A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is ‘hidden’ from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community.

Database URL:http://neuinfo.org

Efficacy and tolerability of methotrexate therapy for refractory Crohn's disease: a large single-centre experience

BACKGROUND

Randomised controlled trials demonstrate that methotrexate is effective in inducing remission and preventing relapse of Crohn's disease (CD) as a first-line immunosuppressant, but efficacy data after failure with, or intolerance to, thiopurines are limited.

AIMS

To report efficacy of methotrexate in a cohort of refractory CD patients, most of whom had not responded to, or were intolerant of, thiopurines.

METHODS

Data were collected for patients receiving methotrexate for active CD. Response to methotrexate induction therapy at 4 months, and sustained clinical benefit at last point of follow-up with maintenance therapy, were assessed via physician's global assessment. Demographic and disease factors predicting response, or sustained clinical benefit, were examined by univariate and multivariate analysis.

RESULTS

Sixty-six [38 (54%) female patients, mean age at diagnosis 29.4 years] patients received methotrexate between 2001 and 2010, 61 (92%) of whom received the drug parenterally. Sixty patients had failed, or were intolerant of, thiopurines. Response to therapy at 4 months occurred in 54 (82%) patients. However, sustained clinical benefit occurred in only 19 (29%) patients at last point of follow-up, including six patients who discontinued the drug for family planning reasons. No predictors of response or sustained clinical benefit were identified. Adverse events occurred in 20 (30%) patients.

CONCLUSIONS

These data suggest that methotrexate is effective in terms of initial response in Crohn's disease patients who have failed, or are intolerant of, thiopurines. However, efficacy is not sustained in the long term.

The effect of player positional groups on the nature of tackles that result in tackle-related injuries in professional rugby league matches

AIM

The aim of this study was to describe the effect of player positional groups on the nature of tackles that result in tackle-related injuries in professional rugby league matches.

METHODS

Prospective observational epidemiology analyses for tackle-related injuries and video analyses for the nature of tackles were conducted for a single team in the National Rugby League (NRL) throughout the 2007 and 2008 competitions for a total of 48 games. Risk ratios (RR) were calculated for comparisons between positional groups (adjustable, hit-up forwards or outside backs).

RESULTS

The total missed match tackle-related injury rate was 57.8 per 1 000 player hours. Hit-up forwards recorded significantly more total tackle-related injuries than outside backs (RR: 1.3; P=0.049), but not more than adjustables (RR: 1.0; P=0.922). Hit-up forwards recorded significantly more chest-back tackle-related injuries than adjustables (RR: 6.0; P=0.008). Outside backs recorded significantly more tackle injuries as the ball carrier than the tackler (RR: 2.4; P=0.015) while adjustables recorded significantly more tackle injuries as the tackler than the ball carrier (RR: 1.8; P<0.001). Hit-up forwards had a higher incidence of contusions, and sprains while adjustables had a higher incidence of fracture/dislocations. There were no differences in injury severity between the positional groups.

CONCLUSION

Player positional group had an effect on tackle-related injury type and injury site. Hit-up forwards and outside backs recorded more tackle-related injuries as a ball carrier than as a tackler, while in contrast, adjustables recorded more tackle-related injuries as the tackler than the ball carrier.

A retrospective review over 1999 to 2007 of head, shoulder and knee soft tissue and fracture dislocation injuries and associated costs for rugby league in New Zealand

King et al. reported that of 5 941 moderate to serious claims resulting in medical treatment for rugby league injuries, the knee, shoulder, and head and neck body sites and soft tissue and fracture-dislocation injuries were most frequent and costly in the New Zealand national no-fault injury compensation corporation database during 1999 to 2007. However, additional analyses of knee, shoulder and head and neck body sites by soft tissue and fracture-dislocation injury types was required to enable a greater understanding of the nature of injuries most likely to be seen by sports medical personnel dealing with rugby league players. From 1999 to 2007 the injury claims and costs for head and neck soft tissue, fracture-dislocations, shoulders soft tissue significantly increased. Knee soft tissue injury claims and costs significantly decreased from 1999 to 2007. There was no significant difference in knee fracture-dislocation injury claims but there was a significant increase in knee fracture-dislocation injury costs from 1999 to 2007. Changes in the nature of injuries may be related to changes in defensive techniques employed in rugby league during this time. Sports medical personnel dealing with rugby league players should focus their injury prevention strategies on reducing musculoskeletal injuries to the head and shoulder. There should be a focus on increasing awareness of correct tackling technique, head injury awareness and management of suspected cervical spine injuries.

A patient and relative centred evaluation of treatment escalation plans: a replacement for the do-not-resuscitate process

The Treatment Escalation Plan (TEP) was introduced into our trust in an attempt to improve patient involvement and experience of their treatment in hospital and to embrace and clarify a wider remit of treatment options than the Do Not Resuscitate (DNR) order currently offers. Our experience suggests that the patient and family are rarely engaged in DNR discussions. This is acutely relevant considering that the Mental Capacity Act (MCA) now obliges these discussions to take place. The TEP is a form that the doctor completes, ideally with the competent patient or close relative, documenting what treatment options would be appropriate if that patient were to become acutely unwell. Ventilation of the lungs, cardiac resuscitation, renal replacement therapy, intravenous fluids and antibiotics are all discussed. The study evaluated patient and relative experiences with the TEP. 55 patients or their relatives were interviewed regarding their experience of the TEP and thoughts regarding the process. 96% of patients and relatives evaluated thought that the TEP was a good idea. Free text comments were all positive and only 34% of patients claimed to feel anxious when completing the form. Following this study, the TEP has been expanded hospital wide and into the community within our trust. Discussions are currently taking place in hospitals within our region to introduce the TEP form into other local trusts.

Velocity-dependent fatigue crack paths in nanograined Pt films

Studies of crack growth in nanograined films assert that mechanical damage accumulates at grain boundaries irrespective of the crack velocity and loading conditions. This work shows that crack advance in nanograined Pt films involves a dislocation-slip mechanism that is a function of the crack growth rate and mode of loading. Crack paths in Pt were initially intergranular, but transitioned to a transgranular mode that persisted until catastrophic failure. This research demonstrates that crack growth mechanisms modeled for nanograined Ni cannot be generalized to other pure, metallic systems.