bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary structural features of SR-like protein acinusS govern the phosphorylation mechanism by SRPK2
Authors: Liang Ning , Zeng Chuyue , Tao Kin Pong , Sou Weng Hong , Hsia Ho Pan , Qu Dan , Lau Sze Nga , Ngo Jacky Chi Ki 
Published: January 2014

SRPKs (serine/arginine protein kinases) are highly specific kinases that recognize and phosphorylate RS (Arg-Ser) dipeptide repeats. It has been shown previously that SRPK1 phosphorylates the RS domain of SRSF1 (serine/arginine splicing factor 1) at multiple sites using a directional and processive mechanism. Such ability to processively phosphorylate substrates is proposed to be an inherent characteristic of SRPKs. SRPK2 is highly related to SRPK1 in sequence and in vitro properties, yet it has been shown to have distinct substrate specificity and physiological function in vivo. To study the molecular basis for substrate specificity of SRPK2, we investigated the roles of the non-kinase regions and a conserved docking groove of SRPK2 in the recognition and phosphorylation of different substrates: SRSF1 and acinusS. Our results reveal that a conserved electronegative docking groove in SRPK2, but not its non-kinase regions, is responsible for substrate binding regardless of their identities. Although SRPK2 phosphorylates SRSF1 in a processive manner as predicted, an electronegative region on acinusS restricts SRPK2 phosphorylation to a single specific site despite the presence of multiple RS dipeptides. These results suggest that primary structural elements on the substrates serve as key regulatory roles in determining the phosphorylation mechanism of SRPK2.
Tunable gaps and enhanced mobilities in strain-engineered silicane
Authors: Restrepo Oscar D. , Mishra Rohan , Goldberger Joshua E. , Windl Wolfgang 
Published: January 2014

The recent demonstration of single-atom thick, sp3-hybridized group 14 analogues of graphene enables the creation of materials with electronic structures that are manipulated by the nature of the covalently bound substituents above and below the sheet. These analogues can be electronically derived from isolated (111) layers of the bulk diamond lattice. Here, we perform systematic Density Functional Theory calculations to understand how the band dispersions, effective masses, and band gaps change as the bulk silicon (111) layers are continuously separated from each other until they are electronically isolated, and then passivated with hydrogen. High-level calculations based on HSE06 hybrid functionals were performed on each endpoint to compare directly with experimental values. We find that the change in the electronic structure due to variations in the Si-H bond length, Si-Si-Si bond angle, and most significantly the Si-Si bond length can tune the nature of the band gap from indirect to direct with dramatic effects on the transport properties. First-principles calculations of the phonon-limited electron mobility predict a value of 464 cm2/Vs for relaxed indirect band gap Si-H monolayers at room temperature. However, for 1.6% tensile strain, the band gap becomes direct, which increases the mobility significantly (8 551 cm2/Vs at 4% tensile strain). In total, this analysis of Si-based monolayers suggests that strain can change the nature of the band gap from indirect to direct and increase the electron mobility more than 18-fold.
Comparison of magnetic probe calibration at nano and millitesla magnitudes
Authors: Pahl Ryan A. , Rovey Joshua L. , Pommerenke David J. 
Published: January 2014

Magnetic field probes are invaluable diagnostics for pulsed inductive plasma devices where field magnitudes on the order of tenths of tesla or larger are common. Typical methods of providing a broadband calibration of \documentclass[12pt]{minimal}\begin{document}$\dot{\rm{B}}$\end{document}Ḃ probes involve either a Helmholtz coil driven by a function generator or a network analyzer. Both calibration methods typically produce field magnitudes of tens of microtesla or less, at least three and as many as six orders of magnitude lower than their intended use. This calibration factor is then assumed constant regardless of magnetic field magnitude and the effects of experimental setup are ignored. This work quantifies the variation in calibration factor observed when calibrating magnetic field probes in low field magnitudes. Calibration of two \documentclass[12pt]{minimal}\begin{document}$\dot{\rm{B}}$\end{document}Ḃ probe designs as functions of frequency and field magnitude are presented. The first \documentclass[12pt]{minimal}\begin{document}$\dot{\rm{B}}$\end{document}Ḃ probe design is the most commonly used design and is constructed from two hand-wound inductors in a differential configuration. The second probe uses surface mounted inductors in a differential configuration with balanced shielding to further reduce common mode noise. Calibration factors are determined experimentally using an 80.4 mm radius Helmholtz coil in two separate configurations over a frequency range of 100–1000 kHz. A conventional low magnitude calibration using a vector network analyzer produced a field magnitude of 158 nT and yielded calibration factors of 15 663 ± 1.7% and 4920 ± 0.6% \documentclass[12pt]{minimal}\begin{document}$\frac{\rm{T}}{\rm{V}\, \rm{s}}$\end{document}TVs at 457 kHz for the surface mounted and hand-wound probes, respectively. A relevant magnitude calibration using a pulsed-power setup with field magnitudes of 8.7–354 mT yielded calibration factors of 14 615 ± 0.3% and 4507 ± 0.4% \documentclass[12pt]{minimal}\begin{document}$\frac{\rm{T}}{\rm{V}\, \rm{s}}$\end{document}TVs at 457 kHz for the surface mounted inductor and hand-wound probe, respectively. Low-magnitude calibration resulted in a larger calibration factor, with an average difference of 9.7% for the surface mounted probe and 12.0% for the hand-wound probe. The maximum difference between relevant and low magnitude tests was 21.5%.
ChREBP, a glucose-responsive transcriptional factor, enhances glucose metabolism to support biosynthesis in human cytomegalovirus-infected cells
Authors: Yu Yongjun , Maguire Tobi G. , Alwine James C. 
Published: January 2014

Significance
Human cytomegalovirus (HCMV)-infected cells and tumor cells produce similar alterations in glucose metabolism, including increasing glucose uptake and glycolysis and redirecting glucose carbon to support synthesis of biomolecules. We show that HCMV infection induces the glucose-responsive transcriptional factor carbohydrate-response element binding protein to reprogram glucose metabolism to support lipid and nucleotide synthesis. This study provides insight into viral mechanisms of pathogenesis.
Acoustic droplet vaporization is initiated by superharmonic focusing
Authors: Shpak Oleksandr , Verweij Martin , Vos Hendrik J. , de Jong Nico , Lohse Detlef , Versluis Michel 
Published: January 2014

SignificanceThis work explains the long-standing puzzle of the physical mechanisms underlying acoustic droplet vaporization (ADV). ADV makes use of low-boiling-point perfluorocarbon droplets that become metastable once injected into the body, where they can be activated by high-intensity ultrasound. How ultrasound can physically trigger the vaporization remained elusive, also given the large mismatch between the ultrasound wavelength and the droplet size. Here we show that vaporization is preceded by nonlinear propagation of the ultrasound wave generating superharmonics. These high-frequency waves focus efficiently within the droplet, triggering vaporization. ADV shows great potential for advanced medical diagnosis and therapy. Our new understanding allows for further reduction of the required pressure amplitudes, thereby minimizing the adverse effects on healthy tissue.
China’s international trade and air pollution in the United States
Authors: Lin Jintai , Pan Da , Davis Steven J. , Zhang Qiang , He Kebin , Wang Can , Streets David G. , Wuebbles Donald J. , Guan Dabo 
Published: January 2014

Significance
International trade affects global air pollution and transport by redistributing emissions related to production of goods and services and by potentially altering the total amount of global emissions. Here we analyze the trade influences by combining an economic-emission analysis on China’s bilateral trade and atmospheric chemical transport modeling. Our focused analysis on US air quality shows that Chinese air pollution related to production for exports contributes, at a maximum on a daily basis, 12–24% of sulfate pollution over the western United States. The US outsourcing of manufacturing to China might have reduced air quality in the western United States with an improvement in the east, due to the combined effects of changes in emissions and atmospheric transport.
Self-replicating colloidal clusters
Authors: Zeravcic Zorana , Brenner Michael P. 
Published: January 2014

Significance
One of the hallmarks of living systems is self-replication. Mimicking nature’s ability to self-replicate would not only give more insight into biological mechanisms of self-replication but also could potentially revolutionize material science and nanotechnology. Over the past 60 y, much research, both theoretical and experimental, has been focused on understanding and realizing self-replicating systems. However, artificial systems that efficiently self-replicate remained elusive. In this paper, we construct schemes for self-replication of small clusters of isotropic particles. By manipulating the energy landscape of the process, we show how exponential replication can be achieved. As a proof of principle, we show exponential self-replication of an octahedral cluster using finite-temperature computer simulations.
Chiral symmetry breaking and surface faceting in chromonic liquid crystal droplets with giant elastic anisotropy
Authors: Jeong Joonwoo , Davidson Zoey S. , Collings Peter J. , Lubensky Tom C. , Yodh A. G. 
Published: January 2014

Significance
Lyotropic chronomic liquid crystals (LCLCs) are water-based systems consisting of planar molecules that form aligned stacks in the nematic phase that develop two-dimensional crystalline order upon cooling to the columnar phase. They are characterized by an unusually small resistance to twist distortions. This work explores the interplay of giant elastic anisotropy and geometrical frustration imposed by boundary conditions in droplets, demonstrating, in particular, spontaneous formation in the nematic phase of chiral patterns from achiral building blocks and of central line defects and surface faceting in the columnar phase. Because LCLCs are water-loving, these findings about the combined effects of anisotropic elasticity, confinement, and frustration take steps toward tapping applications for liquid crystals in aqueous environments.
Essential role of poly(ADP-ribosyl)ation in cocaine action
Authors: Scobie Kimberly N. , Damez-Werno Diane , Sun HaoSheng , Shao NingYi , Gancarz Amy , Panganiban Clarisse H. , Dias Caroline , Koo JaWook , Caiafa Paola , Kaufman Lewis , Neve Rachael L. , Dietz David M. , Shen Li , Nestler Eric J. 
Published: January 2014

Significance
We demonstrate that chronic cocaine, including cocaine self-administration, induces poly(ADP-ribose) polymerase-1 (PARP-1) in the nucleus accumbens (NAc). Using a combination of viral-mediated gene transfer and pharmacological tools, we show that upregulation of PARP-1 in NAc dramatically enhances behavioral responses to cocaine, whereas downregulation of PARP-1 has the opposite effect. We used chromatin immunoprecipitation sequencing to map genome-wide binding of PARP-1 in NAc. The data demonstrate upregulation of PARP-1 binding across the genome after cocaine administration and identify numerous target genes for PARP-1. Among these is sidekick-1 (SDK1), previously implicated in regulating synaptic connections during development. We confirm SDK1 induction in NAc after chronic cocaine and demonstrate its ability to promote both cocaine’s behavioral effects and induction of dendritic plasticity in NAc.
Induced multipotency in adult keratinocytes through down-regulation of
ΔNp63
or
DGCR8
Authors: Chakravarti Deepavali , Su Xiaohua , Cho Min Soon , Bui Ngoc Hoang Bao , Coarfa Cristian , Venkatanarayan Avinashnarayan , Benham Ashley L. , Flores González Ramón E. , Alana Jennifer , Xiao Weimin , Leung Marco L. , Vin Harina , Chan Io Long , Aquino Arianexys , Müller Nicole , Wang Hongran , Cooney Austin J. , Parker-Thornburg Jan , Tsai Kenneth Y. , Gunaratne Preethi H. , Flores Elsa R. 
Published: January 2014

Significance
The p53 family member deltaNp63 (ΔNp63) is required for transcriptional activation of the microprocessor complex subunit DGCR8 in epidermal cells, leading to terminal differentiation of tissues such as the epidermis. We show here that loss of ΔNp63 leads to the generation of cells with self-renewing but limited differentiation capacity. When DGCR8 is reexpressed in cells deficient for ΔNp63, these cells can terminally differentiate into all three germ layers. We dubbed these cells induced multipotent stem cells because of their remarkable plasticity and ability to differentiate into multiple cell lineages. Based on our results using human keratinocytes, we predict that epidermal cells can be extracted from patient skin biopsies and reprogrammed into multipotent stem cells by knockdown of ΔNp63 or DGCR8.
Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family
Authors: Goulet Adeline , Major Jennifer , Jun Yonggun , Gross Steven P. , Rosenfeld Steven S. , Moores Carolyn A. 
Published: January 2014

Significance
Kinesins are a superfamily of ATP-dependent motors that are important for a wide variety of microtubule-based functions in eukaryotic cells. Kinesins have evolved to allow variable tuning of their motor properties, but the link between molecular variation and motor function is largely unknown. To understand this link, we have studied an essential mitotic kinesin, kinesin-5, which is the target of anticancer drugs. We used cryo-electron microscopy to visualize directly sequential conformational changes of structural elements during the motor ATPase cycle. We have identified the contribution of kinesin-5–specific variations to motor function indicating that kinesins indeed are precisely tuned according to cellular function. This insight will be important in designing kinesin-specific inhibitors in different disease contexts.
Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations
Authors: Fu Glenn K. , Xu Weihong , Wilhelmy Julie , Mindrinos Michael N. , Davis Ronald W. , Xiao Wenzhong , Fodor Stephen P. A. 
Published: January 2014

Significance
RNA sequencing (RNA-Seq) is a common tool for measuring relative gene expression levels. However, as an absolute quantitative tool, the data are prone to various distortions due to biases from library preparation. We improve the quantitative aspects of RNA-Seq by barcoding individual cDNA molecules to correct for amplification bias, distinguish clonal replicates, and obtain absolute measurements of gene expression. We have also developed a set of barcoded synthetic RNAs that can be spiked into samples as easy-to-use quantitative controls. Additionally, we demonstrate the combined use of capture enrichment with molecular barcoding for the sequencing of targeted genes. These results demonstrate low library preparation efficiency leading to the stochastic loss of low-abundance transcripts, which cannot be overcome by simply increasing sequencing depth.
Different modes of endothelial–smooth muscle cell interaction elicit differential β-catenin phosphorylations and endothelial functions
Authors: Chang Shun-Fu , Chen Li-Jing , Lee Pei-Ling , Lee Ding-Yu , Chien Shu , Chiu Jeng-Jiann 
Published: January 2014

Significance
β-Catenin is an important versatile protein in most types of cells and its activity is regulated by differential phosphorylations and, hence, affects cellular functions. In this study, we defined a unique mechanism by which different modes of heterocellular interaction between vascular endothelial cells (ECs) and smooth muscle cells (SMCs) play differential roles in regulating EC β-catenin phosphorylations and functions. Direct physical interaction of SMCs to ECs causes their β-catenin Tyr142-phosphorylation via connexin 43/Fer to induce EC inflammation. In contrast, paracrine interaction of SMCs to ECs induces Ser45/Thr41-phosphorylation of VE-cadherin–associated β-catenin in ECs to cause their barrier dysfunction, with increased permeability. Our findings suggest that different phosphorylated forms of β-catenin play important roles in modulating vascular pathophysiology through different heterocellular interactions.
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
Authors: Starruß Jörn , de Back Walter , Brusch Lutz , Deutsch Andreas 
Published: January 2014

Abstract
Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.
Availability and implementation: Binary packages are available at http://imc.zih.tu-dresden.de/wiki/morpheus for Linux, Mac OSX and MS Windows.
Contact: walter.deback@tu-dresden.de
Supplementary information: Supplementary data are available at Bioinformatics online.
estMOI: estimating multiplicity of infection using parasite deep sequencing data
Authors: Assefa Samuel A. , Preston Mark D. , Campino Susana , Ocholla Harold , Sutherland Colin J. , Clark Taane G. 
Published: January 2014

Abstract
Summary: Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum, genotyping of the merozoite surface protein (MSP1/2) genes is a standard method for assessing MOI, despite the apparent problem of underestimation. The availability of deep coverage data from massively parallizable sequencing technologies means that MOI can be detected genome wide by considering the abundance of heterozygous genotypes. Here, we present a method to estimate MOI, which considers unique combinations of polymorphisms from sequence reads. The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission.
Availability and implementation: estMOI is freely available from http://pathogenseq.lshtm.ac.uk.
Contact: samuel.assefa@lshtm.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
Authors: Silva Ricardo R. , Jourdan Fabien , Salvanha Diego M. , Letisse Fabien , Jamin Emilien L. , Guidetti-Gonzalez Simone , Labate Carlos A. , Vêncio Ricardo Z. N. 
Published: January 2014

Abstract
Summary: We present ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography–mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and (ii) allow sensitive selection of biologically meaningful biochemical reaction databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand-alone versions.
Availability and implementation: ProbMetab was implemented in a modular manner to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/.
Contact: rvencio@usp.br
Supplementary information: Supplementary data are available at Bioinformatics online.
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity
Authors: Malod-Dognin Noël , Pržulj Nataša 
Published: January 2014

Abstract
Motivation: Protein structure alignment is key for transferring information from well-studied proteins to less studied ones. Structural alignment identifies the most precise mapping of equivalent residues, as structures are more conserved during evolution than sequences. Among the methods for aligning protein structures, maximum Contact Map Overlap (CMO) has received sustained attention during the past decade. Yet, known algorithms exhibit modest performance and are not applicable for large-scale comparison.
Results: Graphlets are small induced subgraphs that are used to design sensitive topological similarity measures between nodes and networks. By generalizing graphlets to ordered graphs, we introduce GR-Align, a CMO heuristic that is suited for database searches. On the Proteus_300 set (44 850 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art CMO solvers Apurva, MSVNS and AlEigen7, and its similarity score is in better agreement with the structural classification of proteins. On a large-scale experiment on the Gold-standard benchmark dataset (3 207 270 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art protein structure comparison tools TM-Align, DaliLite, MATT and Yakusa, while achieving similar classification performances. Finally, we illustrate the difference between GR-Align’s flexible alignments and the traditional ones by querying a flexible protein in the Astral-40 database (11 154 protein domains). In this experiment, GR-Align’s top scoring alignments are not only in better agreement with structural classification of proteins, but also that they allow transferring more information across proteins.
Availability and implementation: GR-Align is coded in C++. software and supplementary material are available at: http://bio-nets.doc.ic.ac.uk/home/software/gralign/.
Contact: n.malod-dognin@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.