Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

Permafrost contains an estimated 1672?Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5?°C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.     

The ontology of quantum field theory: Structural realism vindicated?

In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best confirmed theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure.     

On Forecasting Conflict in the Sudan: 2009–2012

This paper considers univariate and multivariate models to forecast monthly conflict events in the Sudan over the out‐of‐sample period 2009–2012. The models used to generate these forecasts were based on a specification from a machine learning algorithm fit to 2000–2008 monthly data. The model that includes previous month's wheat price performs better than a similar model which does not include past wheat prices (the univariate model). Both models did not perform well in forecasting conflict in a neighborhood of the 2012 ‘Heglig crisis’. Copyright © 2015 John Wiley & Sons, Ltd.     

Microscale screening systems for 3D cellular microenvironments: platforms,advances, and challenges

The increasing interest in studying cells using more in vivo-like three-dimensional (3D) microenvironments has created a need for advanced 3D screening platforms with enhanced functionalities and increased throughput. 3D screening platforms that better mimic in vivo microenvironments with enhanced throughput would provide more in-depth understanding of the complexity and heterogeneity of microenvironments. The platforms would also better predict the toxicity and efficacy of potential drugs in physiologically relevant conditions. Traditional 3D culture models (e.g., spinner flasks, gyratory rotation devices, non-adhesive surfaces, polymers) were developed to create 3D multicellular structures. However, these traditional systems require large volumes of reagents and cells, and are not compatible with high-throughput screening (HTS) systems. Microscale technology offers the miniaturization of 3D cultures and allows efficient screening of various conditions. This review will discuss the development, most influential works, and current advantages and challenges of microscale culture systems for screening cells in 3D microenvironments.     

Toward a History of Mathematics Focused on Procedures

Abraham Robinson’s framework for modern infinitesimals was developed half a century ago. It enables a re-evaluation of the procedures of the pioneers of mathematical analysis. Their procedures have been often viewed through the lens of the success of the Weierstrassian foundations. We propose a view without passing through the lens, by means of proxies for such procedures in the modern theory of infinitesimals. The real accomplishments of calculus and analysis had been based primarily on the elaboration of novel techniques for solving problems rather than a quest for ultimate foundations. It may be hopeless to interpret historical foundations in terms of a punctiform continuum, but arguably it is possible to interpret historical techniques and procedures in terms of modern ones. Our proposed formalisations do not mean that Fermat, Gregory, Leibniz, Euler, and Cauchy were pre-Robinsonians, but rather indicate that Robinson’s framework is more helpful in understanding their procedures than a Weierstrassian framework.     

微型化的魅力

下世纪初,只要看一下戴在自己手腕上的微型电话,你就会知道你的朋友在呼叫你。引起变化的方式有许许多多种。有的人采取的是流血的暴力行动,另一些人通过有说服力的辩论来改变我们的生活。而电气工程与计算机科学教授克拉克·尼因则希望通过改变我们的通讯方式来使我们的生活发生革命性的变化。尤其是,他的目的在于缩小移动电话和收音机的尺寸,直到它们变得小到可以安装在手表内或者像最近的电影“星球旅行”中所描述的科幻通讯器可以像缝在衣服上的纽扣那样小为止。在一个微型器件上将一种发射器和接收器的线路组合在一起构成一种发射…     

The role of periostin in lung fibrosis and airway remodeling

Periostin is a protein that plays a key role in development and repair within the biological matrix of the lung. As a matricellular protein that does not contribute to extracellular matrix structure, periostin interacts with other extracellular matrix proteins to regulate the composition of the matrix in the lung and other organs. In this review, we discuss the studies exploring the role of periostin to date in chronic respiratory diseases, namely asthma and idiopathic pulmonary fibrosis. Asthma is a major health problem globally affecting millions of people worldwide with significant associated morbidity and mortality. Periostin is highly expressed in the lungs of asthmatic patients, contributes to mucus secretion, airway fibrosis and remodeling and is recognized as a biomarker of Th2 high inflammation. Idiopathic pulmonary fibrosis is a fatal interstitial lung disease characterized by progressive aberrant fibrosis of the lung matrix and respiratory failure. It predominantly affects adults over 50 years of age and its incidence is increasing worldwide. Periostin is also highly expressed in the lungs of idiopathic pulmonary fibrosis patients. Serum levels of periostin may predict clinical progression in this disease and periostin promotes myofibroblast differentiation and type 1 collagen production to contribute to aberrant lung fibrosis. Studies to date suggest that periostin is a key player in several pathogenic mechanisms within the lung and may provide us with a useful biomarker of clinical progression in both asthma and idiopathic pulmonary fibrosis.