Cracking the code of oscillatory activity

Neural oscillations are ubiquitous measurements of cognitive processes and dynamic routing and gating of information. The fundamental and so far unresolved problem for neuroscience remains to understand how oscillatory activity in the brain codes information for human cognition. In a biologically relevant cognitive task, we instructed six human observers to categorize facial expressions of emotion while we measured the observers' EEG. We combined state-of-the-art stimulus control with statistical information theory analysis to quantify how the three parameters of oscillations (i.e., power, phase, and frequency) code the visual information relevant for behavior in a cognitive task. We make three points: First, we demonstrate that phase codes considerably more information (2.4 times) relating to the cognitive task than power. Second, we show that the conjunction of power and phase coding reflects detailed visual features relevant for behavioral response-that is, features of facial expressions predicted by behavior. Third, we demonstrate, in analogy to communication technology, that oscillatory frequencies in the brain multiplex the coding of visual features, increasing coding capacity. Together, our findings about the fundamental coding properties of neural oscillations will redirect the research agenda in neuroscience by establishing the differential role of frequency, phase, and amplitude in coding behaviorally relevant information in the brai

Making sense of violence risk predictions using clinical notes

Violence risk assessment in psychiatric institutions enables interventions to avoid violence incidents. Clinical notes written by practitioners and available in electronic health records (EHR) are valuable resources that are seldom used to their full potential. Previous studies have attempted to assess violence risk in psychiatric patients using such notes, with acceptable performance. However, they do not explain why classification works and how it can be improved. We explore two methods to better understand the quality of a classifier in the context of clinical note analysis: random forests using topic models, and choice of evaluation metric. These methods allow us to understand both our data and our methodology more profoundly, setting up the groundwork for improved models that build upon this understanding. This is particularly important when it comes to the generalizability of evaluated classifiers to new data, a trustworthiness problem that is of great interest due to the increased availability of new data in electronic format

Comparison of patient-specific computational models vs. clinical follow-up, for adjacent segment disc degeneration and bone remodelling after spinal fusion

Spinal fusion is a standard surgical treatment for patients suffering from low back pain attributed to disc degeneration. However, results are somewhat variable and unpredictable. With fusion the kinematic behaviour of the spine is altered. Fusion and/or stabilizing implants carrying considerable load and prevent rotation of the fused segments. Associated with these changes, a risk for accelerated disc degeneration at the adjacent levels to fusion has been demonstrated. However, there is yet no method to predict the effect of fusion surgery on the adjacent tissue levels, i.e. bone and disc. The aim of this study was to develop a coupled and patient-specific mechanoregulated model to predict disc generation and changes in bone density after spinal fusion and to validate the results relative to patient follow-up data. To do so, a multiscale disc mechanoregulation adaptation framework was developed and coupled with a previously developed bone remodelling algorithm. This made it possible to determine extra cellular matrix changes in the intervertebral disc and bone density changes simultaneously based on changes in loading due to fusion surgery. It was shown that for 10 cases the predicted change in bone density and degeneration grade conforms reasonable well to clinical follow-up data. This approach helps us to understand the effect of surgical intervention on the adjacent tissue remodelling. Thereby, providing the first insight for a spine surgeon as to which patient could potentially be treated successfully by spinal fusion and in which patient has a high risk for adjacent tissue changes

Linking Scottish vital event records using family groups

Funding: This work was supported by ESRC Grants ES/K00574X/2 “Digitising Scotland” and ES/L007487/1 “Administrative Data Research Centre – Scotland.”The reconstitution of populations through linkage of historical records is a powerful approach to generate longitudinal historical microdata resources of interest to researchers in various fields. Here we consider automated linking of the vital events recorded in the civil registers of birth, death and marriage compiled in Scotland, to bring together the various records associated with the demographic events in the life course of each individual in the population. From the histories, the genealogical structure of the population can then be built up. Rather than apply standard linkage techniques to link the individuals on the available certificates, we explore an alternative approach, inspired by the family reconstitution techniques adopted by historical demographers, in which the births of siblings are first linked to form family groups, after which intergenerational links between families can be established. We report a small-scale evaluation of this approach, using two district-level data sets from Scotland in the late nineteenth century, for which sibling links have already been created by demographers. We show that quality measures of up to 83% can be achieved on these data sets (using F-Measure, a combination of precision and recall). In the future, we intend to compare the results with a standard linkage approach and to investigate how these various methods may be used in a project which aims to link the entire Scottish population from 1856 to 1973.PostprintPeer reviewe

The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. during the Influenza A H1N1 Pandemic

Twitter is a free social networking and micro-blogging service that enables its millions of users to send and read each other's “tweets,” or short, 140-character messages. The service has more than 190 million registered users and processes about 55 million tweets per day. Useful information about news and geopolitical events lies embedded in the Twitter stream, which embodies, in the aggregate, Twitter users' perspectives and reactions to current events. By virtue of sheer volume, content embedded in the Twitter stream may be useful for tracking or even forecasting behavior if it can be extracted in an efficient manner. In this study, we examine the use of information embedded in the Twitter stream to (1) track rapidly-evolving public sentiment with respect to H1N1 or swine flu, and (2) track and measure actual disease activity. We also show that Twitter can be used as a measure of public interest or concern about health-related events. Our results show that estimates of influenza-like illness derived from Twitter chatter accurately track reported disease levels

Glycosylation site prediction using ensembles of Support Vector Machine classifiers

Article discussing the performance of different computational methods for prediction of glycosylation sites from amino acid sequences

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

A Folding Pathway-Dependent Score to Recognize Membrane Proteins

While various approaches exist to study protein localization, it is still a challenge to predict where proteins localize. Here, we consider a mechanistic viewpoint for membrane localization. Taking into account the steps for the folding pathway of α-helical membrane proteins and relating biophysical parameters to each of these steps, we create a score capable of predicting the propensity for membrane localization and call it FP3mem. This score is driven from the principal component analysis (PCA) of the biophysical parameters related to membrane localization. FP3mem allows us to rationalize the colocalization of a number of channel proteins with the Cav1.2 channel by their fewer propensities for membrane localization

Calculation of substructural analysis weights using a genetic algorithm

This paper describes a genetic algorithm for the calculation of substructural analysis for use in ligand-based virtual screening. The algorithm is simple in concept and effective in operation, with simulated virtual screening experiments using the MDDR and WOMBAT datasets showing it to be superior to substructural analysis weights based on a naive Bayesian classifier