Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics

The application of gas chromatography–mass spectrometry (GC–MS) to the ‘global’ analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project’s (METAbolomics for Plants Health and OutReach: http://www.meta-phor.eu/) priorities towards robust technology development, a GC–MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GC×GC–TOF/MS was compared with 1 dimensional GC–TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise

Probability landscapes for integrative genomics

<p>Abstract</p> <p>Background</p> <p>The comprehension of the gene regulatory code in eukaryotes is one of the major challenges of systems biology, and is a requirement for the development of novel therapeutic strategies for multifactorial diseases. Its bi-fold degeneration precludes brute force and statistical approaches based on the genomic sequence alone. Rather, recursive integration of systematic, whole-genome experimental data with advanced statistical regulatory sequence predictions needs to be developed. Such experimental approaches as well as the prediction tools are only starting to become available and increasing numbers of genome sequences and empirical sequence annotations are under continual discovery-driven change. Furthermore, given the complexity of the question, a decade(s) long multi-laboratory effort needs to be envisioned. These constraints need to be considered in the creation of a framework that can pave a road to successful comprehension of the gene regulatory code.</p> <p>Results</p> <p>We introduce here a concept for such a framework, based entirely on systematic annotation in terms of probability profiles of genomic sequence using any type of relevant experimental and theoretical information and subsequent cross-correlation analysis in hypothesis-driven model building and testing.</p> <p>Conclusion</p> <p>Probability landscapes, which include as reference set the probabilistic representation of the genomic sequence, can be used efficiently to discover and analyze correlations amongst initially heterogeneous and un-relatable descriptions and genome-wide measurements. Furthermore, this structure is usable as a support for automatically generating and testing hypotheses for alternative gene regulatory grammars and the evaluation of those through statistical analysis of the high-dimensional correlations between genomic sequence, sequence annotations, and experimental data. Finally, this structure provides a concrete and tangible basis for attempting to formulate a mathematical description of gene regulation in eukaryotes on a genome-wide scale.</p

The clinical relevance of PCL index on the reconstruction of anterior cruciate ligament with hamstring tendon autograft

The posterior cruciate ligament index (PCL index) has been reported as a diagnostic and prognostic marker for anterior cruciate ligament (ACL) reconstruction. The clinical relevance of PCL index on the reconstruction of ACL with hamstring tendon autograft has not been described in the literature. The objective of this study is to evaluate the importance of the PCL index as a marker of anatomic reconstruction and of functional improvement of patients undergoing ACL reconstruction with HT autograft. Twenty-four patients were submitted to ACL reconstruction with HT autograft. The PCL index was assessed by magnetic resonance imaging before and after surgery. The functional evaluation was performed through the International Knee Documentation Committee (IKDC) Subjective Knee Evaluation Form© and Knee Society Knee Scoring System© (IKS). Patients presented a significant positive variation of the PCL index, IKDC and IKS scores. There is no significant correlation between PCL index variation and IKDC and IKS scores (p > 0.05). Unlike other studies reporting a relationship between the PCL index, control of rotational kinematics, and functional improvement in patients undergoing ACL reconstruction with bone-patellar tendon-bone autograft, this study does not demonstrate this association. There is evidence in this study to show that the PCL index may be used as an anatomic reconstructive marker of ACL but not to predict the clinical outcome in this type of reconstruction.(undefined

Search for the decay Bs0→D‾0f0(980) {B}_s^0\to {\overline{D}}^0{f}_0(980)

A search for $B_s^0 \to \overline{D}^{0} f_{0}(980)$ decays is performed using $3.0\, {\rm fb}^{-1}$ of $pp$ collision data recorded by the LHCb experiment during 2011 and 2012. The $f_{0}(980)$ meson is reconstructed through its decay to the $\pi^{+}\pi^{-}$ final state in the mass window $900\, {\rm MeV}/c^{2} < m(\pi^{+}\pi^{-}) < 1080\, {\rm MeV}/c^{2}$. No significant signal is observed. The first upper limits on the branching fraction of $\mathcal{B}(B_s^0 \to \overline{D}^{0} f_{0}(980)) < 3.1\,(3.4) \times 10^{-6}$ are set at $90\,\%$ ($95\,\%$) confidence level.Comment: 20 pages, 2 figures, published in JHE

Designs are cultural alloys; STEMPJE in design methodology

... the scholar who says he detests any kind of science is not only ridiculous: his attitude is decidedly harmful. Harmful because it encourages those who are responsible for decisions that may determine the fate of mankind to be intentionally ignorant about the material background against which their decisions should be taken. Harmful also because authors and scholars, while gladly using modern commodities, fail to see the philosophical implications of science and tend to deny scientists and engineers their legitimate place in culture. But we, scientists and engineers, we know that we have not only created material things and above all we know that we contribute to better relations between nations and peoples. For us it is easy to have understanding of and objective appreciation for the work of others, and from there it is not difficult to arrive also at human understanding and appreciation [H.B.G. Casimir, 1965; italics added