Adaptive seeds tame genomic sequence comparison

The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.     

Dislocation of the patella in a patient with Rubinstein-Taybi syndrome--a case study

The Rubinstein-Taybi syndrome is a rare syndrome of congenital disorders whose etiology is still unknown. Most RTS patients have musculoskeletal abnormalities which, if untreated, may significantly affect independent mobility. This paper presents the results of a surgical treatment of a 13-year-old patient with RTS and instability of the patellofemoral joint. The patient was followed up for 3 years. Surgery resulted in complete pain relief, increased knee range of motion and marked improvement in the patient's gait. An extensive plasty of the extensor apparatus of the knee joint increases the likelihood of a good and lasting treatment result in patients with RTS and instability of the patellofemoral joint.     

The use of extracorporeal membrane oxygenation (ECMO) in the treatment of acute respiratory distress syndrome due to pandemic influenza

Pandemic influenza particularly often is associated with symptoms of acute respiratory failure, and in case of refractory hypoxemia patients may have indications for the extracorporeal membrane oxygenation (ECMO). The paper presents a case of a pandemic influenza virus infection, where classical indications for veno-venous ECMO occured. Practical aspects of this kind of treatment in the intensive care unit are discussed.     

Inverse Current Source Density Method in Two Dimensions: Inferring Neural Activation from Multielectrode Recordings

The recent development of large multielectrode recording arrays has made it affordable for an increasing number of laboratories to record from multiple brain regions simultaneously. The development of analytical tools for array data, however, lags behind these technological advances in hardware. In this paper, we present a method based on forward modeling for estimating current source density from electrophysiological signals recorded on a two-dimensional grid using multi-electrode rectangular arrays. This new method, which we call two-dimensional inverse Current Source Density (iCSD 2D), is based upon and extends our previous one- and three-dimensional techniques. We test several variants of our method, both on surrogate data generated from a collection of Gaussian sources, and on model data from a population of layer 5 neocortical pyramidal neurons. We also apply the method to experimental data from the rat subiculum. The main advantages of the proposed method are the explicit specification of its assumptions, the possibility to include system-specific information as it becomes available, the ability to estimate CSD at the grid boundaries, and lower reconstruction errors when compared to the traditional approach. These features make iCSD 2D a substantial improvement over the approaches used so far and a powerful new tool for the analysis of multielectrode array data. We also provide a free GUI-based MATLAB toolbox to analyze and visualize our test data as well as user datasets.     

Cognitive abilities of Alzheimer's disease transgenic mice are modulated by social context and circadian rhythm

In the present study, we used a new training paradigm in the intelliCage automatic behavioral assessment system to investigate cognitive functions of the transgenic mice harboring London mutation of the human amyloid precursor protein (APP.V717I). Three groups of animals: 5-, 12- and 18-24-month old were subjected to both Water Maze training and the IntelliCage-based appetitive conditioning. The spatial memory deficit was observed in all three groups of transgenic mice in both behavioral paradigms. However, the APP mice were capable to learn normally when co-housed with the wild-type (WT) littermates, in contrast to clearly impaired learning observed when the transgenic mice were housed alone. Furthermore, in the transgenic mice kept in the Intellicage alone, the cognitive deficit of the young animals was modulated by the circadian rhythm, namely was prominent only during the active phase of the day. The novel approach to study the transgenic mice cognitive abilities presented in this paper offers new insight into cognitive dysfunctions of the Alzheimer's disease mouse model.     

Ideating Mobile Health Behavioral Support for Compliance to Therapy for Patients with Chronic Disease: A Case Study of Atrial Fibrillation Management

Poor patient compliance to therapy results in a worsening condition that often increases healthcare costs. In the MobiGuide project, we developed an evidence-based clinical decision-support system that delivered personalized reminders and recommendations to patients, helping to achieve higher therapy compliance. Yet compliance could still be improved and therefore building on the MobiGuide project experience, we designed a new component called the Motivational Patient Assistant (MPA) that is integrated within the MobiGuide architecture to further improve compliance. This component draws from psychological theories to provide behavioral support to improve patient engagement and thereby increasing patients’ compliance. Behavior modification interventions are delivered via mobile technology at patients’ home environments. Our approach was inspired by the IDEAS (Integrate, Design, Assess, and Share) framework for developing effective digital interventions to change health behavior; it goes beyond this approach by extending the Ideation phase’ concepts into concrete backend architectural components and graphical user-interface designs that implement behavioral interventions. We describe in detail our ideation approach and how it was applied to design the user interface of MPA for anticoagulation therapy for the atrial fibrillation patients. We report results of a preliminary evaluation involving patients and care providers that shows the potential usefulness of the MPA for improving compliance to anticoagulation therapy.     

Temperature-dependent appearance of forensically useful flies on carcasses

Flies are frequently used for postmortem interval (PMI) estimations. These estimates are usually based on the age of larval or pupal specimens. However, the age defines only the minimum PMI. In order to move forensic entomology further, a method useful for the estimation of an interval preceding insect appearance on a corpse called the pre-appearance interval (PAI) is needed. Recently, it was demonstrated that the PAI of several carrion beetles is closely related to the temperature prevailing throughout this interval. Hence, it was postulated to estimate PAI from temperature. In order to check premises for using this approach with flies, a test of the relationship between adult or oviposition PAI and temperature was made for nine species of European flies. Data on PAI originated from pig carcasses decomposing under various temperatures. Adult PAI of Hydrotaea dentipes, Hydrotaea ignava, Hydrotaea similis, Phormia regina, and Stearibia nigriceps and oviposition PAI of S. nigriceps were exponentially related to temperature. Only S. nigriceps revealed a close relationship, demonstrating solid premises for PAI estimation from temperature alone. Adult and oviposition PAI of Calliphora vomitoria and adult PAI of Hydrotaea pilipes were not related to temperature. Adult and oviposition PAI of Lucilia sericata and Lucilia caesar responded similarly, with an abrupt and large increase in a narrow range of low temperatures and no response in a broad range of high temperatures. Probably, different mechanisms form the basis for the response of PAI to temperature in flies colonizing carcasses shortly after death and flies colonizing carcasses later in the decomposition process.