An Automated Procedure to Identify Biomedical Articles that Contain Cancer-associated Gene Variants

The proliferation of biomedical literature makes it increasingly difficult for researchers to find and manage relevant information. However, identifying research articles containing mutation data, a requisite first step in integrating large and complex mutation data sets, is currently tedious, time-consuming and imprecise. More effective mechanisms for identifying articles containing mutation information would be beneficial both for the curation of mutation databases and for individual researchers. We developed an automated method that uses information extraction, classifier, and relevance ranking techniques to determine the likelihood of MEDLINE abstracts containing information regarding genomic variation data suitable for inclusion in mutation databases. We targeted the CDKN2A (p16) gene and the procedure for document identification currently used by CDKN2A Database curators as a measure of feasibility. A set of abstracts was manually identified from a MEDLINE search as potentially containing specific CDKN2A mutation events. A subset of these abstracts was used as a training set for a maximum entropy classifier to identify text features distinguishing relevant from not relevant abstracts. Each document was represented as a set of indicative word, word pair, and entity tagger-derived genomic variation features. When applied to a test set of 200 candidate abstracts, the classifier predicted 88 articles as being relevant; of these, 29 of 32 manuscripts in which manual curation found CDKN2A sequence variants were positively predicted. Thus, the set of potentially useful articles that a manual curator would have to review was reduced by 56%, maintaining 91% recall (sensitivity) and more than doubling precision (positive predictive value). Subsequent expansion of the training set to 494 articles yielded similar precision and recall rates, and comparison of the original and expanded trials demonstrated that the average precision improved with the larger data set. Our results show that automated systems can effectively identify article subsets relevant to a given task and may prove to be powerful tools for the broader research community. This procedure can be readily adapted to any or all genes, organisms, or sets of documents

Automated recognition of malignancy mentions in biomedical literature

BACKGROUND: The rapid proliferation of biomedical text makes it increasingly difficult for researchers to identify, synthesize, and utilize developed knowledge in their fields of interest. Automated information extraction procedures can assist in the acquisition and management of this knowledge. Previous efforts in biomedical text mining have focused primarily upon named entity recognition of well-defined molecular objects such as genes, but less work has been performed to identify disease-related objects and concepts. Furthermore, promise has been tempered by an inability to efficiently scale approaches in ways that minimize manual efforts and still perform with high accuracy. Here, we have applied a machine-learning approach previously successful for identifying molecular entities to a disease concept to determine if the underlying probabilistic model effectively generalizes to unrelated concepts with minimal manual intervention for model retraining. RESULTS: We developed a named entity recognizer (MTag), an entity tagger for recognizing clinical descriptions of malignancy presented in text. The application uses the machine-learning technique Conditional Random Fields with additional domain-specific features. MTag was tested with 1,010 training and 432 evaluation documents pertaining to cancer genomics. Overall, our experiments resulted in 0.85 precision, 0.83 recall, and 0.84 F-measure on the evaluation set. Compared with a baseline system using string matching of text with a neoplasm term list, MTag performed with a much higher recall rate (92.1% vs. 42.1% recall) and demonstrated the ability to learn new patterns. Application of MTag to all MEDLINE abstracts yielded the identification of 580,002 unique and 9,153,340 overall mentions of malignancy. Significantly, addition of an extensive lexicon of malignancy mentions as a feature set for extraction had minimal impact in performance. CONCLUSION: Together, these results suggest that the identification of disparate biomedical entity classes in free text may be achievable with high accuracy and only moderate additional effort for each new application domain

Magnetoelastic coupling in URu2Si2: Probing multipolar correlations in the hidden order state

Time-reversal symmetry and magnetoelastic correlations are probed by means of high-resolution volume dilatometry in URu 2 Si 2 at cryogenic temperatures, and magnetic fields sufficient to suppress the hidden order state at H HO ( T = 0.66 K ) ≃ 35 T. We report a significant magnetoelastic volume expansion at and above H HO ( T ) , and even above T HO , possibly a consequence of field-induced f -electron localization. We investigate in detail the magnetostriction and magnetization as the temperature is reduced across two decades in temperature from 30 K where the system is paramagnetic, to 0.5 K in the realm of the hidden order state. We find a dominant quadratic-in-field dependence Δ L / L ∝ H 2 , a result consistent with a state that is symmetric under time reversal. The data shows, however, an incipient yet unmistakable asymptotic approach to linear ( Δ L / L ∝ 1 − H / H 0 ) for 15 T < H < H HO ( 0.66 K ) ∼ 40 T at the lowest temperatures. We discuss these results in the framework of a Ginzburg-Landau formalism that proposes a complex order parameter for the HO phase to model the ( H , T , p ) phase diagram.Fil: Wartenbe, Mark. National High Magnetic Field Laboratory; Estados Unidos. Florida State University; Estados UnidosFil: Baumbach, Ryan E.. National High Magnetic Field Laboratory; Estados Unidos. Florida State University; Estados UnidosFil: Shekhter, Arkady. National High Magnetic Field Laboratory; Estados Unidos. Florida State University; Estados UnidosFil: Boebinger, Gregory S.. National High Magnetic Field Laboratory; Estados Unidos. Florida State University; Estados UnidosFil: Bauer, Eric D.. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Corvalán Moya, Carolina del Huerto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte; Argentina. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Harrison, Neil. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: McDonald, Ross D.. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Salamon, Myron B.. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Jaime, Marcelo. Los Alamos National High Magnetic Field Laboratory; Estados Unido

SPECT/CT imaging of the lumbar spine in chronic low back pain: a case report

Mechanical low back pain is a common indication for Nuclear Medicine imaging. Whole-body bone scan is a very sensitive but poorly specific study for the detection of metabolic bone abnormalities. The accurate localisation of metabolically active bone disease is often difficult in 2D imaging but single photon emission computed tomography/computed tomography (SPECT/CT) allows accurate diagnosis and anatomic localisation of osteoblastic and osteolytic lesions in 3D imaging. We present a clinical case of a patient referred for evaluation of chronic lower back pain with no history of trauma, spinal surgery, or cancer. Planar whole-body scan showed heterogeneous tracer uptake in the lumbar spine with intense localisation to the right lateral aspect of L3. Integrated SPECT/CT of the lumbar spine detected active bone metabolism in the right L3/L4 facet joint in the presence of minimal signs of degenerative osteoarthrosis on CT images, while a segment demonstrating more gross degenerative changes was more quiescent with only mild tracer uptake. The usefulness of integrated SPECT/CT for anatomical and functional assessment of back pain opens promising opportunities both for multi-disciplinary clinical assessment and treatment for manual therapists and for research into the effectiveness of manual therapies

‘Dead people don’t claim’: A psychopolitical autopsy of UK austerity suicides

One of the symptoms of post financial crisis austerity in the UK has been an increase in the numbers of suicides, especially by people who have experienced welfare reform. This article develops and utilises an analytic framework of psychopolitical autopsy to explore media coverage of ‘austerity suicide’ and to take seriously the psychic life of austerity (internalisation, shame, anxiety), embedding it in a context of social dis-ease. Drawing on three distinct yet interrelated areas of literature (the politics of affect and psychosocial dynamics of welfare, post and anti-colonial psychopolitics, and critical suicidology), the article aims to better understand how austerity ‘kills’. Key findings include understanding austerity suicides as embedded within an affective economy of the anxiety caused by punitive welfare retrenchment, the stigmatisation of being a recipient of benefits, and the internalisation of market logic that assigns value through ‘productivity’ and conceptualises welfare entitlement as economic ‘burden’. The significance of this approach lies in its ability to widen analytic framing of suicide from an individual and psychocentric focus, to illuminate culpability of government reforms while still retaining the complexity of suicide, and thus to provide relevant policy insights about welfare reform

From covariant to canonical formulations of discrete gravity

Starting from an action for discretized gravity we derive a canonical formalism that exactly reproduces the dynamics and (broken) symmetries of the covariant formalism. For linearized Regge calculus on a flat background -- which exhibits exact gauge symmetries -- we derive local and first class constraints for arbitrary triangulated Cauchy surfaces. These constraints have a clear geometric interpretation and are a first step towards obtaining anomaly--free constraint algebras for canonical lattice gravity. Taking higher order dynamics into account the symmetries of the action are broken. This results in consistency conditions on the background gauge parameters arising from the lowest non--linear equations of motion. In the canonical framework the constraints to quadratic order turn out to depend on the background gauge parameters and are therefore pseudo constraints. These considerations are important for connecting path integral and canonical quantizations of gravity, in particular if one attempts a perturbative expansion.Comment: 37 pages, 5 figures (minor modifications, matches published version + updated references

Internal construct validity of the Warwick-Edinburgh Mental Well-being Scale (WEMWBS): a Rasch analysis using data from the Scottish Health Education Population Survey

Background: The Warwick-Edinburgh Mental Well-Being Scale (WEMWBS) was developed to meet demand for instruments to measure mental well-being. It comprises 14 positively phrased Likert-style items and fulfils classic criteria for scale development. We report here the internal construct validity of WEMWBS from the perspective of the Rasch measurement model. Methods: The model was applied to data collected from 779 respondents in Wave 12 (Autumn 2006) of the Scottish Health Education Population Survey. Respondents were aged 16–74 (average 41.9) yrs. Results: Initial fit to model expectations was poor. The items 'I've been feeling good about myself', 'I've been interested in new things' and 'I've been feeling cheerful' all showed significant misfit to model expectations, and were deleted. This led to a marginal improvement in fit to the model. After further analysis, more items were deleted and a strict unidimensional seven item scale (the Short Warwick Edinburgh Mental Well-Being Scale (SWEMWBS)) was resolved. Many items deleted because of misfit with model expectations showed considerable bias for gender. Two retained items also demonstrated bias for gender but, at the scale level, cancelled out. One further retained item 'I've been feeling optimistic about the future' showed bias for age. The correlation between the 14 item and 7 item versions was 0.954. Given fit to the Rasch model, and strict unidimensionality, SWEMWBS provides an interval scale estimate of mental well-being. Conclusion: A short 7 item version of WEMWBS was found to satisfy the strict unidimensionality expectations of the Rasch model, and be largely free of bias. This scale, SWEMWBS, provides a raw score-interval scale transformation for use in parametric procedures. In terms of face validity, SWEMWBS presents a more restricted view of mental well-being than the 14 item WEMWBS, with most items representing aspects of psychological and eudemonic well-being, and few covering hedonic well-being or affect. However, robust measurement properties combined with brevity make SWEMWBS preferable to WEMWBS at present for monitoring mental well-being in populations. Where face validity is an issue there remain arguments for continuing to collect data on the full 14 item WEMWBS

From absent to present pasts: civil society, democracy and the shifting place of memory in Brazil

This paper takes Alexis de Tocqueville’s concern with the emotional life of citizens as a cue for exploring the role of collective memory within ‘the self-organizing sphere’ and asking how the invocation of memory affects progress towards democracy. The paper hones in on the Brazilian experience, re-assessing Brazil’s amnesiac past as well as its much lauded ‘turn to memory’. Against common assertions that Brazil’s ‘turn to memory’ will enhance the country’s democratic credentials, this paper argues that the move from an ‘absent’ to a ‘present’ past in Brazil in fact bodes rather mixed prospects for the country’s democratic deepening

A Regional Initiative to Reduce Skin Infections amongst Aboriginal Children Living in Remote Communities of the Northern Territory, Australia

Skin infections are endemic in many in remote Australian Aboriginal communities and have been linked to very high rates of chronic heart and kidney disease in this population. We report the results of a regional collaboration that aimed to reduce skin infections amongst children aged less than 15 years in five remote communities. The program included annual mass scabies treatment days offered to all residents and routine screening/follow-up of children. Trained community workers helped conduct over 6000 skin assessments on 2329 children over a three year period. Of every 100 children seen at the commencement of the study, 47 were found to have skin sores and many had multiple sores. We demonstrate a reduction both in the number of children with skin sores and in the severity of those sores. On average, of every 100 children seen per month, there were 14 fewer children with skin sores and seven fewer children with multiple sores. Overall improvement in treatment uptake was a critical factor. We found no discernible impact against scabies. While the burden of skin infections remains unacceptably high, we believe the results presented here are a good news story for local action to address a serious public health problem