How biased are maximum entropy models?

Maximum entropy models have become popular statistical models in neuroscience and other areas in biology, and can be useful tools for obtaining estimates of mutual information in biological systems. However, maximum entropy models fit to small data sets can be subject to sampling bias; i.e. the true entropy of the data can be severely underestimated. Here we study the sampling properties of estimates of the entropy obtained from maximum entropy models. We show that if the data is generated by a distribution that lies in the model class, the bias is equal to the number of parameters divided by twice the number of observations. However, in practice, the true distribution is usually outside the model class, and we show here that this misspecification can lead to much larger bias. We provide a perturbative approximation of the maximally expected bias when the true model is out of model class, and we illustrate our results using numerical simulations of an Ising model; i.e. the second-order maximum entropy distribution on binary data.

Identification of proteins that bind extracellular microRNAs secreted by the parasitic nematode Trichinella spiralis

Small non-coding RNAs such as microRNAs (miRNAs) are conserved across eukaryotes and play key roles in regulating gene expression. In many organisms, miRNAs are also secreted from cells, often encased within vesicles such as exosomes, and sometimes extravesicular. The mechanisms of miRNA secretion, how they are stabilised outside of cells and their functional importance are poorly understood. Recently, we characterised the parasitic nematode Trichinella spiralis as a model to study miRNA secretion. T. spiralis muscle-stage larvae (MSL) secrete abundant miRNAs which are largely extravesicular. Here, we investigated how T. spiralis miRNAs might remain stable outside of cells. Using proteomics, we identified two RNA binding proteins secreted by T. spiralis larvae and characterised their RNA binding properties. One, a homologue of the known RNA binding protein KSRP, binds miRNA in a selective and sequence-specific fashion. Another protein, which is likely a novel RNA binding protein, binds to miRNA without exhibiting sequence specificity. Our results suggest a possible mechanism for miRNA secretion by T. spiralis and may have relevance for understanding the biology of extracellular miRNA more widely

Mining chemical information from Open patents

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured.Peer Reviewe

The Biology of Wahoo (Acanthocybium solandri) in the Western Central Atlantic

This contribution summarizes aspects of the biology of the wahoo, Acanthocybium solandri (Scombridae), that are pertinent to assessment and management of this species in the western central Atlantic (WCA). In this region wahoo is a target species for both commercial and recreational fisheries, and annual landings appear to have increased steadily over the last 30 years to in excess of 2000 mt. Wahoo is believed to be migratory, but little is known of the migration patterns. Significant seasonal variation in catches within the region indicates that it is seasonally abundant in most locations. Periods of peak abundance occur from the fall through spring in the southeastern and northern Caribbean islands, and are restricted to the warmer months (late spring through early fall) in the more northerly locations (northern Gulf of Mexico, North Carolina, and Bermuda). Wahoo exhibits early sexual maturity (within the first year) and a spawning season that extends from at least May to October. Females are multiple batch spawners and are highly fecund. Limited age and growth studies indicate that it is a relatively fast-growing species, has high mortality, and probably lives for 5-6 years. Wahoo is primarily piscivorous, although some invertebrates including squids are eaten. A relatively small number of parasite species have been associated with it. There is no evidence of more than a single shared stock of wahoo in the WCA, and recent genetic studies, using RAPD markers, suggest that stock boundaries may extend beyond this region. The status of the wahoo resource in the WCA remains unclear. Reliable wahoo catch and fishing effort data from the entire WCA, improved knowledge of migration patterns, reproductive characteristics and critical habitat (e.g., preferred spawning areas), validation of age, growth and mortality estimates, and a more comprehensive analysis of stock structure for the entire Atlantic are needed for informed wahoo stock assessment and management

How is the biocompatibilty of dental biomaterials evaluated?

All biomaterials used in dentistry must be evaluated for biocompatibility using screening assays to protect patient health and safety. The purpose of this review is to explain the international biocompatibility guidelines, and to explain the structure of a test program. The test program requires the structured assessment of materials into four phases; general toxicity, local tissue irritation, pre-clinical, and clinical evaluation. Different types of screening assays are available, and it is important to understand the advantages and limitations of the various types of assays that are available, so that they can be selected for appropriateness and interpreted accurately. New scientific advances in terms of the chemical properties of dental materials, tissue engineering, stem cell, genetic transfer, biomaterial, and growth factor therapies are under development. These new therapies create improved opportunities to restore and regenerate oral tissues, but they can also present new hazards to patients. Prior to their clinical use, these new technologies must be proven to be safe, and not hazardous to human health. A structured biocompatibility assessment and advice on the selection of assays are outlined to evaluate these new therapies

Recent Decisions

Comments on recent decisions by James E. Murray, Edmund L. White, Peter H. Lousberg, Wilbur L. Pollard, John L. Rosshirt, and Patrick J. Foley