ALBERT

Description: 〈span〉〈div〉SUMMARY〈/div〉Low-velocity layers within the crust can indicate the presence of melt and lithologic differences with implications for crustal composition and formation. Seismic wave conversions and reverberations across the base of the crust or intracrustal discontinuities, analysed using the receiver function method, can be used to constrain crustal layering. This is commonly accomplished by inverting receiver functions jointly with surface wave dispersion. Recently, the proliferation of model-space search approaches has made this technique a workhorse of crustal seismology. We show that reverberations from shallow layers such as sedimentary basins produce spurious low-velocity zones when inverted for crustal structure with surface wave data of insufficiently high frequency. Therefore, reports of such layers in the literature based on inversions using receiver function data should be re-evaluated. We demonstrate that a simple resonance-removal filter can suppress these effects and yield reliable estimates of crustal structure, and advocate for its use in receiver-function based inversions.〈/span〉

Description: Author(s): B.-L. Li, L. Chang, F. Gao, C. D. Roberts, S. M. Schmidt, and H.-S. Zong A symmetry-preserving truncation of the two-body bound state problem in relativistic quantum field theory is used to compute the leading-twist parton distribution amplitudes (PDAs) for the first radial excitations of the π and K mesons. In common with ground states in these channels, the PDAs are fo… [Phys. Rev. D 93, 114033] Published Wed Jun 29, 2016

Description: Mutations in the retinitis pigmentosa GTPase regulator ( RPGR ) gene account for 〉70% of X-linked retinitis pigmentosa (XLRP) and 15–20% of all inherited retinal degeneration. Gene replacement therapy for RPGR -XLRP was hampered by the relatively slow disease progression in mouse models and by difficulties in cloning the full-length RPGR-ORF15 cDNA that includes a purine-rich 3'-coding region; however, its effectiveness has recently been demonstrated in four dogs with RPGR mutations. To advance the therapy to clinical stage, we generated new stable vectors in AAV8 or AAV9 carrying mouse and human full-length RPGR-ORF15 -coding sequence and conducted a comprehensive long-term dose-efficacy study in Rpgr -knockout mice. After validating their ability to produce full-length proteins that localize to photoreceptor connecting cilia, we evaluated various vector doses in mice during a 2-year study. We demonstrate that eyes treated with a single injection of mouse or human RPGR-ORF15 vector at an optimal dose maintained the expression of RPGR - ORF15 throughout the study duration and exhibited higher electroretinogram amplitude, thicker photoreceptor layer and better targeting of opsins to outer segments compared with sham-treated eyes. Furthermore, mice that received treatment at an advanced age also showed remarkable preservation of retinal structure and function. Retinal toxicity was observed at high vector doses, highlighting the importance of careful dose optimization in future clinical experiments. Our long-term dose-efficacy study should facilitate the design of human trials with human RPGR-ORF15 vector as a clinical candidate.

Description: : Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here, we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared with Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times faster and uses less memory. BS-SNPer also offers higher sensitivity and specificity compared with existing methods. Availability and implementation : BS-SNPer is written in C++ and Perl, and is freely available at https://github.com/hellbelly/BS-Snper . Contact : bolund@biomed.au.dk , kdso@clin.au.dk or orntoft@ki.au.dk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Aims Accurate forecast of ecosystem states is critical for improving natural resource management and climate change mitigation. Assimilating observed data into models is an effective way to reduce uncertainties in ecological forecasting. However, influences of measurement errors on parameter estimation and forecasted state changes have not been carefully examined. This study analyzed the parameter identifiability of a process-based ecosystem carbon cycle model, the sensitivity of parameter estimates and model forecasts to the magnitudes of measurement errors and the information contributions of the assimilated data to model forecasts with a data assimilation approach. Methods We applied a Markov Chain Monte Carlo method to assimilate eight biometric data sets into the Terrestrial ECOsystem model. The data were the observations of foliage biomass, wood biomass, fine root biomass, microbial biomass, litter fall, litter, soil carbon and soil respiration, collected at the Duke Forest free-air CO 2 enrichment facilities from 1996 to 2005. Three levels of measurement errors were assigned to these data sets by halving and doubling their original standard deviations. Important Findings Results showed that only less than half of the 30 parameters could be constrained, though the observations were extensive and the model was relatively simple. Higher measurement errors led to higher uncertainties in parameters estimates and forecasted carbon (C) pool sizes. The long-term predictions of the slow turnover pools were affected less by the measurement errors than those of fast turnover pools. Assimilated data contributed less information for the pools with long residence times in long-term forecasts. These results indicate the residence times of C pools played a key role in regulating propagation of errors from measurements to model forecasts in a data assimilation system. Improving the estimation of parameters of slow turnover C pools is the key to better forecast long-term ecosystem C dynamics.

Description: 〈span〉〈div〉Summary〈/div〉Low-velocity layers within the crust can indicate the presence of melt and lithologic differences with implications for crustal composition and formation. Seismic wave conversions and reverberations across the base of the crust or intra-crustal discontinuities, analyzed using the receiver function method, can be used to constrain crustal layering. This is commonly accomplished by inverting receiver functions jointly with surface wave dispersion. Recently, the proliferation of model-space search approaches has made this technique a workhorse of crustal seismology. We show that reverberations from shallow layers such as sedimentary basins produce spurious low-velocity zones when inverted for crustal structure with surface wave data of insufficiently high frequency. Therefore, reports of such layers in the literature based on inversions using receiver function data should be re-evaluated. We demonstrate that a simple resonance-removal filter can suppress these effects and yield reliable estimates of crustal structure, and advocate for its use in receiver-function based inversions.〈/span〉

Description: Transcriptional regulation plays a critical role in the life cycle of Mycobacterium smegmatis and its related species, M. tuberculosis , the causative microbe for tuberculosis. However, the key transcriptional factors involved in broad regulation of diverse genes remain to be characterized in mycobacteria. In the present study, a TetR-like family transcriptional factor, Ms6564, was characterized in M. smegmatis as a master regulator. A conserved 19 bp-palindromic motif was identified for Ms6564 binding using DNaseI footprinting and EMSA. A total of 339 potential target genes for Ms6564 were further characterized by searching the M. smegmatis genome based on the sequence motif. Notably, Ms6564 bound with the promoters of 37 cell cycle and DNA damage/repair genes and regulated positively their expressions. The Ms6564-overexpressed recombinant strain yielded 5-fold lower mutation rates and mutation frequencies, whereas deletion of Ms6564 resulted in ~5-fold higher mutation rates for the mutant strain compared with the wild-type strain. These findings suggested that Ms6564 may function as a global regulator and might be a sensor necessary for activation of DNA damage/repair genes.

Description: Author(s): M. H. Lee, C.-P. Chang, F.-T. Huang, G. Y. Guo, B. Gao, C. H. Chen, S.-W. Cheong, and M.-W. Chu Hybrid improper ferroelectricity (HIF) denotes a new class of polar instability by the mixture of two octahedral-distortion modes and can feature the coexistence of abundant head-to-head and tail-to-tail polar domains, of which the domain walls tend to be charged due to the respective screening char... [Phys. Rev. Lett. 119, 157601] Published Tue Oct 10, 2017

Description: The study of dense matter at ultrahigh density has a very long history, which is meaningful for us to understand not only cosmic events in extreme circumstances but also fundamental laws of physics. It is well known that the state of cold matter at supranuclear density depends on the non-perturbative nature of quantum chromodynamics (QCD) and is essential for modelling pulsars. A so-called H-cluster matter is proposed in this paper as the nature of dense matter in reality. In compact stars at only a few nuclear densities but low temperature, quarks could be interacting strongly with each other there. That might render quarks grouped in clusters, although the hypothetical quark clusters in cold dense matter have not been confirmed due to the lack of both theoretical and experimental evidence. Motivated by recent lattice QCD simulations of the H-dibaryons (with structure uuddss ), we therefore consider here a possible kind of quark clusters, H-clusters, that could emerge inside compact stars during their initial cooling as the dominant components inside (the degree of freedom could then be H-clusters there). Taking into account the in-medium stiffening effect, we find that at baryon densities of compact stars H-cluster matter could be more stable than nuclear matter. We also find that for the H-cluster matter with lattice structure, the equation of state could be so stiff that it would seem to be ‘superluminal’ in the most dense region. However, the real sound speed for H-cluster matter is in fact difficult to calculate, so at this stage we do not put constraints on our model from the usual requirement of causality. We study the stars composed of H-clusters, i.e. H-cluster stars, and derive the dependence of their maximum mass on the in-medium stiffening effect, showing that the maximum mass could be well above 2 M as observed and that the resultant mass–radius relation fits the measurement of the rapid burster under reasonable parameters. Besides a general understanding of different manifestations of compact stars, we expect further observational and experimental tests for the H-cluster stars in the future.

Description: Motivation: Identification of expression Quantitative Trait Loci (eQTL), the genetic loci that contribute to heritable variation in gene expression, can be obstructed by factors that produce variation in expression profiles if these factors are unmeasured or hidden from direct analysis. Methods: We have developed a method for Hidden Expression Factor analysis (HEFT) that identifies individual and pleiotropic effects of eQTL in the presence of hidden factors. The HEFT model is a combined multivariate regression and factor analysis, where the complete likelihood of the model is used to derive a ridge estimator for simultaneous factor learning and detection of eQTL. HEFT requires no pre-estimation of hidden factor effects; it provides P -values and is extremely fast, requiring just a few hours to complete an eQTL analysis of thousands of expression variables when analyzing hundreds of thousands of single nucleotide polymorphisms on a standard 8 core 2.6 G desktop. Results: By analyzing simulated data, we demonstrate that HEFT can correct for an unknown number of hidden factors and significantly outperforms all related hidden factor methods for eQTL analysis when there are eQTL with univariate and multivariate (pleiotropic) effects. To demonstrate a real-world application, we applied HEFT to identify eQTL affecting gene expression in the human lung for a study that included presumptive hidden factors. HEFT identified all of the cis- eQTL found by other hidden factor methods and 91 additional cis- eQTL. HEFT also identified a number of eQTLs with direct relevance to lung disease that could not be found without a hidden factor analysis, including cis- eQTL for GTF2H1 and MTRR, genes that have been independently associated with lung cancer. Availability: Software is available at http://mezeylab.cb.bscb.cornell.edu/Software.aspx . Supplementary information: Supplementary data are available at Bioinformatics online. Contact: jgm45@cornell.edu