Informed baseline subtraction of proteomic mass spectrometry data aided by a novel sliding window algorithm

Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However, the raw protein profiles suffer from several sources of bias or systematic variation which need to be removed via pre-processing before meaningful downstream analysis of the data can be undertaken. Baseline subtraction, an early pre-processing step that removes the non-peptide signal from the spectra, is complicated by the following: (i) each spectrum has, on average, wider peaks for peptides with higher mass-to-charge ratios (m/z), and (ii) the time-consuming and error-prone trial-and-error process for optimising the baseline subtraction input arguments. With reference to the aforementioned complications, we present an automated pipeline that includes (i) a novel `continuous' line segment algorithm that efficiently operates over data with a transformed m/z-axis to remove the relationship between peptide mass and peak width, and (ii) an input-free algorithm to estimate peak widths on the transformed m/z scale. The automated baseline subtraction method was deployed on six publicly available proteomic MS datasets using six different m/z-axis transformations. Optimality of the automated baseline subtraction pipeline was assessed quantitatively using the mean absolute scaled error (MASE) when compared to a gold-standard baseline subtracted signal. Near-optimal baseline subtraction was achieved using the automated pipeline. The advantages of the proposed pipeline include informed and data specific input arguments for baseline subtraction methods, the avoidance of time-intensive and subjective piecewise baseline subtraction, and the ability to automate baseline subtraction completely. Moreover, individual steps can be adopted as stand-alone routines.Comment: 50 pages, 19 figure

A Study to Assess the Benefits Students Received from Completing the Fire Cadet Program in Chesapeake Public Schools

The following goals were established to guide the research: Identify why the program was started; Determine the current employment status of program completers; Determine if the program had indirect benefits to participants; and Identify why the program was terminated

Growth states of catalytic reaction networks exhibiting energy metabolism

All cells derive nutrition by absorbing some chemical and energy resources from the environment; these resources are used by the cells to reproduce the chemicals within them, which in turn leads to an increase in their volume. In this study, we introduce a protocell model exhibiting catalytic reaction dynamics, energy metabolism, and cell growth. Results of extensive simulations of this model show the existence of four phases with regard to the rates of both the influx of resources and the cell growth. These phases include an active phase with high influx and high growth rates, an inefficient phase with high influx but low growth rates, a quasi-static phase with low influx and low growth rates, and a death phase with negative growth rate. A mean field model well explains the transition among these phases as bifurcations. The statistical distribution of the active phase is characterized by a power law and that of the inefficient phase is characterized by a nearly equilibrium distribution. We also discuss the relevance of the results of this study to distinct states in the existing cells.Comment: 21 pages, 5 figure

Simulation of fractionally damped mechanical systems by means of a Newmark-diffusive scheme

A Newmark-diffusive scheme is presented for the time-domain solution of dynamic systems containing fractional derivatives. This scheme combines a classical Newmark time-integration method used to solve second-order mechanical systems (obtained for example after finite element discretization), with a diffusive representation based on the transformation of the fractional operator into a diagonal system of linear differential equations, which can be seen as internal memory variables. The focus is given on the algorithm implementation into a finite element framework, the strategies for choosing diffusive parameters, and applications to beam structures with a fractional Zener model

Uncovering Policy Response: Primary School Principals in the Netherlands and the Professions in Education Act

Summary: The Netherlands currently has one of the most decentralised education systems in Europe, with a high level of school autonomy and no formal governance levels between the national government and the school. Consequently, school principals have gained more freedom in educational policy, but also face more responsibilities in the provision of schooling. The aim of this study is to discover the ways in which principals in Dutch primary schools respond to governmental policy. The policy focus is the Professions in Education Act (BIO-Act), 2004, which aims to assure the quality of education delivered by school principals, teachers and supporting staff in schools. The research employed a mixed method sequential and phased design approach, collecting and analysing quantitative data (N=103) and augmenting these results with in-depth qualitative data analysis (N=5). The tentative findings from this relatively small study cautiously suggest school principals’ (i) possess a sense of responsibility in needing to respond to policy; (ii) mediate policy response in relation to the culture and history of the school and other key stakeholders; (iii) are engaged in a complex process of ‘creative social action

Microwave-assisted Bohlmann–Rahtz synthesis of highly-substituted 2-aminonicotinates

Microwave irradiation of 2-carbethoxyacetamidine and an ethynyl ketone under acidic or basic conditions in ethanol at 150 °C for 1.5 h facilitated Bohlmann-Rahtz pyridine synthesis to give highly-substituted ethyl 2 aminonicotinates with total regiocontrol and in reasonable to excellent yield, following purification by immobiliza tion upon an acidic resin