Assessing a standardised approach to measuring corticospinal integrity after stroke with DTI

The structural integrity of the corticospinal tract (CST) after stroke is closely linked to the degree of motor impairment. Simple and reliable methods of assessing white matter integrity within the CST would facilitate the use of this measure in routine clinical practice. Commonly, diffusion tensor imaging is used to measure voxel-wise fractional anisotropy (FA) in a variety of regions of interest (ROIs) representing the CST. Several methods are currently in use with no consensus about which approach is best. ROIs are usually either the whole CST or the posterior limb of the internal capsule (PLIC). These are created manually on brain images or with reference to an individual's CST determined by tractography. Once the ROI has been defined, the FA can be reported as an absolute measure from the ipsilesional side or as a ratio in comparison to the contralesional side. Both corticospinal tracking and manual ROI definition in individual stroke patients are time consuming and subject to bias. Here, we investigated whether using a CST template derived from healthy volunteers was a feasible method for defining the appropriate ROI within which to measure changes in FA. We reconstructed the CST connecting the primary motor cortex to the ipsilateral pons in 23 age-matched control subjects and 21 stroke patients. An average healthy CST template was created from the 23 control subjects. For each patient, FA values were then calculated for both the template CST and for their own CST. We compared patients' FA metrics between the two tracts by considering four measures (FA in the ipsilesional side, FA in the contralesional side, FA ratio of the ipsilesional side to the contralesional side and FA asymmetry between the two sides) and in two tract-based ROIs (whole tract and tract section traversing the PLIC). There were no significant differences in FA metrics for either method, except for contralesional FA. Furthermore, we found that FA metrics relating to CST damage all correlated with motor ability post-stroke equally well. These results suggest that the healthy CST template could be a surrogate structure for defining tract-based ROIs with which to measure stroke patients' FA metrics, avoiding the necessity for CST tracking in individual patients. CST template-based automated quantification of structural integrity would greatly facilitate implementation of practical clinical applications of diffusion tensor imaging

TEDI: the TripleSpec Exoplanet Discovery Instrument

The TEDI (TripleSpec - Exoplanet Discovery Instrument) will be the first instrument fielded specifically for finding low-mass stellar companions. The instrument is a near infra-red interferometric spectrometer used as a radial velocimeter. TEDI joins Externally Dispersed Interferometery (EDI) with an efficient, medium-resolution, near IR (0.9 - 2.4 micron) echelle spectrometer, TripleSpec, at the Palomar 200" telescope. We describe the instrument and its radial velocimetry demonstration program to observe cool stars.Comment: 6 Pages, To Appear in SPIE Volume 6693, Techniques and Instrumentation for Detection of Exoplanets II

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

© 2015 Becraft, Wood, Rusch, Kühl, Jensen, Bryant, Roberts, Cohan and Ward. Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same putative ecotype formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the putative ecotypes are ecologically distinct, the members of each ecotype are ecologically homogeneous. Putative ecotypes responded differently to experimental perturbations of temperature and light, but the genetic variation within each putative ecotype was maintained as the relative abundances of putative ecotypes changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to putative ecotypes that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for putative ecotypes that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time

Lunch and Learn Small Discussion Groups

Mini-conversations in which attendees self-select. There will be a discussant at each table to assist in guiding the dialogues. Alexia Hudson-Ward: Situating Our Work Within the Mission in a Liberal Arts SettingStrategies on how to strategically communicate and steward the importance of this work to the faculty and senior leaders of our institutions as a mission-centered imperative. Laura Perrings: Educational Opportunities Provided by Rare Book SchoolLearn more about the educational opportunities provided by Rare Book School, such as the Lang Fellowship. Ken Grossi and Ed Vermue: Building Professional CommunityWe all need our people. This dialogue will explore how one can share and support a cohort of colleagues across the disciplines to maintain this critical work. Anne Cuyler Salsich, Megan Mitchell, and Heath Patten: Discoverability, Presentation and Promotion of Your Existing CollectionsThis session explores questions of outreach and how to present and promote your existing objects with faculty and students. Angela Vanden Elzen: Making as Pedagogy with Makerspaces and Digital GamingWe will review the concept of making as pedagogy with makerspaces, digital projects, and exhibitions and how to engage students, faculty, and the community in this growing area

Lessons from dynamic cadaver and invasive bone pin studies: do we know how the foot really moves during gait?

Background: This paper provides a summary of a Keynote lecture delivered at the 2009 Australasian Podiatry Conference. The aim of the paper is to review recent research that has adopted dynamic cadaver and invasive kinematics research approaches to better understand foot and ankle kinematics during gait. It is not intended to systematically cover all literature related to foot and ankle kinematics (such as research using surface mounted markers). Since the paper is based on a keynote presentation its focuses on the authors own experiences and work in the main, drawing on the work of others where appropriate Methods: Two approaches to the problem of accessing and measuring the kinematics of individual anatomical structures in the foot have been taken, (i) static and dynamic cadaver models, and (ii) invasive in-vivo research. Cadaver models offer the advantage that there is complete access to all the tissues of the foot, but the cadaver must be manipulated and loaded in a manner which replicates how the foot would have performed when in-vivo. The key value of invasive in-vivo foot kinematics research is the validity of the description of foot kinematics, but the key difficulty is how generalisable this data is to the wider population. Results: Through these techniques a great deal has been learnt. We better understand the valuable contribution mid and forefoot joints make to foot biomechanics, and how the ankle and subtalar joints can have almost comparable roles. Variation between people in foot kinematics is high and normal. This includes variation in how specific joints move and how combinations of joints move. The foot continues to demonstrate its flexibility in enabling us to get from A to B via a large number of different kinematic solutions. Conclusion: Rather than continue to apply a poorly founded model of foot type whose basis is to make all feet meet criteria for the mechanical 'ideal' or 'normal' foot, we should embrace variation between feet and identify it as an opportunity to develop patient-specific clinical models of foot function

Tracking digital impact (TDI) tool.

The Tracking Digital Impact (TDI) tool is designed to help researchers, research groups, projects and institutions assess their current and future digital engagement strategies in an objective and informed way to support the development of new and improved strategies that more effectively enable good engagement with businesses, communities, the public, governing bodies and other researchers to facilitate better engagement and greater impact. The TDI tool was developed as part of a JISC funded project which focused on identifying, synthesising and embedding business, community and public (BCE) engagement best practices. The TDI tool examined the best practices at the dot.rural Digital Economies hub at the University of Aberdeen and translated those (accompanied by new guidance) into the TDI tool. Parts of this document were sourced from 'Brief Notes on Social Media for Research' by Jennifer Holden (University of Aberdeen, October, 2012). This document describes the TDI tool and its use

Supratentorial and spinal pediatric ependymomas display a hypermethylated phenotype which includes the loss of tumor suppressor genes involved in the control of cell growth and death

Epigenetic alterations, including methylation, have been shown to be an important mechanism of gene silencing in cancer. Ependymoma has been well characterized at the DNA copy number and mRNA expression levels. However little is known about DNA methylation changes. To gain a more global view of the methylation profile of ependymoma we conducted an array-based analysis. Our data demonstrated tumors to segregate according to their location in the CNS, which was associated with a difference in the global level of methylation. Supratentorial and spinal tumors displayed significantly more hypermethylated genes than posterior fossa tumors, similar to the ‘CpG island methylator phenotype’ (CIMP) identified in glioma and colon carcinoma. This hypermethylated profile was associated with an increase in expression of genes encoding for proteins involved in methylating DNA, suggesting an underlying mechanism. An integrated analysis of methylation and mRNA expression array data allowed us to identify methylation-induced expression changes. Most notably genes involved in the control of cell growth and death and the immune system were identified, including members of the JNK pathway and PPARG. In conclusion, we have generated a global view of the methylation profile of ependymoma. The data suggests epigenetic silencing of tumor suppressor genes is an important mechanism in the pathogenesis of supratentorial and spinal, but not posterior fossa ependymomas. Hypermethylation correlated with a decrease in expression of a number of tumor suppressor genes and pathways that could be playing an important role in tumor pathogenesis