Статті в журналах: "Lsm Domain"

1

Tritschler, Felix, Ana Eulalio, Vincent Truffault, Marcus D. Hartmann, Sigrun Helms, Steffen Schmidt, Murray Coles, Elisa Izaurralde, and Oliver Weichenrieder. "A Divergent Sm Fold in EDC3 Proteins Mediates DCP1 Binding and P-Body Targeting." Molecular and Cellular Biology 27, no. 24 (October 8, 2007): 8600–8611. http://dx.doi.org/10.1128/mcb.01506-07.

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ABSTRACT Members of the (L)Sm (Sm and Sm-like) protein family are found across all kingdoms of life and play crucial roles in RNA metabolism. The P-body component EDC3 (enhancer of decapping 3) is a divergent member of this family that functions in mRNA decapping. EDC3 is composed of a N-terminal LSm domain, a central FDF domain, and a C-terminal YjeF-N domain. We show that this modular architecture enables EDC3 to interact with multiple components of the decapping machinery, including DCP1, DCP2, and Me31B. The LSm domain mediates DCP1 binding and P-body localization. We determined the three-dimensional structures of the LSm domains of Drosophila melanogaster and human EDC3 and show that the domain adopts a divergent Sm fold that lacks the characteristic N-terminal α-helix and has a disrupted β4-strand. This domain remains monomeric in solution and lacks several features that canonical (L)Sm domains require for binding RNA. The structures also revealed a conserved patch of surface residues that are required for the interaction with DCP1 but not for P-body localization. The conservation of surface and of critical structural residues indicates that LSm domains in EDC3 proteins adopt a similar fold that has separable novel functions that are absent in canonical (L)Sm proteins.

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2

Payá, Gloria, Vanesa Bautista, Mónica Camacho, Julia Esclapez, and María-José Bonete. "Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain." Microorganisms 11, no. 5 (May 3, 2023): 1196. http://dx.doi.org/10.3390/microorganisms11051196.

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The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.

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3

Guo, Song, and Huazhong Wang. "Image domain least-squares migration with a Hessian matrix estimated by non-stationary matching filters." Journal of Geophysics and Engineering 17, no. 1 (November 22, 2019): 148–59. http://dx.doi.org/10.1093/jge/gxz098.

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Abstract Assuming that an accurate background velocity is obtained, least-squares migration (LSM) can be used to estimate underground reflectivity. LSM can be implemented in either the data domain or image domain. The data domain LSM (DDLSM) is not very practical because of its huge computational cost and slow convergence rate. The image domain LSM (IDLSM) might be a flexible alternative if estimating the Hessian matrix using a cheap and accurate approach. It has practical potential to analyse convenient Hessian approximation methods because the Hessian matrix is too huge to compute and save. In this paper, the Hessian matrix is approximated with non-stationary matching filters. The filters are calculated to match the conventional migration image to the demigration/remigration image. The two images are linked by the Hessian matrix. An image deblurring problem is solved with the estimated filters for the IDLSM result. The combined sparse and total variation regularisations are used to produce accurate and reasonable inversion results. The numerical experiments based on part of Sigsbee model, Marmousi model and a 2D field data set illustrate that the non-stationary matching filters can give a good approximation for the Hessian matrix, and the results of the image deblurring problem with combined regularisations can provide high-resolution and true-amplitude reflectivity estimations.

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4

Böhringer, H. J., D. Boller, J. Leppert, U. Knopp, E. Lankenau, E. Reusche, G. Hüttmann, and A. Giese. "Time-domain and spectral-domain optical coherence tomography in the analysis of brain tumor tissue." Lasers in Surgery and Medicine 38, no. 6 (May 30, 2006): 588–97. http://dx.doi.org/10.1002/lsm.20353.

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5

Tritschler, Felix, Ana Eulalio, Sigrun Helms, Steffen Schmidt, Murray Coles, Oliver Weichenrieder, Elisa Izaurralde, and Vincent Truffault. "Similar Modes of Interaction Enable Trailer Hitch and EDC3 To Associate with DCP1 and Me31B in Distinct Protein Complexes." Molecular and Cellular Biology 28, no. 21 (September 2, 2008): 6695–708. http://dx.doi.org/10.1128/mcb.00759-08.

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ABSTRACT Trailer Hitch (Tral or LSm15) and enhancer of decapping-3 (EDC3 or LSm16) are conserved eukaryotic members of the (L)Sm (Sm and Like-Sm) protein family. They have a similar domain organization, characterized by an N-terminal LSm domain and a central FDF motif; however, in Tral, the FDF motif is flanked by regions rich in charged residues, whereas in EDC3 the FDF motif is followed by a YjeF_N domain. We show that in Drosophila cells, Tral and EDC3 specifically interact with the decapping activator DCP1 and the DEAD-box helicase Me31B. Nevertheless, only Tral associates with the translational repressor CUP, whereas EDC3 associates with the decapping enzyme DCP2. Like EDC3, Tral interacts with DCP1 and localizes to mRNA processing bodies (P bodies) via the LSm domain. This domain remains monomeric in solution and adopts a divergent Sm fold that lacks the characteristic N-terminal α-helix, as determined by nuclear magnetic resonance analyses. Mutational analysis revealed that the structural integrity of the LSm domain is required for Tral both to interact with DCP1 and CUP and to localize to P-bodies. Furthermore, both Tral and EDC3 interact with the C-terminal RecA-like domain of Me31B through their FDF motifs. Together with previous studies, our results show that Tral and EDC3 are structurally related and use a similar mode to associate with common partners in distinct protein complexes.

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6

Osorio, Luana Nobre, Bruno Pereira-Dias, André Bulcão, and Luiz Landau. "Migration deconvolution using domain decomposition." GEOPHYSICS 86, no. 3 (April 21, 2021): S247—S256. http://dx.doi.org/10.1190/geo2020-0352.1.

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Least-squares migration (LSM) is an effective technique for mitigating blurring effects and migration artifacts generated by limited data frequency bandwidth, incomplete coverage of geometry, source signature, and unbalanced amplitudes caused by complex wavefield propagation in the subsurface. Migration deconvolution (MD) is an image-domain approach for LSM that approximates the Hessian operator using a set of precomputed point spread functions. We have developed a new workflow by integrating the MD and domain decomposition (DD) methods. DD techniques aim to solve large and complex linear systems by splitting problems into smaller parts, facilitating parallel computing, and providing a higher convergence in iterative algorithms. We suggest that instead of solving the problem in a unique domain, as conventionally performed, splitting the problem into subdomains that overlap and solve each of them independently. We accelerate the convergence rate of the conjugate-gradient solver by applying the DD methods to retrieve better reflectivity, which is mainly visible in regions with low amplitudes. Moreover, using the pseudo-Hessian operator, the convergence of the algorithm is accelerated, suggesting that the inverse problem becomes better conditioned. Experiments using the synthetic Pluto model demonstrate that our algorithm dramatically reduces the required number of iterations while providing a considerable enhancement in image resolution and better continuity of poorly illuminated events.

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7

Fromont-Racine, Micheline, Andrew E. Mayes, Adeline Brunet-Simon, Jean-Christophe Rain, Alan Colley, Ian Dix, Laurence Decourty, et al. "Genome-Wide Protein Interaction Screens Reveal Functional Networks Involving Sm-Like Proteins." Yeast 1, no. 2 (January 1, 2000): 95–110. http://dx.doi.org/10.1155/2000/919260.

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A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence of Saccharomyces cerevisiae has identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (L¯ike Sm¯) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein–protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale.

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8

Fromont-Racine, Micheline, Andrew E. Mayes, Adeline Brunet-Simon, Jean-Christophe Rain, Alan Colley, Ian Dix, Laurence Decourty, et al. "Genome-Wide Protein Interaction Screens Reveal Functional Networks Involving Sm-Like Proteins." Yeast 1, no. 2 (2000): 95–110. http://dx.doi.org/10.1002/1097-0061(20000630)17:2<95::aid-yea16>3.0.co;2-h.

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A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence ofSaccharomyces cerevisiaehas identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (L¯ike Sm¯) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein–protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale.

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9

Bhatta, Krishna M., and Norman S. Nishioka. "Effect of pulse duration on microsecond-domain laser lithotripsy." Lasers in Surgery and Medicine 9, no. 5 (1989): 454–57. http://dx.doi.org/10.1002/lsm.1900090505.

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10

Li, Bo, Minao Sun, Chen Xiang, and Yingzhe Bai. "Least-Squares Reverse Time Migration in Imaging Domain Based on Global Space-Varying Deconvolution." Applied Sciences 12, no. 5 (February 24, 2022): 2361. http://dx.doi.org/10.3390/app12052361.

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The classical least-squares migration (LSM) translates seismic imaging into a data-fitting optimization problem to obtain high-resolution images. However, the classical LSM is highly dependent on the precision of seismic wavelet and velocity models, and thus it suffers from an unstable convergence and excessive computational costs. In this paper, we propose a new LSM method in the imaging domain. It selects a spatial-varying point spread function to approximate the accurate Hessian operator and uses a high-dimensional spatial deconvolution algorithm to replace the common-used iterative inversion. To keep a balance between the inversion precision and the computational efficiency, this method is implemented based on the strategy of regional division, and the point spread function is computed using only one-time demigration/migration and inverted individually in each region. Numerical experiments reveal the differences in the spatial variation of point spread functions and highlight the importance to use a space-varying deconvolution algorithm. A 3D field case in Northwest China can demonstrate the effectiveness of this method on improving spatial resolution and providing better characterizations for small-scale fracture and cave units of carbonate reservoirs.

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11

Xu, Huipu, Wenjie Lu, and Meng Joo Er. "An Integrated Strategy toward the Extraction of Contour and Region of Sonar Images." Journal of Marine Science and Engineering 8, no. 8 (August 10, 2020): 595. http://dx.doi.org/10.3390/jmse8080595.

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In this paper, an integrated underwater sonar image extraction strategy, which combines two improved methods, namely the level set method (LSM) and the Lattice Boltzmann Method (LBM), is proposed. First, sonar images are processed by a clustering method and a connected domain analysis to generate the target minimum rectangle frame. Next, the segmentation task is decomposed into two subtasks, namely a coarse segmentation task to obtain the initial contour and a fine segmentation task after embedding the initial contour. Finally, the improved LSM is used to obtain the target contour, and the coarse contour of the segment is embedded into the LBM to obtain the region segmentation of the target in the sonar images. The main contributions of the paper are as follows: (1) The contours and regions of the sonar images are extracted simultaneously. (2) The original LBM method is enhanced to solve the level set iteration problem. (3) The region segmentation with the original image background is extracted, and a more intuitive region segmentation result than that of directly extracting the contour of the level set is achieved. Experimental results based on four evaluation indices of image segmentation show that our method is effective, accurate, and superior to other existing methods.

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12

Wan, Xiang Kui, Kang Hui Yan, and Ming Gui Li. "Detecting and Quantifying T Wave Alternans Using Linear Least Squares Curve Fitting Method." Applied Mechanics and Materials 239-240 (December 2012): 1404–8. http://dx.doi.org/10.4028/www.scientific.net/amm.239-240.1404.

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Evaluatement of T-wave alternans (TWA) is a non-invasive method to identify patients at risk for sudden cardiac death. A novel time-domain algorithm based on linear least squares method (LSM) for TWA analysis is developed in this paper. And the LSM’s ability to TWA analaysis in comparison with the modified moving average (MMA) method was demonstrated. In a simulation study LSM and MMA can both detected TWA with high accuracy, but under lower SNR levels LSM was found more robust, and its evaluated TWA values are closer to true TWA value. The algorithm was subsequently used to analyze the clinical ECGs from T-Wave Alternans Challenge Database, which showed that the results from this method vs. MMA had the correlation coefficients of 0.89.

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13

Smirnova, Tatiana G., John M. Brown, Stanley G. Benjamin, and Jaymes S. Kenyon. "Modifications to the Rapid Update Cycle Land Surface Model (RUC LSM) Available in the Weather Research and Forecasting (WRF) Model." Monthly Weather Review 144, no. 5 (May 2016): 1851–65. http://dx.doi.org/10.1175/mwr-d-15-0198.1.

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The land surface model (LSM) described in this manuscript was originally developed as part of the NOAA Rapid Update Cycle (RUC) model development effort; with ongoing modifications, it is now used as an option for the WRF community model. The RUC model and its WRF-based NOAA successor, the Rapid Refresh (RAP), are hourly updated and have an emphasis on short-range, near-surface forecasts including aviation-impact variables and preconvective environment. Therefore, coupling to this LSM (hereafter the RUC LSM) has been critical to provide more accurate lower boundary conditions. This paper describes changes made to the RUC LSM since earlier descriptions, including extension from six to nine levels, improved snow treatment, and new land-use data from MODIS. The RUC LSM became operational at the NOAA/National Centers for Environmental Prediction (NCEP) as part of the RUC from 1998–2012 and as part of the RAP from 2012 through the present. The simple treatments of basic land surface processes in the RUC LSM have proven to be physically robust and capable of realistically representing the evolution of soil moisture, soil temperature, and snow in cycled models. Extension of the RAP domain to encompass all of North America and adjacent high-latitude ocean areas necessitated further development of the RUC LSM for application in the tundra permafrost regions and over Arctic sea ice. Other modifications include refinements in the snow model and a more accurate specification of albedo, roughness length, and other surface properties. These recent modifications in the RUC LSM are described and evaluated in this paper.

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14

Pellet, Cécile, and Christian Hauck. "Monitoring soil moisture from middle to high elevation in Switzerland: set-up and first results from the SOMOMOUNT network." Hydrology and Earth System Sciences 21, no. 6 (June 29, 2017): 3199–220. http://dx.doi.org/10.5194/hess-21-3199-2017.

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Abstract. Besides its important role in the energy and water balance at the soil–atmosphere interface, soil moisture can be a particular important factor in mountain environments since it influences the amount of freezing and thawing in the subsurface and can affect the stability of slopes. In spite of its importance, the technical challenges and its strong spatial variability usually prevents soil moisture from being measured operationally at high and/or middle altitudes. This study describes the new Swiss soil moisture monitoring network SOMOMOUNT (soil moisture in mountainous terrain) launched in 2013. It consists of six entirely automated soil moisture stations distributed along an altitudinal gradient between the Jura Mountains and the Swiss Alps, ranging from 1205 to 3410 m a.s.l. in elevation. In addition to the standard instrumentation comprising frequency domain sensor and time domain reflectometry (TDR) sensors along vertical profiles, soil probes and meteorological data are available at each station. In this contribution we present a detailed description of the SOMOMOUNT instrumentation and calibration procedures. Additionally, the liquid soil moisture (LSM) data collected during the first 3 years of the project are discussed with regard to their soil type and climate dependency as well as their altitudinal distribution. The observed elevation dependency of LSM is found to be non-linear, with an increase of the mean annual values up to ∼ 2000 m a.s.l. followed by a decreasing trend towards higher elevations. This altitude threshold marks the change between precipitation-/evaporation-controlled and frost-affected LSM regimes. The former is characterized by high LSM throughout the year and minimum values in summer, whereas the latter typically exhibits long-lasting winter minimum LSM values and high variability during the summer.

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15

Dutta, Gaurav, Matteo Giboli, Cyril Agut, Paul Williamson, and Gerard T. Schuster. "Least-squares reverse time migration with local Radon-based preconditioning." GEOPHYSICS 82, no. 2 (March 1, 2017): S75—S84. http://dx.doi.org/10.1190/geo2016-0117.1.

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Least-squares migration (LSM) can produce images with better balanced amplitudes and fewer artifacts than standard migration. The conventional objective function used for LSM minimizes the L2-norm of the data residual between the predicted and the observed data. However, for field-data applications in which the recorded data are noisy and undersampled, the conventional formulation of LSM fails to provide the desired uplift in the quality of the inverted image. We have developed a least-squares reverse time migration (LSRTM) method using local Radon-based preconditioning to overcome the low signal-to-noise ratio (S/N) problem of noisy or severely undersampled data. A high-resolution local Radon transform of the reflectivity is used, and sparseness constraints are imposed on the inverted reflectivity in the local Radon domain. The sparseness constraint is that the inverted reflectivity is sparse in the Radon domain and each location of the subsurface is represented by a limited number of geologic dips. The forward and the inverse mapping of the reflectivity to the local Radon domain and vice versa is done through 3D Fourier-based discrete Radon transform operators. The weights for the preconditioning are chosen to be varying locally based on the relative amplitudes of the local dips or assigned using quantile measures. Numerical tests on synthetic and field data validate the effectiveness of our approach in producing images with good S/N and fewer aliasing artifacts when compared with standard RTM or standard LSRTM.

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16

Baños, Ana, Martin Wolf, Claudia Grawe, Michèle Stahel, Daniel Haensse, Daniel Fink, and René Hornung. "Frequency domain near-infrared spectroscopy of the uterine cervix during cervical ripening." Lasers in Surgery and Medicine 39, no. 8 (2007): 641–46. http://dx.doi.org/10.1002/lsm.20542.

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17

Bernstein, Eric F., Kevin T. Schomacker, Lisa D. Basilavecchio, Jessica M. Plugis, and Jayant D. Bhawalkar. "A novel dual‐wavelength, Nd:YAG, picosecond‐domain laser safely and effectively removes multicolor tattoos." Lasers in Surgery and Medicine 47, no. 7 (July 14, 2015): 542–48. http://dx.doi.org/10.1002/lsm.22391.

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18

Kim, Jung E., Jeong Y. Hong, Ho J. Lee, Sung Y. Lee, and Hyun J. Kim. "Picosecond‐Domain Fractional Laser Treatment Over Hyaluronic Acid Fillers: In Vivo and Clinical Studies." Lasers in Surgery and Medicine 52, no. 10 (April 29, 2020): 928–34. http://dx.doi.org/10.1002/lsm.23254.

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19

Yang, Jizhong, Yuzhu Liu, and Liangguo Dong. "Least-squares reverse time migration in the presence of density variations." GEOPHYSICS 81, no. 6 (November 1, 2016): S497—S509. http://dx.doi.org/10.1190/geo2016-0075.1.

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Least-squares migration (LSM) is commonly regarded as an amplitude-preserving or true amplitude migration algorithm that, compared with conventional migration, can provide migrated images with reduced migration artifacts, balanced amplitudes, and enhanced spatial resolution. Most applications of LSM are based on the constant-density assumption, which is not the case in the real earth. Consequently, the amplitude performance of LSM is not appropriate. To partially remedy this problem, we have developed a least-squares reverse time migration (LSRTM) scheme suitable for density variations in the acoustic approximation. An improved scattering-integral approach is adopted for implementation of LSRTM in the frequency domain. LSRTM images associated with velocity and density perturbations are simultaneously used to generate the simulated data, which better matches the recorded data in amplitudes. Summation of these two images provides a reflectivity model related to impedance perturbation that is in better accordance with the true one, than are the velocity and density images separately. Numerical examples based on a two-layer model and a small part of the Sigsbee2A model verify the effectiveness of our method.

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20

Bernstein, Eric F., Jayant Bhawalkar, and Kevin T. Schomacker. "A novel titanium sapphire picosecond-domain laser safely and effectively removes purple, blue, and green tattoo inks." Lasers in Surgery and Medicine 50, no. 7 (May 20, 2018): 704–10. http://dx.doi.org/10.1002/lsm.22942.

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21

Mazhar, Amaan, Seyed A. Sharif, J. David Cuccia, J. Stuart Nelson, Kristen M. Kelly, and Anthony J. Durkin. "Spatial frequency domain imaging of port wine stain biochemical composition in response to laser therapy: A pilot study." Lasers in Surgery and Medicine 44, no. 8 (August 21, 2012): 611–21. http://dx.doi.org/10.1002/lsm.22067.

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22

Livneh, Ben, Youlong Xia, Kenneth E. Mitchell, Michael B. Ek, and Dennis P. Lettenmaier. "Noah LSM Snow Model Diagnostics and Enhancements." Journal of Hydrometeorology 11, no. 3 (June 1, 2010): 721–38. http://dx.doi.org/10.1175/2009jhm1174.1.

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Abstract A negative snow water equivalent (SWE) bias in the snow model of the Noah land surface scheme used in the NCEP suite of numerical weather and climate prediction models has been noted by several investigators. This bias motivated a series of offline tests of model extensions and improvements intended to reduce or eliminate the bias. These improvements consist of changes to the model’s albedo formulation that include a parameterization for snowpack aging, changes to how pack temperature is computed, and inclusion of a provision for refreeze of liquid water in the pack. Less extensive testing was done on the performance of model extensions with alternate areal depletion parameterizations. Model improvements were evaluated through comparisons of point simulations with National Resources Conservation Service (NRCS) Snowpack Telemetry (SNOTEL) SWE data for deep-mountain snowpacks at selected stations in the western United States, as well as simulations of snow areal extent over the conterminous United States (CONUS) domain, compared with observational data from the NOAA Interactive Multisensor Snow and Ice Mapping System (IMS). The combination of snow-albedo decay and liquid-water refreeze results in substantial improvements in the magnitude and timing of peak SWE, as well as increased snow-covered extent at large scales. Modifications to areal snow depletion thresholds yielded more realistic snow-covered albedos at large scales.

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Zaric, Bozidarka, Mohamed Chami, Hervé Rémigy, Andreas Engel, Kurt Ballmer-Hofer, Fritz K. Winkler, and Christian Kambach. "Reconstitution of Two Recombinant LSm Protein Complexes Reveals Aspects of Their Architecture, Assembly, and Function." Journal of Biological Chemistry 280, no. 16 (February 11, 2005): 16066–75. http://dx.doi.org/10.1074/jbc.m414481200.

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Sm and Sm-like (LSm) proteins form complexes engaging in various RNA-processing events. Composition and architecture of the complexes determine their intracellular distribution, RNA targets, and function. We have reconstituted the human LSm1–7 and LSm2–8 complexes from their constituent componentsin vitro. Based on the assembly pathway of the canonical Sm core domain, we used heterodimeric and heterotrimeric sub-complexes to assemble LSm1–7 and LSm2–8. Isolated sub-complexes form ring-like higher order structures. LSm1–7 is assembled and stable in the absence of RNA. LSm1–7 forms ring-like structures very similar to LSm2–8 at the EM level. Ourin vitroreconstitution results illustrate likely features of the LSm complex assembly pathway. We prove the complexes to be functional both in an RNA bandshift and anin vivocellular transport assay.

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Yafi, Amr, Fuad K. Muakkassa, Tejasvi Pasupneti, Judy Fulton, David J. Cuccia, Amaan Mazhar, Kimberly N. Blasiole, and Eliot N. Mostow. "Quantitative skin assessment using spatial frequency domain imaging (SFDI) in patients with or at high risk for pressure ulcers." Lasers in Surgery and Medicine 49, no. 9 (June 6, 2017): 827–34. http://dx.doi.org/10.1002/lsm.22692.

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25

Bernstein, Eric F., Kevin T. Schomacker, Lisa D. Basilavecchio, Jessica M. Plugis, and Jayant D. Bhawalkar. "Treatment of acne scarring with a novel fractionated, dual-wavelength, picosecond-domain laser incorporating a novel holographic beam-splitter." Lasers in Surgery and Medicine 49, no. 9 (September 28, 2017): 796–802. http://dx.doi.org/10.1002/lsm.22734.

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26

Krüger, Timothy, Mario Hofweber, and Susanne Kramer. "SCD6 induces ribonucleoprotein granule formation in trypanosomes in a translation-independent manner, regulated by its Lsm and RGG domains." Molecular Biology of the Cell 24, no. 13 (July 2013): 2098–111. http://dx.doi.org/10.1091/mbc.e13-01-0068.

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Ribonucleoprotein (RNP) granules are cytoplasmic, microscopically visible structures composed of RNA and protein with proposed functions in mRNA decay and storage. Trypanosomes have several types of RNP granules, but lack most of the granule core components identified in yeast and humans. The exception is SCD6/Rap55, which is essential for processing body (P-body) formation. In this study, we analyzed the role of trypanosome SCD6 in RNP granule formation. Upon overexpression, the majority of SCD6 aggregates to multiple granules enriched at the nuclear periphery that recruit both P-body and stress granule proteins, as well as mRNAs. Granule protein composition depends on granule distance to the nucleus. In contrast to findings in yeast and humans, granule formation does not correlate with translational repression and can also take place in the nucleus after nuclear targeting of SCD6. While the SCD6 Lsm domain alone is both necessary and sufficient for granule induction, the RGG motif determines granule type and number: the absence of an intact RGG motif results in the formation of fewer granules that resemble P-bodies. The differences in granule number remain after nuclear targeting, indicating translation-independent functions of the RGG domain. We propose that, in trypanosomes, a local increase in SCD6 concentration may be sufficient to induce granules by recruiting mRNA. Proteins that bind selectively to the RGG and/or Lsm domain of SCD6 could be responsible for regulating granule type and number.

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Ponticorvo, Adrien, David M. Burmeister, Rebecca Rowland, Melissa Baldado, Gordon T. Kennedy, Rolf Saager, Nicole Bernal, Bernard Choi, and Anthony J. Durkin. "Quantitative long-term measurements of burns in a rat model using Spatial Frequency Domain Imaging (SFDI) and Laser Speckle Imaging (LSI)." Lasers in Surgery and Medicine 49, no. 3 (February 21, 2017): 293–304. http://dx.doi.org/10.1002/lsm.22647.

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Clayton, Anita H., Julie C. Locklear, Henrik Svedsäter, and Roger S. McIntyre. "Sexual functioning in patients with major depressive disorder in randomized placebo-controlled studies of extended release quetiapine fumarate." CNS Spectrums 19, no. 2 (September 25, 2013): 182–96. http://dx.doi.org/10.1017/s1092852913000631.

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ObjectiveWe evaluated sexual functioning from 6 acute, randomized, placebo-controlled studies (6–10 weeks) of once-daily extended release quetiapine fumarate (quetiapine XR) 50, 150, or 300 mg/day as monotherapy (Studies 1–4) or adjunct therapy (Studies 6–7) in major depressive disorder (MDD).MethodsWe present a pre-planned, non-inferiority analysis of quetiapine XR monotherapy versus placebo using Changes in Sexual Functioning Questionnaire (CSFQ) total score change (Studies 1–4). Post hoc analyses evaluated CSFQ total and domain scores for fixed-dose monotherapy (Studies 1–2), modified fixed-dose (Studies 3–4), and adjunct therapy studies (Studies 6–7). CSFQ data for active comparators (duloxetine [Study 2], escitalopram [Study 4]) are reported.ResultsQuetiapine XR monotherapy was non-inferior to placebo for sexual functioning (least squares mean [LSM] difference in CSFQ score change versus placebo, 0.16 [95% confidence interval: −0.59, 0.92]); LSM change in CSFQ score: 1.90, quetiapine XR (all doses) and 1.73, placebo. LSM differences versus placebo (95% confidence interval): 0.18 (−1.40, 1.75), duloxetine (Study 2); 0.16 (−1.77, 2.10), escitalopram (Study 4). LSM differences with adjunct quetiapine XR 150 mg/day (0.52; p = 0.338) or 300 mg/day (0.22; p = 0.679) were comparable with placebo plus antidepressants. Post hoc all-patient and gender-specific analyses were comparable for CSFQ total scores versus placebo with quetiapine XR 50, 150, or 300 mg/day, duloxetine, and escitalopram.DiscussionLack of negative effects on sexual functioning in patients with MDD may improve treatment acceptability.ConclusionQuetiapine XR (monotherapy or adjunct therapy) had an impact on sexual function that was comparable with placebo.

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Stanĕk, David, Stephen D. Rader, Mirko Klingauf, and Karla M. Neugebauer. "Targeting of U4/U6 small nuclear RNP assembly factor SART3/p110 to Cajal bodies." Journal of Cell Biology 160, no. 4 (February 10, 2003): 505–16. http://dx.doi.org/10.1083/jcb.200210087.

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The spliceosomal small nuclear RNAs (snRNAs) are distributed throughout the nucleoplasm and concentrated in nuclear inclusions termed Cajal bodies (CBs). A role for CBs in the metabolism of snRNPs has been proposed but is not well understood. The SART3/p110 protein interacts transiently with the U6 and U4/U6 snRNPs and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. Here we report that SART3/p110 is enriched in CBs but not in gems or residual CBs lacking coilin. The U6 snRNP Sm-like (LSm) proteins, also involved in U4/U6 snRNP assembly, were localized to CBs as well. The levels of SART3/p110 and LSm proteins in CBs were reduced upon treatment with the transcription inhibitor α-amanitin, suggesting that CB localization reflects active processes dependent on transcription/splicing. The NH2-terminal HAT domain of SART3/p110 was necessary and sufficient for specific protein targeting to CBs. Overexpression of truncation mutants containing the HAT domain had dominant negative effects on U6 snRNP localization to CBs, indicating that endogenous SART3/p110 plays a role in targeting the U6 snRNP to CBs. We propose that U4 and U6 snRNPs accumulate in CBs for the purpose of assembly into U4/U6 snRNPs by SART3/p110.

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Saager, R. B., D. J. Cuccia, S. Saggese, K. M. Kelly, and A. J. Durkin. "A Light Emitting Diode (LED) Based Spatial Frequency Domain Imaging System for Optimization of Photodynamic Therapy of Nonmelanoma Skin Cancer: Quantitative Reflectance Imaging." Lasers in Surgery and Medicine 45, no. 4 (April 2013): 207–15. http://dx.doi.org/10.1002/lsm.22139.

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Li, Yunlei, Yanyan Sun, Aixin Ni, Lei Shi, Panlin Wang, Adamu Mani Isa, Pingzhuang Ge, et al. "Seminal Plasma Proteome as an Indicator of Sperm Dysfunction and Low Sperm Motility in Chickens." Molecular & Cellular Proteomics 19, no. 6 (April 20, 2020): 1035–46. http://dx.doi.org/10.1074/mcp.ra120.002017.

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Molecular mechanisms underlying sperm motility have not been fully explained, particularly in chickens. The objective was to identify seminal plasma proteins associated with chicken sperm motility by comparing the seminal plasma proteomic profile of roosters with low sperm motility (LSM, n = 4) and high sperm motility (HSM, n = 4). Using a label-free MS-based method, a total of 522 seminal plasma proteins were identified, including 386 (∼74%) previously reported and 136 novel ones. A total of 70 differentially abundant proteins were defined, including 48 more-abundant, 15 less-abundant, and seven proteins unique to the LSM group (specific proteins). Key secretory proteins like less-abundant adhesion G-protein coupled receptor G2 (ADGRG2) and more-abundant serine peptidase inhibitor Kazal-type 2 (SPINK2) in the LSM suggested that the corresponding secretory tissues played a crucial role in maintaining sperm motility. Majority (80%) of the more-abundant and five specific proteins were annotated to the cytoplasmic domain which might be a result of higher plasma membrane damage and acrosome dysfunction in LSM. Additionally, more-abundant mitochondrial proteins were detected in LSM seminal plasma associated with lower spermatozoa mitochondrial membrane potential (ΔΨm) and ATP concentrations. Further studies showed that the spermatozoa might be suffering from oxidative stress, as the amount of spermatozoa reactive oxygen species (ROS) were largely enhanced, seminal malondialdehyde (MDA) concentrations were increased, and the seminal plasma total antioxidant capacity (T-AOC) were decreased. Our study provides an additional catalogue of chicken seminal plasma proteome and supports the idea that seminal plasma could be as an indicator of spermatozoa physiology. More-abundant of acrosome, mitochondria and sperm cytoskeleton proteins in the seminal plasma could be a marker of sperm dysfunction and loss of motility. The degeneration of spermatozoa caused by the reduced seminal T-AOC and enhanced oxidative stress might be potential determinants of low sperm motility. These results could extend our understanding of sperm motility and sperm physiology regulation.

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Bagnerini, Patrizia, Matteo Neviani, and Ombretta Paladino. "Simulation of the rising of gas bubbles in a pilot-scale external loop airlift photobioreactor." E3S Web of Conferences 113 (2019): 03023. http://dx.doi.org/10.1051/e3sconf/201911303023.

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Air-lift reactors offer an interesting option as a microalgae cultivation system, especially for biorefineries. To optimize this application, a precise description of the moving interfaces formed by the liquid and gas phase is critical. In this paper, a coupled Level Set Method (LSM) and finite difference method is used to simulate gas bubbles dynamics in a pilot-scale external loop air-lift photobioreactor in which microalgae are used to capture CO2 from flue gas and to treat wastewater. Numerical simulations are carried out on a rectangular domain representing the section on the vertical axis of the riser. The data employed were either acquired from previous experimental campaigns carried out in the ALR or found in the literature. The rise, shape dynamics and coalescence process of the bubbles of flue gas are studied. The issue of volume loss characteristic of standard LSM is dealt with the conservative level set method. Computation results show good correspondence with the experimental ones.

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Hou, Jie, and William W. Symes. "Accelerating extended least-squares migration with weighted conjugate gradient iteration." GEOPHYSICS 81, no. 4 (July 2016): S165—S179. http://dx.doi.org/10.1190/geo2015-0499.1.

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Least-squares migration (LSM) iteratively achieves a mean-square best fit to seismic reflection data, provided that a kinematically accurate velocity model is available. The subsurface offset extension adds extra degrees of freedom to the model, thereby allowing LSM to fit the data even in the event of significant velocity error. This type of extension also implies additional computational expense per iteration from crosscorrelating source and receiver wavefields over the subsurface offset, and therefore places a premium on rapid convergence. We have accelerated the convergence of extended least-squares migration by combining the conjugate gradient algorithm with weighted norms in range (data) and domain (model) spaces that render the extended Born modeling operator approximately unitary. We have developed numerical examples that demonstrate that the proposed algorithm dramatically reduces the number of iterations required to achieve a given level of fit or gradient reduction compared with conjugate gradient iteration with Euclidean (unweighted) norms.

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Yerramilli, Anjaneyulu, Venkata Srinivas Challa, Venkata Bhaskar Rao Dodla, Hari Prasad Dasari, John H. Young, Chuck Patrick, Julius M. Baham, Robert L. Hughes, Mark G. Hardy, and Shelton J. Swanier. "Simulation of Surface Ozone Pollution in the Central Gulf Coast Region Using WRF/Chem Model: Sensitivity to PBL and Land Surface Physics." Advances in Meteorology 2010 (2010): 1–24. http://dx.doi.org/10.1155/2010/319138.

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The fully coupled WRF/Chem (Weather Research and Forecasting/Chemistry) model is used to simulate air quality in the Mississippi Gulf coastal region at a high resolution (4 km) for a moderately severe summer ozone episode between 18 CST 7 and 18 CST 10 June 2006. The model sensitivity is studied for meteorological and gaseous criteria pollutants (O3, NO2) using three Planetary Boundary Layer (PBL) and four land surface model (LSM) schemes and comparison of model results with monitoring station observations. Results indicated that a few combinations of PBL and LSMs could reasonably produce realistic meteorological fields and that the combination of Yonsei University (YSU) PBL and NOAH LSM provides best predictions for winds, temperature, humidity and mixed layer depth in the study region for the period of study. The diurnal range in ozone concentration is better estimated by the YSU PBL in association with either 5-layer or NOAH land surface model. The model seems to underestimate the ozone concentrations in the study domain because of underestimation of temperatures and overestimation of winds. The underestimation of NO2by model suggests the necessity of examining the emission data in respect of its accurate representation at model resolution. Quantitative analysis for most monitoring stations indicates that the combination of YSU PBL with NOAH LSM provides the best results for various chemical species with minimum BIAS, RMSE, and high correlation values.

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Dai, Ying‐Xiu, Ying‐Yen Chuang, Po‐Yu Chen, and Chih‐Chiang Chen. "Efficacy and Safety of Ablative Resurfacing With A High‐Energy 1,064 Nd‐YAG Picosecond‐domain Laser for the Treatment of Facial Acne Scars in Asians." Lasers in Surgery and Medicine 52, no. 5 (September 4, 2019): 389–95. http://dx.doi.org/10.1002/lsm.23151.

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Gossec, Laure, Vibeke Strand, Clare Proudfoot, Chieh-I. Chen, Sophie Guillonneau, Toshio Kimura, Hubert van Hoogstraten, Erin Mangan, and Matthew Reaney. "Effects of Sarilumab on Rheumatoid Arthritis as Reported by Patients Using the Rheumatoid Arthritis Impact of Disease Scale." Journal of Rheumatology 46, no. 10 (March 15, 2019): 1259–67. http://dx.doi.org/10.3899/jrheum.180904.

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Objective.We evaluated the effect of sarilumab on patient-perceived impact of rheumatoid arthritis (RA) using the 7-domain RA Impact of Disease (RAID) scale.Methods.Two phase III, randomized, controlled trials of sarilumab in patients with active, longstanding RA were analyzed: (1) sarilumab 150 mg and 200 mg every 2 weeks plus conventional synthetic disease-modifying antirheumatic drugs (+csDMARD) versus placebo + csDMARD [TARGET (NCT01709578)]; and (2) sarilumab 200 mg versus adalimumab (ADA) 40 mg monotherapy [MONARCH (NCT02332590)]. Least-squares mean (LSM) differences in RAID total score (range 0–10) and 7 key RA symptoms, including pain and fatigue (baseline to Weeks 12 and 24), were compared. “Responders” by RAID total score were defined by improvements from baseline ≥ minimal clinically important difference (MCID), and ≥ patient-acceptable symptom-state (PASS) at endpoint.Results.Sarilumab 150 mg and 200 mg + csDMARD were nominally superior (p < 0.05) versus placebo + csDMARD and 200 mg sarilumab versus ADA 40 mg in LSM differences for RAID total score at weeks 12 (−0.93 and −1.13; −0.49, respectively) and 24 (−0.75 and −1.01; −0.78), and all effects of RA (except functional impairment in MONARCH Week 12). Effects were greater in physical domains (e.g., pain) than mental domains (e.g., emotional well-being). More patients receiving sarilumab versus placebo or ADA reported improvements ≥ MCID and PASS in total RAID scores at both assessments.Conclusion.Based on the RAID, sarilumab + csDMARD or as monotherapy reduced the effect of RA on patients’ lives to a greater extent than placebo + csDMARD or ADA monotherapy. (ClinicalTrials.gov: NCT01709578 and NCT02332590)

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Ling, Sharon H. M., Carolyn J. Decker, Martin A. Walsh, Meipei She, Roy Parker, and Haiwei Song. "Crystal Structure of Human Edc3 and Its Functional Implications." Molecular and Cellular Biology 28, no. 19 (August 4, 2008): 5965–76. http://dx.doi.org/10.1128/mcb.00761-08.

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ABSTRACT Edc3 is an enhancer of decapping and serves as a scaffold that aggregates mRNA ribonucleoproteins together for P-body formation. Edc3 forms a network of interactions with the components of the mRNA decapping machinery and has a modular domain architecture consisting of an N-terminal Lsm domain, a central FDF domain, and a C-terminal YjeF-N domain. We have determined the crystal structure of the N-terminally truncated human Edc3 at a resolution of 2.2 Å. The structure reveals that the YjeF-N domain of Edc3 possesses a divergent Rossmann fold topology that forms a dimer, which is supported by sedimentation velocity and sedimentation equilibrium analysis in solution. The dimerization interface of Edc3 is highly conserved in eukaryotes despite the overall low sequence homology across species. Structure-based site-directed mutagenesis revealed dimerization is required for efficient RNA binding, P-body formation, and likely for regulating the yeast Rps28B mRNA as well, suggesting that the dimeric form of Edc3 is a structural and functional unit in mRNA degradation.

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MacKellar, N. C., S. J. Dadson, M. New, and P. Wolski. "Evaluation of the JULES land surface model in simulating catchment hydrology in Southern Africa." Hydrology and Earth System Sciences Discussions 10, no. 8 (August 22, 2013): 11093–128. http://dx.doi.org/10.5194/hessd-10-11093-2013.

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Abstract. Land surface models (LSMs) are advanced tools which can be used to estimate energy, water and biogeochemical exchanges at regional scales. The inclusion of a river flow routing module in an LSM allows for the simulation of river discharge from a catchment and offers an approach to evaluate the response of the system to variations in climate and land-use, which can provide useful information for regional water resource management. This study offers insight into some of the pragmatic considerations of applying an LSM over a regional domain in Southern Africa. The objectives are to identify key parameter sensitivities and investigate differences between two runoff production schemes in physically contrasted catchments. The Joint UK Land Environment Simulator (JULES) LSM was configured for a domain covering Southern Africa at a 0.5° resolution. The model was forced with meteorological input from the WATCH Forcing Data for the period 1981–2001 and sensitivity to various model configurations and parameter settings were tested. Both the PDM and TOPMODEL sub-grid scale runoff generation schemes were tested for parameter sensitivities, with the evaluation focussing on simulated river discharge in sub-catchments of the Orange, Okavango and Zambezi rivers. It was found that three catchments respond differently to the model configurations and there is no single runoff parameterization scheme or parameter values that yield optimal results across all catchments. The PDM scheme performs well in the upper Orange catchment, but poorly in the Okavango and Zambezi, whereas TOPMODEL grossly underestimates discharge in the upper Orange and shows marked improvement over PDM for the Okavango and Zambezi. A major shortcoming of PDM is that it does not realistically represent subsurface runoff in the deep, porous soils typical of the Okavango and Zambezi headwaters. The dry-season discharge in these catchments is therefore not replicated by PDM. TOPMODEL, however, simulates a more realistic seasonal cycle of subsurface runoff and hence improved dry-season flow.

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Lu, Shaoping, Lingyun Qiu, and Xiang Li. "Addressing the crosstalk issue in imaging using seismic multiple wavefields." GEOPHYSICS 86, no. 3 (April 21, 2021): S235—S245. http://dx.doi.org/10.1190/geo2020-0364.1.

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Surface-related-multiple wavefields constitute redundant information in conventional migration and can often be difficult to attenuate. However, when used for migration, multiple wavefields can improve subsurface illumination. Unfortunately, the process of imaging using multiples involves the management of crosstalk, which largely restricts its application. Crosstalk causes phantom images formed by spurious correlation of unrelated events in a migration process. These events can be unrelated orders of multiples in the source and receiver wavefields; they can also be one event associated with a reflector in the source wavefield and another event generated by a different reflector in the receiver wavefield. We have first examined crosstalk by explicitly investigating its generation mechanisms in a migration process and classifying it into different categories based on causality. Following this analysis, crosstalk can be predicted in a migration process and subtracted in the image domain; however, this method is usually difficult to apply due to the complexity of wavefield separation and adaptive subtraction. Furthermore, we develop different algorithms to attenuate the crosstalk, including a deconvolution imaging condition, a least-squares migration (LSM) method, and an advanced algorithm combining LSM with a deconvolution imaging condition. We evaluate these different strategies with synthetic examples. A deconvolution imaging condition can attenuate some crosstalk, but it is less effective at suppressing strong coherent crosstalk events. However, the LSM method can fundamentally address the crosstalk issue, and this approach is further optimized when combined with a deconvolution imaging condition.

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Meena, Sansar Raj, Silvia Puliero, Kushanav Bhuyan, Mario Floris, and Filippo Catani. "Assessing the importance of conditioning factor selection in landslide susceptibility for the province of Belluno (region of Veneto, northeastern Italy)." Natural Hazards and Earth System Sciences 22, no. 4 (April 21, 2022): 1395–417. http://dx.doi.org/10.5194/nhess-22-1395-2022.

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Abstract. In the domain of landslide risk science, landslide susceptibility mapping (LSM) is very important, as it helps spatially identify potential landslide-prone regions. This study used a statistical ensemble model (frequency ratio and evidence belief function) and two machine learning (ML) models (random forest and XGBoost; eXtreme Gradient Boosting) for LSM in the province of Belluno (region of Veneto, northeastern Italy). The study investigated the importance of the conditioning factors in predicting landslide occurrences using the mentioned models. In this paper, we evaluated the importance of the conditioning factors in the overall prediction capabilities of the statistical and ML algorithms. By the trial-and-error method, we eliminated the least “important” features by using a common threshold of 0.30 for statistical and 0.03 for ML algorithms. Conclusively, we found that removing the least important features does not impact the overall accuracy of LSM for all three models. Based on the results of our study, the most commonly available features, for example, the topographic features, contributes to comparable results after removing the least important ones, namely the aspect plan and profile curvature, topographic wetness index (TWI), topographic roughness index (TRI), and normalized difference vegetation index (NDVI) in the case of the statistical model and the plan and profile curvature, TWI, and topographic position index (TPI) for ML algorithms. This confirms that the requirement for the important conditioning factor maps can be assessed based on the physiography of the region.

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Gomes-Filho, José Vicente, Michael Daume, and Lennart Randau. "Unique Archaeal Small RNAs." Annual Review of Genetics 52, no. 1 (November 23, 2018): 465–87. http://dx.doi.org/10.1146/annurev-genet-120417-031300.

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Advances in genome-wide sequence technologies allow for detailed insights into the complexity of RNA landscapes of organisms from all three domains of life. Recent analyses of archaeal transcriptomes identified interaction and regulation networks of noncoding RNAs in this understudied domain. Here, we review current knowledge of small, noncoding RNAs with important functions for the archaeal lifestyle, which often requires adaptation to extreme environments. One focus is RNA metabolism at elevated temperatures in hyperthermophilic archaea, which reveals elevated amounts of RNA-guided RNA modification and virus defense strategies. Genome rearrangement events result in unique fragmentation patterns of noncoding RNA genes that require elaborate maturation pathways to yield functional transcripts. RNA-binding proteins, e.g., L7Ae and LSm, are important for many posttranscriptional control functions of RNA molecules in archaeal cells. We also discuss recent insights into the regulatory potential of their noncoding RNA partners.

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Armuzzi, A., D. T. Rubin, S. Schreiber, J. Panés, M. Fellmann, L. Bartolome, M. Goetsch, et al. "P465 Health-related quality of life from the Inflammatory Bowel Disease Questionnaire in patients with ulcerative colitis treated with etrasimod in the phase 3 ELEVATE UC 52 and ELEVATE UC 12 trials." Journal of Crohn's and Colitis 17, Supplement_1 (January 30, 2023): i593—i594. http://dx.doi.org/10.1093/ecco-jcc/jjac190.0595.

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Abstract Background Etrasimod is an investigational, once-daily, oral, selective sphingosine 1-phosphate receptor 1,4,5 modulator (S1P1,4,5) in development for the treatment of moderately to severely active ulcerative colitis (UC). ELEVATE UC 52 and ELEVATE UC 12 were two phase 3 studies that demonstrated efficacy and safety of etrasimod in patients with UC in which several patient-reported outcomes were collected. Health-related quality of life (HRQoL) was assessed in a post hoc analysis of the ELEVATE programme with the validated Inflammatory Bowel Disease Questionnaire (IBDQ).1 Methods In ELEVATE UC 52 (NCT03945188) and ELEVATE UC 12 (NCT03996369), patients (16-80 years) with moderately to severely active UC were randomised 2:1 to once-daily etrasimod 2 mg or placebo (PBO). Patients in the full analysis set with modified Mayo Scores 5-9 with a completed 32-item IBDQ questionnaire at baseline, week 12 (both trials) and week 52 (ELEVATE UC 52 only) were included in this analysis. Least squares mean (LSM) change from baseline for IBDQ total score and IBDQ domain scores were compared between etrasimod and PBO arms in both trials at each time point (data as observed), along with the proportion of patients who achieved IBDQ remission (IBDQ total score ≥170; nonresponder imputation). Results At baseline, a total of 237 and 191 etrasimod-treated patients and 112 and 96 PBO-treated patients completed the IBDQ for ELEVATE UC 52 and ELEVATE UC 12, respectively. LSM change from baseline in IBDQ total scores for etrasimod vs PBO were 42.8 vs 27.4 (difference [95% CI] 15.4 [6.5, 24.4]; P<0.001) and 55.8 vs 38.1 (difference [95% CI] 17.7 [6.6, 28.6]; P=0.002) at week 12 and week 52, respectively, in ELEVATE UC 52, and 47.5 vs 30.2 (difference [95% CI] 17.3 [8.5, 26.2]; P<0.001) at week 12 in ELEVATE UC 12 (Figure 1A). A greater proportion of etrasimod-treated patients achieved IBDQ remission at week 12 in both trials and week 52 in ELEVATE UC 52 (Figure 1B). Etrasimod-treated patients demonstrated significant improvements from baseline vs PBO in all 4 IBDQ domains in both trials (Figure 2). Across all IBDQ domains, improvements were seen at 12 weeks and the LSM change from baseline was greatest among etrasimod-treated patients at all time points. Conclusion Patients treated with etrasimod demonstrated greater improvement from baseline in total and all 4 domain scores of the IBDQ at the end of the 12-week induction phase and 52-week maintenance phase in comparison with PBO. These findings demonstrate the benefits of etrasimod on disease-specific HRQoL and support the clinical findings from the ELEVATE programme. Reference: 1. Chen XL, et al. Health Qual Life Outcomes. 2017;15:1-13.

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Abri Aghdam, Kaveh, Florian Seidensticker, Amelie Pielen, Carsten Framme, and Bernd Junker. "The short-term effects of aflibercept on the size of choroidal neovascularization lesion in treatment-resistant neovascular age-related macular degeneration as determined by spectral-domain optical coherence tomography." Lasers in Surgery and Medicine 48, no. 7 (April 25, 2016): 668–77. http://dx.doi.org/10.1002/lsm.22531.

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Aldibaja, Mohammad, Naoki Suganuma, and Ryo Yanase. "2.5D Layered Sub-Image LIDAR Maps for Autonomous Driving in Multilevel Environments." Remote Sensing 14, no. 22 (November 18, 2022): 5847. http://dx.doi.org/10.3390/rs14225847.

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This paper proposes a reliable framework to map multilevel road structures in the 2D image domain called layered sub-image maps (LSM). The road is divided into a set of sub-areas providing IDs in the XY plane. Each sub-area is decomposed into several layered images using LIDAR intensity and elevation data to form a 2.5D map image. The layered elevation images are given IDs in the Z plane to represent the height of the contained road features in meter-order whereas the elevation pixels indicate the cm-order of the road slope in the range of 200 cm. The layered intensity images are then created to describe the road surface in conjunction with the number of the layered elevation images and the corresponding pixel distributions. A significant map retrieval strategy during autonomous driving has been designed based on the LSM implementation tactic and the IDs in the XYZ plane. The system’s reliability has been proved by a unique localization module to localize an autonomous vehicle in a challenging multilevel environment consisting of four stacked loops with an average accuracy of 5 cm in lateral, longitudinal and altitudinal directions.

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Spennemann, Pablo C., Juan A. Rivera, A. Celeste Saulo, and Olga C. Penalba. "A Comparison of GLDAS Soil Moisture Anomalies against Standardized Precipitation Index and Multisatellite Estimations over South America." Journal of Hydrometeorology 16, no. 1 (February 1, 2015): 158–71. http://dx.doi.org/10.1175/jhm-d-13-0190.1.

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Abstract This study aims to compare simulated soil moisture anomalies derived from different versions of the Global Land Data Assimilation System (GLDAS), the standardized precipitation index (SPI), and a new multisatellite surface soil moisture product over southern South America. The main motivation is the need for assessing the reliability of GLDAS variables to be used in the characterization of soil state and its variability at the regional scale. The focus is on the southeastern part of South America (SESA), which is part of the La Plata basin, one of the largest basins of the world, where agriculture is the main source of income. The results show that GLDAS data capture soil moisture anomalies and their variability, taking into account regional and seasonal dependencies and showing correspondence with other proxies used to characterize soil states. Over large portions of the domain, and particularly over SESA, the correlation with the SPI is very high, with the second version of GLDAS, version 2 (GLDAS-2 v2), exhibiting the highest values regardless of the season. Similar results were obtained by comparing the surface soil moisture anomalies from the GLDAS land surface model (LSM) against the satellite estimations for a shorter period of time. This work documents that the precipitation dataset used to force each LSM and the choice of the LSM are of major relevance for representing soil conditions in an adequate manner. The results are considered to support the use of GLDAS as an indicator of soil moisture states and for developing new soil moisture–monitoring indices that can be applied, for example, in the context of agricultural production management.

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Dvorak, Elizabeth L., Davetrina S. Gadson, Elizabeth H. Lacey, Andrew T. DeMarco, and Peter E. Turkeltaub. "Domains of Health-Related Quality of Life Are Associated With Specific Deficits and Lesion Locations in Chronic Aphasia." Neurorehabilitation and Neural Repair 35, no. 7 (May 21, 2021): 634–43. http://dx.doi.org/10.1177/15459683211017507.

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Background Health-related quality of life (HRQL) in stroke survivors is related to numerous factors, but more research is needed to delineate factors related to HRQL in people with aphasia. Objective To examine the relationship between HRQL and demographic factors, impairment-based measures, and lesion characteristics in chronic aphasia. Methods A total of 41 left-hemisphere stroke survivors with aphasia underwent cognitive testing and magnetic resonance imaging. To address relationships with demographic and impairment-based measures, test scores were entered into a principal component analysis (PCA) and multiple linear regression was performed for overall and domain (physical, communication, psychosocial) scores of the Stroke and Aphasia Quality of Life Scale (SAQOL-39g). Independent variables included factor scores from the PCA, motricity, lesion volume, depressed mood, and demographic variables. To address relationships with lesion location, multivariate support vector regression lesion-symptom mapping (SVR-LSM) was used to localize lesions associated with SAQOL-39g scores. Results The PCA yielded 3 factors, which were labeled Language Production, Nonlinguistic Cognition, and Language Comprehension. Multiple linear regression revealed that depression symptoms predicted lower SAQOL-39g average and domain scores. Lower motricity scores predicted lower SAQOL-39g average and physical scores, and lower Language Production factor scores predicted lower communication scores. SVR-LSM demonstrated that basal ganglia lesions were associated with lower physical scores, and inferior frontal lesions were associated with lower psychosocial scores. Conclusions HRQL in chronic left-hemisphere stroke survivors with aphasia relates to lesion location, depression symptoms, and impairment-based measures. This information may help identify individuals at risk for specific aspects of low HRQL and facilitate targeted interventions to improve well-being.

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Gavrilieva, Uygulana, Maria Vasilyeva, and Eric T. Chung. "Generalized Multiscale Finite Element Method for Elastic Wave Propagation in the Frequency Domain." Computation 8, no. 3 (July 7, 2020): 63. http://dx.doi.org/10.3390/computation8030063.

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In this work, we consider elastic wave propagation in fractured media. The mathematical model is described by the Helmholtz problem related to wave propagation with specific interface conditions (Linear Slip Model, LSM) on the fracture in the frequency domain. For the numerical solution, we construct a fine grid that resolves all fracture interfaces on the grid level and construct approximation using a finite element method. We use a discontinuous Galerkin method for the approximation by space that helps to weakly impose interface conditions on fractures. Such approximation leads to a large system of equations and is computationally expensive. In this work, we construct a coarse grid approximation for an effective solution using the Generalized Multiscale Finite Element Method (GMsFEM). We construct and compare two types of the multiscale methods—Continuous Galerkin Generalized Multiscale Finite Element Method (CG-GMsFEM) and Discontinuous Galerkin Generalized Multiscale Finite Element Method (DG-GMsFEM). Multiscale basis functions are constructed by solving local spectral problems in each local domains to extract dominant modes of the local solution. In CG-GMsFEM, we construct continuous multiscale basis functions that are defined in the local domains associated with the coarse grid node and contain four coarse grid cells for the structured quadratic coarse grid. The multiscale basis functions in DG-GMsFEM are discontinuous and defined in each coarse grid cell. The results of the numerical solution for the two-dimensional Helmholtz equation are presented for CG-GMsFEM and DG-GMsFEM for different numbers of multiscale basis functions.

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Zinzani, Pier Luigi, Radhakrishnan Ramchandren, Armando Santoro, Ewa Paszkiewicz-Kozik, Robin Gasiorowski, Nathalie A. Johnson, Jose S. R. de Oliveira, et al. "Quality-of-life analysis of pembrolizumab vs brentuximab vedotin for relapsed/refractory classical Hodgkin lymphoma." Blood Advances 6, no. 2 (January 19, 2022): 590–99. http://dx.doi.org/10.1182/bloodadvances.2021004970.

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Abstract KEYNOTE-204 (NCT02684292) demonstrated a progression-free survival advantage for pembrolizumab over brentuximab vedotin (BV) in patients who had relapsed or refractory classical Hodgkin lymphoma (R/R cHL) following, or who were ineligible for, autologous stem cell transplantation (ASCT). Health-related quality of life (HRQoL), measured by patient-reported outcomes (PROs) from KEYNOTE-204, are reported from patients who received ≥1 dose of study treatment and completed ≥1 PRO assessment. The EORTC QoL Questionnaire Core 30 (QLQ-C30) and EuroQoL EQ-5D were administered at baseline, every 6 weeks until week 24, and every 12 weeks thereafter. Prespecified end points included least squares mean (LSM) changes from baseline to week 24 and time to true deterioration (TTD; ≥10-point decline from baseline). Comparisons were evaluated using 2-sided P values uncontrolled for multiplicity. High compliance at baseline (>90%) and through week 24 (>80%) was demonstrated across treatment groups (PRO analysis set: pembrolizumab, n = 146; BV, n = 150). The EORTC QLQ-C30 global health status (GHS)/quality of life (QoL) score improved from baseline to week 24 on pembrolizumab and worsened on BV and demonstrated significant LSM differences at 24 weeks (GHS/QoL: 8.60 [95% confidence interval, 3.89-13.31]; P = .0004). Significant improvements were observed in each QLQ-C30 domain except emotional and cognitive functioning. Compared with BV, pembrolizumab prolonged TTD for GHS/QoL (hazard ratio, 0.40 [95% CI, 0.22-0.74]; P = .003) and each QLQ-C30 domain except cognitive functioning. In conclusion, pembrolizumab demonstrated overall improvements in PROs of HRQoL measures over BV in the KEYNOTE-204 study. These data and previously reported efficacy results support pembrolizumab as the preferred treatment option for patients with R/R cHL who are ineligible for or experience relapse after ASCT.

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Strand, V., P. J. Mease, A. Deodhar, J. Ye, M. Nowak, J. Choi, and B. Becker. "AB0886 The Impact of Deucravacitinib on Health-Related Quality of Life Measured by the Short Form Health Survey 36-Item Questionnaire: Analysis of a Phase 2 Trial in Patients With Active Psoriatic Arthritis." Annals of the Rheumatic Diseases 81, Suppl 1 (May 23, 2022): 1567.1–1567. http://dx.doi.org/10.1136/annrheumdis-2022-eular.1283.

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BackgroundPatients (pts) with psoriatic arthritis (PsA) experience pain, loss of physical function, joint damage, and significant impairments in social and emotional well-being. The Short Form Health Survey 36-item questionnaire (SF-36v2), a generic measure of pt-reported health-related quality of life (HRQOL), includes 36 items and measures 8 domains—physical functioning (PF), role-physical (RP), bodily pain (BP), general health (GH), vitality (VT), social functioning (SF), role-emotional (RE), and mental health (MH)—that contribute to both physical component summary (PCS) and mental component summary (MCS) scores. Deucravacitinib (DEUC) is a novel, oral, selective, allosteric inhibitor of tyrosine kinase 2 (TYK2), an intracellular kinase that mediates cytokine signalling pathways implicated in PsA pathogenesis. In a Phase 2 trial in pts with active PsA, DEUC was well tolerated and significantly more efficacious than placebo (PBO) after 16 weeks (wks) of treatment.1ObjectivesTo further evaluate the effect of DEUC treatment on SF-36 scores.MethodsThis double-blind Phase 2 trial (NCT03881059) enrolled pts with a PsA diagnosis ≥6 months who fulfilled Classification Criteria for Psoriatic Arthritis at screening and had active joint disease (≥3 tender and ≥3 swollen joints), high-sensitivity CRP ≥3 mg/L, and ≥1 plaque psoriasis lesion (≥2 cm). Pts failed or were intolerant to ≥1 nonsteroidal anti-inflammatory, conventional synthetic DMARD, and/or 1 TNF inhibitor (≤30%). Pts were randomised 1:1:1 to DEUC 6 mg once daily (QD) or 12 mg QD, or PBO. Changes from baseline (BL) in SF-36 PCS and MCS scores at Wk 16 were prespecified key secondary and additional endpoints, respectively. The 8 SF-36 domain scores were evaluated at Wk 16. The proportions of pts reporting improvements ≥2.5 and ≥5 points (the minimum clinically important difference [MCID]) in SF-36 summary and domain scores, respectively, were evaluated.ResultsOf 203 pts randomised, 180 (89%) completed 16 wks of treatment (DEUC 6 mg QD, 63/70 [90%]; DEUC 12 mg QD, 59/67 [88%]; PBO, 58/66 [88%]). Demographic and BL disease characteristics were similar across groups. BL mean SF-36 PCS and MCS scores were similar among DEUC 6 mg QD, 12 mg QD, and PBO groups (PCS: 34.0, 34.5, and 33.4; MCS: 45.4, 46.9, and 47.5, respectively). At Wk 16, adjusted mean changes from BL in SF-36 PCS and MCS scores were significantly improved with DEUC 6 and 12 mg QD treatment vs PBO (PCS: 5.6, 5.8, and 2.3; MCS: 3.6, 3.5, and 0.7, respectively; P<0.05). Reported improvements in domain scores with both doses exceeded MCID and were significant in 5 of 8 domains with DEUC 6 mg QD (PF, RP, BP, VT, and SF) and 6 of 8 domains with DEUC 12 mg QD (RE in addition; Figure 1 and Table 1).Table 1.Improvements reported in SF-36 domains with deucravacitinib 6 mg QD and 12 mg QD vs placebo at Week 16PFRPBPGHVTSFREMHDeucravacitinib 6 mg – BL41.942.932.539.639.057.069.558.4Deucravacitinib 12 mg – BL44.146.033.438.543.065.571.559.2Placebo – BL42.442.831.740.338.863.875.159.9Deucravacitinib 6 mg – LSM Wk 1614.612.315.99.511.713.26.98.1Deucravacitinib 12 mg – LSM Wk 1613.313.519.58.412.110.58.78.2Placebo – LSM Wk 163.35.37.06.24.2-0.21.63.6Protocol A/G norms81.181.972.570.259.185.188.076.2Domain scores range from 0-100, with higher scores indicating better health status.A/G, age/gender; BL, baseline; BP, bodily pain; GH, general health; LSM, least square mean change; MH, mental health; PF, physical functioning; QD, once daily; RE, role-emotional; RP-role-physical; SF, social functioning; SF-36, Short Form-36; VT, vitality; Wk, week.ConclusionPts with PsA treated with DEUC reported clinically meaningful and significant improvements in HRQOL, including fatigue, social functioning and role emotional in addition to physical functioning, role physical and pain, at Wk 16.References[1]Mease PJ et al. Efficacy and Safety of Selective TYK2 Inhibitor, Deucravacitinib, in a Phase 2 Trial in Psoriatic Arthritis. Ann Rheum Dis. (In Press)AcknowledgementsThe study was sponsored by Bristol Myers Squibb. Professional medical writing assistance from Julianne Hatfield, PhD was provided by Peloton Advantage, LLC, an OPEN Health company, Parsippany, NJ, USA, and funded by Bristol Myers Squibb.Disclosure of InterestsVibeke Strand Consultant of: AbbVie, Amgen, BMS, Boehringer Ingelheim, Celltrion, Galapagos, Gilead, Janssen, Lilly, Merck, Novartis, Pfizer, Rheos, Samsung, Sandoz, Sun Pharma, UCB., Philip J Mease Consultant of: AbbVie, Amgen, Boehringer Ingelheim, Bristol Myers Squibb, Eli Lilly, Galapagos, Gilead, GlaxoSmithKline, Janssen, Novartis, Pfizer, SUN Pharma, UCB, Grant/research support from: AbbVie, Amgen, Boehringer Ingelheim, Bristol Myers Squibb, Eli Lilly, Galapagos, Gilead, GlaxoSmithKline, Janssen, Novartis, Pfizer, SUN Pharma, UCB, Atul Deodhar Consultant of: Consulting and/or advisory boards: AbbVie, Amgen, Aurinia, Bristol Myers Squibb, Eli Lilly, GlaxoSmithKline, Janssen, MoonLake, Novartis, Pfizer, and UCB, Grant/research support from: AbbVie, Eli Lilly, GlaxoSmithKline, Novartis, Pfizer, UCB, June Ye Shareholder of: Bristol Myers Squibb, Employee of: Bristol Myers Squibb, Miroslawa Nowak Shareholder of: Bristol Myers Squibb, Employee of: Bristol Myers Squibb, Jiyoon Choi Shareholder of: Employee of Bristol Myers Squibb at time of study conduct, Employee of: Employee of Bristol Myers Squibb at time of study conduct, Brandon Becker Shareholder of: Bristol Myers Squibb, Employee of: Bristol Myers Squibb

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Forrester, Mary M., and Reed M. Maxwell. "Impact of Lateral Groundwater Flow and Subsurface Lower Boundary Conditions on Atmospheric Boundary Layer Development over Complex Terrain." Journal of Hydrometeorology 21, no. 6 (June 2020): 1133–60. http://dx.doi.org/10.1175/jhm-d-19-0029.1.

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AbstractCredible soil moisture redistribution schemes are essential to meteorological models, as lower boundary moisture influences the balance of surface turbulent fluxes and atmospheric boundary layer (ABL) development. While land surface models (LSMs) have vastly improved in their hydrologic representation, several commonly held assumptions, such as free-draining lower boundary, one-dimensional moisture flux, and lack of groundwater representation, can bias the terrestrial water balance. This study explores the impact of LSM hydrology representation on ABL development in the Weather Research and Forecasting (WRF) meteorological model. The results of summertime WRF simulations with Noah LSM, characterized by 2-m-thick soil and one-dimensional flow, are shown for a domain in the Colorado Rocky Mountain headwaters region. A reference WRF simulation is compared to 1) the same model with soil moisture initialized by the hydrologic model ParFlow; 2) a deep, free-draining simulation; and 3) WRF coupled to ParFlow, a three-dimensional, integrated groundwater-surface water model. Results show that both lateral transport of groundwater and the rate of drainage from the lower soil layer can weaken or reverse the coupling strength between evaporative fraction and ABL over a 5-month summer period. The resulting shifts in low-level moist convection in river valleys and thermally driven airflows yield strengthened anabatic upslope winds and perturbations to regional precipitation.

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