Simple Muscle Architecture Analysis (SMA): an ImageJ macro tool to automate measurements in B-mode ultrasound scans

In vivo measurements of muscle architecture (i.e. the spatial arrangement of muscle fascicles) are routinely included in research and clinical settings to monitor muscle structure, function and plasticity. However, in most cases such measurements are performed manually, and more reliable and time-efficient automated methods are either lacking completely, or are inaccessible to those without expertise in image analysis. In this work, we propose an ImageJ script to automate the entire analysis process of muscle architecture in ultrasound images: Simple Muscle Architecture Analysis (SMA). Images are filtered in the spatial and frequency domains with built-in commands and external plugins to highlight aponeuroses and fascicles. Fascicle dominant orientation is then computed in regions of interest using the OrientationJ plugin. Bland-Altman plots of analyses performed manually or with SMA indicates that the automated analysis does not induce any systematic bias and that both methods agree equally through the range of measurements. Our test results illustrate the suitability of SMA to analyse images from superficial muscles acquired with a broad range of ultrasound settings.Comment: 8 pages, 7 figures, 1 appendi

Triceps Surae Short Latency Stretch Reflexes Contribute to Ankle Stiffness Regulation during Human Running

During human running, short latency stretch reflexes (SLRs) are elicited in the triceps surae muscles, but the function of these responses is still a matter of controversy. As the SLR is primarily mediated by Ia afferent nerve fibres, various methods have been used to examine SLR function by selectively blocking the Ia pathway in seated, standing and walking paradigms, but stretch reflex function has not been examined in detail during running. The purpose of this study was to examine triceps surae SLR function at different running speeds using Achilles tendon vibration to modify SLR size. Ten healthy participants ran on an instrumented treadmill at speeds between 7 and 15 km/h under 2 Achilles tendon vibration conditions: no vibration and 90 Hz vibration. Surface EMG from the triceps surae and tibialis anterior muscles, and 3D lower limb kinematics and ground reaction forces were simultaneously collected. In response to vibration, the SLR was depressed in the triceps surae muscles at all speeds. This coincided with short-lasting yielding at the ankle joint at speeds between 7 and 12 km/h, suggesting that the SLR contributes to muscle stiffness regulation by minimising ankle yielding during the early contact phase of running. Furthermore, at the fastest speed of 15 km/h, the SLR was still depressed by vibration in all muscles but yielding was no longer evident. This finding suggests that the SLR has greater functional importance at slow to intermediate running speeds than at faster speeds

Medial gastrocnemius muscle fascicle function during heel-rise after non-operative repair of Achilles tendon rupture

Background: To better understand muscle remodelling in dynamic conditions after an Achilles tendon rupture, this study examined the length of medial gastrocnemius muscle fascicles during a heel-rise at 6- and 12-months after non-operative ATR treatment. Methods: Participants (15 M, 3F) were diagnosed with acute Achilles tendon rupture. Medial gastrocnemius subtendon length, fascicle length and pennation angle were assessed in resting conditions, and fascicle shortening during bi- and unilateral heel-rises. Findings: Fascicle shortening was smaller on the injured side (mean difference [95% CI]: −9. 7 mm [−14.7 to −4.7 mm]; −11.1 mm [−16.5 to −5.8 mm]) and increased from 6- to 12 months (4.5 mm [2.8–6.3 mm]; 3.2 mm [1.4–4.9 mm]) in bi- and unilateral heel-rise, respectively. The injured tendon was longer compared to contralateral limb (2.16 cm [0.54–3.79 cm]) and the length decreased over time (−0.78 cm [−1.28 to −0.29 cm]). Tendon length correlated with fascicle shortening in bilateral (r = −0.671, p = 0.002; r = −0.666, p = 0.003) and unilateral (r = −0.773, p ≤ 0.001; r = −0.616, p = 0.006) heel-rise, at 6- and 12-months, respectively. In the injured limb, the change over time in fascicle shortening correlated with change in subtendon length in unilateral heel-rise (r = 0.544, p = 0.02). Interpretation: This study showed that the lengths of the injured tendon and associated muscle can adapt throughout the first year after rupture when patients continue physiotherapy and physical exercises. For muscle, measures of resting length may not be very informative about adaptations, which manifest themselves during functional tasks such as unilateral heel-rise

TeV Particle Astrophysics II: Summary comments

A unifying theme of this conference was the use of different approaches to understand astrophysical sources of energetic particles in the TeV range and above. In this summary I review how gamma-ray astronomy, neutrino astronomy and (to some extent) gravitational wave astronomy provide complementary avenues to understanding the origin and role of high-energy particles in energetic astrophysical sources.Comment: 6 pages, 4 figures; Conference summary talk for "TeV Particle Astrophysics II" at University of Wisconsin, Madison, 28-31 August 200

Mechanisms of Adaptation from a Multiple to a Single Step Recovery Strategy following Repeated Exposure to Forward Loss of Balance in Older Adults

When released from an initial, static, forward lean angle and instructed to recover with a single step, some older adults are able to meet the task requirements, whereas others either stumble or fall. The purpose of the present study was to use the concept of margin of stability (MoS) to investigate balance recovery responses in the anterior-posterior direction exhibited by older single steppers, multiple steppers and those that are able to adapt from multiple to single steps following exposure to repeated forward loss of balance. One hundred and fifty-one healthy, community dwelling, older adults, aged 65–80 years, participated in the study. Participants performed four trials of the balance recovery task from each of three initial lean angles. Balance recovery responses in the anterior-posterior direction were quantified at three events; cable release (CR), toe-off (TO) and foot contact (FC), for trials performed at the intermediate lean angle. MoS was computed as the anterior-posterior distance between the forward boundary of the Base of Support (BoS) and the vertical projection of the velocity adjusted centre of mass position (XCoM). Approximately one-third of participants adapted from a multiple to a single step recovery strategy following repeated exposure to the task. MoS at FC for the single and multiple step trials in the adaptation group were intermediate between the exclusively single step group and the exclusively multiple step group, with the single step trials having a significant, 3.7 times higher MoS at FC than the multiple step trials. Consistent with differences between single and multiple steppers, adaptation from multiple to single steps was attributed to an increased BoS at FC, a reduced XCoM at FC and an increased rate of BoS displacement from TO to FC. Adaptations occurred within a single test session and suggest older adults that are close to the threshold of successful recovery can rapidly improve dynamic stability following repeated exposure to a forward loss of balance

Impulsive noise pollution in the Northeast Atlantic: Reported activity during 2015-2017

Underwater noise pollution from impulsive sources (e.g. explosions, seismic airguns, percussive pile driving) can affect marine fauna through mortality, physical injury, auditory damage, physiological stress, acoustic masking, and behavioural responses. Given the potential for large-scale impact on marine ecosystems, some countries are now monitoring impulsive noise activity, coordinated internationally through Regional Seas Conventions. Here, we assess impulsive noise activity in the Northeast Atlantic reported during 2015-2017 to the first international impulsive noise register (INR), established in 2016 under the OSPAR Convention. Seismic airgun surveys were the dominant noise source (67%-83% of annual activity) and declined by 38% during 2015-2017. Reported pile driving activity increased 46%. Explosions and sonar/acoustic deterrent devices both had overall increases in reported activity. Some increases were attributable to more comprehensive reporting in later years. We discuss utilising the INR for risk assessment, target setting, and forward planning, and the implementation of similar systems in other regions

Reconstructing promoter activity from Lux bioluminescent reporters

The bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has also been adapted for eukaryotic cells, and can be used for whole cell biosensors, or in real time with live animals without the need for euthanasia. However, correct interpretation of bioluminescent data is limited: the bioluminescence is different from gene expression because of nonlinear molecular and enzyme dynamics of the Lux system. We have developed a computational approach that, for the first time, allows users of Lux assays to infer gene transcription levels from the light output. This approach is based upon a new mathematical model for Lux activity, that includes the actions of LuxAB, LuxEC and Fre, with improved mechanisms for all reactions, as well as synthesis and turn-over of Lux proteins. The model is calibrated with new experimental data for the LuxAB and Fre reactions from Photorhabdus luminescens --- the source of modern Lux reporters --- while literature data has been used for LuxEC. Importantly, the data show clear evidence for previously unreported product inhibition for the LuxAB reaction. Model simulations show that predicted bioluminescent profiles can be very different from changes in gene expression, with transient peaks of light output, very similar to light output seen in some experimental data sets. By incorporating the calibrated model into a Bayesian inference scheme, we can reverse engineer promoter activity from the bioluminescence. We show examples where a decrease in bioluminescence would be better interpreted as a switching off of the promoter, or where an increase in bioluminescence would be better interpreted as a longer period of gene expression. This approach could benefit all users of Lux technology

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure