Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.

Inferring the historical patterns of biological evolution

The specialized junction between a T lymphocyte and an antigen-presenting cell, the immunological synapse, consists of a central cluster of T cell receptors surrounded by a ring of adhesion molecules. Immunological synapse formation is now shown to be an active and dynamic mechanism that allows T cells to distinguish potential antigenic ligands. Initially, T cell receptor ligands were engaged in an outermost ring of the nascent synapse. Transport of these complexes into the central cluster was dependent on T cell receptor—ligand interaction kinetics. Finally, formation of a stable central cluster at the heart of the synapse was a determinative event for T cell proliferation. A critical event in the initiation of the adaptive

https://www.med.nyu.edu/skirball-lab/dustinlab/pdfs/The%20immunological%20synapse%20%20A%20molecular%20machine%20controlling%20T%20cell%20activation.pdf

The Immunological Synapse: A Molecular Machine Controlling T Cell Activation

Big Data concern large-volume, complex, growing data sets with multiple, autonomous sources. With the fast development of networking, data storage, and the data collection capacity, Big Data are now rapidly expanding in all science and engineering domains, including physical, biological and biomedical sciences. This paper presents a HACE theorem that characterizes the features of the Big Data revolution, and proposes a Big Data processing model, from the data mining perspective. This data-driven model involves demand-driven aggregation of information sources, mining and analysis, user interest modeling, and security and privacy considerations. We analyze the challenging issues in the data-driven model and also in the Big Data revolution.

https://www.cs.umb.edu/%7Eding/papers/TKDE2013.pdf

Data mining with big data

Random fluctuations in genetic networks are inevitable as chemical reactions are probabilistic and many genes, RNAs and proteins are present in low numbers per cell. Such 'noise' affects all life processes and has recently been measured using green fluorescent protein (GFP). Two studies show that negative feedback suppresses noise, and three others identify the sources of noise in gene expression. Here I critically analyse these studies and present a simple equation that unifies and extends both the mathematical and biological perspectives.

Summing up the noise in gene networks

https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(13)62229-1.pdf

How to increase value and reduce waste when research priorities are set

A federal effort is under way to improve the nation9s ability to manage, understand, and act upon the 1.2 zettabytes (1021) of electronic data generated each year. Its goal is to increase fundamental understanding of the technologies needed to manipulate and mine massive amounts of information; apply that knowledge to other scientific fields; address national goals in health, energy, defense, and education; and train more researchers to work with those technologies. The impetus for the initiative, to be managed by the Office of Science and Technology Policy, comes from a December 2010 report by a presidential task force that concluded the nation was "underinvesting" in the field. Computer scientists welcome the spotlight that the White House is shining on big-data research.

Agencies Rally to Tackle Big Data

Two opposing forces--competition and cooperation--are beginning to coexist at Japanese universities as they enter an era of increased funding, increased demand for graduate students, and increased pressure to contribute to the country9s economic growth. The new environment promises to be a challenging one, with great rewards for those who succeed and great risks for those who fail to keep pace. On the competitive side, there is the unprecedented bidding for talented students, the growing use of peer review to make awards, and the emerging recognition that lifetime tenure, tiny but equitable grants, and immobility are not compatible with cutting-edge science. Those below the top tier--dominated by the University of Tokyo and Kyoto University--liken the new atmosphere to the law of the jungle: "I have to get everything for my team by myself, like a small yakuza [organized crime] boss," says one researcher at Waseda University. But cooperation is too deeply ingrained in Japanese culture to be driven out by the latest demands on science. From high school teachers sharing their ideas on improving the precollege science curriculum to universities putting out the welcome mat for foreign scientists, increased domestic and international collaboration are seen as vital to a successful transformation of academic science. The stories in this special section are intended to be a snapshot of life on campus and the issues affecting academic research in Japan. It is part of our broader, ongoing effort to report on the country9s vibrant and growing scientific enterprise. We welcome your comments and your ideas for future coverage. Jeffrey Mervis Choice of Ph.D. or job This section was reported and written by Dennis Normile, head of the Japan news bureau of Science, and June Kinoshita, a science writer based in Belmont, Massachusetts. For more information on career opportunities, see Science9s Next Wave9s forum on “sTraining Young Scientists in Asia for the 21st Century.”

http://science.sciencemag.org/content/sci/274/5284/43.full.pdf

Science in Japan: Competition on Campus

Data check: U.S. government share of basic research funding falls below 50%

With costs soaring, every major pharmaceutical company says it9s becoming more efficient. But what exactly does that mean?

http://science.sciencemag.org/content/sci/309/5735/726.full.pdf

Productivity Counts--But the Definition Is Key

A new report from the National Academies says that improving introductory courses is one of many steps needed to increase the number of students obtaining degrees in the fields of science, technology, engineering, and mathematics (STEM) and, in particular, the percentage of minorities in the scientific and engineering workforce. The new report says that retaining STEM majors will require better academic, social, and financial support for students.

https://science.sciencemag.org/content/sci/330/6002/306.full.pdf

Jeffrey Mervis

Papers

Agencies Rally to Tackle Big Data

Science in Japan: Competition on Campus

Data check: U.S. government share of basic research funding falls below 50%

Productivity Counts--But the Definition Is Key

Better Intro Courses Seen as Key to Reducing Attrition of STEM Majors