An optimal subgradient algorithm for large-scale convex optimization in simple domains

This paper shows that the optimal subgradient algorithm, OSGA, proposed in \cite{NeuO} can be used for solving structured large-scale convex constrained optimization problems. Only first-order information is required, and the optimal complexity bounds for both smooth and nonsmooth problems are attained. More specifically, we consider two classes of problems: (i) a convex objective with a simple closed convex domain, where the orthogonal projection on this feasible domain is efficiently available; (ii) a convex objective with a simple convex functional constraint. If we equip OSGA with an appropriate prox-function, the OSGA subproblem can be solved either in a closed form or by a simple iterative scheme, which is especially important for large-scale problems. We report numerical results for some applications to show the efficiency of the proposed scheme. A software package implementing OSGA for above domains is available

MS²PIP: a tool for MS/MS peak intensity prediction

Motivation: Tandem mass spectrometry provides the means tomatch mass spectrometry signal observations with the chemical entities that generated them. The technology produces signal spectra that contain information about the chemical dissociation pattern of a peptide that was forced to fragment using methods like collision-induced dissociation. The ability to predict these MS 2 signals and to understand this fragmentation process is important for sensitive high-throughput proteomics research. Results: We present a new tool called (MSPIP)-P-2 for predicting the intensity of the most important fragment ion signal peaks from a peptide sequence. (MSPIP)-P-2 pre-processes a large dataset with confident peptide-to-spectrum matches to facilitate data-driven model induction using a random forest regression learning algorithm. The intensity predictions of (MSPIP)-P-2 were evaluated on several independent evaluation sets and found to correlate significantly better with the observed fragment-ion intensities as compared with the current state-of-the-art PeptideART tool

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains

Cultural Properties as a Source for Learning History: A Case Study in Cilacap Regency, Indonesia

Abstract. This research aims to identify the potential of cultural property in Cilacap Regency as a source for learning history. The research is conducted using qualitative approach through three stages, namely identifying cultural property that can be used as a source for learning history and educational tourism, assessing the response of history teachers on the use of cultural property as a source for learning history, and assessing the strategy of using cultural property as learning sources. The results show that (1) Cilacap has 84 potential cultural properties that can be developed as learning resources. (2) The potential of the cultural properties has not been fully utilized by teachers as a source for learning history. (3) The reasons behind this are the teacher's lack of information about the cultural properties and the distance between the location of the cultural properties and the school. (4) History teachers in Cilacap use project-based learning as a method of using cultural properties as a learning resource

A Theory of Electrodynamic Responses for Bounded Metals: Surface Capacitive Effects

We report a general macroscopic theory for the electrodynamic response of semi-infinite metals (SIMs). The theory includes the hitherto overlooked capacitive effects due to the finite spatial extension of a surface. The basic structure of this theory is independent of the particulars of electron dynamics. Analytical expressions have been obtained of the charge density-density response function, which is naturally parsed into two parts. One of them represents a bulk property while the other a pure surface property. We apply the theory to study the responses according to several electronic dynamics models and provide a unified view of their validity and limitations. The models studied include the local dielectric model (DM), the dispersive hydrodynamic model (HDM) and specular reflection model (SRM), as well as the less common semi-classical model (SCM) based on Boltzmann's transport equation. We show that, in terms of their basic equations, the SRM is an extension of the HDM, just as the HDM is an extension of the DM. The SCM improves over the SRM critically through the inclusion of translation symmetry breaking and surface roughness effects. We then employ the response function to evaluate the so-called dynamical structure factor, which plays an important role in particle scattering. As expected, this factor reveals a peak due to the excitation of surface plasma waves (SPWs). Surprisingly, however, the peak is shown to be considerably sharper in the SCM than in other models, indicating an incipient instability of the system according to this model. We also study the distribution of charges induced by a charged particle grazing over a SIM surface at constant speed. This distribution is shown to contain model-specific features that are of immediate experimental interest.Comment: 24 pages, 10 figures, a few more references are added and discussed, abstract and introduction modified to improve presentation over older versions, more experimental aspects are discusse

Performance of the Roche Total Mycophenolic Acid® assay on the Cobas Integra 400®, Cobas 6000® and comparison to LC-MS/MS in liver transplant patients

Background: Mycophenolic acid (MPA) is an immunosuppressant for which therapeutic drug monitoring (TDM) is performed for optimal prophylaxis and avoidance of toxicity in transplant patients. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is ideally suited for TDM of MPA. There have been several method comparisons of the Roche Total MPA assay, but none have been performed with respect to liver transplant patients. Methods: We validated the Roche Total MPA assay on the Cobas Integra 400 and Cobas 6000 and compared it to a validated LC-MS/MS (API 2000 (TM)) method. Fifty-five EDTA plasma samples from liver transplant patients were measured with the Roche assay on these platforms and compared to the LC-MS/MS results. Results: Validation of the LC-MS/MS, Cobas Integra 400 and 6000 was performed with good results. The LC-MS/MS/Integra 400/Cobas 6000 were linear up to 30, 15 and 17 mg/L, respectively. Imprecision was <10% for LC-MS/MS and <7% for the Roche assay on both platforms. The samples showed good agreement with LC-MS/MS. Passing-Bablok regression analysis showed Cobas Integra (mg/L) = 1.02 x LC-MS/MS (mg/L)-0.50 and Cobas 6000 (mg/L) = 0.98 x LC-MS/MS-0.47. Conclusions: The Roche Total Mycophenolic Acid-assay is suitable for measuring total MPA in plasma from liver transplant patients and is a good alternative for LC-MS/MS

The Economic Impacts of GM Contamination Incidents on the Organic Sector

This paper examines the economic impact of GM co-existence on the global organic sector to date through GM contamination of organic food and crops. A total of 15 GM contamination incidents in the organic sector are identified, occurring either from cross-pollination from GM crops being grown in the area or due to contamination in the post-harvest supply chain. The financial losses incurred by organic farmers and food companies due to GM contamination are considerable, through lost markets, lost sales, lower prices, negative publicity, withdrawal of organic certification and product recalls. It is important that co-existence regimes address all of these impacts, with the GM sector being held accountabl

Impact of glucuronide interferences on therapeutic drug monitoring of posaconazole by tandem mass spectrometry

Background: Posaconazole is a novel antifungal drug for oral application intended especially for therapy of invasive mycoses. Due to variable gastrointestinal absorption, adverse side effects, and suspected drug-drug interactions, therapeutic drug monitoring (TDM) of posaconazole is recommended. Method: A fast ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for quantification of posaconazole with a run-time &lt;3 min was developed and compared to a LC-MS/MS method and HPLC method with fluorescence detection. Results: During evaluation of UPLC-MS/MS, two earlier eluting peaks were observed in the MRM trace of posaconazole. This was only seen in patient samples, but not in spiked calibrator samples. Comparison with LC-MS/MS disclosed a significant bias with higher concentrations measured by LC-MS/MS, while UPLC-MS/MS showed excellent agreement with the commercially available HPLC method. In the LC-MS/MS procedure, comparably wide and left side shifted peaks were noticed. This could be ascribed to in-source fragmentation of conjugate metabolites during electrospray ionisation. Precursor and product ion scans confirmed the assumption that the additional compounds are posaconazole glucuronides. Reducing the cone voltage led to disappearance of the glucuronide peaks. Slight modification of the LC-MS/MS method enabled separation of the main interference, leading to significantly reduced deviation. Conclusions: These results highlight the necessity to reliably eliminate interference from labile drug metabolites for correct TDM results, either by sufficient separation or selective MS conditions. The presented UPLC-MS/MS method provides a reliable and fast assay for TDM of posaconazole. Clin Chem Lab Med 2010; 48:1723-31