PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined, reference gene expression profiles of the constituent populations in these samples. However, the expression profiles of the actual constituent populations are often perturbed from those of the reference profiles due to gene expression changes in cells associated with microenvironmental or developmental effects. Existing deconvolution algorithms do not account for these changes and give incorrect results when benchmarked against those measured by well-established flow cytometry, even after batch correction was applied. We introduce PERT, a new probabilistic expression deconvolution method that detects and accounts for a shared, multiplicative perturbation in the reference profiles when performing expression deconvolution. We applied PERT and three other state-of-the-art expression deconvolution methods to predict cell frequencies within heterogeneous human blood samples that were collected under several conditions (uncultured mono-nucleated and lineage-depleted cells, and culture-derived lineage-depleted cells). Only PERT's predicted proportions of the constituent populations matched those assigned by flow cytometry. Genes associated with cell cycle processes were highly enriched among those with the largest predicted expression changes between the cultured and uncultured conditions. We anticipate that PERT will be widely applicable to expression deconvolution strategies that use profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular phenotypic identity

Transposed-letter priming effects in reading aloud words and nonwords

A masked nonword prime generated by transposing adjacent inner letters in a word (e.g., jugde) facilitates the recognition of the target word (JUDGE) more than a prime in which the relevant letters are replaced by different letters (e.g., junpe). This transposed-letter (TL) priming effect has been widely interpreted as evidence that the coding of letter position is flexible, rather than precise. Although the TL priming effect has been extensively investigated in the domain of visual word recognition using the lexical decision task, very few studies have investigated this empirical phenomenon in reading aloud. In the present study, we investigated TL priming effects in reading aloud words and nonwords and found that these effects are of equal magnitude for the two types of items. We take this result as support for the view that the TL priming effect arises from noisy perception of letter order within the prime prior to the mapping of orthography to phonology.6 page(s

Envelope Determinants of Equine Lentiviral Vaccine Protection

Lentiviral envelope (Env) antigenic variation and associated immune evasion present major obstacles to vaccine development. The concept that Env is a critical determinant for vaccine efficacy is well accepted, however defined correlates of protection associated with Env variation have yet to be determined. We reported an attenuated equine infectious anemia virus (EIAV) vaccine study that directly examined the effect of lentiviral Env sequence variation on vaccine efficacy. The study identified a significant, inverse, linear correlation between vaccine efficacy and increasing divergence of the challenge virus Env gp90 protein compared to the vaccine virus gp90. The report demonstrated approximately 100% protection of immunized ponies from disease after challenge by virus with a homologous gp90 (EV0), and roughly 40% protection against challenge by virus (EV13) with a gp90 13% divergent from the vaccine strain. In the current study we examine whether the protection observed when challenging with the EV0 strain could be conferred to animals via chimeric challenge viruses between the EV0 and EV13 strains, allowing for mapping of protection to specific Env sequences. Viruses containing the EV13 proviral backbone and selected domains of the EV0 gp90 were constructed and in vitro and in vivo infectivity examined. Vaccine efficacy studies indicated that homology between the vaccine strain gp90 and the N-terminus of the challenge strain gp90 was capable of inducing immunity that resulted in significantly lower levels of post-challenge virus and significantly delayed the onset of disease. However, a homologous N-terminal region alone inserted in the EV13 backbone could not impart the 100% protection observed with the EV0 strain. Data presented here denote the complicated and potentially contradictory relationship between in vitro virulence and in vivo pathogenicity. The study highlights the importance of structural conformation for immunogens and emphasizes the need for antibody binding, not neutralizing, assays that correlate with vaccine protection. © 2013 Craigo et al

Recommendations for a core outcome set for measuring standing balance in adult populations: a consensus-based approach

Standing balance is imperative for mobility and avoiding falls. Use of an excessive number of standing balance measures has limited the synthesis of balance intervention data and hampered consistent clinical practice.To develop recommendations for a core outcome set (COS) of standing balance measures for research and practice among adults.A combination of scoping reviews, literature appraisal, anonymous voting and face-to-face meetings with fourteen invited experts from a range of disciplines with international recognition in balance measurement and falls prevention. Consensus was sought over three rounds using pre-established criteria.The scoping review identified 56 existing standing balance measures validated in adult populations with evidence of use in the past five years, and these were considered for inclusion in the COS.Fifteen measures were excluded after the first round of scoring and a further 36 after round two. Five measures were considered in round three. Two measures reached consensus for recommendation, and the expert panel recommended that at a minimum, either the Berg Balance Scale or Mini Balance Evaluation Systems Test be used when measuring standing balance in adult populations.Inclusion of two measures in the COS may increase the feasibility of potential uptake, but poses challenges for data synthesis. Adoption of the standing balance COS does not constitute a comprehensive balance assessment for any population, and users should include additional validated measures as appropriate.The absence of a gold standard for measuring standing balance has contributed to the proliferation of outcome measures. These recommendations represent an important first step towards greater standardization in the assessment and measurement of this critical skill and will inform clinical research and practice internationally

Identification of Behaviour in Freely Moving Dogs (Canis familiaris) Using Inertial Sensors

Monitoring and describing the physical movements and body postures of animals is one of the most fundamental tasks of ethology. The more precise the observations are the more sophisticated the interpretations can be about the biology of a certain individual or species. Animal-borne data loggers have recently contributed much to the collection of motion-data from individuals, however, the problem of translating these measurements to distinct behavioural categories to create an ethogram is not overcome yet. The objective of the present study was to develop a “behaviour tracker”: a system composed of a multiple sensor data-logger device (with a tri-axial accelerometer and a tri-axial gyroscope) and a supervised learning algorithm as means of automated identification of the behaviour of freely moving dogs. We collected parallel sensor measurements and video recordings of each of our subjects (Belgian Malinois, N=12; Labrador Retrievers, N=12) that were guided through a predetermined series of standard activities. Seven behavioural categories (lay, sit, stand, walk, trot, gallop, canter) were pre-defined and each video recording was tagged accordingly. Evaluation of the measurements was performed by support vector machine (SVM) classification. During the analysis we used different combinations of independent measurements for training and validation (belonging to the same or different individuals or using different training data size) to determine the robustness of the application. We reached an overall accuracy of above 90% perfect identification of all the defined seven categories of behaviour when both training and validation data belonged to the same individual, and over 80% perfect recognition rate using a generalized training data set of multiple subjects. Our results indicate that the present method provides a good model for an easily applicable, fast, automatic behaviour classification system that can be trained with arbitrary motion patterns and potentially be applied to a wide range of species and situations

The integration of occlusion and disparity information for judging depth in autism spectrum disorder

In autism spectrum disorder (ASD), atypical integration of visual depth cues may be due to flattened perceptual priors or selective fusion. The current study attempts to disentangle these explanations by psychophysically assessing within-modality integration of ordinal (occlusion) and metric (disparity) depth cues while accounting for sensitivity to stereoscopic information. Participants included 22 individuals with ASD and 23 typically developing matched controls. Although adults with ASD were found to have significantly poorer stereoacuity, they were still able to automatically integrate conflicting depth cues, lending support to the idea that priors are intact in ASD. However, dissimilarities in response speed variability between the ASD and TD groups suggests that there may be differences in the perceptual decision-making aspect of the task

Steps toward Massage Therapy Guidelines: A First Report to the Profession

Over the last two decades, the massage profession has grown rapidly. As it does with business startups that begin informally and successfully grow into mature enterprises, growth brings new organizational challenges along with greater visibility and opportunity. The maturation of massage as a healthcare profession creates an increasing need for a process to formalize the synthesis of massage therapy knowledge from clinical experience and research. As a profession, we need more expedient means to collect what we know and to make such baseline knowledge widely available to practitioners, consumers, and other healthcare stakeholders. In short, we need to create a process for creating guidelines. This paper lays out the motivations and framework for creating guidelines for massage therapy that are informed both by research and clinical experience. It represents a report to the massage therapy profession and to other stakeholders of the work of the Best Practices Committee (BPC) of the Massage Therapy Foundation over the previous two years. Because there is little or no existing referenceable literature basis for such discussion in the context of massage, the paper also bears the additional goal of providing a healthcare literature basis for future academic massage discussions. The concept of guidelines is discussed based on a definition from the Institute of Medicine (IOM) and research on the nature of expertise. Guidelines are targeted for submission to the National Guideline Clearinghouse. Challenges in creating guidelines for massage therapy are discussed. Different stakeholders are considered, with their needs and potential benefits from guidelines presented as scenarios. Current literature from the wider scope of healthcare is extensively reviewed. Topics include guideline creation, credentialing of complementary and alternative medicine (CAM) practitioners, definition of competence, and the increasing role of technology (i.e. informatics) in managing training and task-necessary competencies. At first glance separate, these topics are interlinked by a healthcare quality initiative from the IOM, by a resultant process of healthcare self-reflection, and by extensive defense and technology industry efforts to create new capabilities and data standards for learning and competency communication and management. Finally, a process for creation of massage therapy guidelines is proposed. A central feature of the proposal is the use of a “World Café” symposium to elicit knowledge and solutions from a diverse collection of experts. The symposium would be aimed at vetting and refining the proposed guideline process by applying it to creation of guidelines for massage interventions for stress management, low-back pain, and lymphedema. The role of transparency and a wide and open peer-review is stressed as essential to the usability and credibility of guidelines

The history of falls and the association of the timed up and go test to falls and near-falls in older adults with hip osteoarthritis

Abstract Background Falling accounts for a significant number of hospital and long-term care admissions in older adults. Many adults with the combination of advancing age and functional decline associated with lower extremity osteoarthritis (OA), are at an even greater risk. The purpose of this study was to describe fall and near-fall history, location, circumstances and injuries from falls in a community-dwelling population of adults over aged 65 with hip OA and to determine the ability of the timed up and go test (TUG) to classify fallers and near-fallers. Method A retrospective observational study of 106 older men and women with hip pain for six months or longer, meeting a clinical criteria for the presence of hip OA at one or both hips. An interview for fall and near-fall history and administration of the TUG were administered on one occasion. Results Forty-five percent of the sample had at least one fall in the past year, seventy-seven percent reported occasional or frequent near-falls. The majority of falls occurred during ambulation and ascending or descending steps. Forty percent experienced an injury from the fall. The TUG was not associated with history of falls, but was associated with near-falls. Higher TUG scores occurred for those who were older, less mobile, and with greater number of co-morbidities. Conclusion A high percentage of older adults with hip OA experience falls and near-falls which may be attributed to gait impairments related to hip OA. The TUG could be a useful screening instrument to predict those who have frequent near-falls, and thus might be useful in predicting risk of future falls in this population.</p

A versatile synthesis method of dendrites-free segmented nanowires with a precise size control

We report an innovative strategy to obtain cylindrical nanowires combining well established and low-cost bottom-up methods such as template-assisted nanowires synthesis and electrodeposition process. This approach allows the growth of single-layer or multi-segmented nanowires with precise control over their length (from few nanometers to several micrometers). The employed techniques give rise to branched pores at the bottom of the templates and consequently dendrites at the end of the nanowires. With our method, these undesired features are easily removed from the nanowires by a selective chemical etching. This is crucial for magnetic characterizations where such non-homogeneous branches may introduce undesired features into the final magnetic response. The obtained structures show extremely narrow distributions in diameter and length, improved robustness and high-yield, making this versatile approach strongly compatible with large scale production at an industrial level. Finally, we show the possibility to tune accurately the size of the nanostructures and consequently provide an easy control over the magnetic properties of these nanostructures