Entropy, Ergodicity and Stem Cell Multipotency

Populations of mammalian stem cells commonly exhibit considerable cell-cell variability. However, the functional role of this diversity is unclear. Here, we analyze expression fluctuations of the stem cell surface marker Sca1 in mouse hematopoietic progenitor cells using a simple stochastic model and find that the observed dynamics naturally lie close to a critical state, thereby producing a diverse population that is able to respond rapidly to environmental changes. We propose an information-theoretic interpretation of these results that views cellular multipotency as an instance of maximum entropy statistical inference.Comment: 6 pages, 3 figure

Persistent urinary incontinence and delivery mode history: a six-year longitudinal study.

Objective: To investigate the prevalence of persistent and long term postpartum urinary incontinence and associations with mode of first and subsequent delivery. Setting: Maternity units in Aberdeen (Scotland), Birmingham (England) and Dunedin (New Zealand). Design: Longitudinal study Population: 4214 women who returned postal questionnaires 3 months and 6 years after the index birth. Methods: Symptom data were obtained from both questionnaires and obstetric data from case-notes for the index birth and the second questionnaire for subsequent births. Logistic regression investigated the independent effects of mode of first delivery and delivery mode history. Main outcome measures: Urinary incontinence – persistent (at 3 months and 6 years after index birth) and long-term (at 6 years after index birth). Results: The prevalence of persistent urinary incontinence was 24%. Delivering exclusively by Caesarean section was associated with both less persistent (OR= 0.46, 95% CI 0.32 to 0.68) and long term urinary incontinence (OR=0.50, 95% CI 0.40 to 0.63). Caesarean section birth in addition to vaginal delivery however was not associated with significantly less persistent incontinence (OR 0.93, 95%CI 0.67 to 1.29). There were no significant associations between persistent or long-term urinary incontinence and forceps or vacuum extraction delivery. Other significantly associated factors were increasing number of births and older maternal age. Conclusions: The risk of persistent and long term urinary incontinence is significantly lower following Caesarean section deliveries but not if there is another vaginal birth. Even when delivering exclusively by Caesarean section, the prevalence of persistent symptoms (14%) is still high

Twelve-year follow-up of conservative management of postnatal urinary and faecal incontinence and prolapse outcomes : randomised controlled trial

© 2013 Royal College of Obstetricians and Gynaecologists. Funded by Royal College of Obstetricians and Gynaecologists, London, UK; Health Research Council of New Zealand. Grant Number: RG 819/06 New Zealand Lottery Grant Board Health Services Research Unit, University of Aberdeen Chief Scientist Office of the Scottish Government Health DirectoratesPeer reviewedPostprin

Faecal incontinence persisting after childbirth : a 12 year longitudinal study

© 2012 The Authors BJOG An International Journal of Obstetrics and Gynaecology © 2012 RCOG.Peer reviewedPostprin

School Playground Surfacing and Arm Fractures in Children: A Cluster Randomized Trial Comparing Sand to Wood Chip Surfaces

In a randomized trial of elementary schools in Toronto, Andrew Howard and colleagues show that granitic sand playground surfaces reduce the risk of arm fractures from playground falls when compared with wood fiber surfaces

Analyses of Special Hazards and Flooding Problems in Tropical Island Environments

Data and results summarized in this paper show that development of urban projects and design of flood control works in tropical island catchments must consider clear water flooding as well as special hazards such as landslides, flow bulking, high sediment concentrations, mud and debris flows and flow avulsions. The needs for and methods to estimate peak flows, event volumes and the potential extent and depths of flooding during severe storm events in urbanizing tropical environments are described

Terrestrial Alteration Mineral Assemblages in the NWA 10416 Olivine Phyric Shergottite

We report on the alteration history of the olivine-phyric, highly depleted (HD) shergottite, Northwest Africa (NWA) 10416, paying particular attention to the origin of the aqueous alteration seen affecting the meteorite’s olivine megacrysts. The rock’s interior displays 1 mm, zoned, altered olivine megacrysts set in a groundmass of clinopyroxene, unzoned olivine, and interstitial plagioclase and maskelynite. Synchrotron micro X-ray diffraction (µ-XRD) and transmission electron microscopy (TEM) show that plagioclase and maskelynite have been partially replaced by kaolinite. The relict olivine megacryst cores display a unique concentric colouration for Martian meteorites, having central amber-coloured zones surrounded by a brown mantle zone, with the rims remaining clear and unaltered. This colouration is a result of fluid alteration and partial replacement, with hydration. TEM analysis revealed the ∼200 nm scale banded and largely amorphous nature of the alteration, but with some (∼ 20%) relict crystalline olivine patches. Although the coloured olivine zones show cation and anion site vacancies compared to stoichiometric olivine, a relict igneous compositional trend is preserved in the megacrysts, from Mg-rich altered cores (Mg# = 76) to unaltered stoichiometric rims (Fo53). Synchrotron Fe-K X-ray absorption near-edge structure (XANES) analysis revealed that the coloured zones of the megacryst have different Fe oxidation values. High ferric contents are present in the brown mantle zones (Fe3+/ΣFe ≤ 0.92) and the amber zones (Fe3+/ΣFe ≤ 0.30), whereas the clear rims are ferrous. This suggests alteration occurred in an oxidising environment and that the sharp contrast in colour of the megacryst (brown to clear) is a record of a relict fluid reaction front. In order to test the terrestrial or extraterrestrial origin of the alteration, olivine material from a shock-melt vein was analysed by TEM. The analysis revealed 0.952 nm curved d-spacing’s from clay alteration undisturbed by any shock effects, strongly suggesting a terrestrial origin. The d-spacing values most likely represent a collapsed saponite or vermiculite, showing that in some places olivine has been replaced by crystalline clay. Oxygen isotope analysis of bulk (Δ17O = 0.309 ± 0.009 (2σ) ‰) and amber-coloured megacryst material (= 0.271 ± 0.002 (2σ) ‰), are also consistent with terrestrial alteration. We propose a model in which, during the meteorite’s time in Northwest Africa, low-temperature, likely acidic, groundwater exploited fractures. The fluid altered the olivine megacrysts in a way that was controlled by the pre-existing, igneous compositional zonation, with Mg-rich olivine being more susceptible to alteration in this fluid environment. The plagioclase and maskelynite were also altered to a high degree. After the alteration event it is likely that NWA 10416 had a significant residence time in Northwest Africa, accounting for terrestrial calcite and the dehydration of some clay phases

Fundamental differences in physiology of Bordetella pertussis dependent on the two-component system Bvg revealed by gene essentiality studies.

The identification of genes essential for a bacterium's growth reveals much about its basic physiology under different conditions. Bordetella pertussis, the causative agent of whooping cough, adopts both virulent and avirulent states through the activity of the two-component system, Bvg. The genes essential for B. pertussis growth in vitro were defined using transposon sequencing, for different Bvg-determined growth states. In addition, comparison of the insertion indices of each gene between Bvg phases identified those genes whose mutation exerted a significantly different fitness cost between phases. As expected, many of the genes identified as essential for growth in other bacteria were also essential for B. pertussis. However, the essentiality of some genes was dependent on Bvg. In particular, a number of key cell wall biosynthesis genes, including the entire mre/mrd locus, were essential for growth of the avirulent (Bvg minus) phase but not the virulent (Bvg plus) phase. In addition, cell wall biosynthesis was identified as a fundamental process that when disrupted produced greater fitness costs for the Bvg minus phase compared to the Bvg plus phase. Bvg minus phase growth was more susceptible than Bvg plus phase growth to the cell wall-disrupting antibiotic ampicillin, demonstrating the increased susceptibility of the Bvg minus phase to disruption of cell wall synthesis. This Bvg-dependent conditional essentiality was not due to Bvg-regulation of expression of cell wall biosynthesis genes; suggesting that this fundamental process differs between the Bvg phases in B. pertussis and is more susceptible to disruption in the Bvg minus phase. The ability of a bacterium to modify its cell wall synthesis is important when considering the action of antibiotics, particularly if developing novel drugs targeting cell wall synthesis

HI: haplotype improver using paired-end short reads

Summary: We present a program to improve haplotype reconstruction by incorporating information from paired-end reads, and demonstrate its utility on simulated data. We find that given a fixed coverage, longer reads (implying fewer of them) are preferable