ComplexViewer: visualization of curated macromolecular complexes.

SUMMARY: Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions. Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex. AVAILABILITY AND IMPLEMENTATION: freely available under Apache version 2 license; EMBL-EBI Complex Portal: http://www.ebi.ac.uk/complexportal; Source code: https://github.com/MICommunity/ComplexViewer; Package: https://www.npmjs.com/package/complexviewer; http://biojs.io/d/complexviewer. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. CONTACT: [email protected] or [email protected]

Insights into olfactory ensheathing cell development from a laser-microdissection and transcriptome-profiling approach.

Olfactory ensheathing cells (OECs) are neural crest-derived glia that ensheath bundles of olfactory axons from their peripheral origins in the olfactory epithelium to their central targets in the olfactory bulb. We took an unbiased laser microdissection and differential RNA-seq approach, validated by in situ hybridization, to identify candidate molecular mechanisms underlying mouse OEC development and differences with the neural crest-derived Schwann cells developing on other peripheral nerves. We identified 25 novel markers for developing OECs in the olfactory mucosa and/or the olfactory nerve layer surrounding the olfactory bulb, of which 15 were OEC-specific (that is, not expressed by Schwann cells). One pan-OEC-specific gene, Ptprz1, encodes a receptor-like tyrosine phosphatase that blocks oligodendrocyte differentiation. Mutant analysis suggests Ptprz1 may also act as a brake on OEC differentiation, and that its loss disrupts olfactory axon targeting. Overall, our results provide new insights into OEC development and the diversification of neural crest-derived glia.Cambridge Commonwealth Trust Cambridge Philosophical Societ

Molecular Characterization and Patient Outcome of Melanoma Nodal Metastases and an Unknown Primary Site

Background Melanoma of unknown primary site (MUP) is not a completely understood entity with nodal metastases as the most common first clinical manifestation. The aim of this multicentric study was to assess frequency and type of oncogenic BRAF/NRAS/KIT mutations in MUP with clinically detected nodal metastases in relation to clinicopathologic features and outcome. Materials and Methods We analyzed series of 103 MUP patients (period: 1992-2010) after therapeutic lymphadenectomy (LND): 40 axillary, 47 groin, 16 cervical, none treated with BRAF inhibitors. We performed molecular characterization of BRAF/NRAS/KIT mutational status in nodal metastases using direct sequencing of respective coding sequences. Median follow-up time was 53 months. Results BRAF mutations were detected in 55 cases (53 %) (51 V600E, 93 %; 4 others, 7 %), and mutually exclusive NRAS mutations were found in 14 cases (14 %) (7 p.Q61R, 4 p.Q61K, 2 p.Q61H, 1 p.Q13R). We have not detected any mutations in KIT. The 5-year overall survival (OS) was 34 %; median was 24 months. We have not found significant correlation between mutational status (BRAF/NRAS) and OS; however, for BRAF or NRAS mutated melanomas we observed significantly shorter disease-free survival (DFS) when compared with wild-type melanoma patients (p = .04; 5-year DFS, 18 vs 19 vs 31 %, respectively). The most important factor influencing OS was number of metastatic lymph nodes >1 (p = .03). Conclusions Our large study on molecular characterization of MUP with nodal metastases showed that MUPs had molecular features similar to sporadic non-chronic-sun-damaged melanomas. BRAF/NRAS mutational status had negative impact on DFS in this group of patients. These observations might have potential implication for molecular-targeted therapy in MUPs

Correction to Severe depression is associated with increased microglial quinolinic acid in subregions of the anterior cingulate gyrus: Evidence for an immune-modulated glutamatergic neurotransmission? [Journal of Neuroinflammation (2013) 10, 34] 10.1186/1742-2094-10-34

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Identified baryon and meson distributions at large transverse momenta from Au+Au collisions at sNN=200\sqrt{s_{_{NN}}} = 200 GeV

Transverse momentum spectra of $\pi^{\pm}$, $p$ and $\bar{p}$ up to 12 GeV/c at mid-rapidity in centrality selected Au+Au collisions at $\sqrt{s_{_{NN}}} = 200$ GeV are presented. In central Au+Au collisions, both $\pi^{\pm}$ and $p(\bar{p})$ show significant suppression with respect to binary scaling at $p_T >$ 4 GeV/c. Protons and anti-protons are less suppressed than $\pi^{\pm}$, in the range 1.5 $< p_{T} <$6 GeV/c. The $\pi^-/\pi^+$ and $\bar{p}/p$ ratios show at most a weak $p_T$ dependence and no significant centrality dependence. The $p/\pi$ ratios in central Au+Au collisions approach the values in p+p and d+Au collisions at $p_T >$ 5 GeV/c. The results at high $p_T$ indicate that the partonic sources of $\pi^{\pm}$, $p$ and $\bar{p}$ have similar energy loss when traversing the nuclear medium.Comment: 6 pages, 4 figure

Longitudinal double-spin asymmetry and cross section for inclusive jet production in polarized proton collisions at sqrt(s) = 200 GeV

We report a measurement of the longitudinal double-spin asymmetry A_LL and the differential cross section for inclusive midrapidity jet production in polarized proton collisions at sqrt(s)=200 GeV. The cross section data cover transverse momenta 5 < pT < 50 GeV/c and agree with next-to-leading order perturbative QCD evaluations. The A_LL data cover 5 < pT < 17 GeV/c and disfavor at 98% C.L. maximal positive gluon polarization in the polarized nucleon.Comment: 6 pages, 3 figures. Minor changes from review process in Phys. Rev. Lett. Plain text tables of data in STAR publications may be found at http://www.star.bnl.gov/central/publications

Strangelet search at RHIC

Two position sensitive Shower Maximum Detector (SMDs) for Zero-Degree Calorimeters (ZDCs) were installed by STAR before run 2004 at both upstream and downstream from the interaction point along the beam axis where particles with small rigidity are swept away by strong magnetic field. The ZDC-SMDs provides information about neutral energy deposition as a function of transverse position in ZDCs. We report the preliminary results of strangelet search from a triggered data-set sampling 100 million Au+Au collisions at top RHIC energy.Comment: Strange Quark Matter 2004 conference proceedin

Multiplicity and Pseudorapidity Distributions of Charged Particles and Photons at Forward Pseudorapidity in Au + Au Collisions at sqrt{s_NN} = 62.4 GeV

We present the centrality dependent measurement of multiplicity and pseudorapidity distributions of charged particles and photons in Au + Au collisions at sqrt{s_NN} = 62.4 GeV. The charged particles and photons are measured in the pseudorapidity region 2.9 < eta < 3.9 and 2.3 < eta < 3.7, respectively. We have studied the scaling of particle production with the number of participating nucleons and the number of binary collisions. The photon and charged particle production in the measured pseudorapidity range has been shown to be consistent with energy independent limiting fragmentation behavior. The photons are observed to follow a centrality independent limiting fragmentation behavior while for the charged particles it is centrality dependent. We have carried out a comparative study of the pseudorapidity distributions of positively charged hadrons, negatively charged hadrons, photons, pions, net protons in nucleus--nucleus collisions and pseudorapidity distributions from p+p collisions. From these comparisons we conclude that baryons in the inclusive charged particle distribution are responsible for the observed centrality dependence of limiting fragmentation. The mesons are found to follow an energy independent behavior of limiting fragmentation while the behavior of baryons seems to be energy dependent.Comment: 17 pages and 20 figure