Recent studies suggest a role for the microbiota in autism spectrum disorders (ASD), potentially arising from their role in modulating the immune system and gastrointestinal (GI) function or from gut–brain interactions dependent or independent from the immune system. GI problems such as chronic constipation and/or diarrhea are common in children with ASD, and significantly worsen their behavior and their quality of life. Here we first summarize previously published data supporting that GI dysfunction is common in individuals with ASD and the role of the microbiota in ASD. Second, by comparing with other publically available microbiome datasets, we provide some evidence that the shifted microbiota can be a result of westernization and that this shift could also be framing an altered immune system. Third, we explore the possibility that gut–brain interactions could also be a direct result of microbially produced metabolites.
Health care providers (HCPs) are an important source of physical activity (PA) information. Two studies were conducted to qualitatively and quantitatively examine nurse practitioners'(NPs) and physician assistants' current PA counseling practices, knowledge and confidence to provide PA counseling and providers' perceptions about their current PA counseling practices. The specific aims for these two studies included quantitatively and qualitatively identifying the prevalence of PA counseling, perceived counseling knowledge and confidence, and educational training related to counseling. In study 1, survey respondents were currently practicing NPs and physician assistants. Participants completed a modified version of the Promotion of Physical Activity by Nurse Practitioners Questionnaire either online or in person during a population specific conference. The majority of both NP and physician assistant respondents reported routinely counseling patients about PA. There were no differences in perceived knowledge or confidence to provide PA counseling between the two populations. Approximately half of all respondents reported receiving training to provide PA counseling as part of their educational preparation for becoming a health practitioner. Nearly three-quarters of respondents reported interest in receiving additional PA counseling training. In study 2, five focus groups (FGs), stratified by practice type, were conducted with NPs and physician assistants. Both NPs and physician assistants reported discussing PA with their patients, particularly those with chronic illness. Participants reported that discussing lifestyle modifications with patients was the most common type of PA counseling provided. Increased confidence to counsel was associated with having PA knowledge and providing simple counseling, such as lifestyle modifications. Barriers to counseling included having more important things to discuss, lack of time during appointments, the current healthcare system, lack of reimbursement and perceived patient financial barriers. PA recommendation knowledge was highly variable, with few participants reporting specific guidelines. FG participants, while not familiar with the American College of Sports Medicines' "Exercise is Medicine" initiative indicated interest in its use and learning more about it. The findings of these two studies indicate that while NPs and physician assistants are knowledgeable, confident and currently providing some amount of PA counseling to patients, additional training in PA counseling is needed and desired.
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison.
Results
We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach.
Conclusion
In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.
“Stoichioproteomics” relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels.
Results
Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline.
Conclusions
The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.