ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples

Optimizing the Post Sandvik Nanoflex material model using inverse optimization and the finite element method

This article describes an inverse optimization method for the Sandvik Nanoflex steel in cold forming\ud processes. The optimization revolves around measured samples and calculations using the Finite Element\ud Method. Sandvik Nanoflex is part of the group of meta-stable stainless steels. These materials are characterized\ud by a good corrosion resistance, high strength, good formability and crack resistance. In addition, Sandvik\ud Nanoflex has a strain-induced transformation and, depending on austenising conditions and chemical composition,\ud a stress-assisted transformation can occur. The martensite phase of this material shows a substantial aging\ud response. The inverse optimization is a sub-category of the optimization techniques. The inverse optimization\ud method uses a top down approach, as the name implies. The starting point is a prototype state where the current\ud state is to converge on. In our experiment the test specimen is used as prototype and a calculation result as\ud current state. The calculation is then adapted so that the result converges towards the test example. An iterative\ud numerical optimization algorithm controls the adaptation. For the inverse optimization method two parameters\ud are defined: shape of the product and martensite profile. These parameters are extracted from both calculation\ud and test specimen, using Fourier analysis and integrals. An optimization parameter is then formulated from\ud the extracted parameters. The method uses this optimization parameter to increase the accuracy of ”The Post”\ud material model for Sandvik Nanoflex. [1] The article will describe a method to optimize material models, using\ud a combination practical experiments, Finite Element Method and parameter extraction

Free edge strain concentrations in real composite laminates: Experimental-theoretical correlation

The magnitude of the maximum shear strain at the free edge of axially loaded theta (2)/-theta(2)(s) and (+ or - theta(2) (s) composite laminates was investigated experimentally and numerically to ascertain the actual value of strain concentration in resin matrix laminates and to determine the accuracy of finite element results. Experimental results using moire interferometry show large, but finite, shear strain concentrations at the free edge of graphite-epoxy and graphite-polyimide laminates. Comparison of the experimental results with those obtained using several different finite element representations showed that a four node isoparametric finite element provided the best and most trouble free numerical results. The results indicate that the ratio of maxium shear strain at the free edge to applied axial strain varies with fiber orientation and does not exceed nine for the most critical angle which is 15 deg

A New Pathway for the Preparation of Highly Qualified Teachers: The Master of Arts in Teaching (MAT)

This article reports on the development and initial implementation of a Master of Arts in Teaching (MAT) degree, an accelerated graduate program that encourages and scaffolds individuals with existing disciplinary expertise in entering the teaching profession. First, the context for developing the program is outlined. Next, the unique structure of the 15-month program, which consists of three blocks, is described. Expectations about students are then shared, quality control features of the program are highlighted, and the lessons we learned about program development and implementation are detailed. Finally, thoughts about the future of this program and others of its type are shared based upon our experience

Advances in Moire interferometry for thermal response of composites

An experimental technique for the precise measurement of the thermal response of both sides of a laminated composite coupon specimen uses Moire interferometry with fringe multiplication which yields a sensitivity of 833 nm (32.8 micro in.) per fringe. The reference gratings used are virtual gratings and are formed by partially mirrorized glass prisms in close proximity to the specimen. Results are compared with both results obtained from tests which used Moire interferometry on one side of composite laminates, and with those predicted by classical lamination theory. The technique is shown to be capable of producing the sensitivity and accuracy necessary to measure a wide range of thermal responses and to detect small side to side variations in the measured response. Tests were conducted on four laminate configurations of T300/5208 graphite epoxy over a temperature range of 297 K (75 F) to 422 K (300 F). The technique presented allows for the generation of reference gratings for temperature regimes well outside that used in these tests

Semirelativistic stability of N-boson systems bound by 1/r pair potentials

We analyze a system of self-gravitating identical bosons by means of a semirelativistic Hamiltonian comprising the relativistic kinetic energies of the involved particles and added (instantaneous) Newtonian gravitational pair potentials. With the help of an improved lower bound to the bottom of the spectrum of this Hamiltonian, we are able to enlarge the known region for relativistic stability for such boson systems against gravitational collapse and to sharpen the predictions for their maximum stable mass.Comment: 11 pages, considerably enlarged introduction and motivation, remainder of the paper unchange

Convergence of resonances on thin branched quantum wave guides

We prove an abstract criterion stating resolvent convergence in the case of operators acting in different Hilbert spaces. This result is then applied to the case of Laplacians on a family X_\eps of branched quantum waveguides. Combining it with an exterior complex scaling we show, in particular, that the resonances on X_\eps approximate those of the Laplacian with ``free'' boundary conditions on $X_0$, the skeleton graph of X_\eps.Comment: 48 pages, 1 figur

Corrections to Sirlin's Theorem in O(p6)O(p^6) Chiral Perturbation Theory

We present the results of the first two-loop calculation of a form factor in full $SU(3) \times SU(3)$ Chiral Perturbation Theory. We choose a specific linear combination of $\pi^+, K^+, K^0$ and $K\pi$ form factors (the one appearing in Sirlin's theorem) which does not get contributions from order $p^6$ operators with unknown constants. For the charge radii, the correction to the previous one-loop result turns out to be significant, but still there is no agreement with the present data due to large experimental uncertainties in the kaon charge radii.Comment: 6 pages, Latex, 2 LaTeX figure

Electronic Scattering Effects in Europium-Based Iron Pnictides

In a comprehensive study, we investigate the electronic scattering effects in EuFe$_{2}$(As$_{1-x}$P$_{x}$)$_{2}$ by using Fourier-transform infrared spectroscopy. In spite of the fact that Eu$^{2+}$ local moments order around $T_\text{Eu} \approx 20$\,K, the overall optical response is strikingly similar to the one of the well-known Ba-122 pnictides. The main difference lies within the suppression of the lower spin-density-wave gap feature. By analysing our spectra with a multi-component model, we find that the high-energy feature around 0.7\,eV -- often associated with Hund's rule coupling -- is highly sensitive to the spin-density-wave ordering, this further confirms its direct relationship to the dynamics of itinerant carriers. The same model is also used to investigate the in-plane anisotropy of magnetically detwinned EuFe$_{2}$As$_{2}$ in the antiferromagnetically ordered state, yielding a higher Drude weight and lower scattering rate along the crystallographic $a$-axis. Finally, we analyse the development of the room temperature spectra with isovalent phosphor substitution and highlight changes in the scattering rate of hole-like carriers induced by a Lifshitz transition