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Mike's Tech Notes for 1/29/2012. Boltzmann machine. A graphical representation of an example Boltzmann machine.

Boltzmann machine

Each undirected edge represents dependency. In this example there are 3 hidden units and 4 visible units. Demonstrations of Kilobot collective behaivors on up to 29 robots. Infinispan - Open Source Data Grids. Distributed in-memory key/value data grid and cache Latest news Clustered cache quickstart updates As developers, it's always easy for us to "forget" about documentation and tutorials, and let them get out of date.

Infinispan - Open Source Data Grids

Open Source Ecology. Center for Models of Life - CMOL: Models / Interactive Java Applets. Coverage of mRNA by Ribosomes and mRNA Half Life Bacterial mRNAs are translated by closely spaced ribosomes and degraded from the 5′-end, with half-lives of around 2 min at 37 °C in most cases.

Center for Models of Life - CMOL: Models / Interactive Java Applets

Ribosome-free or “naked” mRNA is known to be readily degraded, but the initial event that inactivates the mRNA functionally has not been fully described. Here, we characterize a determinant of the functional stability of an mRNA, which is located in the early coding region. Using literature values for the mRNA half-lives of variant lacZ mRNAs in Escherichia coli, we modeled how the ribosome spacing is affected by the translation rate of the individual codons. When comparing the ribosome spacing at various segments of the mRNA to its functional half-life, we found a clear correlation between the functional mRNA half-life and the ribosome spacing in the mRNA region approximately between codon 20 and codon 45. Genome comparison of ants establishes new model species for molecular research. By comparing two species of ants, Shelley Berger, PhD, the Daniel S.

Genome comparison of ants establishes new model species for molecular research

Och University Professor at the University of Pennsylvania, and colleagues Danny Reinberg, PhD, New York University, and Juergen Liebig, PhD, Arizona State University, have established an important new avenue of research for epigenetics -- the study of how the expression or suppression of particular genes affects an organism's characteristics, development, and even behavior. Ants, the new model system used in this study, organize themselves into caste-based societies in which most of the individuals are sterile females, limited to highly specialized roles such as workers and soldiers.

Only one queen and the relatively small contingent of male ants are fertile and able to reproduce. Yet despite such extreme differences in behavior and physical form, all females within the colony appear to be genetically identical. Manipulating microbes in the gut may remedy disease and enhance health. We are what we eat, but who are "we"?

Manipulating microbes in the gut may remedy disease and enhance health

New, high-powered genomic analytical techniques have established that as many as 1,000 different single-celled species coexist in relative harmony in every healthy human gut. "For each human cell in your body there are 10 microbial cells, most of them living in the gut and helping us digest things we can't digest on our own," said Justin Sonnenburg, PhD, assistant professor of microbiology and immunology at the Stanford University School of Medicine. "In turn, what you eat is proving to be one of the major determinants of the components of your 'inner self' -- that community of bacteria living in your intestine.

" Each individual's microbial ecosystem is different in its relative composition, with potential implications for our health. Natural selection alone can explain eusociality, scientists say. Scientists at Harvard University have sketched a new map of the "evolutionary labyrinth" species must traverse to reach eusociality, the rare but spectacularly successful social structure where individuals cooperate to raise offspring.

Natural selection alone can explain eusociality, scientists say

Mathematical biologists Martin A. Nowak and Corina E. Tarnita and evolutionary biologist Edward O. Increased honey bee diversity means fewer pathogens, more helpful bacteria. A novel study of honey bee genetic diversity co-authored by an Indiana University biologist has for the first time found that greater diversity in worker bees leads to colonies with fewer pathogens and more abundant helpful bacteria like probiotic species.

Increased honey bee diversity means fewer pathogens, more helpful bacteria

Led by IU Bloomington assistant professor Irene L.G. Newton and Wellesley College assistant professor Heather Mattila, and co-authors from Wellesley College and the Netherlands Organisation for Applied Scientific Research, the new work describes the communities of active bacteria harbored by honey bee colonies. The study, which was conducted at Wellesley College in 2010, is also the first to identify four important microbes in bee colonies that have previously been associated with fermentation in humans and other animals: Succinivibrio (associated with cow rumens), Oenococcus (wine fermentation), Paralactobacillus (food fermentation) and Bifidobacterium (yogurt). Biologist discovers 'stop' signal in honey bee communication. A biologist at UC San Diego has discovered that honey bees warn their nest mates about dangers they encounter while feeding with a special signal that's akin to a "stop" sign for bees.

Biologist discovers 'stop' signal in honey bee communication

The discovery, detailed in a paper in the February 23 issue of the journal Current Biology, which appears online February 11, resulted from a series of experiments on honey bees foraging for food that were attacked by competitors from nearby colonies fighting for food at an experimental feeder. The bees that were attacked then produced a specific signal to stop nest mates who were recruiting others for this dangerous location. Honey bees use a waggle dance to communicate the location of food and other resources. Attacked bees directed "stop" signals at nest mates waggle dancing for the dangerous location. Social Insects Could Offer Clues About Genetic Conflict. From universities, journals, and other organizations Date: April 15, 2002 Source: Rice University Summary:

Social Insects Could Offer Clues About Genetic Conflict

Darwin Was Right About How Evolution Can Affect Whole Group. Worker ants of the world, unite!

Darwin Was Right About How Evolution Can Affect Whole Group

You have nothing to lose but your fertility. The highly specialized worker castes in ants represent the pinnacle of social organization in the insect world. As in any society, however, ant colonies are filled with internal strife and conflict. So what binds them together? More than 150 years ago, Charles Darwin had an idea and now he's been proven right. Colonies of bacteria fight for resources with lethal protein. Rival colonies of bacteria can produce a lethal chemical that keeps competitors at bay, scientists report. By halting the growth of nearby colonies and even killing some of the cells, groups of bacteria preserve scarce resources for themselves, even when the encroaching colony is closely related. "It supports the notion that each colony is a superorganism, a multicellular organism with it's own identity," said Eshel Ben-Jacob, an adjunct senior scientist at UC San Diego's Center for Theoretical Biological Physics and professor of physics at Tel Aviv University.

Ben-Jacob and lead author Avraham Be'er of the University of Texas, Austin, and other colleagues at these institutions report their discovery in the early online edition of the Proceedings of the National Academy of Sciences. Alone in a dish, colonies of the bacterium Paenibacillus dendritiformis will send branches of cells in all directions. Bugs In The Gut Could Play Key Role In Understanding Human Disease And Drug Toxicity. Understanding how microbes in the gut interact with the body could lead scientists and doctors to new a understanding and novel treatments for diseases say scientists from Imperial College London and Astra Zeneca. In a review published today in Nature Biotechnology, researchers describe how microbes in the gut form the second largest metabolic 'organ' in the body and play a key role in disease processes alongside genetic and environmental factors.

Microbes in the gut can weigh up to one kilogram in a normal adult human, and collectively can contain more genes than the host. The combination of interacting genes from the body and gut microbes can be considered a 'super-organism', capable of co-ordinating many physiological and metabolic responses, say the researchers. Insect colonies operate as 'superorganisms', new research finds. New A team of researchers including scientists from the University of Florida has shown insect colonies follow some of the same biological "rules" as individuals, a finding that suggests insect societies operate like a single "superorganism" in terms of their physiology and life cycle. For more than a century, biologists have marveled at the highly cooperative nature of ants, bees and other social insects that work together to determine the survival and growth of a colony.

The social interactions are much like cells working together in a single body, hence the term "superorganism" -- an organism comprised of many organisms, according to James Gillooly, Ph.D., an assistant professor in the department of biology at UF's College of Liberal Arts and Sciences. Competition, Loss Of Selfishness Mark Shift To Supersociety. How social or altruistic behavior evolved has been a central and hotly debated question, particularly by those researchers engaged in the study of social insect societies – ants, bees and wasps. In these groups, this question of what drives altruism also becomes critical to further understanding of how ancestral or primitive social organizations (with hierarchies and dominance fights, and poorly developed division of labor) evolve to become the more highly sophisticated networks found in some eusocial insect collectives termed “superorganisms.”

'Autoantibodies' May Be Created In Response To Bacterial DNA. Autoimmune diseases have long been regarded as illnesses in which the immune system creates autoantibodies to attack the body itself. But, researchers at the California non-profit Autoimmunity Research Foundation (ARF) explain that the antibodies observed in autoimmune disease actually result from alteration of human genes and gene products by hidden bacteria. Not long ago, scientists believed they had located all bacteria capable of causing human disease, But DNA discoveries in the last decade have led the NIH Human Microbiome Project to now estimate that as many as 90% of cells in the body are bacterial in origin. Many of these bacteria, which have yet to be named and characterized, have been implicated in the progression of autoimmune disease.