Finite mixtures of matrix-variate Poisson-log normal distributions for three-way count data

Three-way data structures, characterized by three entities, the units, the variables and the occasions, are frequent in biological studies. In RNA sequencing, three-way data structures are obtained when high-throughput transcriptome sequencing data are collected for n genes across p conditions at r occasions. Matrix-variate distributions offer a natural way to model three-way data and mixtures of matrix-variate distributions can be used to cluster three-way data. Clustering of gene expression data is carried out as means to discovering gene co-expression networks. In this work, a mixture of matrix-variate Poisson-log normal distributions is proposed for clustering read counts from RNA sequencing. By considering the matrix-variate structure, full information on the conditions and occasions of the RNA sequencing dataset is simultaneously considered, and the number of covariance parameters to be estimated is reduced. A Markov chain Monte Carlo expectation-maximization algorithm is used for parameter estimation and information criteria are used for model selection. The models are applied to both real and simulated data, giving favourable clustering results

Density functional study of FeS, FeSe and FeTe: Electronic structure, magnetism, phonons and superconductivity

We report density functional calculations of the electronic structure, Fermi surface, phonon spectrum, magnetism and electron-phonon coupling for the superconducting phase FeSe, as well as the related compounds FeS and FeTe. We find that the Fermi surface structure of these compounds is very similar to that of the Fe-As based superconductors, with cylindrical electron sections at the zone corner, cylindrical hole surface sections, and depending on the compound, other small hole sections at the zone center. As in the Fe-As based materials, these surfaces are separated by a 2D nesting vector at ($\pi$,$\pi$). The density of states, nesting and Fermi surface size increase going from FeSe to FeTe. Both FeSe and FeTe show spin density wave ground states, while FeS is close to an instability. In a scenario where superconductivity is mediated by spin fluctuations at the SDW nesting vector, the strongest superconductor in this series would be doped FeTe.Comment: Added note regarding recent experimental observations of superconductivity under pressure. Some additional discussio

Agro-environmental project duration and effectiveness in South-east Asia

Considerable emphasis has been placed on developing technologies for agricultural sustainability. Many bilateral projects are working to achieve this outcome. A desk review was conducted to study the importance of project duration for the effectiveness of sustainable agricultural projects. Longer-duration projects were successful in addressing more holistic issues than short projects. However, funding agencies tend to fund shorter-duration projects, so projects become progressively shorter. At the same time, the number of projects implemented each year is increasing. Despite the decrease in total development assistance, increases in project numbers, particularly since 1986, appear to be at the cost of project duration. Short project duration was one of the most cited reasons for not completing essential dissemination activities for wider adoption, whereas longer- duration projects were usually considered more successful in addressing more holistic issues. It is difficult to produce tangible outputs from agricultural and soil conservation projects within five years. Considering the slow changes in the system and in agricultural and environmental sustainability, the authors suggest that project developers should be advised to plan for a minimum of 5–10 years, depending on the nature of activities. It is time for funding agencies to reconsider their tendency to fund shorter-duration projects

Integrating immunology and microfluidics for single immune cell analysis

The field of immunoengineering aims to develop novel therapies and modern vaccines to manipulate and modulate the immune system and applies innovative technologies toward improved understanding of the immune system in health and disease. Microfluidics has proven to be an excellent technology for analytics in biology and chemistry. From simple microsystem chips to complex microfluidic designs, these platforms have witnessed an immense growth over the last decades with frequent emergence of new designs. Microfluidics provides a highly robust and precise tool which led to its widespread application in single-cell analysis of immune cells. Single-cell analysis allows scientists to account for the heterogeneous behavior of immune cells which often gets overshadowed when conventional bulk study methods are used. Application of single-cell analysis using microfluidics has facilitated the identification of several novel functional immune cell subsets, quantification of signaling molecules, and understanding of cellular communication and signaling pathways. Single-cell analysis research in combination with microfluidics has paved the way for the development of novel therapies, point-of-care diagnostics, and even more complex microfluidic platforms that aid in creating in vitro cellular microenvironments for applications in drug and toxicity screening. In this review, we provide a comprehensive overview on the integration of microsystems and microfluidics with immunology and focus on different designs developed to decode single immune cell behavior and cellular communication. We have categorized the microfluidic designs in three specific categories: microfluidic chips with cell traps, valve-based microfluidics, and droplet microfluidics that have facilitated the ongoing research in the field of immunology at single-cell level

Electronic Structure, Magnetism and Superconductivity of Layered Iron Compounds

The layered iron superconductors are discussed using electronic structure calculations. The four families of compounds discovered so far, including Fe(Se,Te) have closely related electronic structures. The Fermi surface consists of disconnected hole and electron cylinders and additional hole sections that depend on the specific material. This places the materials in proximity to itinerant magnetism, both due to the high density of states and due to nesting. Comparison of density functional results and experiment provides strong evidence for itinerant spin fluctuations, which are discussed in relation to superconductivity. It is proposed that the intermediate phase between the structural transition and the SDW transition in the oxy-pnictides is a nematic phase.Comment: Proceedings ISS200