Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.

The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment.Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome.These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies

New Geometric Algorithms for Fully Connected Staged Self-Assembly

We consider staged self-assembly systems, in which square-shaped tiles can be added to bins in several stages. Within these bins, the tiles may connect to each other, depending on the glue types of their edges. Previous work by Demaine et al. showed that a relatively small number of tile types suffices to produce arbitrary shapes in this model. However, these constructions were only based on a spanning tree of the geometric shape, so they did not produce full connectivity of the underlying grid graph in the case of shapes with holes; designing fully connected assemblies with a polylogarithmic number of stages was left as a major open problem. We resolve this challenge by presenting new systems for staged assembly that produce fully connected polyominoes in O(log^2 n) stages, for various scale factors and temperature {\tau} = 2 as well as {\tau} = 1. Our constructions work even for shapes with holes and uses only a constant number of glues and tiles. Moreover, the underlying approach is more geometric in nature, implying that it promised to be more feasible for shapes with compact geometric description.Comment: 21 pages, 14 figures; full version of conference paper in DNA2

State Complexity of Reversals of Deterministic Finite Automata with Output

We investigate the worst-case state complexity of reversals of deterministic finite automata with output (DFAOs). In these automata, each state is assigned some output value, rather than simply being labelled final or non-final. This directly generalizes the well-studied problem of determining the worst-case state complexity of reversals of ordinary deterministic finite automata. If a DFAO has $n$ states and $k$ possible output values, there is a known upper bound of $k^n$ for the state complexity of reversal. We show this bound can be reached with a ternary input alphabet. We conjecture it cannot be reached with a binary input alphabet except when $k = 2$, and give a lower bound for the case $3 \le k < n$. We prove that the state complexity of reversal depends solely on the transition monoid of the DFAO and the mapping that assigns output values to states.Comment: 18 pages, 3 tables. Added missing affiliation/funding informatio

Remarks on Income Contingent Loans: How Effective Can They Be at Mitigating Risk?

A well-known principle holds that equity provides better risk sharing opportunities than debt, but that there are greater enforcement problems associated with equity. Income contingent loans (ICL) represent an efficient (low transactions cost) way of implementing equity contracts for human capital.1 The amount the individual repays is dependent on his or her income. While it seems natural to link ICL with investments that increase the value of human capital — most notably education — there is no necessary reason to limit it to such investments

Prevalence and causes of blindness and visual impairment in Muyuka: a rural health district in South West Province, Cameroon.

AIM: To estimate the prevalence and causes of blindness and visual impairment in the population aged 40 years and over in Muyuka, a rural district in the South West Province of Cameroon. METHODS: A multistage cluster random sampling methodology was used to select 20 clusters of 100 people each. In each cluster households were randomly selected and all eligible people had their visual acuity (VA) measured by an ophthalmic nurse. Those with VA <6/18 were examined by an ophthalmologist. RESULTS: 1787 people were examined (response rate 89.3%). The prevalence of binocular blindness was 1.6% (95% CI: 0.8% to 2.4%), 2.2% (1.% to 3.1%) for binocular severe visual impairment, and 6.4% (5.0% to 7.8%) for binocular visual impairment. Cataract was the main cause of blindness (62.1%), severe visual impairment (65.0%), and visual impairment (40.0%). Refractive error was an important cause of severe visual impairment (15.0%) and visual impairment (22.5%). The cataract surgical coverage for people was 55% at the <3/60 level and 33% at the <6/60 level. 64.3% of eyes operated for cataract had poor visual outcome (presenting VA<6/60). CONCLUSIONS: Strategies should be developed to make cataract services affordable and accessible to the population in the rural areas. There is an urgent need to improve the outcome of cataract surgery. Refractive error services should be provided at the community level

User-driven design of robot costume for child-robot interactions among children with cognitive impairment

The involvement of arts and psychology elements in robotics research for children with cognitive impairment is still limited. However, the combination of robots, arts, psychology and education in the development of robots could significantly contribute to the improvement of social interaction skills among children with cognitive impairment. In this article, we would like to share our work on building and innovating the costume of LUCA's robot, which incorporating the positive psychological perspectives and arts values for children with cognitive impairment. Our goals are (1) to educate arts students in secondary arts school on the importance of social robot appearance for children with cognitive impairment, and (2) to select the best costume for future child-robot interaction study with children with cognitive impairments

Regulated Inositol‐Requiring Protein 1‐Dependent Decay as a Mechanism of Corin RNA and Protein Deficiency in Advanced Human Systolic Heart Failure

BACKGROUND: The compensatory actions of the endogenous natriuretic peptide system require adequate processing of natriuretic peptide pro‐hormones into biologically active, carboxyl‐terminal fragments. Natriuretic peptide pro‐peptide processing is accomplished by corin, a transmembrane serine protease expressed by cardiomyocytes. Brain natriuretic peptide (BNP) processing is inadequate in advanced heart failure and is independently associated with adverse outcomes; however, the molecular mechanisms causing impaired BNP processing are not understood. We hypothesized that the development of endoplasmic reticulum stress in cardiomyocytes in advanced heart failure triggers inositol‐requiring protein 1 (IRE1)‐dependent corin mRNA decay, which would favor a molecular substrate favoring impaired natriuretic peptide pro‐peptide processing. METHODS AND RESULTS: Two independent samples of hearts obtained from patients with advanced heart failure at transplant demonstrated that corin RNA was reduced as Atrial natriuretic peptide (ANP)/BNP RNA increased. Increases in spliced X‐box protein 1, a marker for IRE1‐endoribonuclease activity, were associated with decreased corin RNA. Moreover, ≈50% of the hearts demonstrated significant reductions in corin RNA and protein as compared to the nonfailing control sample. In vitro experiments demonstrated that induction of endoplasmic reticulum stress in cultured cardiomyocytes with thapsigargin activated IRE1s endoribonuclease activity and time‐dependent reductions in corin mRNA. In HL‐1 cells, overexpression of IRE1 activated IRE1 endoribonuclease activity and caused corin mRNA decay, whereas IRE1‐RNA interference with shRNA attenuated corin mRNA decay after induction of endoplasmic reticulum stress with thapsigargin. Pre‐treatment of cells with Actinomycin D to inhibit transcription did not alter the magnitude or time course of thapsigargin‐induced corin mRNA decline, supporting the hypothesis that this was the result of IRE1‐mediated corin mRNA degradation. CONCLUSIONS: These data support the hypothesis that endoplasmic reticulum stress‐mediated, IRE1‐dependent targeted corin mRNA decay is a mechanism leading to corin mRNA resulting in corresponding corin protein deficiency may contribute to the pathophysiology of impaired natriuretic peptide pro‐hormone processing in humans processing in humans with advanced systolic heart failure

Impaired decidual natural killer cell regulation of vascular remodelling in early human pregnancies with high uterine artery resistance

During human pregnancy, natural killer (NK) cells accumulate in the maternal decidua, but their specific roles remain to be determined. Decidual NK (dNK) cells are present during trophoblast invasion and uterine spiral artery remodelling. These events are crucial for successful placentation and the provision of an adequate blood supply to the developing fetus. Remodelling of spiral arteries is impaired in the dangerous pregnancy complication pre-eclampsia. We studied dNK cells isolated from pregnancies at 9-14 weeks' gestation, screened by uterine artery Doppler ultrasound to determine resistance indices which relate to the extent of spiral artery remodelling. dNK cells were able to promote the invasive behaviour of fetal trophoblast cells, partly through HGF. Cells isolated from pregnancies with higher resistance indices were less able to do this and secreted fewer pro-invasive factors. dNK cells from pregnancies with normal resistance indices could induce apoptotic changes in vascular smooth muscle and endothelial cells in vitro, events of importance in vessel remodelling, partly through Fas signalling. dNK cells isolated from high resistance index pregnancies failed to induce vascular apoptosis and secreted fewer pro-apoptotic factors. We have modelled the cellular interactions at the maternal-fetal interface and provide the first demonstration of a functional role for dNK cells in influencing vascular cells. A potential mechanism contributing to impaired vessel remodelling in pregnancies with a higher uterine artery resistance is presented. These findings may be informative in determining the cellular interactions contributing to the pathology of pregnancy disorders where remodelling is impaired, such as pre-eclampsia. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd

Black funnels

The Hartle-Hawking state of $\mathcal{N}=4$ SYM at strong coupling and large $N$ on a fixed black hole background has two proposed gravitational duals: a black funnel or a black droplet. We construct the black funnel solutions that are dual to the Hartle-Hawking state on a Schwarzschild black hole and on a class of three-dimensional asymptotically flat black hole backgrounds. We compute their holographic stress tensor and argue for the stability of these solutions