Multiplicative random walk Metropolis-Hastings on the real line

In this article we propose multiplication based random walk Metropolis Hastings (MH) algorithm on the real line. We call it the random dive MH (RDMH) algorithm. This algorithm, even if simple to apply, was not studied earlier in Markov chain Monte Carlo literature. The associated kernel is shown to have standard properties like irreducibility, aperiodicity and Harris recurrence under some mild assumptions. These ensure basic convergence (ergodicity) of the kernel. Further the kernel is shown to be geometric ergodic for a large class of target densities on $\mathbb{R}$. This class even contains realistic target densities for which random walk or Langevin MH are not geometrically ergodic. Three simulation studies are given to demonstrate the mixing property and superiority of RDMH to standard MH algorithms on real line. A share-price return data is also analyzed and the results are compared with those available in the literature

Imaginary-time matrix product state impurity solver for dynamical mean-field theory

We present a new impurity solver for dynamical mean-field theory based on imaginary-time evolution of matrix product states. This converges the self-consistency loop on the imaginary-frequency axis and obtains real-frequency information in a final real-time evolution. Relative to computations on the real-frequency axis, required bath sizes are much smaller and less entanglement is generated, so much larger systems can be studied. The power of the method is demonstrated by solutions of a three band model in the single and two-site dynamical mean-field approximation. Technical issues are discussed, including details of the method, efficiency as compared to other matrix product state based impurity solvers, bath construction and its relation to real-frequency computations and the analytic continuation problem of quantum Monte Carlo, the choice of basis in dynamical cluster approximation, and perspectives for off-diagonal hybridization functions.Comment: 8 pages + 4 pages appendix, 9 figure

Evaluation of some industrial effluents in Jos metropolis, Plateau State, Nigeria

Industrial effluents are generally discharged into receiving water bodies or disposed on land. These effluents are often used by the communities around for domestic activities like farming. Sometimes effluents gain access into wells or streams within the community. Analyses aimed to determine the strength of effluents of three different industries in Jos metropolis: industry A (a food industry), industry B (a pharmaceutical outfit) and Industry C (a water treatment plant) using  parameters such as physicochemical, chemical and  microbiological tests. Analyses revealed that National Environmental Standards and Regulations Enforcement Agency (NESREA) limits for pH, chloride, oil and grease, zinc, copper and sodium were met by the industries. Industries A and B passed the test for BOD5 but industry C failed. Only industry C passed the test for COD. All the industries failed the tests for sulphide, iron and lead while only Industry A failed the test for free chlorine and nitrates. The most probable number per 100 mL maximum limit was met by industry C alone. High concentrations of microbiological, chemical and physicochemical pollutants being discharged into the environment can be checked by continual monitoring and surveillance by regulatory authorities and education of communities to ensure a healthy environment. Key words: Chemical, microbiological and physicochemical tests, industrial effluents, NESREA limits

Bell inequality violation with two remote atomic qubits

We observe violation of a Bell inequality between the quantum states of two remote Yb ions separated by a distance of about one meter with the detection loophole closed. The heralded entanglement of two ions is established via interference and joint detection of two emitted photons, whose polarization is entangled with each ion. The entanglement of remote qubits is also characterized by full quantum state tomography.Comment: 4 pages, 4 figure

Advances, obstacles, and opportunities for machine learning in proteomics

The fields of proteomics and machine learning are both large disciplines, each producing well over 5,000 publications per year. However, studies combining both fields are still relatively rare, with only about 2% of recent proteomics papers including machine learning. This review, which focuses on the intersection of the fields, is intended to inspire proteomics researchers to develop skills and knowledge in the application of machine learning. A brief tutorial introduction to machine learning is provided, and research advances that rely on both fields, particularly as they relate to proteomics tools development and biomarker discovery, are highlighted. Key knowledge gaps and opportunities for scientific advancement are also enumerated

Advances, obstacles, and opportunities for machine learning in proteomics

The fields of proteomics and machine learning are both large disciplines, each producing well over 5,000 publications per year. However, studies combining both fields are still relatively rare, with only about 2% of recent proteomics papers including machine learning. This review, which focuses on the intersection of the fields, is intended to inspire proteomics researchers to develop skills and knowledge in the application of machine learning. A brief tutorial introduction to machine learning is provided, and research advances that rely on both fields, particularly as they relate to proteomics tools development and biomarker discovery, are highlighted. Key knowledge gaps and opportunities for scientific advancement are also enumerated

Absolute Quantitation of Glycosylation Site Occupancy Using Isotopically Labeled Standards and LC-MS

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1007/s13361-014-0859-2.N-linked glycans are required to maintain appropriate biological functions on proteins. Underglycosylation leads to many diseases in plants and animals; therefore, characterizing the extent of glycosylation on proteins is an important step in understanding, diagnosing, and treating diseases. To determine the glycosylation site occupancy, protein N-glycosidase F (PNGase F) is typically used to detach the glycan from the protein, during which the formerly glycosylated asparagine undergoes deamidation to become an aspartic acid. By comparing the abundance of the resulting peptide containing aspartic acid against the one containing non-glycosylated asparagine, the glycosylation site occupancy can be evaluated. However, this approach can give inaccurate results when spontaneous chemical deamidation of the non-glycosylated asparagine occurs. To overcome this limitation, we developed a new method to measure the glycosylation site occupancy that does not rely on converting glycosylated peptides to their deglycosylated forms. Specifically, the overall protein concentration and the non-glycosylated portion of the protein are quantified simultaneously by using heavy isotope-labeled internal standards coupled with LC-MS analysis, and the extent of site occupancy is accurately determined. The efficacy of the method was demonstrated by quantifying the occupancy of a glycosylation site on bovine fetuin. The developed method is the first work that measures the glycosylation site occupancy without using PNGase F, and it can be done in parallel with glycopeptide analysis because the glycan remains intact throughout the workflow

The effect of metal ions released from different dental implant-abutment couples on osteoblast function and secretion of bone resorbing mediators

OBJECTIVES: The etiology of the reduced marginal bone loss observed around platform-switched implant-abutment connections is not clear but could be related to the release of variable amounts of corrosion products. The present study evaluated the effect of different concentrations of metal ions released from different implant abutment couples on osteoblastic cell viability, apoptosis and expression of genes related to bone resorption. METHODS: Osteoblastic cells were exposed to five conditions of culture media prepared containing metal ions (titanium, aluminum, vanadium, cobalt, chromium and molybdenum) in different concentrations representing the amounts released from platform-matched and platform-switched implant-abutment couples as a result of an earlier accelerated corrosion experiment. Cell viability was evaluated over 21days using the Alamar Blue assay. Induction of apoptosis was measured after 24h of exposure using flow cytometry. Expression of interleukin-6, interleukin-8, cyclooxygenase-2, caspase-8, osteoprotegerin and receptor activator of nuclear factor kappa-B ligand (RANKL) by osteoblastic cells were analysed after exposure for 1, 3 and 21days using real-time quantitative polymerase chain reaction assay RESULTS: Metal ions in concentrations representing the platform-matched groups led to a reduction in cell viability (P<0.01) up to 7days of exposure. Stimulated cells showed higher rates of early apoptosis (P<0.01) compared to non-treated cells. Metal ions up-regulated the expression of interleukin-6, interleukin-8, cyclooxygenase-2 and RANKL in a dose dependent manner after 1day of exposure (P<0.05). The up-regulation was more pronounced in the groups containing the corrosion products of platform-matched implant-abutment couples. CONCLUSION: Osteoblastic cell viability, apoptosis, and regulation of bone resorbing mediators were significantly altered in the presence of metal ions. The change in cytokine levels expressed was directly proportional to the metal ion concentration. CLINICAL SIGNIFICANCE: The observed biological responses to decreased amounts of metal ions released from platform-switched implant-abutment couples compared to platform-matched couples may partly explain the positive radiographic findings in respect to crestal bone level when utilising the "platform-switching" concept, which highlights the possible role of corrosion products in the mediation of crestal bone loss around dental implants