ALBERT

Description: Determination of reliable hypocenters of earthquakes is crucial to earthquake seismology and to evaluate hazards associated with earthquakes. There are many associated computer codes for this purpose; however, most of the location algorithms are designed to determine hypocentral parameters based on previously determined velocity models. In contrast, we employed a location method that is independent of the initial velocity model, using a genetic algorithm (GA) to determine an optimal 1D velocity model and the locations of earthquakes. Using this GA, we relocated earthquakes that occurred in the New Madrid Seismic Zone (NMSZ) in the central United States between October 1989 and August 1992. The goal of this work was to delineate the possible fault planes by reliable relocation of those earthquakes and to determine a 1D velocity structure for the NMSZ. A total of 502 earthquakes recorded by 37 Portable Array for Numerical Data Acquisition (PANDA) stations were used in the relocation study. In the relocation process, the root mean square travel-time residuals were reduced by ~35%, corresponding to an average of 2.3 km deeper in depth, 0.7 km shift in latitude, and 0.8 km shift in longitude compared with those in the initial catalog locations. The hypocenters of the earthquakes can be subdivided into four groups based on their spatial distributions. The group that corresponds to the Cottonwood Grove fault (CGF) in the southwestern NMSZ represents a very steep plane, whereas the other three groups fall into Reelfoot fault (RF). We inverted P - and S -wave travel times from the new hypocentral parameters to determine 1D velocity models. The resulting eight-layered velocity models consist of a 2 km thick surface layer followed by seven 2 km thick layers, with V P ranges from 5.36 to 6.74 km/s and V S ranges from 2.83 to 3.90 km/s for both CGF and RF regions. Online Material: Interactive visualizations of hypocentral distributions.

Description: : Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multipanel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. The project manager handles multiple samples of multiple groups. The read alignment is imported in BAM file format. Implemented features comprise sorting, zooming, highlighting, editing, filtering, saving, exporting, etc. Currently, miRseqViewer supports 84 organisms whose annotation is available at miRBase. Availability and implementation: miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr . Contact: sanghyuk@ewha.ac.kr

Description: Texas Air Quality Study field campaigns took place in eastern Texas in August–October of 2000 and 2006. Several flights of NOAA and NCAR research aircraft were dedicated to characterizing anthropogenic emissions over Houston. We present results from an inverse modeling technique that uses three atmospheric transport models and these aircraft observations to assess and improve existing emission inventories. We used inverse modeling techniques to improve the spatial and temporal emissions' distribution of CO, NOy, and SO2 predicted by the 4 km resolution U.S. Environmental Protection Agency (EPA) National Emission Inventory (NEI) for 2005. Differences between the prior and posterior inventories are discussed in detail. In September 2006, we found that the prior daytime CO emissions in the Houston urban area have to be reduced by 41% ± 8%. Over the Houston Ship Channel, where industrial emissions are predominant, the prior emissions have to be decreased by 43% ± 5% for CO and 51% ± 5% for NOy. Prior NOy emissions from other major ports around Houston also have to be reduced, probably owing to uncertain nearshore ship emissions in the EPA NEI inventory. Using the measurements from the two field campaigns, we assessed the emissions' variability between August 2000 and September 2006. Daytime CO emissions from the Houston urban area have decreased by 8% ± 3%, while the NOy emissions have increased by 20% ± 6%. In the Houston Ship Channel, daytime NOy emissions have increased by 13% ± 7%. Our results show qualitative consistencies with known changes in Houston emissions' sources.

Description: Author(s): V. Kuznetsov, M. V. Polyakov, V. Bellini, T. Boiko, S. Chebotaryov, H.-S. Dho, G. Gervino, F. Ghio, A. Giusa, A. Kim, W. Kim, F. Mammoliti, E. Milman, A. Ni, I. A. Perevalova, C. Randieri, G. Russo, M. L. Sperduto, C. M. Sutera, and A. N. Vall The study of quasifree Compton scattering on the neutron in the energy range of E_{γ} =0.75–1.5 GeV is presented. The data reveal a narrow peak at W~1.685 GeV. This result, being considered in conjunction with the recent evidence for a narrow structure at W~1.68 GeV in η photoproduction on the n... [Phys. Rev. C 83, 022201] Published Fri Feb 11, 2011

Description: Motivation: Clustering methods can be useful for automatically grouping documents into meaningful clusters, improving human comprehension of a document collection. Although there are clustering algorithms that can achieve the goal for relatively large document collections, they do not always work well for small and homogenous datasets. Methods: In this article, we present Retro—a novel clustering algorithm that extracts meaningful clusters along with concise and descriptive titles from small and homogenous document collections. Unlike common clustering approaches, our algorithm predicts cluster titles before clustering. It relies on the hypergeometric distribution model to discover key phrases, and generates candidate clusters by assigning documents to these phrases. Further, the statistical significance of candidate clusters is tested using supervised learning methods, and a multiple testing correction technique is used to control the overall quality of clustering. Results: We test our system on five disease datasets from OMIM ® and evaluate the results based on MeSH ® term assignments. We further compare our method with several baseline and state-of-the-art methods, including K-means, expectation maximization, latent Dirichlet allocation-based clustering, Lingo, OPTIMSRC and adapted GK-means. The experimental results on the 20-Newsgroup and ODP-239 collections demonstrate that our method is successful at extracting significant clusters and is superior to existing methods in terms of quality of clusters. Finally, we apply our system to a collection of 6248 topical sets from the HomoloGene ® database, a resource in PubMed ® . Empirical evaluation confirms the method is useful for small homogenous datasets in producing meaningful clusters with descriptive titles. Availability and implementation: A web-based demonstration of the algorithm applied to a collection of sets from the HomoloGene database is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Wilbur/IRET/CLUSTERING_HOMOLOGENE/index.html . Contact: lana.yeganova@nih.gov Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Fish respire through gills, which have evolved to extract aqueous oxygen. Fish gills consist of filaments with well-ordered lamellar structures, which play a role in maximizing oxygen diffusion. It is interesting that when we anatomically observe the gills of various fish species, gill interlamellar distances (d) vary little among them,...

Description: We critically re-examine the concept of a throat in a porous medium as a geometric quantity defined independently of an entry meniscus in a drainage process. To maintain the standard notion of a throat as a locally minimum-area cross section in the pore network, we demonstrate with examples that throats must intersect each other. Using flow simulation we show that these intersecting throats correspond to capillary pressure controlled entry points during drainage. We have designed a throat finding algorithm that explicitly locates intersecting throats, using a planar approximation for robustness and speed. The capability of the new algorithm was compared against an existing algorithm in the construction of pore-throat networks from X-ray computed tomography images of consolidated sandstones (7.5% to 22% porosity) and of an unconsolidated sand pack (32.5% porosity). We show that the probability of throat intersection increases significantly with porosity above 20%; in the sand pack, over 1/4 of all throats intersect with another.

Description: (ADP-ribose) polymerase 1 and AMP-activated protein kinase mediate progressive dopaminergic neuronal degeneration in a mouse model of Parkinson’s disease Cell Death and Disease 4, e919 (November 2013). doi:10.1038/cddis.2013.447 Authors: T W Kim, H M Cho, S Y Choi, Y Suguira, T Hayasaka, M Setou, H C Koh, E Mi Hwang, J Y Park, S J Kang, H S Kim, H Kim & W Sun

Description: Anthocyanins are a group of colorful and bioactive natural pigments with important physiological and ecological functions in plants. We found an MYB transcription factor (PtrMYB119) from Populus trichocarpa that positively regulates anthocyanin production when expressed under the control of the CaMV 35S promoter in transgenic Arabidopsis . Amino acid sequence analysis revealed that PtrMYB119 is highly homologous to Arabidopsis PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT1), a well-known transcriptional activator of anthocyanin biosynthesis. Independently produced transgenic poplars overexpressing PtrMYB119 or PtrMYB120 (a paralogous gene to PtrMYB119 ) (i.e., 35S::PtrMYB119 and 35S::PtrMYB120, respectively) showed elevated accumulation of anthocyanins in the whole plants, including leaf, stem and even root tissues. Using a reverse-phase high-performance liquid chromatography, we confirmed that the majority of the accumulated anthocyanin in our transgenic poplar is cyanidin-3- O -glucoside. Gene expression analyses revealed that most of the genes involved in the anthocyanin biosynthetic pathway were highly upregulated in 35S::PtrMYB119 poplars compared with the nontransformed control poplar. Among these genes, expression of PtrCHS1 ( Chalcone Synthase1 ) and PtrANS2 ( Anthocyanin Synthase2 ), which catalyze the initial and last steps of anthocyanin biosynthesis, respectively, was upregulated by up to 350-fold. Subsequent transient activation assays confirmed that PtrMYB119 activated the transcription of both PtrCHS1 and PtrANS2 . Interestingly, expression of MYB182 , a repressor of both anthocyanin and proanthocyanidin (PA) biosynthesis, was largely suppressed in 35S::PtrMYB119 poplars, while expression of MYB134 , an activator of PA biosynthesis, was not changed significantly. More interestingly, high-level accumulation of anthocyanins in 35S::PtrMYB119 poplars did not have an adverse effect on plant growth. Taken together, our results demonstrate that PtrMYB119 and PtrMYB120 function as transcriptional activators of anthocyanin accumulation in both Arabidopsis and poplar.

Description: Mutations in the serine-threonine kinase with-no-lysine 4 (WNK4) cause pseudohypoaldosteronism type 2 (PHAII), a Mendelian form of human hypertension. WNK4 regulates diverse ion transporters in the kidney, and dysregulation of renal transporters is considered the main cause of the WNK4 mutation-associated hypertension. Another determinant of hypertension is vascular tone that is regulated by Ca2+-dependent blood vessel constriction. However, the role of WNK4 in vasoconstriction as part of its function to regulate blood pressure is not known. Here, we report that WNK4 is a unique modulator of blood pressure by restricting Ca2+ influx via the transient receptor potential canonical 3 (TRPC3) channel in the vasculature. Loss of WNK4 markedly augmented TRPC3-mediated Ca2+ influx in vascular smooth muscle cells (VSMCs) in response to α-adrenoreceptor stimulation, which is the pathological hallmark of hypertension in resistance arteries. Notably, WNK4 depletion induced hypertrophic cell growth in VSMCs and increased vasoconstriction in small mesenteric arteries via TRPC3-mediated Ca2+ influx. In addition, WNK4 mutants harboring the Q562E PHAII-causing or the D318A kinase-inactive mutation failed to mediate TRPC3 inhibition. These results define a previously undescribed function of WNK4 and reveal a unique therapeutic target to control blood pressure in WNK4-related hypertension.