Frame-by-frame annotation of video recordings using deep neural networks

Funding: Scottish Government (Grant Number(s): Marine Mammal Scientific Support Research Program); Homebrew Films; National Research Foundation of South Africa (Grant Number(s): 105782, 90782).Video data are widely collected in ecological studies, but manual annotation is a challenging and time‐consuming task, and has become a bottleneck for scientific research. Classification models based on convolutional neural networks (CNNs) have proved successful in annotating images, but few applications have extended these to video classification. We demonstrate an approach that combines a standard CNN summarizing each video frame with a recurrent neural network (RNN) that models the temporal component of video. The approach is illustrated using two datasets: one collected by static video cameras detecting seal activity inside coastal salmon nets and another collected by animal‐borne cameras deployed on African penguins, used to classify behavior. The combined RNN‐CNN led to a relative improvement in test set classification accuracy over an image‐only model of 25% for penguins (80% to 85%), and substantially improved classification precision or recall for four of six behavior classes (12–17%). Image‐only and video models classified seal activity with very similar accuracy (88 and 89%), and no seal visits were missed entirely by either model. Temporal patterns related to movement provide valuable information about animal behavior, and classifiers benefit from including these explicitly. We recommend the inclusion of temporal information whenever manual inspection suggests that movement is predictive of class membership.Publisher PDFPeer reviewe

Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'

Proteinase-activated receptor 2 modulates OA-related pain, cartilage and bone pathology

Objective Proteinase-activated receptor 2 (PAR2) deficiency protects against cartilage degradation in experimental osteoarthritis (OA). The wider impact of this pathway upon OA-associated pathologies such as osteophyte formation and pain is unknown. Herein, we investigated early temporal bone and cartilage changes in experimental OA in order to further elucidate the role of PAR2 in OA pathogenesis. Methods OA was induced in wild-type (WT) and PAR2-deficient (PAR2−/−) mice by destabilisation of the medial meniscus (DMM). Inflammation, cartilage degradation and bone changes were monitored using histology and microCT. In gene rescue experiments, PAR2−/− mice were intra-articularly injected with human PAR2 (hPAR2)-expressing adenovirus. Dynamic weight bearing was used as a surrogate of OA-related pain. Results Osteophytes formed within 7 days post-DMM in WT mice but osteosclerosis was only evident from 14 days post induction. Importantly, PAR2 was expressed in the proliferative/hypertrophic chondrocytes present within osteophytes. In PAR2−/− mice, osteophytes developed significantly less frequently but, when present, were smaller and of greater density; no osteosclerosis was observed in these mice up to day 28. The pattern of weight bearing was altered in PAR2−/− mice, suggesting reduced pain perception. The expression of hPAR2 in PAR2−/− mice recapitulated osteophyte formation and cartilage damage similar to that observed in WT mice. However, osteosclerosis was absent, consistent with lack of hPAR2 expression in subchondral bone. Conclusions This study clearly demonstrates PAR2 plays a critical role, via chondrocytes, in osteophyte development and subchondral bone changes, which occur prior to PAR2-mediated cartilage damage. The latter likely occurs independently of OA-related bone changes

Ecosystem service assessment of selected wetlands of Kolkata and the Indian Gangetic Delta: multi-beneficial systems under differentiated management stress

© 2019, The Author(s). A structured literature review using the search term ‘ecosystem services’ found few relevant studies relating to three contrasting wetlands in West Bengal: the unpopulated Sudhanyakhali Island in the Sundarbans National Park, the populated Gosaba Island separated from Sudhanyakhali Island by a narrow channel, and the East Kolkata Wetland (EKW). Subsequent structured review focused on the EKW using specific service-related terms located only 2 provisioning, 6 regulating, 1 cultural and 3 supporting services. Few services are currently recognized in the literature, with significant gaps in whole service categories. Significantly, there was no published evidence of a systemic overview of service production at these sites. Field observations and stakeholder dialogue informed assessment of ecosystem services using the Rapid Assessment of Wetland Ecosystem Services (RAWES) approach, adopted by the Ramsar Commission, on both islands and three discretely different areas of the EKW. The RAWES surveys found that 32 of 36 ecosystem services were produced from at least one assessed wetland site. Despite low sample size, statistically significant differences were observed in the range of services produced between the five wetland sites and the geographical range at which benefits accrued, explained by differing wetland characteristics and management regimes. Were decisions based solely on evidence provided by existing published knowledge, few ecosystem services would be considered and, potentially, whole ecosystem service categories might be overlooked. Importantly, there would also be no systemic account of service production and interdependencies. RAWES assessment serves as a practical, rapid and systemic approach, taking account of interdependent ecosystem services, supporting protection of the ecological character and achievement of wise use of wetlands. RAWES can also help redress perceptions that the values of peri-urban wetlands are currently under-represented

The IĸB protein BCL3 controls osteogenesis and bone health

Objective: IĸB protein B-cell lymphoma 3-encoded protein (BCL3) is a regulator of the NF-κB family of transcription factors. NF-κB signalling fundamentally influences the fate of bone-forming osteoblasts and bone-resorbing osteoclasts, but the role of BCL3 in bone biology has not been investigated. The objective of this study was to evaluate BCL3 in skeletal development, maintenance and osteoarthritic pathology. Methods: To assess the contribution of BCL3 to skeletal homeostasis, neonatal mice (n = 6-14) lacking BCL3 (Bcl3−/−) and WT controls were characterised for bone phenotype and density. To reveal the contribution to bone phenotype by the osteoblast compartment in Bcl3−/− mice, transcriptomic analysis of early osteogenic differentiation and cellular function (n = 3-7) were assessed. Osteoclast differentiation and function in Bcl3−/− mice (n = 3-5) was assessed. Adult 20-week Bcl3−/− and WT mice bone phenotype, strength and turnover were assessed. A destabilisation of the medial meniscus (DMM) model of osteoarthritic ostephytogenesis was utilised to understand adult bone formation in Bcl3−/− mice (n = 11-13). Results: Evaluation of Bcl3−/− mice revealed congenitally increased bone density, long bone dwarfism, increased bone biomechanical strength and altered bone turnover. Molecular and cellular characterisation of mesenchymal precursors showed that Bcl3−/− cells display an accelerated osteogenic transcriptional profile that leads to enhanced differentiation into osteoblasts with increased functional activity; which could be reversed with a mimetic peptide. In a model of osteoarthritis-induced osteophytogenesis, Bcl3−/− mice exhibit decreased pathological osteophyte formation (P < 0.05). Conclusion: Cumulatively, these findings demonstrate that BCL3 controls developmental mineralisation to enable appropriate bone formation, whilst in a pathological setting it contributes to skeletal pathology

Effectiveness of prolonged use of continuous passive motion (CPM), as an adjunct to physiotherapy, after total knee arthroplasty

<p>Abstract</p> <p>Background</p> <p>Adequate and intensive rehabilitation is an important requirement for successful total knee arthroplasty.</p> <p>Although research suggests that Continuous Passive Motion (CPM) should be implemented in the first rehabilitation phase after surgery, there is substantial debate about the duration of each session and the total period of CPM application. A Cochrane review on this topic concluded that short-term use of CPM leads to greater short-term range of motion. It also suggested, however, that future research should concentrate on the treatment period during which CPM should be administered.</p> <p>Methods</p> <p>In a randomised controlled trial we investigated the effectiveness of prolonged CPM use in the home situation as an adjunct to standardised PT. Efficacy was assessed in terms of faster improvements in range of motion (RoM) and functional recovery, measured at the end of the active treatment period, 17 days after surgery.</p> <p>Sixty patients with knee osteoarthritis undergoing TKA and experiencing early postoperative flexion impairment were randomised over two treatment groups. The experimental group received CPM + PT for 17 consecutive days after surgery, whereas the usual care group received the same treatment during the in-hospital phase (i.e. about four days), followed by PT alone (usual care) in the first two weeks after hospital discharge.</p> <p>From 18 days to three months after surgery, both groups received standardised PT. The primary focus of rehabilitation was functional recovery (e.g. ambulation) and regaining RoM in the knee.</p> <p>Results</p> <p>Prolonged use of CPM slightly improved short-term RoM in patients with limited RoM at the time of discharge after total knee arthroplasty when added to a semi-standard PT programme. Assessment at 6 weeks and three months after surgery found no long-term effects of this intervention Neither did we detect functional benefits of the improved RoM at any of the outcome assessments.</p> <p>Conclusion</p> <p>Although results indicate that prolonged CPM use might have a small short-term effect on RoM, routine use of prolonged CPM in patients with limited RoM at hospital discharge should be reconsidered, since neither long-term effects nor transfer to better functional performance was detected.</p> <p>Trial Registration</p> <p>ISRCTN85759656</p

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes