HotSwap for bioinformatics: A STRAP tutorial

BACKGROUND: Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique. RESULTS: Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. Saving changes to the Java file causes STRAP to recompile the plugin and automatically update its user interface without requiring recompilation of STRAP or reloading of protein data. This article presents a tutorial on how to develop HotSwap plugins. STRAP is available at and . CONCLUSION: HotSwap is a useful and time-saving technique for bioinformatics developers. HotSwap can be used to efficiently develop bioinformatics applications that require loading large amounts of data into memory

Eg versus x relation from photoluminescence and electron microprobe investigations in p-type Hg1−xCdxTe (0.35 =< x =< 0.7)

Combined photoluminescence (at 10 T 300 K) and electron microprobe investigations have been carried out with HgCdTe samples grown from the melt or from solution. By exciting the samples through metallic masks with 200 μm diameter holes fixed with respect to the sample care was taken to pick-up both characteristic X-ray radiation as well as the photoluminescence from the same sample area. The Eg versus x relation determined in this way at T = 30 K has been compared with data from the interband absorption edge by other authors

Horizontal travelling heater method growth of Hg1−xCdxTe with crucible rotation

A horizontal travelling heater method (THM) for growing cylindrical cyrstals from a partially filled solution zone has been investigated for the first time. By applying ampoule rotation, the whole cross section of the crystal is successively brought into contact with the liquid solution, which is effectively stirred by forced convection. This approach was used to grow single-crystalline Hg1−xCdxTe ingots from a Te-rich solution zone. The structural perfection and metallurgical homogeneity are equivalent to vertically-grown THM material

Diagnosis of Fanconi Anemia: Mutation Analysis by Multiplex Ligation-Dependent Probe Amplification and PCR-Based Sanger Sequencing

Fanconi anemia (FA) is a rare inherited disease characterized by developmental defects, short stature, bone marrow failure, and a high risk of malignancies. FA is heterogeneous: 15 genetic subtypes have been distinguished so far. A clinical diagnosis of FA needs to be confirmed by testing cells for sensitivity to cross-linking agents in a chromosomal breakage test. As a second step, DNA testing can be employed to elucidate the genetic subtype of the patient and to identify the familial mutations. This knowledge allows preimplantation genetic diagnosis (PGD) and enables prenatal DNA testing in future pregnancies. Although simultaneous testing of all FA genes by next generation sequencing will be possible in the near future, this technique will not be available immediately for all laboratories. In addition, in populations with strong founder mutations, a limited test using Sanger sequencing and MLPA will be a cost-effective alternative. We describe a strategy and optimized conditions for the screening of FANCA, FANCB, FANCC, FANCE, FANCF, and FANCG and present the results obtained in a cohort of 54 patients referred to our diagnostic service since 2008. In addition, the follow up with respect to genetic counseling and carrier screening in the families is discussed

Spin properties of dense near-surface ensembles of nitrogen-vacancy centres in diamond

We present a study of the spin properties of dense layers of near-surface nitrogen-vacancy (NV) centres in diamond created by nitrogen ion implantation. The optically detected magnetic resonance contrast and linewidth, spin coherence time, and spin relaxation time, are measured as a function of implantation energy, dose, annealing temperature and surface treatment. To track the presence of damage and surface-related spin defects, we perform in situ electron spin resonance spectroscopy through both double electron-electron resonance and cross-relaxation spectroscopy on the NV centres. We find that, for the energy ($4-30$~keV) and dose ($5\times10^{11}-10^{13}$~ions/cm$^2$) ranges considered, the NV spin properties are mainly governed by the dose via residual implantation-induced paramagnetic defects, but that the resulting magnetic sensitivity is essentially independent of both dose and energy. We then show that the magnetic sensitivity is significantly improved by high-temperature annealing at $\geq1100^\circ$C. Moreover, the spin properties are not significantly affected by oxygen annealing, apart from the spin relaxation time, which is dramatically decreased. Finally, the average NV depth is determined by nuclear magnetic resonance measurements, giving $\approx10$-17~nm at 4-6 keV implantation energy. This study sheds light on the optimal conditions to create dense layers of near-surface NV centres for high-sensitivity sensing and imaging applications.Comment: 12 pages, 7 figure

Equivariant pretheories and invariants of torsors

In the present paper we introduce and study the notion of an equivariant pretheory: basic examples include equivariant Chow groups, equivariant K-theory and equivariant algebraic cobordism. To extend this set of examples we define an equivariant (co)homology theory with coefficients in a Rost cycle module and provide a version of Merkurjev's (equivariant K-theory) spectral sequence for such a theory. As an application we generalize the theorem of Karpenko-Merkurjev on G-torsors and rational cycles; to every G-torsor E and a G-equivariant pretheory we associate a graded ring which serves as an invariant of E. In the case of Chow groups this ring encodes the information concerning the motivic J-invariant of E and in the case of Grothendieck's K_0 -- indexes of the respective Tits algebras.Comment: 23 pages; this is an essentially extended version of the previous preprint: the construction of an equivariant cycle (co)homology and the spectral sequence (generalizing the long exact localization sequence) are adde

Superfluid Helium Tanker (SFHT) study

Replenishment of superfluid helium (SFHe) offers the potential of extending the on-orbit life of observatories, satellite instruments, sensors and laboratories which operate in the 2 K temperature regime. A reference set of resupply customers was identified as representing realistic helium servicing requirements and interfaces for the first 10 years of superfluid helium tanker (SFHT) operations. These included the Space Infrared Telescope Facility (SIRTF), the Advanced X-ray Astrophysics Facility (AXAF), the Particle Astrophysics Magnet Facility (Astromag), and the Microgravity and Materials Processing Sciences Facility (MMPS)/Critical Point Phenomena Facility (CPPF). A mixed-fleet approach to SFHT utilization was considered. The tanker permits servicing from the Shuttle cargo bay, in situ when attached to the OMV and carried to the user spacecraft, and as a depot at the Space Station. A SFHT Dewar ground servicing concept was developed which uses a dedicated ground cooling heat exchanger to convert all the liquid, after initial fill as normal fluid, to superfluid for launch. This concept permits the tanker to be filled to a near full condition, and then cooled without any loss of fluid. The final load condition can be saturated superfluid with any desired ullage volume, or the tank can be totally filed and pressurized. The SFHT Dewar and helium plumbing system design has sufficient component redundancy to meet fail-operational, fail-safe requirements, and is designed structurally to meet a 50 mission life usage requirement. Technology development recommendations were made for the selected SFHT concept, and a Program Plan and cost estimate prepared for a phase C/D program spanning 72 months from initiation through first launch in 1997

Synthesis and characterization of tantalum(V) boronate clusters : multifunctional Lewis acid cages for binding guests

Open and shut cases: Tantalum(V) boronate clusters [(Cp*Ta)3(μ2‐η2‐RBO2)3(μ2‐O)2(μ2‐OH)(μ3‐OH)] (Cp*=η5‐C5Me5; 1: R=Ph, 2: R=iBu) with Lewis acidic cavities were prepared. Whereas the cavity of 2 is blocked by the iBu groups, that of 1 is open and can bind Lewis basic guests such as ketones (see picture) by interaction with one boronate and one μ3‐OH ligand

Chain dynamics in entangled polymers: Power laws of the proton and deuteron spin-lattice relaxation dispersions

Chain modes of entangled polymer melts can directly be probed in a frequency range 102 Hz <v<108 Hz with the aid of field-cycling proton or deuteron relaxometry. The frequency dispersion of proton spin-lattice relaxation universally shows crossovers between the power laws T1 ∝ν0.5±0.05 (region I), T1∝ν0.25±0.05 (region II), and T1∝ν0.45±0.05 (region III) from high to low frequencies. Regions I and II are identified as limits of a theory based on the renormalized Rouse model assuming intrasegment dipolar interactions. Region III does not appear in distinct form in the deuteron T1 dispersion of perdeuterated chains. It is inferred that proton relaxation in region III is influenced by intersegment interactions which are negligible with deuterons. A corresponding formalism is given. The comparison with the experimental data suggests some multi-chain correlation of the displacement dynamics. © 1998 American Institute of Physics

Inflammatory and metabolic responses to high-fat meals with and without dairy products in men.

Postprandial inflammation is an important factor for human health since chronic low-grade inflammation is associated with chronic diseases. Dairy products have a weak but significant anti-inflammatory effect on postprandial inflammation. The objective of the present study was to compare the effect of a high-fat dairy meal (HFD meal), a high-fat non-dairy meal supplemented with milk (HFM meal) and a high-fat non-dairy control meal (HFC meal) on postprandial inflammatory and metabolic responses in healthy men. A cross-over study was conducted in nineteen male subjects. Blood samples were collected before and 1, 2, 4 and 6 h after consumption of the test meals. Plasma concentrations of insulin, glucose, total cholesterol, LDL-cholesterol, HDL-cholesterol, TAG and C-reactive protein (CRP) were measured at each time point. IL-6, TNF-α and endotoxin concentrations were assessed at baseline and endpoint (6 h). Time-dependent curves of these metabolic parameters were plotted, and the net incremental AUC were found to be significantly higher for TAG and lower for CRP after consumption of the HFM meal compared with the HFD meal; however, the HFM and HFD meals were not different from the HFC meal. Alterations in IL-6, TNF-α and endotoxin concentrations were not significantly different between the test meals. The results suggest that full-fat milk and dairy products (cheese and butter) have no significant impact on the inflammatory response to a high-fat meal