MM Algorithms for Geometric and Signomial Programming

This paper derives new algorithms for signomial programming, a generalization of geometric programming. The algorithms are based on a generic principle for optimization called the MM algorithm. In this setting, one can apply the geometric-arithmetic mean inequality and a supporting hyperplane inequality to create a surrogate function with parameters separated. Thus, unconstrained signomial programming reduces to a sequence of one-dimensional minimization problems. Simple examples demonstrate that the MM algorithm derived can converge to a boundary point or to one point of a continuum of minimum points. Conditions under which the minimum point is unique or occurs in the interior of parameter space are proved for geometric programming. Convergence to an interior point occurs at a linear rate. Finally, the MM framework easily accommodates equality and inequality constraints of signomial type. For the most important special case, constrained quadratic programming, the MM algorithm involves very simple updates.Comment: 16 pages, 1 figur

Multiresolution eXtended Free-Form Deformations (XFFD) for non-rigid registration with discontinuous transforms

Image registration is an essential technique to obtain point correspondences between anatomical structures from different images. Conventional non-rigid registration methods assume a continuous and smooth deformation field throughout the image. However, the deformation field at the interface of different organs is not necessarily continuous, since the organs may slide over or separate from each other. Therefore, imposing continuity and smoothness ubiquitously would lead to artifacts and increased errors near the discontinuity interface. In computational mechanics, the eXtended Finite Element Method (XFEM) was introduced to handle discontinuities without using computational meshes that conform to the discontinuity geometry. Instead, the interpolation bases themselves were enriched with discontinuous functional terms. Borrowing this concept, we propose a multiresolution eXtented Free-Form Deformation (XFFD) framework that seamlessly integrates within and extends the standard Free-Form Deformation (FFD) approach. Discontinuities are incorporated by enriching the B-spline basis functions coupled with extra degrees of freedom, which are only introduced near the discontinuity interface. In contrast with most previous methods, restricted to sliding motion, no ad hoc penalties or constraints are introduced to reduce gaps and overlaps. This allows XFFD to describe more general discontinuous motions. In addition, we integrate XFFD into a rigorously formulated multiresolution framework by introducing an exact parameter upsampling method. The proposed method has been evaluated in two publicly available datasets: 4D pulmonary CT images from the DIR-Lab dataset and 4D CT liver datasets. The XFFD achieved a Target Registration Error (TRE) of 1.17 ± 0.85 mm in the DIR-lab dataset and 1.94 ± 1.01 mm in the liver dataset, which significantly improves on the performance of the state-of-the-art methods handling discontinuities

Intervertebral disc classification by its degree of degeneration from T2-weighted magnetic resonance images

Purpose: The primary goal of this article is to achieve an automatic and objective method to compute the Pfirrmann’s degeneration grade of intervertebral discs (IVD) from MRI. This grading system is used in the diagnosis and management of patients with low back pain (LBP). In addition, biomechanical models, which are employed to assess the treatment on patients with LBP, require this grading value to compute proper material properties. Materials and methods: T2-weighted MR images of 48 patients were employed in this work. The 240 lumbar IVDs were divided into a training set (140) and a testing set (100). Three experts manually classified the whole set of IVDs using the Pfirrmann’s grading system and the ground truth was selected as the most voted value among them. The developed method employs active contour models to delineate the boundaries of the IVD. Subsequently, the classification is achieved using a trained Neural Network (NN) with eight designed features that contain shape and intensity information of the IVDs. Results: The classification method was evaluated using the testing set, resulting in a mean specificity (95.5 %) and sensitivity (87.3 %) comparable to those of every expert with respect to the ground truth. Conclusions: Our results show that the automatic method and humans perform equally well in terms of the classification accuracy. However, human annotations have inherent inter- and intra-observer variabilities, which lead to inconsistent assessments. In contrast, the proposed automatic method is objective, being only dependent on the input MRI

Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity

Background Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps. Results We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes. Conclusions Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA

Psychological interventions in asthma

Asthma is a multifactorial chronic respiratory disease characterised by recurrent episodes of airway obstruction. The current management of asthma focuses principally on pharmacological treatments, which have a strong evidence base underlying their use. However, in clinical practice, poor symptom control remains a common problem for patients with asthma. Living with asthma has been linked with psychological co-morbidity including anxiety, depression, panic attacks and behavioural factors such as poor adherence and suboptimal self-management. Psychological disorders have a higher-than-expected prevalence in patients with difficult-to-control asthma. As psychological considerations play an important role in the management of people with asthma, it is not surprising that many psychological therapies have been applied in the management of asthma. There are case reports which support their use as an adjunct to pharmacological therapy in selected individuals, and in some clinical trials, benefit is demonstrated, but the evidence is not consistent. When findings are quantitatively synthesised in meta-analyses, no firm conclusions are able to be drawn and no guidelines recommend psychological interventions. These inconsistencies in findings may in part be due to poor study design, the combining of results of studies using different interventions and the diversity of ways patient benefit is assessed. Despite this weak evidence base, the rationale for psychological therapies is plausible, and this therapeutic modality is appealing to both patients and their clinicians as an adjunct to conventional pharmacological treatments. What are urgently required are rigorous evaluations of psychological therapies in asthma, on a par to the quality of pharmaceutical trials. From this evidence base, we can then determine which interventions are beneficial for our patients with asthma management and more specifically which psychological therapy is best suited for each patient

IFNβ Protects Neurons from Damage in a Murine Model of HIV-1 Associated Brain Injury.

Infection with human immunodeficiency virus-1 (HIV-1) causes brain injury. Type I interferons (IFNα/β) are critical mediators of any anti-viral immune response and IFNβ has been implicated in the temporary control of lentiviral infection in the brain. Here we show that transgenic mice expressing HIV-1 envelope glycoprotein 120 in their central nervous system (HIVgp120tg) mount a transient IFNβ response and provide evidence that IFNβ confers neuronal protection against HIVgp120 toxicity. In cerebrocortical cell cultures, neuroprotection by IFNβ against gp120 toxicity is dependent on IFNα receptor 1 (IFNAR1) and the β-chemokine CCL4, as IFNAR1 deficiency and neutralizing antibodies against CCL4, respectively, abolish the neuroprotective effects. We find in vivo that IFNβ mRNA is significantly increased in HIVgp120tg brains at 1.5, but not 3 or 6 months of age. However, a four-week intranasal IFNβ treatment of HIVgp120tg mice starting at 3.5 months of age increases expression of CCL4 and concomitantly protects neuronal dendrites and pre-synaptic terminals in cortex and hippocampus from gp120-induced damage. Moreover, in vivo and in vitro data suggests astrocytes are a major source of IFNβ-induced CCL4. Altogether, our results suggest exogenous IFNβ as a neuroprotective factor that has potential to ameliorate in vivo HIVgp120-induced brain injury

Non-Equilibrium Field Dynamics of an Honest Holographic Superconductor

Most holographic models of superconducting systems neglect the effects of dynamical boundary gauge fields during the process of spontaneous symmetry-breaking. Usually a global symmetry gets broken. This yields a superfluid, which then is gauged "weakly" afterwards. In this work we build (and probe the dynamics of) a holographic model in which a local boundary symmetry is spontaneously broken instead. We compute two-point functions of dynamical non-Abelian gauge fields in the normal and in the broken phase, and find non-trivial gapless modes. Our AdS3 gravity dual realizes a p-wave superconductor in (1+1) dimensions. The ground state of this model also breaks (1+1)-dimensional parity spontaneously, while the Hamiltonian is parity-invariant. We discuss possible implications of our results for a wider class of holographic liquids.Comment: 32 pages, 12 figures; v3: string theory derivation of setup added (section 3.1), improved presentation, version accepted by JHEP; v2: paragraph added to discussion, figure added, references added, typos correcte

Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)

PMCID: PMC3581519This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited