iTriplet, a rule-based nucleic acid sequence motif finder

<p>Abstract</p> <p>Background</p> <p>With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides) motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing.</p> <p>Results</p> <p>We have conducted a comprehensive assessment on the performance and sensitivity-specificity of iTriplet in analyzing artificial and real biological sequences in various genomic regions. The results show that iTriplet is able to solve challenging cases. Furthermore we have confirmed the utility of iTriplet by showing it accurately predicts polyA-site-related motifs using a dual Luciferase reporter assay.</p> <p>Conclusion</p> <p>iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems.</p

Toward a neuroscience of interactive parent–infant dyad empathy

In accord with social neuroscience's progression to include interactive experimental paradigms, parents' brains have been activated by emotionally charged infant stimuli - especially of their own infant - including baby cry and picture. More recent research includes the use of brief video clips and opportunities for maternal response. Among brain systems important to parenting are those involved in empathy. This research may inform recent studies of decreased societal empathy, offer mechanisms and solutions

Facilitating the systematic nanoscale study of battery materials by atom probe tomography through in-situ metal coating

Through its capability for 3D mapping of Li at the nanoscale, atom probe tomography (APT) is poised to play a key role in understanding the microstructural degradation of lithium-ion batteries (LIB) during successive charge and discharge cycles. However, APT application to materials for LIB is plagued by the field induced delithiation (deintercalation) of Li-ions during the analysis itself that prevents the precise assessment of the Li distribution. Here, we showcase how a thin Cr-coating, in-situ formed on APT specimens of NMC811 in the focused-ion beam (FIB), preserves the sample's integrity and circumvent this deleterious delithiation. Cr-coated specimens demonstrated remarkable improvements in data quality and virtually eliminated premature specimen failures, allowing for more precise measurements via. improved statistics. Through improved data analysis, we reveal substantial cation fluctuations in commercial grade NMC811, including complete grains of LiMnO. The current methodology stands out for its simplicity and cost-effectiveness and is a viable approach to prepare battery cathodes and anodes for systematic APT studies

Nanocomposites from Stable Dispersions of Carbon Nanotubes in Polymeric Matrices Using Dispersion Interaction

Stable dispersions of carbon nanotubes (CNTs) in polymeric matrices include CNTs dispersed in a host polymer or copolymer whose monomers have delocalized electron orbitals, so that a dispersion interaction results between the host polymer or copolymer and the CNTs dispersed therein. Nanocomposite products, which are presented in bulk, or when fabricated as a film, fiber, foam, coating, adhesive, paste, or molding, are prepared by standard means from the present stable dispersions of CNTs in polymeric matrices, employing dispersion interactions, as presented hereinabove

Upregulation of SOCS-3 and PIAS-3 Impairs IL-12-Mediated Interferon-Gamma Response in CD56+ T Cells in HCV-Infected Heroin Users

CD56(+) T cells are abundant in liver and play an important role in host innate immunity against viral infections, including hepatitis C virus (HCV) infection, a common infection among heroin abusers. We thus investigated the in vivo impact of heroin use or heroin use plus HCV infection on the CD56(+) T cell frequency and function.A total of 37 heroin users with (17) or without (20) HCV infection and 17 healthy subjects were included in the study. Although there was no significant difference in CD56(+) T cell frequency in PBMCs among three study groups, CD56(+) T cells isolated from the heroin users had significantly lower levels of constitutive interferon-gamma (IFN-gamma) expression than those from the normal subjects. In addition, when stimulated by interleukin (IL)-12, CD56(+) natural T cells from HCV-infected heroin users produced significantly lower levels of IFN-gamma than those from the normal subjects. This diminished ability to produce IFN-gamma by CD56(+) T cells was associated with the increased plasma HCV viral loads in the HCV-infected heroin users. Investigation of the mechanisms showed that although heroin use or heroin use plus HCV infection had little impact on the expression of the key positive regulators (IL-12 receptors, STAT-1, 3, 4, 5, JAK-2, and TYK-2) in IL-12 pathway, heroin use or heroin use plus HCV infection induced the expression of suppressor of cytokine signaling protein-3 (SOCS-3) and protein inhibitors of activated STAT-3 (PIAS-3), two key inhibitors of IL-12 pathway.These findings provide compelling in vivo evidence that heroin use or heroin use plus HCV infection impairs CD56(+) T cell-mediated innate immune function, which may account for HCV infection and persistence in liver

Thermal and magnetic properties of a low-temperature antiferromagnet Ce4_4Pt12_{12}Sn25_{25}

We report specific heat ($C$) and magnetization ($M$) of single crystalline Ce$_4$Pt$_{12}$Sn$_{25}$ at temperature down to $\sim$50mK and in fields up to 3T. $C/T$ exhibits a sharp anomaly at 180mK, with a large $\Delta C/T\sim$30J/molK$^2$-Ce, which, together with the corresponding cusp-like magnetization anomaly, indicates an antiferromagnetic (AFM) ground state with a N\'eel temperature $T_N$=180mK. Numerical calculations based on a Heisenberg model reproduce both zero-field $C$ and $M$ data, thus placing Ce$_4$Pt$_{12}$Sn$_{25}$ in the weak exchange coupling $J<J_c$ limit of the Doniach diagram, with a very small Kondo scale $T_K\ll T_N$. Magnetic field suppresses the AFM state at $H^*\approx$0.7T, much more effectively than expected from the Heisenberg model, indicating additional effects possibly due to frustration or residual Kondo screening.Comment: 8 pages, 7 figures, accepted for publication in Phys. Rev.

An ancient role for Gata-1/2/3 and Scl transcription factor homologs in the development of immunocytes

AbstractAlthough vertebrate hematopoiesis is the focus of intense study, immunocyte development is well-characterized in only a few invertebrate groups. The sea urchin embryo provides a morphologically simple model for immune cell development in an organism that is phylogenetically allied to vertebrates. Larval immunocytes, including pigment cells and several blastocoelar cell subtypes, emerge from a population of non-skeletal mesodermal (NSM) precursors that is specified at the blastula stage. This ring of cells is first partitioned into oral and aboral fields with distinct blastocoelar and pigment cell gene regulatory programs. The oral field is subsequently specified into several distinct immune and non-immune cell types during gastrulation. Here we characterize the oral NSM expression and downstream function of two homologs of key vertebrate hematopoietic transcription factors: SpGatac, an ortholog of vertebrate Gata-1/2/3 and SpScl, an ortholog of Scl/Tal-2/Lyl-1. Perturbation of SpGatac affects blastocoelar cell migration at gastrulation and later expression of immune effector genes, whereas interference with SpScl function disrupts segregation of pigment and blastocoelar cell precursors. Homologs of several transcription regulators that interact with Gata-1/2/3 and Scl factors in vertebrate hematopoiesis are also co-expressed in the oral NSM, including SpE-protein, the sea urchin homolog of vertebrate E2A/HEB/E2-2 and SpLmo2, an ortholog of a dedicated cofactor of the Scl–GATA transcription complex. Regulatory analysis of SpGatac indicates that oral NSM identity is directly suppressed in presumptive pigment cells by the transcription factor SpGcm. These findings provide part of a comparative basis to understand the evolutionary origins and regulatory biology of deuterostome immune cell differentiation in the context of a tractable gene regulatory network model

Sex differences in atheroma burden and endothelial function in patients with early coronary atherosclerosis

Aims Women and men have different clinical presentations and outcomes in coronary artery disease (CAD). We tested the hypothesis that sex differences may influence coronary atherosclerotic burden and coronary endothelial function before development of obstructive CAD. Methods and results A total of 142 patients (53 men, 89 women; mean ± SD age, 49.3 ± 11.7 years) with early CAD simultaneously underwent intravascular ultrasonography and coronary endothelial function assessment. Atheroma burden in the left main and proximal left anterior descending (LAD) arteries was significantly greater in men than women (median, 23.0% vs. 14.1%, P = 0.002; median, 40.1% vs. 29.3%, P = 0.001, respectively). Atheroma eccentricity in the proximal LAD artery was significantly higher in men than women (median, 0.89 vs. 0.80, P = 0.04). The length of the coronary segments with endothelial dysfunction was significantly longer in men than women (median, 39.2 vs. 11.1 mm, P = 0.002). In contrast, maximal coronary flow reserve was significantly lower in women than men (2.80 vs. 3.30, P < 0.001). Sex was an independent predictor of atheroma burden in the left main and proximal LAD arteries (both P < 0.05) by multivariate analysis. Conclusion Men have greater atheroma burden, more eccentric atheroma, and more diffuse epicardial endothelial dysfunction than women. These results suggest that men have more severe structural and functional abnormalities in epicardial coronary arteries than women, even in patients with early atherosclerosis, which may result in the higher incidence rates of CAD and ST-segment myocardial infarction in men than wome

On the single mode approximation in spinor-1 atomic condensate

We investigate the validity conditions of the single mode approximation (SMA) in spinor-1 atomic condensate when effects due to residual magnetic fields are negligible. For atomic interactions of the ferromagnetic type, the SMA is shown to be exact, with a mode function different from what is commonly used. However, the quantitative deviation is small under current experimental conditions (for $^{87}$Rb atoms). For anti-ferromagnetic interactions, we find that the SMA becomes invalid in general. The differences among the mean field mode functions for the three spin components are shown to depend strongly on the system magnetization. Our results can be important for studies of beyond mean field quantum correlations, such as fragmentation, spin squeezing, and multi-partite entanglement.Comment: Revised, newly found analytic proof adde