Customized baseline correction

Baseline correction is an important pre-processing technique used to separate true spectroscopic signals from interference effects or remove background effects, stains or traces of compounds, e.g. in 2D gel electrophoresis. In some cases parts of the spectra or images need correction using rigid baselines (limited curvature) while other parts need more flexible baselines (more curvature). Often one has to make a compromise that is not optimal over the whole spectral range, or focus on one part and let the rest be treated sub-optimally. A customizing wrapper is proposed that rescales the spectrum abscissa and therefore makes the baseline correction algorithm behave right in all parts of the spectra. Improvements are demonstrated both visually and through regression using recently reported Raman spectra on melted fat from pork adipose tissue.     

Do two-dimensional "noble gas atoms" produce molecular honeycombs at a metal surface?

Anthraquinone self-assembles on Cu(111) into a giant honeycomb network with exactly three molecules on each side. Here we propose that the exceptional degree of order achieved in this system can be explained as a consequence of the confinement of substrate electrons in the pores, with the pore size tailored so that the confined electrons can adopt a noble-gas-like two-dimensional quasi-atom configuration with two filled shells. Formation of identical pores in a related adsorption system (at different overall periodicity due to the different molecule size) corroborates this concept. A combination of photoemission spectroscopy with density functional theory computations (including van der Waals interactions) of adsorbate-substrate interactions allows quantum mechanical modeling of the spectra of the resultant quasi-atoms and their energetics.     

Rational Design of Alpha‐Helical Antimicrobial Peptides: Do's and Don'ts

Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure–activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin (GLLKRIKTLL‐NH₂) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic activity can be achieved through subtle increases in the hydrophobicity of the hydrophobic face or through subtle increases in the polarity of the hydrophilic face of the helix, or—most efficiently—a combination of both. A set of guidelines based on the results is given, for assistance in how to modify cationic α‐helical AMPs in order to control activity and selectivity. The guidelines are finally tested on a different peptide.     

Apex Resection in Zebrafish (Danio rerio) as a Model of Heart Regeneration: A Video-Assisted Guide

Ischemic heart disease is one of the leading causes of deaths worldwide. A major hindrance to resolving this challenge lies in the mammalian hearts inability to regenerate after injury. In contrast, zebrafish retain a regenerative capacity of the heart throughout their lifetimes. Apex resection (AR) is a popular zebrafish model for studying heart regeneration, and entails resecting 10–20% of the heart in the apex region, whereafter the regeneration process is monitored until the heart is fully regenerated within 60 days. Despite this popularity, video tutorials describing this technique in detail are lacking. In this paper we visualize and describe the entire AR procedure including anaesthesia, surgery, and recovery. In addition, we show that the concentration and duration of anaesthesia are important parameters to consider, to balance sufficient levels of sedation and minimizing mortality. Moreover, we provide examples of how zebrafish heart regeneration can be assessed both in 2D (immunohistochemistry of heart sections) and 3D (analyses of whole, tissue cleared hearts using multiphoton imaging). In summary, this paper aims to aid beginners in establishing and conducting the AR model in their laboratory, but also to spur further interest in improving the model and its evaluation.     

Tutoring executives online: what drives perceived quality?

Studies of learning and student satisfaction in the context of online university programmes have largely neglected programmes catering specifically to business executives. Such executives have typically been away from higher education for a number of years, and have collected substantial practical experience in the subject matters they are taught. Their expectations in terms of both content and delivery may therefore be different from non-executive students. We explore perceptions of the quality of tutoring in the context of an online executive MBA programme through participant interviews. We find that in addition to some of the tutor behaviours already discussed in the literature, executive students look specifically for practical industry knowledge and experience in tutors, when judging how effective a tutor is. This has implications for both the recruitment and training of online executive MBA tutors.     

Development of Air Concentration on Chute Spillways

To protect hydraulic structures such as spillways, chutes, and bottom outlets against cavitation damage, air is normally added by means of aerators in regions where the cavitation number falls below a critical value. Although aerators have been investigated for more than 30 years, the current design methods for aerator spacing are not reliable. The detrainment process was not previously investigated in detail because of limited laboratory instrumentation. The research presented in this paper provides new model data for hydraulic chutes of variable bottom slope. An advanced remote-controlled, fiber-optical instrumentation was employed to investigate the streamwise development of air concentration contours, velocity contours, and air bubble size along a 14-m model chute. The main hydraulic parameters such as bottom slope, inflow Froude number, inflow depth, and two distinctly different air supply devices for air-water flow generation were employed. Results enable prediction of the reduction of bottom and average air concentration, depending on the inflow air concentration and the chute slope. The minimum air concentration is proven to be a function of the streamwise Froude number. The point of minimum air concentration is constrained by the point of air inception. Downstream of this point the air concentration increases from the surface aeration, depending on the chute slope.     

Microstructure of Precipitation Hardenable Powder Metallurgical Ni Alloys Containing 35 to 45 pct Cr and 3.5 to 6 pct Nb

Ni-based alloys with high Cr contents are not only known for their excellent high temperature and hot corrosion resistance, but are also known for poor mechanical properties and difficult workability. Powder metallurgical (PM) manufacturing of alloys may overcome several of the shortcomings encountered in materials manufacturing involving solidification. In the present work, six PM Ni-based alloys containing 35 to 45 wt pct Cr and 3.5 to 6 wt pct Nb were produced and compacted via hot isostatic pressing. Samples were heat treated for up to 1656 hours at either 923 K or 973 K (650 °C or 700 °C), and the microstructures and mechanical properties were quantified and compared to thermodynamic calculations. For the majority of the investigated alloys, the high Cr and Nb contents caused development of primary populations of globular α-Cr and δ (Ni₃Nb). Transmission electron microscopy of selected alloys confirmed the additional presence of metastable γ″ (Ni₃Nb). A co-dependent growth morphology was found, where the preferred growth direction of γ″, the {001} planes of γ-Ni, caused precipitates of both α-Cr and δ to appear in the form of mutually perpendicular oriented disks or plates. Solution heat treatment at 1373 K (1100 °C) followed by aging at 973 K (700 °C) produced a significant strength increase for all alloys, and an aged yield strength of 990 MPa combined with an elongation of 21 pct is documented for Ni 40 wt pct Cr 3.5 wt pct Nb.     

Rigidified Clicked Dimeric Ligands for Studying the Dynamics of the PDZ1‐2 Supramodule of PSD‐95

PSD‐95 is a scaffolding protein of the MAGUK protein family, and engages in several vital protein–protein interactions in the brain with its PDZ domains. It has been suggested that PSD‐95 is composed of two supramodules, one of which is the PDZ1‐2 tandem domain. Here we have developed rigidified high‐affinity dimeric ligands that target the PDZ1‐2 supramodule, and established the biophysical parameters of the dynamic PDZ1‐2/ligand interactions. By employing ITC, protein NMR, and stopped‐flow kinetics this study provides a detailed insight into the overall conformational energetics of the interaction between dimeric ligands and tandem PDZ domains. Our findings expand our understanding of the dynamics of PSD‐95 with potential relevance to its biological role in interacting with multivalent receptor complexes and development of novel drugs.     

MontePython: Implementing Quantum Monte Carlo using Python

We present a cross-language C++/Python program for simulations of quantum mechanical systems with the use of Quantum Monte Carlo (QMC) methods. We describe a system for which to apply QMC, the algorithms of variational Monte Carlo and diffusion Monte Carlo and we describe how to implement theses methods in pure C++ and C++/Python. Furthermore we check the efficiency of the implementations in serial and parallel cases to show that the overhead using Python can be negligible.

Program summary

Program title: MontePythonCatalogue identifier: ADZP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZP_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 49 519No. of bytes in distributed program, including test data, etc.: 114 484Distribution format: tar.gzProgramming language: C++, PythonComputer: PC, IBM RS6000/320, HP, ALPHAOperating system: LINUXHas the code been vectorised or parallelized?: Yes, parallelized with MPINumber of processors used: 1-96RAM: Depends on physical system to be simulatedClassification: 7.6; 16.1Nature of problem: Investigating ab initio quantum mechanical systems, specifically Bose-Einstein condensation in dilute gases of ⁸⁷RbSolution method: Quantum Monte CarloRunning time: 225 min with 20 particles (with 4800 walkers moved in 1750 time steps) on 1 AMD Opteron^TM Processor 2218 processor; Production run for, e.g., 200 particles takes around 24 hours on 32 such processors.