How Gaussian competition leads to lumpy or uniform species distributions

A central model in theoretical ecology considers the competition of a range of species for a broad spectrum of resources. Recent studies have shown that essentially two different outcomes are possible. Either the species surviving competition are more or less uniformly distributed over the resource spectrum, or their distribution is 'lumped' (or 'clumped'), consisting of clusters of species with similar resource use that are separated by gaps in resource space. Which of these outcomes will occur crucially depends on the competition kernel, which reflects the shape of the resource utilization pattern of the competing species. Most models considered in the literature assume a Gaussian competition kernel. This is unfortunate, since predictions based on such a Gaussian assumption are not robust. In fact, Gaussian kernels are a border case scenario, and slight deviations from this function can lead to either uniform or lumped species distributions. Here we illustrate the non-robustness of the Gaussian assumption by simulating different implementations of the standard competition model with constant carrying capacity. In this scenario, lumped species distributions can come about by secondary ecological or evolutionary mechanisms or by details of the numerical implementation of the model. We analyze the origin of this sensitivity and discuss it in the context of recent applications of the model.Comment: 11 pages, 3 figures, revised versio

A phase-space approach to non-stationary nonlinear systems

A phase-space formulation of non-stationary nonlinear dynamics including both Hamiltonian (e.g., quantum-cosmological) and dissipative (e.g., dissipative laser) systems reveals an unexpected affinity between seemly different branches of physics such as nonlinear dynamics far from equilibrium, statistical mechanics, thermodynamics, and quantum physics. One of the key insights is a clear distinction between the "vacuum" and "squeezed" states of a non-stationary system. For a dissipative system, the "squeezed state" (or the coherent "concentrate") mimics vacuum one and can be very attractable in praxis, in particular, for energy harvesting at the ultrashort time scales in a laser or "material laser" physics including quantum computing. The promising advantage of the phase-space formulation of the dissipative soliton dynamics is the possibility of direct calculation of statistical (including quantum) properties of coherent, partially-coherent, and non-coherent dissipative structure without numerically consuming statistic harvesting.Comment: 11th CHAOS Conference, 5 - 8 June 2018, Rome, Italy; 13 pages, 9 figure

Single nucleotide polymorphisms and breast cancer: not yet a success story

Numerous studies have examined low penetrance susceptibility polymorphisms in candidate genes, with some reporting significant findings. However, for the most part these associations could not be replicated in subsequent studies, suggesting that the original observations were due to chance. The failure to identify meaningful common genetic variation in relation to breast cancer should give us pause for thought and make us reconsider our current research strategies. The most recent directions of pooling samples to increase statistical power and pursuing whole genome screens may overcome some obstacles while also creating new challenges. Future studies should perhaps also consider alternative designs such as using surrogate (preferably continuous) markers of breast cancer, focusing on high-risk populations, and defining pathologically distinct outcomes

Single nucleotide polymorphisms and breast cancer: not yet a success story

Numerous studies have examined low penetrance susceptibility polymorphisms in candidate genes, with some reporting significant findings. However, for the most part these associations could not be replicated in subsequent studies, suggesting that the original observations were due to chance. The failure to identify meaningful common genetic variation in relation to breast cancer should give us pause for thought and make us reconsider our current research strategies. The most recent directions of pooling samples to increase statistical power and pursuing whole genome screens may overcome some obstacles while also creating new challenges. Future studies should perhaps also consider alternative designs such as using surrogate (preferably continuous) markers of breast cancer, focusing on high-risk populations, and defining pathologically distinct outcomes

GLAST: Understanding the High Energy Gamma-Ray Sky

We discuss the ability of the GLAST Large Area Telescope (LAT) to identify, resolve, and study the high energy gamma-ray sky. Compared to previous instruments the telescope will have greatly improved sensitivity and ability to localize gamma-ray point sources. The ability to resolve the location and identity of EGRET unidentified sources is described. We summarize the current knowledge of the high energy gamma-ray sky and discuss the astrophysics of known and some prospective classes of gamma-ray emitters. In addition, we also describe the potential of GLAST to resolve old puzzles and to discover new classes of sources.Comment: To appear in Cosmic Gamma Ray Sources, Kluwer ASSL Series, Edited by K.S. Cheng and G.E. Romer

Impact of FTO genotypes on BMI and weight in polycystic ovary syndrome : a systematic review and meta-analysis

Aims/hypothesis FTO gene single nucleotide polymorphisms (SNPs) have been shown to be associated with obesity-related traits and type 2 diabetes. Several small studies have suggested a greater than expected effect of the FTO rs9939609 SNP on weight in polycystic ovary syndrome (PCOS). We therefore aimed to examine the impact of FTO genotype on BMI and weight in PCOS. Methods A systematic search of medical databases (PubMed, EMBASE and Cochrane CENTRAL) was conducted up to the end of April 2011. Seven studies describing eight distinct PCOS cohorts were retrieved; seven were genotyped for SNP rs9939609 and one for SNP rs1421085. The per allele effect on BMI and body weight increase was calculated and subjected to meta-analysis. Results A total of 2,548 women with PCOS were included in the study; 762 were TT homozygotes, 1,253 had an AT/CT genotype, and 533 were AA/CC homozygotes. Each additional copy of the effect allele (A/C) increased the BMI by a mean of 0.19 z score units (95% CI 0.13, 0.24; p = 2.26 × 10−11) and body weight by a mean of 0.20 z score units (95% CI 0.14, 0.26; p = 1.02 × 10−10). This translated into an approximately 3.3 kg/m2 increase in BMI and an approximately 9.6 kg gain in body weight between TT and AA/CC homozygotes. The association between FTO genotypes and BMI was stronger in the cohorts with PCOS than in the general female populations from large genome-wide association studies. Deviation from an additive genetic model was observed in heavier populations. Conclusions/interpretation The effect of FTO SNPs on obesity-related traits in PCOS seems to be more than two times greater than the effect found in large population-based studies. This suggests an interaction between FTO and the metabolic context or polygenic background of PCOS

Modelling study of dimerization in mammalian defensins

BACKGROUND: Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are considered key factors for their action. Based on structural information on human β-defensin 2, we examine homologous defensins from various mammalian species for conserved functional physico-chemical characteristics. RESULTS: Based on homology greater than 40%, structural models of 8 homologs of HBD-2 were constructed. A conserved pattern of electrostatics and dynamics was observed across 6 of the examined defensins; models backed by energetics suggest that the defensins in these 6 organisms are characterized by dimerization-linked enhanced functional potentials. In contrast, dimerization is not energetically favoured in the sheep, goat and mouse defensins, suggesting that they function efficiently as monomers. CONCLUSION: β-defensin 2 from some mammals may work as monomers while those in others, including humans, work as oligomers. This could potentially be used to design human defensins that may be effective at lower concentrations and hence have therapeutic benefits

Evaluation of the current knowledge limitations in breast cancer research: a gap analysis

BACKGROUND A gap analysis was conducted to determine which areas of breast cancer research, if targeted by researchers and funding bodies, could produce the greatest impact on patients. METHODS Fifty-six Breast Cancer Campaign grant holders and prominent UK breast cancer researchers participated in a gap analysis of current breast cancer research. Before, during and following the meeting, groups in seven key research areas participated in cycles of presentation, literature review and discussion. Summary papers were prepared by each group and collated into this position paper highlighting the research gaps, with recommendations for action. RESULTS Gaps were identified in all seven themes. General barriers to progress were lack of financial and practical resources, and poor collaboration between disciplines. Critical gaps in each theme included: (1) genetics (knowledge of genetic changes, their effects and interactions); (2) initiation of breast cancer (how developmental signalling pathways cause ductal elongation and branching at the cellular level and influence stem cell dynamics, and how their disruption initiates tumour formation); (3) progression of breast cancer (deciphering the intracellular and extracellular regulators of early progression, tumour growth, angiogenesis and metastasis); (4) therapies and targets (understanding who develops advanced disease); (5) disease markers (incorporating intelligent trial design into all studies to ensure new treatments are tested in patient groups stratified using biomarkers); (6) prevention (strategies to prevent oestrogen-receptor negative tumours and the long-term effects of chemoprevention for oestrogen-receptor positive tumours); (7) psychosocial aspects of cancer (the use of appropriate psychosocial interventions, and the personal impact of all stages of the disease among patients from a range of ethnic and demographic backgrounds). CONCLUSION Through recommendations to address these gaps with future research, the long-term benefits to patients will include: better estimation of risk in families with breast cancer and strategies to reduce risk; better prediction of drug response and patient prognosis; improved tailoring of treatments to patient subgroups and development of new therapeutic approaches; earlier initiation of treatment; more effective use of resources for screening populations; and an enhanced experience for people with or at risk of breast cancer and their families. The challenge to funding bodies and researchers in all disciplines is to focus on these gaps and to drive advances in knowledge into improvements in patient care

Synergy between trastuzumab and pertuzumab for human epidermal growth factor 2 (Her2) from colocalization: an in silico based mechanism

10.1186/bcr2888Breast Cancer Research133-BCRR

Association between retinal vein occlusion, axial length and vitreous chamber depth measured by optical low coherence reflectometry.

BACKGROUND: Results of ocular biometric measurements in retinal vein occlusion (RVO) eyes are still inconclusive and controversial. The aim of this study was to evaluate the association between ocular axial length (AL), vitreous chamber depth (VCD) and both central (CRVO) and branch retinal vein occlusions (BRVO) using optical low coherence reflectometry (OLCR). METHODS: Both eyes of 37 patients with unilateral CRVO (mean age: 66 +/- 14 years, male:female - 21:16) and 46 patients with unilateral BRVO (mean age: 63 +/- 12 years, male:female - 24:22) were enrolled in this study. The control group consisted of randomly selected single eyes of 67 age and gender matched volunteers without the presence or history of RVO (mean age: 64 +/- 14 years, male:female - 34:33). Optical biometry was performed by OLCR biometer (LenStar LS 900). Average keratometry readings, central corneal thickness (CCT), anterior chamber depth (ACD), lens thickness (LT), AL and VCD of eyes with RVO were compared with those of fellow eyes using paired t-tests and with those of control eyes using independent t-tests. RESULTS: Mean CCT, ACD and LT, average keratometry readings of affected RVO eyes, unaffected fellow eyes and control eyes was not statistically different in either groups. In eyes with CRVO mean AL and VCD of affected eyes were significantly shorter than those of control eyes (p < 0.001, p < 0.05), mean difference in AL and VCD between the affected and control eyes was 0.56 +/- 0.15 mm and 0.45 +/- 0.19 mm, respectively. In eyes with BRVO, mean AL of the affected eyes was significantly shorter with a mean difference of 0.57 +/- 0.15 mm (p < 0.001) and the VCD was significantly shorter with a mean difference of 0.61 +/- 0.15 mm (p < 0.001) comparing with the control eyes. CONCLUSION: Shorter AL and VCD might be a potential anatomical predisposing factor for development either of CRVO or BRVO