Superpixel-based segmentation of muscle fibers in multi-channel microscopy

Background Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is segmenting the cell boundaries, which is a very different problem from segmenting color images from the real world. This paper addresses the difficulties and presents a superpixel-based framework for segmentation of regenerated muscle fibers in mice. Results We propose to integrate an edge detector into a superpixel algorithm and customize the method for multi-channel images. The enhanced superpixel method outperforms the original and another advanced superpixel algorithm in terms of both boundary recall and under-segmentation error. Our framework was applied to cross-section and lateral section images of regenerated muscle fibers from confetti-fluorescent mice. Compared with “ground-truth” segmentations, our framework yielded median Dice similarity coefficients of 0.92 and higher. Conclusion Our segmentation framework is flexible and provides very good segmentations of multi-color muscle fibers. We anticipate our methods will be useful for segmenting a variety of tissues in confetti fluorecent mice and in mice with similar multi-color labels.National University of Singapore (Duke-NUS SRP Phase 2 Research Block Grant)Singapore. National Research Foundation (CREATE programme)Singapore-MIT Alliance for Research and Technology (SMART

Effects of Explicit Convection on Future Projections of Mesoscale Circulations, Rainfall, and Rainfall Extremes over Eastern Africa

Eastern Africa’s fast-growing population is vulnerable to changing rainfall and extremes. Using the first pan-African climate change simulations that explicitly model the rainfall-generating convection, we investigate both the climate change response of key mesoscale drivers of eastern African rainfall, such as sea and lake breezes, and the spatial heterogeneity of rainfall responses. The explicit model shows widespread increases at the end of the century in mean (~40%) and extreme (~50%) rain rates, whereas the sign of changes in rainfall frequency has large spatial heterogeneity (from −50% to over +90%). In comparison, an equivalent parameterized simulation has greater moisture convergence and total rainfall increase over the eastern Congo and less over eastern Africa. The parameterized model also does not capture 1) the large heterogeneity of changes in rain frequency; 2) the widespread and large increases in extreme rainfall, which result from increased rainfall per humidity change; and 3) the response of rainfall to the changing sea breeze, even though the sea-breeze change is captured. Consequently, previous rainfall projections are likely inadequate for informing many climate-sensitive decisions—for example, for infrastructure in coastal cities. We consider the physics revealed here and its implications to be relevant for many other vulnerable tropical regions, especially those with coastal convection

The Genetics of Prey Susceptibility to Myxobacterial Predation:A Review, including an Investigation into Pseudomonas aeruginosa Mutations Affecting Predation by Myxococcus xanthus

Bacterial predation is a ubiquitous and fundamental biological process, which influences the community composition of microbial ecosystems. Among the best characterised bacterial predators are the myxobacteria, which include the model organism Myxococcus xanthus. Predation by M. xanthus involves the secretion of antibiotic metabolites and hydrolytic enzymes, which results in the lysis of prey organisms and release of prey nutrients into the extracellular milieu. Due to the generalist nature of this predatory mechanism, M. xanthus has a broad prey range, being able to kill and consume Gram-negative/positive bacteria and fungi. Potential prey organisms have evolved a range of behaviours which protect themselves from attack by predators. In recent years, several investigations have studied the molecular responses of a broad variety of prey organisms to M. xanthus predation. It seems that the diverse mechanisms employed by prey belong to a much smaller number of general "predation resistance" strategies. In this mini-review, we present the current state of knowledge regarding M. xanthus predation, and how prey organisms resist predation. As previous molecular studies of prey susceptibility have focussed on individual genes/metabolites, we have also undertaken a genome-wide screen for genes of Pseudomonas aeruginosa which contribute to its ability to resist predation. P. aeruginosa is a World Health Organisation priority 1 antibiotic-resistant pathogen. It is metabolically versatile and has an array of pathogenic mechanisms, leading to its prevalence as an opportunistic pathogen. Using a library of nearly 5,500 defined transposon insertion mutants, we screened for "prey genes", which when mutated allowed increased predation by a fluorescent strain of M. xanthus. A set of candidate "prey proteins" were identified, which shared common functional roles and whose nature suggested that predation resistance by P. aeruginosa requires an effective metal/oxidative stress system, an intact motility system, and mechanisms for de-toxifying antimicrobial peptides

Assessment of Chemical Inhibitor Addition to Improve the Gas Production from Biowaste

The coexistence of sulphate-reducing bacteria and methanogenic archaea in the reactors during the anaerobic digestion from sulphate-containing waste could favor the accumulation of sulfide on the biogas, and therefore reduce its quality. In this study, the effect of sulphate-reducing bacteria inhibitor (MoO−2 4 ) addition in a two phase system from sulphate-containing municipal solid waste to improve the quality of the biogas has been investigated. The results showed that although SRB and sulphide production decreased, the use of inhibitor was not effective to improve the anaerobic digestion in a two phase system from sulphate-containing waste, since a significant decrease on biogas and organic matter removal were observed. Before MoO−2 4 addition the average values of volatile solid were around 12 g/kg, after 5 days of inhibitor use, those values did exceed to 28 g/kg. Molybdate caused acidification in the reactor and it was according to decrease in the pH values. In relation to microbial consortia, the effect of inhibitor was a decrease in Bacteria (44%; 60% in sulphate-reducing bacteria) and Archaea (38%) population

African Lightning and its Relation to Rainfall and Climate Change in a Convection‐Permitting Model

Global climate models struggle to simulate both the convection and cloud ice fundamental to lightning formation. We use the first convection‐permitting, future climate simulations for the lightning hot spot of Africa, at the same time utilizing an ice‐based lightning parametrization. Both the model and observations show that lightning over Africa's drier areas, as well as the moist Congo, have more lightning per rainfall than other regions. Contrary to results in the literature, the future projection shows little increase in total lightning (~107 flashes (or 2%) per degree warming). This is a consequence of increased stability reducing the number of lightning days, largely offsetting the increased graupel and updraft velocity driving an increase in lightning per lightning day. The next step is to establish if these results are robust across other models and, if combined with parametrized‐convection models, whether ensemble‐based information on the possible responses of lightning to climate change can be investigated. Plain Language Summary Lightning depends on ascending air in thunderstorms and the collision of cloud ice particles, which charge the thundercloud. Many climate models have too coarse a resolution to reliably capture these processes. We focus on Africa, which has some of the most frequent lightning in the world. We use a model that is much higher resolution than usual, and this allows us to explicitly simulate the deep convection associated with thunderstorms as well as provide more detailed representation of the distribution of cloud ice particles. Our results show that in drier regions, as well as the much wetter Congo, there is relatively more lightning per kilogram of surface rainfall than there is in other parts of the continent. Lightning does increase across the continent under climate change, but by a relatively small amount. This is despite the number of days with lightning decreasing as the lower atmosphere becomes more stable. On days with lightning, there are more lightning flashes because there is an increase in cloud ice and intensity of convection. This study gives much more detailed information about African lightning than previous work. However, it is a single simulation. Future research should look at these results across other climate models

The spatial context of clinic-reported sexually transmitted infection in Hong Kong

<p>Abstract</p> <p>Background</p> <p>The incidence and prevalence of sexually transmitted infection (STI) in China has been on the rise in the past decade. Delineation of epidemiologic pattern is often hampered by its uneven distribution. Spatial distribution is often a neglected aspect of STI research, the description of which may enhance epidemiologic surveillance and inform service development.</p> <p>Methods</p> <p>Over a one month-period, all first time attendees of 6 public STI clinics in Hong Kong were interviewed before clinical consultation using a standard questionnaire to assess their demographic, clinical and behavioural characteristics. A GIS (geographic information system)-based approach was adopted with mapping performed. The cases attending the clinics in different locations were profiled. A comparison was made between neighbourhood cases (patients living near a clinic) and distant cases (those farther off), by calculating the odds ratio for demographic, behavioural and geographic characteristics.</p> <p>Results</p> <p>Of the 1142 STI patients evaluated, the residence locations of 1029 (90.1%) could be geocoded, of which 95.6% were ethnic Chinese and 63.4% male. Geographically only about a quarter lived in the same district as the clinic. STI patients aged 55 or above were more likely to be living in the vicinity of the clinic, located in the same or adjacent tertiary planning unit (a small geographic unit below district level). A majority of patients came from locations a few kilometers from the clinic, the distance of which varies between clinics. Overall, more syphilis cases were reported in patients residing in the same or adjacent tertiary planning unit, while distant cases tended to give a higher risk of inconsistent condom use. There were otherwise no significant clinical and epidemiologic differences between neighbourhood and distant STI cases.</p> <p>Conclusions</p> <p>There was no specific relationship between STI and the residence location of patients as regards their clinical and epidemiologic characteristics in the territory of Hong Kong. Older STI patients were however more inclined to attend the nearby STI clinics. Most patients have travelled a variable distance to access the STI service. The relationship between STI clinic cases and distance could be a complex issue intertwined between psychosocial characteristics and STI service coverage.</p

A classification model for non-alcoholic steatohepatitis (NASH) using confocal Raman micro-spectroscopy

We combined Raman micro-spectroscopy and machine learning techniques to develop a classification model based on a well-established non-alcoholic steatohepatitis (NASH) mouse model, using spectrum pre-processing, biochemical component analysis (BCA) and logistic regression

A Multilevel Analysis of the Impact of Socio-Structural and Environmental Influences on Condom Use Among Female Sex Workers

This study uses multilevel analysis to examine individual, organizational and community levels of influence on condom use among female commercial sex workers (FSW) in the Philippines. A randomized controlled study involving 1,382 female commercial sex workers assigned to three intervention groups consisting of peer education, managerial training, combined peer and managerial intervention and a usual care control group was conducted. The results of the multilevel analysis show that FSWs who work in establishments with condom use rules tend to have a higher level of condom use (β = .70, P < 0.01). Among the different intervention groups, the combined peer and managerial intervention had the largest effect on condom use (β = 1.30, P < 0.01) compared with the usual care group. Using a three-level hierarchical model, we found that 62% of the variation lies within individuals, whereas 24% and 14% of the variation lies between establishments, and communities, respectively. Standard errors were underestimated when clustering of the FSWs in the different establishments and communities were not taken into consideration. The results demonstrate the importance of using multilevel analysis for community-based HIV/AIDS intervention programs to examine individual, establishment and community effects