A Hadamard transform electron ionization time-of-flight mass spectrometer

We describe the first Hadamard transform time-of-flight mass spectrometer (HT-TOFMS) that incorporates an electron (impact) ionization source. This implementation was realized in an existent TOF instrument using commercially available components and simple modifications to the ion source. In the present apparatus, a Hadamard mask is expressed by modulating the ion generation process within the ion source; thus, the present approach differs from previous designs that use external electrostatic devices to modulate a continuous ion stream. The present implementation may be operated in conventional TOF mode at 12.5 kHz and in HT-TOF mode at 20-40 MHz. In Hadamard mode the design can operate using any circulant simplex code, allowing the operator much flexibility for optimizing resolution and mass range and for eliminating nonstochastic fluctuations, e.g., encoding errors and signal hum. We demonstrate typical performance of the HT-TOFMS in standard and reflectron geometries using sequences of three constructions and of varied length, generating HT-TOF mass spectra of molecules that match conventional reference spectra. The auxiliary material includes an electrical schematic for the floating high-speed encoding amplifier, which is also of use in other high-speed electrostatic optics applications, and a list of 537 validated vectors comprising the first row of each circulant simplex sequence (S(n)=3-8219) derived using maximal shift register (n=2(m)-1), quadratic residue (n=4m-3), and twin prime constructions [n=p(p+2)].     

On the adaptive finite element analysis of the Kohn–Sham equations: methods,algorithms, and implementation

In this paper, details of an implementation of a numerical code for computing the Kohn–Sham equations are presented and discussed. A fully self‐consistent method of solving the quantum many‐body problem within the context of density functional theory using a real‐space method based on finite element discretisation of realspace is considered. Various numerical issues are explored such as (i) initial mesh motion aimed at co‐aligning ions and vertices; (ii) a priori and a posteriori optimization of the mesh based on Kelly's error estimate; (iii) the influence of the quadrature rule and variation of the polynomial degree of interpolation in the finite element discretisation on the resulting total energy. Additionally, (iv) explicit, implicit and Gaussian approaches to treat the ionic potential are compared. A quadrupole expansion is employed to provide boundary conditions for the Poisson problem. To exemplify the soundness of our method, accurate computations are performed for hydrogen, helium, lithium, carbon, oxygen, neon, the hydrogen molecule ion and the carbon‐monoxide molecule. Our methods, algorithms and implementation are shown to be stable with respect to convergence of the total energy in a parallel computational environment. Copyright © 2015 John Wiley & Sons, Ltd.     

Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq

Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNAs. Previously, we showed that the Hfq C-terminal region forms an amyloid-like structure and that these fibrils interact with membranes. The immediate consequence of this interaction is a disruption of the membrane, but the effect on Hfq structure was unknown. To investigate details of the mechanism of interaction, the present work uses different in vitro biophysical approaches. We show that the Hfq C-terminal region influences membrane integrity and, conversely, that the membrane specifically affects the amyloid assembly. The reported effect of this bacterial master regulator on membrane integrity is discussed in light of the possible consequence on small regulatory RNA-based regulation.     

Next-Generation Grade and Survival Expression Biomarkers of Human Gliomas Based on Algorithmically Reconstructed Molecular Pathways

In gliomas, expression of certain marker genes is strongly associated with survival and tumor type and often exceeds histological assessments. Using a human interactome model, we algorithmically reconstructed 7494 new-type molecular pathways that are centered each on an individual protein. Each single-gene expression and gene-centric pathway activation was tested as a survival and tumor grade biomarker in gliomas and their diagnostic subgroups (IDH mutant or wild type, IDH mutant with 1p/19q co-deletion, MGMT promoter methylated or unmethylated), including the three major molecular subtypes of glioblastoma (proneural, mesenchymal, classical). We used three datasets from The Cancer Genome Atlas and the Chinese Glioma Genome Atlas, which in total include 527 glioblastoma and 1097 low grade glioma profiles. We identified 2724 such gene and 2418 pathway survival biomarkers out of total 17,717 genes and 7494 pathways analyzed. We then assessed tumor grade and molecular subtype biomarkers and with the threshold of AUC > 0.7 identified 1322/982 gene biomarkers and 472/537 pathway biomarkers. This suggests roughly two times greater efficacy of the reconstructed pathway approach compared to gene biomarkers. Thus, we conclude that activation levels of algorithmically reconstructed gene-centric pathways are a potent class of new-generation diagnostic and prognostic biomarkers for gliomas.     

Back and forth between continuous and discrete for the working computer scientist

This paper gives a perfect, ideal, discretization of continuous notions. This is a very convenient frame to treat continuous problems or theories with the help of a computer. This is illustrated by the conversion of algorithms using real numbers into algorithms using integers only and the founding of discrete geometry.     

Twelve-Nitrogen-Atom Cyclic Structure Stabilized by 3d-Element Atoms: Quantum Chemical Modeling

Using various versions of density functional theory (DFT), DFT M06/TZVP, DFT B3PW91/TZVP, DFT OPBE/TZVP, and, partially, the MP2 method, the possibility of the existence of 3d-element (M) compounds with nitrogen having unusual M: nitrogen ratio 1:12, unknown for these elements at the present, was shown. Structural parameter data were presented. It was shown that all MN4 groupings have tetragonal-pyramidal structure. It was noted that the bond lengths formed by nitrogen atoms and an M atom were equal to each other only in the case of M = Ti, V, Cr and Co, whereas for other Ms, they were slightly different; moreover, the bond angles formed by nitrogen atoms and an M atom were equal to 90.0°, or practically did not differ from this value. Thermodynamic parameters, NBO analysis data and HOMO/LUMO images for this compound were also presented. Good agreement between the calculated data obtained using the above three quantum chemical methods was also noted.     

Lignite oxidative desulphurization: notice 3—process technological aspects and application of products

International Journal of Coal Science & Technology - The study reviews the process of oxidative desulphurization of high-sulphur Ukrainian lignite, which was performed by coal treatment using...     

Individual and area socioeconomic inequalities in cause-specific unintentional injury mortality: 11-Year follow-up study of 2.7 million Canadians

This study investigated the association between individual and area socioeconomic status (SES) and leading causes of unintentional injury mortality in Canadian adults. Using the 1991–2001 Canadian Census Mortality Follow-up Study cohort (N = 2,735,152), Cox proportional hazard regression was used to calculate hazard ratios and 95% confidence intervals for all-cause unintentional injury, motor vehicle collision (MVC), fall, poisoning, suffocation, fire/burn, and drowning deaths. Results indicated that associations with SES differed by cause of injury, and were generally more pronounced for males. Low education was associated with an elevated risk of mortality from all-cause unintentional injury and MVC (males only) and poisoning and drowning (both sexes). Low income was strongly associated with most causes of injury mortality, particularly fire/burn and poisoning. Having no occupation or low occupational status was associated with higher risks of all-cause injury, fall, poisoning and suffocation (both sexes) and MVC deaths among men. Associations with area deprivation were weak, and only areas with high deprivation had elevated risk of all-cause injury, MVC (males only), poisoning and drowning (both sexes). This study reveals the importance of examining SES differentials by cause of death from a multilevel perspective. Future research is needed to clarify the mechanisms underlying these differences to implement equity-oriented approaches for reducing differential exposures, vulnerability or consequences of injury mortality.