Comparison of data acquisition methods for the identification and quantification of histone post-translational modifications on a Q Exactive HF hybrid quadrupole Orbitrap mass spectrometer.

RATIONALE: Histone PTMs play key roles in regulating eukaryotic gene expression. Mass spectrometry (MS) has emerged as a powerful method to characterize and quantify histone PTMs as it allows unbiased identification and quantification of multiple histone PTMs including combinations of the modifications present. METHODS: In this study we compared a range of data acquisition methods for the identification and quantification of the histone PTMs using a Q Exactive HF Orbitrap. We compared three different data-dependent analysis (DDA) methods with MS2 resolutions of 120K, 60K, 30K. We also compared a range of data-independent analysis (DIA) methods using MS2 isolation windows of 20 m/z and DIAvw to identify and quantify histone PTMs in Chinese Hamster Ovary (CHO) cells. RESULTS: The increased number of MS2 scans afforded by the lower resolution methods resulted in a higher number of queries, peptide sequence matches (PSMs) and a higher number of peptide proteoforms with a Mascot Ion score greater than 46. No difference in the proportion of peptide proteoforms with Delta scores >17 was observed. Comparing the data acquisition methods increased repeatability in terms of lower CVs afforded by DIA MS1 60K MS2 30K 20m/z isolation windows was observed. CONCLUSION: We observed that DIA which offers advantages in flexibility and identification of isobaric peptide proteoforms performs as well as DDA in the analysis of histone PTMs. We were able to identify 71 modified histone peptides for histone H3 and H4 and quantified 64 across each of the different acquisition methods

Planning an integrated agriculture and health program and designing its evaluation: Experience from Western Kenya.

AbstractMulti-sectoral programs that involve stakeholders in agriculture, nutrition and health care are essential for responding to nutrition problems such as vitamin A deficiency among pregnant and lactating women and their infants in many poor areas of lower income countries. Yet planning such multi-sectoral programs and designing appropriate evaluations, to respond to different disciplinary cultures of evidence, remain a challenge. We describe the context, program development process, and evaluation design of the Mama SASHA project (Sweetpotato Action for Security and Health in Africa) which promoted production and consumption of a bio-fortified, orange-fleshed sweetpotato (OFSP). In planning the program we drew upon information from needs assessments, stakeholder consultations, and a first round of the implementation evaluation of a pilot project. The multi-disciplinary team worked with partner organizations to develop a program theory of change and an impact pathway which identified aspects of the program that would be monitored and established evaluation methods. Responding to the growing demand for greater rigour in impact evaluations, we carried out quasi-experimental allocation by health facility catchment area, repeat village surveys for assessment of change in intervention and control areas, and longitudinal tracking of individual mother-child pairs. Mid-course corrections in program implementation were informed by program monitoring, regular feedback from implementers and partners’ meetings. To assess economic efficiency and provide evidence for scaling we collected data on resources used and project expenses. Managing the multi-sectoral program and the mixed methods evaluation involved bargaining and trade-offs that were deemed essential to respond to the array of stakeholders, program funders and disciplines involved

Advances in the proposed electromagnetic zero-point field theory of inertia

A NASA-funded research effort has been underway at the Lockheed Martin Advanced Technology Center in Palo Alto and at California State University in Long Beach to develop and test a recently published theory that Newton's equation of motion can be derived from Maxwell's equations of electrodynamics as applied to the zero-point field (ZPF) of the quantum vacuum. In this ZPF-inertia theory, mass is postulated to be not an intrinsic property of matter but rather a kind of electromagnetic drag force that proves to be acceleration dependent by virtue of the spectral characteristics of the ZPF. The theory proposes that interactions between the ZPF and matter take place at the level of quarks and electrons, hence would account for the mass of a composite neutral particle such as the neutron. An effort to generalize the exploratory study of Haisch, Rueda and Puthoff (1994) into a proper relativistic formulation has been successful. Moreover the principle of equivalence implies that in this view gravitation would also be electromagnetic in origin along the lines proposed by Sakharov (1968). With regard to exotic propulsion we can definitively rule out one speculatively hypothesized mechanism: matter possessing negative inertial mass, a concept originated by Bondi (1957) is shown to be logically impossible. On the other hand, the linked ZPF-inertia and ZPF-gravity concepts open the conceptual possibility of manipulation of inertia and gravitation, since both are postulated to be electromagnetic phenomena. It is hoped that this will someday translate into actual technological potential. A key question is whether the proposed ZPF-matter interactions generating the phenomenon of mass might involve one or more resonances. This is presently under investigation.Comment: Revised version of invited presentation at 34th AIAA/ASME/SAE/ASEE Joint Propulsion Conference, July 13-15, 1998, Cleveland, OH, 10 pages, no figure

Eigenmodes of index-modulated layers with lateral PMLs

Maxwell equations are solved in a layer comprising a finite number of homogeneous isotropic dielectric regions ended by anisotropic perfectly matched layers (PMLs). The boundary-value problem is solved and the dispersion relation inside the PML is derived. The general expression of the eigenvalues equation for an arbitrary number of regions in each layer is obtained, and both polarization modes are considered. The modal functions of a single layer ended by PMLs are found, and their orthogonality relation is derived. The present method is useful to simulate scattering problems from dielectric objects as well as propagation in planar slab waveguides. Its potential to deal with more complex problems such as the scattering from an object with arbitrary cross section in open space using the multilayer modal method is briefly discussed.Comment: 17 pages, 4 figure

Role of livestock in human nutrition and health for poverty reduction in developing countries

Livestock keeping is critical for many of the poor in the developing world, often contributing to multiple livelihood objectives and offering pathways out of poverty. Livestock keeping also affects an indispensable asset of the poor, their human capital, through its impact on their own nutrition and health. This paper outlines the linkages between livestock keeping and the physical well-being of the poor, and examines a number of commonly held beliefs that misrepresent livestock development issues related to these linkages. These beliefs limit the scope of intervention programs to promote livestock and limit their potential contribution to poverty reduction. Recognition of the complexity of the role livestock play in household decision-making and of the opportunities foregone due to these misconceptions can enhance the ability of livestock to contribute to human well-being in the developing world

Blackbody Radiation and the Scaling Symmetry of Relativistic Classical Electron Theory with Classical Electromagnetic Zero-Point Radiation

It is pointed out that relativistic classical electron theory with classical electromagnetic zero-point radiation has a scaling symmetry which is suitable for understanding the equilibrium behavior of classical thermal radiation at a spectrum other than the Rayleigh-Jeans spectrum. In relativistic classical electron theory, the masses of the particles are the only scale-giving parameters associated with mechanics while the action-angle variables are scale invariant. The theory thus separates the interaction of the action variables of matter and radiation from the scale-giving parameters. Classical zero-point radiation is invariant under scattering by the charged particles of relativistic classical electron theory. The basic ideas of the matter -radiation interaction are illustrated in a simple relativistic classical electromagnetic example.Comment: 18 page

Density and well width dependences of the effective mass of twodimensional holes in (100) GaAs quantum wells measured by cyclotron resonance at microwave frequencies

Cyclotron resonance at microwave frequencies is used to measure the band mass (m_b) of the two-dimensional holes (2DH's) in carbon-doped (100) GaAs/AlxGa1-xAs heterostructures. The measured m_b shows strong dependences on both the 2DH density(p) and the GaAs quantum well width (W). For a fixed W, in the density range (0.4x10^11 to 1.1x10^11 cm^-2) studied here, m_b increases with p, consistent with previous studies of the 2DHs on the (311)A surface. For a fixed p = 1.1x10^11 cm^-2, mb increases from 0.22 m_e at W = 10 nm to 0.50 m_e at W = 30 nm, and saturates around 0.51 m_e for W > 30 nm.Comment: to appear in Solid State Communication

Talk the talk, walk the walk: Defining Critical Race Theory in research

Over the last decade there has been a noticeable growth in published works citing Critical Race Theory (CRT). This has led to a growth in interest in the UK of practical research projects utilising CRT as their framework. It is clear that research on 'race' is an emerging topic of study. What is less visible is a debate on how CRT is positioned in relation to methodic practice, substantive theory and epistemological underpinnings. The efficacy of categories of data gathering tools, both traditional and non-traditional is a discussion point here to explore the complexities underpinning decisions to advocate a CRT framework. Notwithstanding intersectional issues, a CRT methodology is recognisable by how philosophical, political and ethical questions are established and maintained in relation to racialised problematics. This paper examines these tensions in establishing CRT methodologies and explores some of the essential criteria for researchers to consider in utilising a CRT framework. © 2012 Copyright Taylor and Francis Group, LLC