The range of axial rotation of the glenohumeral joint.

Accepted versio

Determining rotational dynamics of the guanidino group of arginine side chains in proteins by carbon-detected NMR

Arginine residues are imperative for many active sites and protein-interaction interfaces. A new NMR-based method is presented to determine the rotational dynamics around the Nε-Cζ bond of arginine side chains. An application to a 19 kDa protein shows that the strengths of interactions involving arginine side chains can be characterised

A framework for the simulation of regional decadal variability for agricultural and other applications

The SimGen software, including ancillary files and scripts, can be found at http://iri.columbia.edu/~amg/CCAFS/simgen/Climate prediction on decadal time scales is currently an active area of research. Although there are indications that predictions from dynamical models may have skill in some regions, assessment of this skill is still underway, and reliable model-based predictions of regional ‘near-term’ climate change, particularly for terrestrial regions, have not yet been demonstrated. Given the absence of such forecasts, synthetic data sequences that capture the statistical properties of observed near-term climate variability have potential value. Incorporation of a climate change component in such sequences can aid in estimating likelihoods for a range of climatic stresses, perhaps lying outside the range of past experience. Such simulations can be used to drive agricultural, hydrological or other application models, enabling resilience testing of adaptation or decision systems. The use of statistically-based methods enables the efficient generation of a large ensemble of synthetic sequences as well as the creation of well-defined probabilistic risk estimates. In this report we discuss procedures for the generation of synthetic climate sequences that incorporate both the statistics of observed variability and expectations regarding future regional climate change. Model fitting and simulation are conditioned by requirements particular to the decadal climate problem. A method for downscaling annualized simulations to the daily time step while preserving both spatial and temporal subannual statistical properties is presented and other possible methods discussed. A ‘case-study’ realization of the proposed framework is described

A scapular coordinate frame for clinical and kinematic analyses.

Accepted versio

Deuteros 2.0: Peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry

Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming increasing routine for monitoring changes in the structural dynamics of proteins. Differential HDX-MS allows comparison of protein states, such as in the absence or presence of a ligand. This can be used to attribute changes in conformation to binding events, allowing the mapping of entire conformational networks. As such, the number of necessary cross-state comparisons quickly increases as additional states are introduced to the system of study. There are currently very few software packages available that offer quick and informative comparison of HDX-MS datasets and even fewer which offer statistical analysis and advanced visualization. Following the feedback from our original software Deuteros, we present Deuteros 2.0 which has been redesigned from the ground up to fulfill a greater role in the HDX-MS analysis pipeline. Deuteros 2.0 features a repertoire of facilities for back exchange correction, data summarization, peptide-level statistical analysis and advanced data plotting features

Sustainability performance measurement : a preliminary classification framework of models and indicators

In this position paper we focus on the diversity of sustainability measurements. Based on existing research on performance measurement, we propose a preliminary classification framework summarizing sustainability models and indicators. By describing illustrative examples, we claim that several models and indicators can be distinguished with their own peculiarities. Having such a framework is interesting for both academia and business to structure the range of models and indicators and to ultimately select the appropriate sustainability measurement approach. The proposed framework should be validated by further research

Smectic and columnar ordering in length-polydisperse fluids of parallel hard cylinders

We apply a recently proposed density functional for mixtures of parallel hard cylinders, based on Rosenfeld's fundamental measure theory, to study the effect of length-polydispersity on the relative stability between the smectic and columnar liquid crystal phases.To this purpose we derive from this functional an expression for the direct correlation function and use it to perform a bifurcation analysis. We compare the results with those obtained with a second and a third virial approximation of this function. All three approximations lead to the same conclusion: there is a terminal polydispersity beyond which the smectic phase is less stable than the columnar phase. This result is in agreement with previous Monte Carlo simulations conducted on a freely rotating length-polydisperse hard spherocylinder fluid, although the theories always overestimate the terminal polydispersity because the nematic-columnar phase transition is first order and exhibits a wide coexistence gap. Both, the fundamental-measure functional and the third virial approximation, predict a metastable nematic-nematic demixing. Conversely, according to second virial approximation this demixing might be stable at high values of the polydispersity, something that is observed neither in simulations nor in experiments. The results of the fundamental-measure functional are quantitatively superior to those obtained from the other two approximations. Thus this functional provides a promising route to map out the full phase diagram of this system.Comment: 7 pages, 2 figure

Symmetries of degenerate center singularities of plane vector fields

Let $D$ be a closed unit $2$-disk on the plane centered at the origin $O$, and $F$ be a smooth vector field such that $O$ is a unique singular point of $F$ and all other orbits of $F$ are simple closed curves wrapping once around $O$. Thus topologically $O$ is a "center" singularity. Let also $\mathrm{Diff}(F)$ be the group of all diffeomorphisms of $D$ which preserve orientation and orbits of $F$. In arXiv:0907.0359 the author described the homotopy type of $\mathrm{Diff}(F)$ under assumption that the $1$-jet of $F$ at $O$ is non-degenerate. In this paper degenerate case is considered. Under additional "non-degeneracy assumptions" on $F$ the path components of $\mathrm{Diff}(F)$ with respect to distinct weak topologies are described.Comment: 21 page, 3 figure

The relationship between the systemic inflammatory response, tumour proliferative activity, T-lymphocytic and macrophage infiltration, microvessel density and survival in patients with primary operable breast cancer

The significance of the inter-relationship between tumour and host local/systemic inflammatory responses in primary operable invasive breast cancer is limited. The inter-relationship between the systemic inflammatory response (pre-operative white cell count, C-reactive protein and albumin concentrations), standard clinicopathological factors, tumour T-lymphocytic (CD4+ and CD8+) and macrophage (CD68+) infiltration, proliferative (Ki-67) index and microvessel density (CD34+) was examined using immunohistochemistry and slide-counting techniques, and their prognostic values were examined in 168 patients with potentially curative resection of early-stage invasive breast cancer. Increased tumour grade and proliferative activity were associated with greater tumour T-lymphocyte (P<0.05) and macrophage (P<0.05) infiltration and microvessel density (P<0.01). The median follow-up of survivors was 72 months. During this period, 31 patients died; 18 died of their cancer. On univariate analysis, increased lymph-node involvement (P<0.01), negative hormonal receptor (P<0.10), lower albumin concentrations (P<0.01), increased tumour proliferation (P<0.05), increased tumour microvessel density (P<0.05), the extent of locoregional control (P<0.0001) and limited systemic treatment (Pless than or equal to0.01) were associated with cancer-specific survival. On multivariate analysis of these significant covariates, albumin (HR 4.77, 95% CI 1.35–16.85, P=0.015), locoregional treatment (HR 3.64, 95% CI 1.04–12.72, P=0.043) and systemic treatment (HR 2.29, 95% CI 1.23–4.27, P=0.009) were significant independent predictors of cancer-specific survival. Among tumour-based inflammatory factors, only tumour microvessel density (P<0.05) was independently associated with poorer cancer-specific survival. The host inflammatory responses are closely associated with poor tumour differentiation, proliferation and malignant disease progression in breast cancer

Cerebral malaria: Gamma-interferon redux

There are two theories that seek to explain the pathogenesis of cerebral malaria, the mechanical obstruction hypothesis and the immunopathology hypothesis. Evidence consistent with both ideas has accumulated from studies of the human disease and experimental models. Thus, some combination of these concepts seems necessary to explain the very complex pattern of changes seen in cerebral malaria. The interactions between malaria parasites, erythrocytes, the cerebral microvascular endothelium, brain parenchymal cells, platelets and microparticles need to be considered. One factor that seems able to knit together much of this complexity is the cytokine interferon-gamma (IFN-?). In this review we consider findings from the clinical disease, in vitro models and the murine counterpart of human cerebral malaria in order to evaluate the roles played by IFN-? in the pathogenesis of this often fatal and debilitating condition. © 2014 Hunt, Ball, Hansen, Khaw, Guo, Bakmiwewa, Mitchell, Combes and Grau