IonFlow: a galaxy tool for the analysis of ionomics data sets.

INTRODUCTION: Inductively coupled plasma mass spectrometry (ICP-MS) experiments generate complex multi-dimensional data sets that require specialist data analysis tools. OBJECTIVE: Here we describe tools to facilitate analysis of the ionome composed of high-throughput elemental profiling data. METHODS: IonFlow is a Galaxy tool written in R for ionomics data analysis and is freely accessible at https://github.com/wanchanglin/ionflow . It is designed as a pipeline that can process raw data to enable exploration and interpretation using multivariate statistical techniques and network-based algorithms, including principal components analysis, hierarchical clustering, relevance network extraction and analysis, and gene set enrichment analysis. RESULTS AND CONCLUSION: The pipeline is described and tested on two benchmark data sets of the haploid S. Cerevisiae ionome and of the human HeLa cell ionome

Non-functional immunoglobulin G transcripts in a case of hyper-immunoglobulin M syndrome similar to type 4

86% of immunoglobulin G (IgG) heavy-chain gene transcripts were found to be non-functional in the peripheral blood B cells of a patient initially diagnosed with common variable immunodeficiency, who later developed raised IgM, whereas no non-functionally rearranged transcripts were found in the cells of seven healthy control subjects. All the patient's IgM heavy-chain and κ light-chain transcripts were functional, suggesting that either non-functional rearrangements were being selectively class-switched to IgG, or that receptor editing was rendering genes non-functional after class-switching. The functional γ-chain sequences showed a normal rate of somatic hypermutation while non-functional sequences contained few somatic mutations, suggesting that most came from cells that had no functional gene and therefore were not receiving signals for hypermutation. However, apoptosis of peripheral blood lymphocytes was not impaired. No defects have been found in any of the genes currently known to be responsible for hyper-IgM syndrome but the phenotype fits best to type 4

Tropical Dominating Sets in Vertex-Coloured Graphs

Given a vertex-coloured graph, a dominating set is said to be tropical if every colour of the graph appears at least once in the set. Here, we study minimum tropical dominating sets from structural and algorithmic points of view. First, we prove that the tropical dominating set problem is NP-complete even when restricted to a simple path. Then, we establish upper bounds related to various parameters of the graph such as minimum degree and number of edges. We also give upper bounds for random graphs. Last, we give approximability and inapproximability results for general and restricted classes of graphs, and establish a FPT algorithm for interval graphs.Comment: 19 pages, 4 figure

Parity Doubling and the S Parameter Below the Conformal Window

We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with $N_f = 2$ and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when $N_f$ is increased from 2 to 6, motivating study of these trends as $N_f$ is increased further, toward the critical value for transition from confinement to infrared conformality.Comment: 4 pages, 5 figures; to be submitted to PR

Genomic Expansion of Magnetotactic Bacteria Reveals an Early Common Origin of Magnetotaxis with Lineage-specific Evolution

The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth’s magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and “Candidatus Lambdaproteobacteria” classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB

Dynamic Role-Based Access Control for Decentralized Applications

Access control management is an integral part of maintaining the security of an application. Although there has been significant work in the field of cloud access control mechanisms, however, with the advent of Distributed Ledger Technology (DLT), on-chain access control management frameworks hardly exist. Existing access control management mechanisms are tightly coupled with the business logic, resulting in governance issues, non-coherent with existing Identity Management Solutions, low security, and compromised usability. We propose a novel framework to implement dynamic role-based access control for decentralized applications (dApps). The framework allows for managing access control on a dApp, which is completely decoupled from the business application and integrates seamlessly with any dApps. The smart contract architecture allows for the independent management of business logic and execution of access control policies. It also facilitates secure, low cost, and a high degree of flexibility of access control management. The proposed framework promotes decentralized governance of access control policies and efficient smart contract upgrades. We also provide quantitative and qualitative metrics for the efficacy and efficiency of the framework. Any Turing complete smart contract programming language is an excellent fit to implement the framework. We expect this framework to benefit enterprise and non-enterprise dApps and provide greater access control flexibility and effective integration with traditional and state of the art identity management solutions.Comment: 6 pages, 3 figures, 1 tabl

Clinical implications of increased lymph vessel density in the lymphatic metastasis of early-stage invasive cervical carcinoma: a clinical immunohistochemical method study

<p>Abstract</p> <p>Background</p> <p>Cervical cancer is the most common malignant gynecological cancer, and lymphatic metastasis can occur in the early stage of tumor growth. Lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1), a marker for lymphatic endothelium, provides powerful tools for studying tumor lymphangiogenesis. The purpose of this study is to investigate the clinical implications of lymphangiogenesis in the metastasis of early-stage invasive cervical carcinoma.</p> <p>Methods</p> <p>We used immunohistochemical (IHC) staining with the antibody against LYVE-1 to measure lymph vessel density in 41 cases of early-stage invasive cervical carcinoma and 12 cases of normal cervical samples. We then analyzed the correlation between lymph vessel density and clinicopathological features of the tumors.</p> <p>Results</p> <p>(1) The majority of peritumoral lymphatics were enlarged, dilated, and irregular. In contrast, intratumoral lymph vessels were small and collapsed. The peritumoral lymphatic vessel density (PLVD) was significantly higher than the intratumoral lymphatic vessel density (ILVD) (<it>P </it>< 0.01). (2) Both ILVD and PLVD were significantly higher than the LVD of the control cervixes (<it>P </it>< 0.01). (3) Both ILVD and PLVD were significantly associated with lymph node metastasis (ILVD, <it>P </it>< 0.05; PLVD, <it>P </it>< 0.01) and lymphatic vessel invasion (ILVD, <it>P </it>< 0.05; PLVD, <it>P </it>< 0.01). Both the ILVD and PLVD in patients with histological grade HG2 and HG3 were significantly higher than those with HG1 (<it>P </it>< 0.05).</p> <p>Conclusion</p> <p>Tumor lymphangiogenesis in early-stage invasive cervical carcinoma may play an important role in the process of lymphatic metastasis.</p

Holographic dilepton production in a thermalizing plasma

We determine the out-of-equilibrium production rate of dileptons at rest in strongly coupled N=4 Super Yang-Mills plasma using the AdS/CFT correspondence. Thermalization is achieved via the gravitational collapse of a thin shell of matter in AdS_5 space and the subsequent formation of a black hole, which we describe in a quasistatic approximation. Prior to thermalization, the dilepton spectral function is observed to oscillate as a function of frequency, but the amplitude of the oscillations decreases when thermal equilibrium is approached. At the same time, we follow the flow of the quasinormal spectrum of the corresponding U(1) vector field towards its equilibrium limit.Comment: 21 pages, 7 figures. v2: Version accepted for publication in JHEP; minor modifications, added reference

Holographic Magnetic Star

A warm fermionic AdS star under a homogeneous magnetic field is explored. We obtain the relativistic Landau levels by using Dirac equation and use the Tolman-Oppenheimer-Volkoff (TOV) equation to study the physical profiles of the star. Bulk properties such as sound speed, adiabatic index, and entropy density within the star are calculated analytically and numerically. Bulk temperature increases the mass limit of the AdS star but external magnetic field has the opposite effect. The results are partially interpreted in terms of the pre-thermalization process of the gauge matter at the AdS boundary after the mass injection. The entropy density is found to demonstrate similar temperature dependence as the magnetic black brane in the AdS in certain limits regardless of the different nature of the bulk and Hawking temperatures. Total entropy of the AdS star is also found to be an increasing function of the bulk temperature and a decreasing function of the magnetic field, similar behaviour to the mass limit. Since both total entropy and mass limit are global quantities, they could provide some hints to the value of entropy and energy of the dual gauge matter before and during the thermalization.Comment: 39 pages, 14 figures, 1 table, comments and references added, to appear in JHE