Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry

Motivation: We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Results: Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service

Metabolic Requirements of Farmers/Ranchers Performing Simulated Occupational Tasks: Recommendations for Cardiovascular Rehabilitation

Current ACSM guidelines for cardiac rehabilitation (rehab) return to work state that exercise training should mimic the muscle groups, movements, and energy systems utilized in a patient’s occupational tasks. The aims of this study were to evaluate the metabolic costs of typical farming/ranching tasks, determine the pattern of movement and muscle groups involved in these tasks, and determine the approximate duration of these tasks. Methods: Participants (n=29) were employed in the farming/ranching field and ranged in aged from 18-57 years. The participants performed four tasks: loading 10 hay bales, digging a fence post hole, filling eight seed hoppers, and shoveling grain. Results: Ranges for mean metabolic equivalent (MET) levels of the tasks were 5.9-7.6 while respiratory exchange ratio (RER) values ranged from .85-.93. Mean times (min:sec) for task duration were 1:42-3:34. Conclusion: MET levels recorded in this study are in agreement with the Compendium of Physical Activities for farming tasks and meet the standard requirements for cardiovascular training in cardiac rehab (~ 8 METS). However, these tasks are of high intensity and require an exercise prescription based on specificity of training for the muscle groups and energy systems involved. In accordance to ACSM guidelines, this study includes recommendations for exercise prescription specific to supervised resistance training appropriate for a farmer/rancher population in cardiac rehab settings

Ks-band detection of thermal emission and color constraints to CoRoT-1b: A low-albedo planet with inefficient atmospheric energy redistribution and a temperature inversion

We report the detection in Ks-band of the secondary eclipse of the hot Jupiter CoRoT-1b, from time series photometry with the ARC 3.5-m telescope at Apache Point Observatory. The eclipse shows a depth of 0.336+/-0.042 percent and is centered at phase 0.5022 (+0.0023,-0.0027), consistent with a zero eccentricity orbit ecos{\omega} = 0.0035 (+0.0036,-0.0042). We perform the first optical to near-infrared multi-band photometric analysis of an exoplanet's atmosphere and constrain the reflected and thermal emissions by combining our result with the recent 0.6, 0.71, and 2.09 micron secondary eclipse detections by Snellen et al. (2009), Gillon et al. (2009), and Alonso et al. (2009a). Comparing the multi-wavelength detections to state-of-the-art radiative-convective chemical-equilibrium atmosphere models, we find the near-infrared fluxes difficult to reproduce. The closest blackbody-based and physical models provide the following atmosphere parameters: a temperature T = 2454 (+84,-170) K, a very low Bond albedo A_B = 0.000 (+0.087,-0.000), and an energy redistribution parameter P_n = 0.1, indicating a small but nonzero amount of heat transfer from the day- to night-side. The best physical model suggests a thermal inversion layer with an extra optical absorber of opacity kappa_e =0.05cm^2g^-1, placed near the 0.1-bar atmospheric pressure level. This inversion layer is located ten times deeper in the atmosphere than the absorbers used in models to fit mid-infrared Spitzer detections of other irradiated hot Jupiters.Comment: accepted for publication on Ap

Multidimensional en-face OCT imaging of the retina.

Fast T-scanning (transverse scanning, en-face) was used to build B-scan or C-scan optical coherence tomography (OCT) images of the retina. Several unique signature patterns of en-face (coronal) are reviewed in conjunction with associated confocal images of the fundus and B-scan OCT images. Benefits in combining T-scan OCT with confocal imaging to generate pairs of OCT and confocal images similar to those generated by scanning laser ophthalmoscopy (SLO) are discussed in comparison with the spectral OCT systems. The multichannel potential of the OCT/SLO system is demonstrated with the addition of a third hardware channel which acquires and generates indocyanine green (ICG) fluorescence images. The OCT, confocal SLO and ICG fluorescence images are simultaneously presented in a two or a three screen format. A fourth channel which displays a live mix of frames of the ICG sequence superimposed on the corresponding coronal OCT slices for immediate multidimensional comparison, is also included. OSA ISP software is employed to illustrate the synergy between the simultaneously provided perspectives. This synergy promotes interpretation of information by enhancing diagnostic comparisons and facilitates internal correction of movement artifacts within C-scan and B-scan OCT images using information provided by the SLO channel

Understanding variation in unplanned admissions of people aged 85 and over:a systems-based approach

AIM: To examine system characteristics associated with variations in unplanned admission rates in those aged 85+.DESIGN: Mixed methods.SETTING: Primary care trusts in England were ranked according to changes in admission rates for people aged 85+ between 2007 and 2009, and study sites selected from each end of the distribution: three 'improving' sites where rates had declined by more than 4% and three 'deteriorating' sites where rates had increased by more than 20%. Each site comprised an acute hospital trust, its linked primary care trust/clinical commissioning group, the provider of community health services and adult social care.PARTICIPANTS: A total of 142 representatives from these organisations were interviewed to understand how policies had been developed and implemented. McKinsey's 7S framework was used as a structure for investigation and analysis.RESULTS: In general, improving sites provided more evidence of comprehensive system focused strategies backed by strong leadership, enabling the development and implementation of policies and procedures to avoid unnecessary admissions of older people. In these sites, primary and intermediate care services appeared more comprehensive and better integrated with other parts of the system, and policies in emergency departments were more focused on providing alternatives to admission.CONCLUSIONS: Health and social care communities which have attenuated admissions of people aged 85+ prioritised developing a shared vision and strategy, with sustained implementation of a suite of interventions.</p

Imagination, Reading, and Cognitive Development: Early Insights in Edith Nesbit’s The Enchanted Castle

In “Reading Fiction is Good for Children’s Cognitive, Emotional, and Social Development,” Maria Nikolajeva explains that cognitive theory can contribute much to literary studies and that a fledgling field of study exists that combines cognitive theory and cognitive science with literary criticism to create an approach known as cognitive literary criticism (4). She makes a case for the many useful insights that can be gained from using cognitive literary theory to understand how reading affects young developing minds. Specifically, she focuses on “how fiction stimulates young readers’ perception, attention, imagination, memory and other cognitive activity” (1). Literary critics have long asserted that reading helps stimulate the imagination, which is an essential aspect of cognition that starts to develop in childhood. Furthermore, reading allows one to enter situations and conflicts vicariously as a kind of practice. When a situation similar to one they have read about comes up in the readers’ lives, they will have some simulated experience with it gathered from reading. However, that literature can improve the cognitive abilities of readers appears to be a new insight for the scientific community