Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model

<div><p>Shannon entropy <i>H</i> and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information (“Shannon differentiation”) between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (<i>Sturnus vulgaris</i>) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.</p></div

A study into the behaviour of the formation level of an excavation under different unloading patterns in soft deposits

The construction of basements in urban areas is often associated with the possible damage to existing structures and services. The varying construction processes inevitably lead to different stress unloading patterns and therefore the dissipation of these excess pore-water pressures may lead to non-standard deformation profiles. The three main types of basement construction processes are layered excavation (LE), basin excavation (BE) and island excavation (IE). The effect of the various unloading patterns has been investigated by a three dimensional (3D) effective stress analysis method using the developed computer program 3DBCPE4.0. An excavation of length 50 m, width 50 m and depth 9 m in a certain homogenous and isotropic saturated soft soil was modelled. This included a diaphragm wall of 800-mm thickness embedded 18 m deep into the soft soil. The different excavation deformation profiles under different excavation patterns were related to the different unloading process, the exposure time of excavation face and the dissipation of negative excess pore-water pressures. The most favourable process for controlling the horizontal deformation of a retaining wall or the heave deformation of the formation level is suggested. The ground water potentials within the formation level are also presented

The Main Belt Comets and ice in the Solar System

We review the evidence for buried ice in the asteroid belt; specifically the questions around the so-called Main Belt Comets (MBCs). We summarise the evidence for water throughout the Solar System, and describe the various methods for detecting it, including remote sensing from ultraviolet to radio wavelengths. We review progress in the first decade of study of MBCs, including observations, modelling of ice survival, and discussion on their origins. We then look at which methods will likely be most effective for further progress, including the key challenge of direct detection of (escaping) water in these bodies

Atomic-scale combination of germanium-zinc nanofibers for structural and electrochemical evolution

Alloys are recently receiving considerable attention in the community of rechargeable batteries as possible alternatives to carbonaceous negative electrodes; however, challenges remain for the practical utilization of these materials. Herein, we report the synthesis of germanium-zinc alloy nanofibers through electrospinning and a subsequent calcination step. Evidenced by in situ transmission electron microscopy and electrochemical impedance spectroscopy characterizations, this one-dimensional design possesses unique structures. Both germanium and zinc atoms are homogenously distributed allowing for outstanding electronic conductivity and high available capacity for lithium storage. The as-prepared materials present high rate capability (capacity of similar to 50% at 20 C compared to that at 0.2 C-rate) and cycle retention (73% at 3.0 C-rate) with a retaining capacity of 546 mAh g(-1) even after 1000 cycles. When assembled in a full cell, high energy density can be maintained during 400 cycles, which indicates that the current material has the potential to be used in a large-scale energy storage system

Spin-orbit density wave induced hidden topological order in URu2Si2

The conventional order parameters in quantum matters are often characterized by 'spontaneous' broken symmetries. However, sometimes the broken symmetries may blend with the invariant symmetries to lead to mysterious emergent phases. The heavy fermion metal URu2Si2 is one such example, where the order parameter responsible for a second-order phase transition at Th = 17.5 K has remained a long-standing mystery. Here we propose via ab-initio calculation and effective model that a novel spin-orbit density wave in the f-states is responsible for the hidden-order phase in URu2Si2. The staggered spin-orbit order 'spontaneous' breaks rotational, and translational symmetries while time-reversal symmetry remains intact. Thus it is immune to pressure, but can be destroyed by magnetic field even at T = 0 K, that means at a quantum critical point. We compute topological index of the order parameter to show that the hidden order is topologically invariant. Finally, some verifiable predictions are presented.Comment: (v2) Substantially modified from v1, more calculation and comparison with experiments are include

Human factors for dementia: Evidence based design

Designing care environments for people living with dementia is a complex challenge as the key stakeholder may have difficulty communicating their capabilities, limitations and preferences. This paper describes the use of evidence-based design personas in a multi-disciplinary team with architects and chartered human factors specialists. Four individual personas (Alison, Barry, Christine and David) and a couple persona (Chris and Sally) were used to bring the voices of the people living with different stages of dementia to the design process. Their changing/fluctuating symptoms were communicated in two formats (wheel and matrix) within an inclusive design process to adapt a Victorian semi-detached house. The demonstrator house presents evidence based design, adaptation and support solutions to support people living with dementia to age well at home

Phase II study of weekly oxaliplatin and 24-h infusion of high-dose 5-fluorouracil and folinic acid in the treatment of advanced gastric cancer

[[abstract]]To investigate the efficacy and safety of combining weekly oxaliplatin with weekly 24-h infusion of high-dose 5-fluorouracil (5-FU) and folinic acid ( FA) in treatment of patients with advanced gastric cancer. Patients with histologically confirmed, locally advanced or recurrent/metastatic gastric cancer were studied. Oxaliplatin 65 mg m(-2) 2-h intravenous infusion, and 5-FU 2600 mg m(-2) plus FA 300 mg m(-2) 24-h intravenous infusion, were given on days 1 and 8, repeated every 3 weeks. Between January 2001 through January 2002, 55 patients were enrolled. The median age was 64 years (range: 22-75). In all, 52 patients (94.5%) had recurrent or metastatic disease and three patients had locally advanced disease. Among 50 patients evaluable for tumour response, 28 patients achieved partial response, with an overall response rate of 56% (95% confidence interval (CI): 41.8-70.3%). All 55 patients were evaluated for survival and toxicities. Median time to progression and overall survival were 5.2 and 10.0 months, respectively, during median follow-up time of 24.0 months. Major grades 3-4 toxicities were neutropenia in 23 cycles (7.1%) and thrombocytopenia in 16 cycles (5.0%). Treatment was discontinued for treatment-related toxicities in nine patients (16.4%), of whom eight were due to oxaliplatin-related neurotoxicity. One patient (1.8%) died of neutropenic sepsis. This oxaliplatin-containing regimen is effective in the treatment of advanced gastric cancer. Except for neurotoxicity that often develops after prolonged use of oxaliplatin, the regimen is well tolerated

Respiratory magnetic resonance imaging biomarkers in Duchenne muscular dystrophy

Objective To examine the diaphragm and chest wall dynamics with cine breathing magnetic resonance imaging (MRI) in ambulatory boys with Duchenne muscular dystrophy (DMD) without respiratory symptoms and controls. Methods In 11 DMD boys and 15 controls, cine MRI of maximal breathing was recorded for 10 sec. The lung segmentations were done by an automated pipeline based on a Holistically-Nested Network model (HNN method). Lung areas, diaphragm, and chest wall motion were measured throughout the breathing cycle. Results The HNN method reliably identified the contours of the lung and the diaphragm in every frame of each dataset (~180 frames) within seconds. The lung areas at maximal inspiration and expiration were reduced in DMD patients relative to controls (P = 0.02 and <0.01, respectively). The change in the lung area between inspiration and expiration correlated with percent predicted forced vital capacity (FVC) in patients (rs = 0.75, P = 0.03) and was not significantly different between groups. The diaphragm position, length, contractility, and motion were not significantly different between groups. Chest wall motion was reduced in patients compared to controls (P < 0.01). Interpretation Cine breathing MRI allows independent and reliable assessment of the diaphragm and chest wall dynamics during the breathing cycle in DMD patients and controls. The MRI data indicate that ambulatory DMD patients breathe at lower lung volumes than controls when their FVC is in the normal range. The diaphragm moves normally, whereas chest wall motion is reduced in these boys with DMD

Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM

The β-barrel assembly machinery (BAM) is a ~203 kDa complex of five proteins (BamA-E) which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins into the outer membrane via a poorly understood mechanism. Several current models suggest that BAM functions through a ‘lateral gating’ motion of the β-barrel of BamA. Here we present a cryo-EM structure of the BamABCDE complex, at 4.9 Å resolution. The structure is in a laterally open conformation showing that gating is independent of BamB binding. We describe conformational changes throughout the complex, and interactions between BamA, B, D, and E and the detergent micelle that suggest communication between BAM and the lipid bilayer. Finally, using an enhanced reconstitution protocol and functional assays, we show that for the outer membrane protein OmpT, efficient folding in vitro requires lateral gating in BAM

Health-promoting behaviors and social support of women of reproductive age, and strategies for advancing their health: Protocol for a mixed methods study

<p>Abstract</p> <p>Background</p> <p>Determining the health-promoting behaviors of women during the important period of reproduction provides valuable information for designing appropriate intervention programs for advancing women's health. There is no study on the health-promoting behaviors of women of reproductive age in Iran. Thus, the aim of this study is to explore these health-promoting behaviors for the purpose of developing comprehensive and culturally sensitive health advancement strategies for Iranian women.</p> <p>Methods/Design</p> <p>This study has a sequential explanatory mixed methods design. The follow-up explanation model is used to elaborate the quantitative results by collecting qualitative data from participants who could best assist in elucidating the results. The study is conducted in two sequential phases. The first phase is a population-based cross-sectional survey in which 1350 Iranian women of reproductive age are selected by proportional random multistage cluster sampling of the 22 main municipal sectors of Tehran, Iran. Questionnaires are completed through a face-to-face interview. The second phase is a qualitative study in which participants are selected using purposive sampling in the form of extreme case sampling on the basis of health-promoting behavior scores. The qualitative phase is based on data collected from focus group discussions or individual in-depth interviews. A conventional qualitative content analysis approach is used, and the data are managed with a computer-assisted program. Women's health-promoting strategies are developed using the qualitative and quantitative results, a review of the related literature, and the nominal group technique among experts.</p> <p>Discussion</p> <p>The findings of this mixed methods sequential explanatory study, obtained using a culturally sensitive approach, provide insights into the health behavioral factors that need to be considered if preventive strategies and intervention programs are to be designed to promote women's health in the community.</p