Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data.

Cell fate decisions play a pivotal role in development, but technologies for dissecting them are limited. We developed a multifunction new method, Topographer, to construct a "quantitative" Waddington's landscape of single-cell transcriptomic data. This method is able to identify complex cell-state transition trajectories and to estimate complex cell-type dynamics characterized by fate and transition probabilities. It also infers both marker gene networks and their dynamic changes as well as dynamic characteristics of transcriptional bursting along the cell-state transition trajectories. Applying this method to single-cell RNA-seq data on the differentiation of primary human myoblasts, we not only identified three known cell types, but also estimated both their fate probabilities and transition probabilities among them. We found that the percent of genes expressed in a bursty manner is significantly higher at (or near) the branch point (~97%) than before or after branch (below 80%), and that both gene-gene and cell-cell correlation degrees are apparently lower near the branch point than away from the branching. Topographer allows revealing of cell fate mechanisms in a coherent way at three scales: cell lineage (macroscopic), gene network (mesoscopic), and gene expression (microscopic)

The Research Space: using the career paths of scholars to predict the evolution of the research output of individuals, institutions, and nations

In recent years scholars have built maps of science by connecting the academic fields that cite each other, are cited together, or that cite a similar literature. But since scholars cannot always publish in the fields they cite, or that cite them, these science maps are only rough proxies for the potential of a scholar, organization, or country, to enter a new academic field. Here we use a large dataset of scholarly publications disambiguated at the individual level to create a map of science-or research space-where links connect pairs of fields based on the probability that an individual has published in both of them. We find that the research space is a significantly more accurate predictor of the fields that individuals and organizations will enter in the future than citation based science maps. At the country level, however, the research space and citations based science maps are equally accurate. These findings show that data on career trajectories-the set of fields that individuals have previously published in-provide more accurate predictors of future research output for more focalized units-such as individuals or organizations-than citation based science maps

The geography of .pt top level domain. The internet diffusion in Portugal and its implications for the decrease of spatial disparities.

The radical role of information and communication technology (ICT) is one of the most visible topic in the media today and seems to grow from day to day, as well as telecommunications are gradually becoming the central infrastructure tying together our society. The advent of these technologies during the past decades, and their widespread use, is radically transforming the dynamics of communication and our understanding of spatial relationships (by the reduce of distances and the increase of accessibility to information and new services). If there are many studies, attempting to show how city management and regional development policies can creatively address the complex linkages between ICT and urban and regional prosperity (influencing the objective of increasing urban living conditions, combating inwardness, promoting employment and economic competitiveness and supporting social integration policies), there are also many authors arguing that electronic communications reinforce existing patterns of physical communication rather than create new patterns. These suppositions are usually theoretical discussions, that needs to be rigorously tested with empirical analysis and comparative perspectives. The main objective of this paper is precisely to present a detailed study about Portugal, with the purpose of questioning the decrease of spatial disparities due to the potential influence of ICT’s. This research is mostly based on new spatial statistics, collected, mapped and analysed in order to understand the diffusion process of the most sophisticated, diverse and capable telecommunication infrastructures, and consequently verify the plasticity of space throughout Portugal, and the ways it has been stretched or compressed. We will be focusing the globally-interconnected set of computer networks, known as ‘The Internet’, which is widely used by millions of individuals, firms and institutions every day, as a way to get into an invisible domain, popularly known as cyberspace, in order to seek information, marketing new services and products, and as means of communication within and between organizations. We believe that this invisible territories of the cyberspace do have a geography and, in an attempt to reveal its topography, we should analyse the spatial patterns of the ownership of Internet space. Despite the rapid growth of Internet in recent years, and the gradually recognition of its implications, there is a lack of knowledge about its geographic diffusion and its attendant implication for regional urban development. Specially in what concerns to its effective role to generate substantial adjustments on traditional portuguese regional dichotomies, or instead, if it is an unexpected contribute to reinforce territorial disintegration tendencies. For the empirical research will try to find links between cyberspace and the portuguese physical geography. In our opinion a good way to achieve this goal is discovering which and where are located the portuguese entities that recognize the importance to distribute globally information, about their activities and services, through the use of the Internet. For that we will explore the compulsory registration of all .pt domain names on one single institution –Foundation for National Scientific Computing- (FNSC), which performs all the registration services for the geographical .pt domain.

Application of the plastic optical fibre in domestic multimedia networks

Plastic optical fibre (POF) constitutes an advantageous alternative medium to implement domestic data networks. In this proposal, we develop an in-home network prototype for distributing video, audio and data information based on large core step-index plastic optical fibres (SI-POF). The aim is to demonstrate a viable uncluttered application of the POFs where the up to date technologies converge in a homogeneous domestic system