The first step in the analysis of protein tandem mass spectrometry data typically involves searching the observed spectra against a protein database. During database search, the search engine must ...digest the proteins in the database into peptides, subject to digestion rules that are under user control. The choice of these digestion parameters, as well as selection of post-translational modifications (PTMs), can dramatically affect the size of the search space and hence the statistical power of the search. The Tide search engine separates the creation of the peptide index from the database search step, thereby saving time by allowing a peptide index to be reused in multiple searches. Here we describe an improved implementation of the indexing component of Tide that consumes around four times less resources (CPU and RAM) than the previous version and can generate arbitrarily large peptide databases, limited by only the amount of available disk space. We use this improved implementation to explore the relationship between database size and the parameters controlling digestion and PTMs, as well as database size and statistical power. Our results can help guide practitioners in proper selection of these important parameters.
An inhomogeneous anisotropic physical model of the brain cortex is presented that predicts the emergence of nonevanescent (weakly damped) wave-like modes propagating in the thin cortex layers ...transverse to both the mean neural fiber direction and the cortex spatial gradient. Although the amplitude of these modes stays below the typically observed axon spiking potential, the lifetime of these modes may significantly exceed the spiking potential inverse decay constant. Full-brain numerical simulations based on parameters extracted from diffusion and structural MRI confirm the existence and extended duration of these wave modes. Contrary to the commonly agreed paradigm that the neural fibers determine the pathways for signal propagation in the brain, the signal propagation because of the cortex wave modes in the highly folded areas will exhibit no apparent correlation with the fiber directions. Nonlinear coupling of those linear weakly evanescent wave modes then provides a universal mechanism for the emergence of synchronized brain wave field activity. The resonant and nonresonant terms of nonlinear coupling between multiple modes produce both synchronous spiking-like high-frequency wave activity as well as low-frequency wave rhythms. Numerical simulation of forced multiple-mode dynamics shows that, as forcing increases, there is a transition from damped to oscillatory regime that can then transition quickly to a nonoscillatory state when a critical excitation threshold is reached. The resonant nonlinear coupling results in the emergence of low-frequency rhythms with frequencies that are several orders of magnitude below the linear frequencies of modes taking part in the coupling. The localization and persistence of these weakly evanescent cortical wave modes have significant implications in particular for neuroimaging methods that detect electromagnetic physiological activity, such as EEG and magnetoencephalography, and for the understanding of brain activity in general, including mechanisms of memory.
Eating, or nutrition, environments are believed to contribute to obesity and chronic diseases. There is a need for valid, reliable measures of nutrition environments. This article reports on the ...development and evaluation of measures of nutrition environments in retail food stores.
The Nutrition Environment Measures Study developed observational measures of the nutrition environment within retail food stores (NEMS-S) to assess availability of healthy options, price, and quality. After pretesting, measures were completed by independent raters to evaluate inter-rater reliability and across two occasions to assess test-retest reliability in grocery and convenience stores in four neighborhoods differing on income and community design in the Atlanta metropolitan area. Data were collected and analyzed in 2004 and 2005.
Ten food categories (e.g., fruits) or indicator food items (e.g., ground beef) were evaluated in 85 stores. Inter-rater reliability and test-retest reliability of availability were high: inter-rater reliability kappas were 0.84 to 1.00, and test-retest reliabilities were .73 to 1.00. Inter-rater reliability for quality across fresh produce was moderate (kappas, 0.44 to 1.00). Healthier options were higher priced for hot dogs, lean ground beef, and baked chips. More healthful options were available in grocery than convenience stores and in stores in higher income neighborhoods.
The NEMS-S tool was found to have a high degree of inter-rater and test-retest reliability, and to reveal significant differences across store types and neighborhoods of high and low socioeconomic status. These observational measures of nutrition environments can be applied in multilevel studies of community nutrition, and can inform new approaches to conducting and evaluating nutrition interventions.
The methods of group theory are applied to the problem of characterizing the diffusion measured in high angular resolution MR experiments. This leads to a natural representation of the local ...diffusion in terms of spherical harmonics. In this representation, it is shown that isotropic diffusion, anisotropic diffusion from a single fiber, and anisotropic diffusion from multiple fiber directions fall into distinct and separable channels. This decomposition can be determined for any voxel without any prior information by a spherical harmonic transform, and for special cases the magnitude and orientation of the local diffusion may be determined. Moreover, non‐diffusion–related asymmetries produced by experimental artifacts fall into channels distinct from the fiber channels, thereby allowing their separation and a subsequent reduction in noise from the reconstructed fibers. In the case of a single fiber, the method reduces identically to the standard diffusion tensor method. The method is applied to normal volunteer brain data collected with a stimulated echo spiral high angular resolution diffusion‐weighted (HARD) acquisition. Magn Reson Med 47:1083–1099, 2002. Published 2002 Wiley‐Liss, Inc.
Patient-specific models of cardiac function have the potential to improve diagnosis and management of heart disease by integrating medical images with heterogeneous clinical measurements subject to ...constraints imposed by physical first principles and prior experimental knowledge. We describe new methods for creating three-dimensional patient-specific models of ventricular biomechanics in the failing heart. Three-dimensional bi-ventricular geometry is segmented from cardiac CT images at end-diastole from patients with heart failure. Human myofiber and sheet architecture is modeled using eigenvectors computed from diffusion tensor MR images from an isolated, fixed human organ-donor heart and transformed to the patient-specific geometric model using large deformation diffeomorphic mapping. Semi-automated methods were developed for optimizing the passive material properties while simultaneously computing the unloaded reference geometry of the ventricles for stress analysis. Material properties of active cardiac muscle contraction were optimized to match ventricular pressures measured by cardiac catheterization, and parameters of a lumped-parameter closed-loop model of the circulation were estimated with a circulatory adaptation algorithm making use of information derived from echocardiography. These components were then integrated to create a multi-scale model of the patient-specific heart. These methods were tested in five heart failure patients from the San Diego Veteran’s Affairs Medical Center who gave informed consent. The simulation results showed good agreement with measured echocardiographic and global functional parameters such as ejection fraction and peak cavity pressures.
The authors provide a conceptual model of a healthy nutrition environment, then review the types of measures required to assess various aspects of this environment. Measures fall into priority ...categories of consumer and community environments.
Active transportation has the potential to contribute considerably to overall physical activity levels in adults and is likely to be influenced by neighborhood-related built environment ...characteristics. Previous studies that examined the associations between built environment attributes and active transportation, focused mainly on transport-related walking and were conducted within single countries, limiting environmental variability. We investigated the direction and shape of relationships of perceived neighborhood attributes with transport-related cycling and walking in three countries; and examined whether these associations differed by country and gender.
Data from the USA (Baltimore and Seattle), Australia (Adelaide) and Belgium (Ghent) were pooled. In total, 6,014 adults (20-65 years, 55.7% women) were recruited in high-/low-walkable and high-/low-income neighborhoods. All participants completed the Neighborhood Environmental Walkability Scale and the International Physical Activity Questionnaire. Generalized additive mixed models were used to estimate the strength and shape of the associations.
Proximity to destinations, good walking and cycling facilities, perceiving difficulties in parking near local shopping areas, and perceived aesthetics were included in a 'cyclability' index. This index was linearly positively related to transport-related cycling and no gender- or country-differences were observed. The 'walkability' index consisted of perceived residential density, land use mix access, proximity of destinations and aesthetics. A non-linear positive relationship with transport-related walking was found. This association was stronger in women than in men, and country-specific associations were identified: the strongest association was observed in Seattle, the weakest in Adelaide. In Ghent, the association weakened at higher levels of walkability.
For cycling, consistent correlates were found in the three countries, but associations were less straightforward for transport-related walking. Moreover, the identified neighborhood environmental correlates were different for walking compared to cycling. In order to further clarify the shape of these associations and reach more specific international guidelines for developing walkable and bikeable neighborhoods, future studies should include even more countries to maximize environmental variability.
Evidence documents associations between neighborhood design and active and sedentary forms of travel. Most studies compare travel patterns for people located in different types of neighborhoods at ...one point in time adjusting for demographics. Most fail to account for either underlying neighborhood selection factors (reasons for choosing a neighborhood) or preferences (neighborhoods that are preferred) that impact neighborhood selection and behavior. Known as self-selection, this issue makes it difficult to evaluate causation among built form, behavior, and associated outcomes and to know how much more walking and less driving could occur through creating environments conducive to active transport. The current study controls for neighborhood selection and preference and isolates the effect of the built environment on walking, car use, and obesity. Separate analyses were conducted among 2056 persons in the Atlanta, USA based Strategies for Metropolitan Atlanta's Regional Transportation and Air Quality (SMARTRAQ) travel survey on selection factors and 1466 persons in the SMARTRAQ community preference sub-survey. A significant proportion of the population are “mismatched” and do not live in their preferred neighborhood type. Factors influencing neighborhood selection and individual preferences, and current neighborhood walkability explained vehicle travel distance after controlling for demographic variables. Individuals who preferred and lived in a walkable neighborhood walked most (33.9% walked) and drove 25.8 miles per day on average. Individuals that preferred and lived in car dependent neighborhoods drove the most (43 miles per day) and walked the least (3.3%). Individuals that do not prefer a walkable environment walked little and show no change in obesity prevalence regardless of where they live. About half as many participants were obese (11.7%) who prefer and live in walkable environments than participants who prefer car dependent environments (21.6%). Findings suggest that creating walkable environments may result in higher levels of physical activity and less driving and in slightly lower obesity prevalence for those preferring walkability.
•Five distinct writing profiles were identified among 4th and 5th graders using theory-aligned measures.•Profiles were distinguished not only by level of performance on writing-related skills, but ...also knowledge about writing and writing motivation.•Profile membership predicted students’ performance on three genre-based writing tasks.•Grade, gender, and disability status significantly influenced the probability of being classified as a member of the globally proficient group versus the other groups.
Our goal in this study is to expand the limited research on writer profile using the advantageous model-based approach of latent profile analysis and independent tasks to evaluate aspects of individual knowledge, motivation, and cognitive processes that align with Hayes’ (1996) writing framework, which has received empirical support. We address three research questions. First, what latent profile are observed for late elementary writers using measures aligned with an empirically validated model of writing? Second, do student sociodemographic characteristics—namely grade, gender, race, English learner status, and special education status—influence latent profile membership? Third, how does student performance on narrative, opinion, and informative writing tasks, determined by quality of writing, vary by latent profile? A five-profile model had the best fit statistics and classified student writers as Globally Weak, At Risk, Average Motivated, Average Unmotivated, and Globally Proficient. Overall, fifth graders, female students, White students, native English speakers, and students without disabilities had greater odds of being in the Globally Proficient group of writers. For all three genres, other latent profile were significantly inversely related to the average quality of papers written by students who were classified as Globally Proficient; however, the Globally Weak and At Risk writers were not significantly different in their writing quality, and the Average Motivated and Average Unmotivated writers did not significantly differ from each other with respect to quality. These findings indicate upper elementary students exhibit distinct patterns of writing-related strengths and weaknesses that necessitate comprehensive yet differentiated instruction to address skills, knowledge, and motivation to yield desirable outcomes.
Understanding neighborhood preferences remains a key focus for planners. While many studies document the effects of either neighborhood design or neighborhood preference on health and travel ...behavior, few have explored their combined effect in smaller regions. Using a sample of 2,597 adults in the Region of Waterloo, Ontario, we found an unmet demand for walkable neighborhoods. Results suggest that walkable neighborhoods are independently associated with less vehicle travel after adjusting for sociodemographic and residential preferences. Our study highlights the importance of combining the effects of walkable neighborhoods and preferences for them when addressing health and sustainability goals in suburban communities.
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