Hypothesizing mechanistic links between microbes and disease using knowledge graphs

Knowledge graphs have found broad biomedical applications, providing useful representations of complex knowledge. Although plentiful evidence exists linking the gut microbiome to disease, mechanistic understanding of those relationships remains generally elusive. Here we demonstrate the potential of knowledge graphs to hypothesize plausible mechanistic accounts of host-microbe interactions in disease. To do so, we constructed a knowledge graph of linked microbes, genes and metabolites called MGMLink. Using a semantically constrained shortest path search through the graph and a novel path prioritization methodology based on cosine similarity, we show that this knowledge supports inference of mechanistic hypotheses that explain observed relationships between microbes and disease phenotypes. We discuss specific applications of this methodology in inflammatory bowel disease and Parkinson's disease. This approach enables mechanistic hypotheses surrounding the complex interactions between gut microbes and disease to be generated in a scalable and comprehensive manner.

Pulmonary hypertension in adults completing tuberculosis treatment

Background

Pulmonary hypertension (PH) after tuberculosis (TB) is typically not included among the chronic lung diseases causing PH (group 3 PH), with few data available to support the inclusion.

Objectives

To determine the prevalence of PH in an adult population completing TB treatment.

Methods

This single-centre, cross-sectional study only included patients with their first documented episode of TB, and who were in the second half of treatment or had recently completed treatment. PH was assessed using transthoracic echocardiography. Questionnaires were completed, and spirometry and a 6-minute walk test were performed.

Results

One hundred patients were enrolled, with a mean age of 37.1 years, of whom 58% were male and 46% HIV positive. The median time since initiation of TB treatment was 22 weeks. The mean (standard deviation) measured right ventricular systolic pressure (RVSP) was 23.6 (6.24) mmHg. One participant had PH (defined as RVSP ≥40 mmHg; 95% confidence interval (CI) 0.0 - 3.0) and a further 3 had possible PH (RVSP ≥35 and <40 mmHg), with a combined PH prevalence of 4% (95% CI 0.2 - 7.8). Airflow obstruction on spirometry was found in 13.3% of 98 patients, while 25.5% had a reduced forced vital capacity. There was no association between RVSP or PH/possible PH and sex, age, HIV status, systemic hypertension, spirometry measurements or 6-minute walking distance. Smoking status was associated with RVSP, but not with the presence of PH/possible PH.

Conclusion

There was a significant prevalence of PH in this preliminary study of predominantly young patients completing treatment for a first episode of TB. Larger and more detailed studies are warranted.

Study synopsis

What the study adds. Of 100 adult patients with their first episode of tuberculosis (TB) who underwent echocardiograms near the end of treatment completion to determine the prevalence of pulmonary hypertension (PH), 1 (1%) had PH and a further 3 (3%) had possible PH. There was no association between sex, age, HIV status, lung function or 6-minute walking distance and the presence of PH. The study adds to the growing awareness of the association of TB with pulmonary vascular disease. It shows that even in a young population with a first episode of TB treated in an ambulatory setting, there is a significant prevalence of PH on treatment completion.Implications of the findings. Given that 10.6 million people acquire TB annually, the absolute global burden of cases with PH is likely to be high, but is underappreciated to date. Further work is urgently needed in this field.

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

BETA: a comprehensive benchmark for computational drug-target prediction

Internal validation is the most popular evaluation strategy used for drug-target predictive models. The simple random shuffling in the cross-validation, however, is not always ideal to handle large, diverse and copious datasets as it could potentially introduce bias. Hence, these predictive models cannot be comprehensively evaluated to provide insight into their general performance on a variety of use-cases (e.g. permutations of different levels of connectiveness and categories in drug and target space, as well as validations based on different data sources). In this work, we introduce a benchmark, BETA, that aims to address this gap by (i) providing an extensive multipartite network consisting of 0.97 million biomedical concepts and 8.5 million associations, in addition to 62 million drug-drug and protein-protein similarities and (ii) presenting evaluation strategies that reflect seven cases (i.e. general, screening with different connectivity, target and drug screening based on categories, searching for specific drugs and targets and drug repurposing for specific diseases), a total of seven Tests (consisting of 344 Tasks in total) across multiple sampling and validation strategies. Six state-of-the-art methods covering two broad input data types (chemical structure- and gene sequence-based and network-based) were tested across all the developed Tasks. The best-worst performing cases have been analyzed to demonstrate the ability of the proposed benchmark to identify limitations of the tested methods for running over the benchmark tasks. The results highlight BETA as a benchmark in the selection of computational strategies for drug repurposing and target discovery.

A comparison of trauma scoring systems for injuries presenting to a district-level urban public hospital in Western Cape

BACKGROUND

Trauma is a major public health issue and has an extensive burden on the health system in South Africa. Many trauma scoring systems have been developed to estimate trauma severity and predict mortality. The prediction of mortality between different trauma scoring systems have not been compared at district-level health facilities in South Africa. The objective was to compare four trauma scoring systems (injury severity score (ISS), revised trauma score (RTS), Kampala trauma score (KTS), trauma and injury severity score (TRISS)) in predicting mortality in trauma-related patients presenting to a district-level hospital in Cape Town.

METHODS

A retrospective analysis of all trauma patients managed in the resuscitation unit of Khayelitsha Hospital during a six-month period. Logistic regression was done, and empirical cut-off points used to maximise sensitivity and specificity on receiver operating characteristic curves. The outcome was all-cause in-hospital mortality.

RESULTS

In total, 868 participants were analysed after 50 were excluded due to missing data. The mean (± SD) age was 28 ± 11 years, 726 (83.6%) were males, and penetrating injuries (n = 492, 56.6%) dominated. The mortality rate was 5.2% (n = 45). TRISS was the best mortality predictor (c-statistic 0.93, sensitivity 90%, specificity 87%). All scoring systems had overlapping confidence intervals.

CONCLUSION

TRISS, ISS, RTS and KTS performed equivocally in predicting mortality in trauma-related patients managed at a district-level facility. The appropriate scoring system should be the simplest one which can be practically implemented and will likely differ between facilities.

Clinical and cost implications of using immediate MRI in the management of patients with a suspected scaphoid fracture and negative radiographs results from the SMaRT trial

AIMS

The aim of the Scaphoid Magnetic Resonance Imaging in Trauma (SMaRT) trial was to evaluate the clinical and cost implications of using immediate MRI in the acute management of patients with a suspected fracture of the scaphoid with negative radiographs.

PATIENTS AND METHODS

Patients who presented to the emergency department (ED) with a suspected fracture of the scaphoid and negative radiographs were randomized to a control group, who did not undergo further imaging in the ED, or an intervention group, who had an MRI of the wrist as an additional test during the initial ED attendance. Most participants were male (52% control, 61% intervention), with a mean age of 36.2 years (18 to 73) in the control group and 38.2 years (20 to 71) in the intervention group. The primary outcome was total cost impact at three months post-recruitment. Secondary outcomes included total costs at six months, the assessment of clinical findings, diagnostic accuracy, and the participants' self-reported level of satisfaction. Differences in cost were estimated using generalized linear models with gamma errors.

RESULTS

The mean cost up to three months post-recruitment per participant was £542.40 (sd £855.20, n = 65) for the control group and £368.40 (sd £338.60, n = 67) for the intervention group, leading to an estimated cost difference of £174 (95% confidence interval (CI) -£30 to £378; p = 0.094). The cost difference per participant increased to £266 (95% CI £3.30 to £528; p = 0.047) at six months. Overall, 6.2% of participants (4/65, control group) and 10.4% of participants (7/67, intervention group) had sustained a fracture of the scaphoid (p = 0.37). In addition, 7.7% of participants (5/65, control group) and 22.4% of participants (15/67, intervention group) had other fractures diagnosed (p = 0.019). The use of MRI was associated with higher diagnostic accuracy both in the diagnosis of a fracture of the scaphoid (100.0% vs 93.8%) and of any other fracture (98.5% vs 84.6%).

CONCLUSION

The use of immediate MRI in the management of participants with a suspected fracture of the scaphoid and negative radiographs led to cost savings while improving the pathway's diagnostic accuracy and patient satisfaction. Cite this article: Bone Joint J 2019;101-B:984-994.

Biosurveillance: a systematic review of global infectious disease surveillance systems from 1900 to 2016

Biosurveillance is crucial to detect, identify and minimise the negative consequences of infectious disease. Its value to society and importance to global public health and global health security are growing. Despite the long history and global importance of biosurveillance, a systematic review of all existing biosurveillance systems across the 'One Health' spectrum has not yet been published. This study conducted a systematic review to identify all extant and defunct biosurveillance systems from 1900 to 2016. Of the 815 systems examined, the majority surveyed human, animal or plant data discretely. Some 105 collected human and animal data, whereas only 31 collected data on all three categories. The authors found a large increase in the number of global biosurveillance systems between 1900 and 2008, but a reduction in the number of biosurveillance systems from 2008 to the present. The number of syndromic systems created, versus laboratory-based biosurveillance systems, increased rapidly after 1980 across the globe.

Myocardial deformation in fetuses with coarctation of the aorta: a case-control study

OBJECTIVE

To study myocardial deformation by speckle tracking echocardiography in fetuses with coarctation of the aorta (CoA) compared with gestational age-matched normal controls.

METHODS

This was a retrospective study of 12 fetuses with postnatally confirmed CoA and 12 gestational age-matched controls seen at a tertiary fetal cardiology unit between January 2013 and July 2014. Two-dimensional speckle tracking in standard grayscale four-chamber view of the fetal heart was performed to assess left and right myocardial deformation. Global longitudinal strain, strain rate and velocities, and regional longitudinal strain were analyzed and compared with controls.

RESULTS

Median gestational age at echocardiography was 25 + 4 weeks. Fetuses with CoA presented with a narrower, but not shorter, left ventricle when compared with controls (mitral valve diastolic diameter, 5.90 vs 8.50 mm; P = 0.002; left ventricular diastolic length, 16.50 vs 18.50 mm; P = 0.05). Global longitudinal systolic strain (P = 0.004), systolic strain rate (P = 0.01) and diastolic strain rate (P = 0.004) of the left ventricle were significantly lower in fetuses with CoA compared with controls. Similar findings were observed for longitudinal systolic (P = 0.03) and diastolic (P = 0.01) velocities of the left ventricle. Right ventricular parameters were not different between groups.

CONCLUSIONS

Fetuses with CoA have lower left ventricular longitudinal systolic strain, systolic strain rate and diastolic strain rate when compared with gestational age-matched control fetuses. These differences in deformation might explain, at least in part, the cardiac asymmetry observed in fetuses with CoA. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.

Aging promotes acquisition of naive-like CD8+ memory T cell traits and enhanced functionalities

Protective T cell memory is an acquired trait that is contingent upon the preservation of its constituents and therefore vulnerable to the potentially deleterious effects of organismal aging. Here, however, we have found that long-term T cell memory in a natural murine host-pathogen system can substantially improve over time. Comprehensive molecular, phenotypic, and functional profiling of aging antiviral CD8+ memory T cells (CD8+ TM) revealed a pervasive remodeling process that promotes the gradual acquisition of distinct molecular signatures, of increasingly homogeneous phenotypes, and of diversified functionalities that combine to confer a CD8+ TM-autonomous capacity for enhanced recall responses and immune protection. Notably, the process of CD8+ TM aging is characterized by a progressive harmonization of memory and naive T cell traits, is broadly amenable to experimental acceleration or retardation, and serves as a constitutional component for the "rebound model" of memory T cell maturation. By casting CD8+ TM populations within the temporal framework of their slowly evolving properties, this model establishes a simple ontogenetic perspective on the principal organization of CD8+ T cell memory that may directly inform the development of improved diagnostic, prophylactic, and therapeutic modalities.

The Relationship between Socioeconomic Status and Household Smoking Patterns in Canada

This report uses data from a 1986 Labour Force Survey (LFS) smoking supplement to examine the relationship between education and smoking prevalence within Canadian households and the influence of parental smoking behavior on the smoking behavior of their children. The sample was a national probability sample of 14,469 households and 30,000 respondents.

Over one in two (54 %) Canadian children are exposed to the presence of at least one adult smoker in the household. Parents and children within lower socioeconomic groups are more likely to be regular smokers than their counterparts in upper socioeconomic groups. Children in lower socioeconomic households are three times more likely to be exposed to a family environment in which both parents smoke than children in upper socioeconomic level households. At all socioeconomic levels, there is a gradient in the smoking prevalence among youth and young adults according to parental smoking behavior.

The patterns of smoking within households suggest the possibility of increasing divergence in smoking rates between socioeconomic groups. The findings are discussed in terms of epidemiological and health promotion implications.

Miliary tuberculosis: sonographic pattern in chest ultrasound

Miliary tuberculosis (TB) is characterized by a multitude of small nodular opacities on chest radiography. Despite ultrasound of the chest gaining wider acceptance as a diagnostic tool of lung infections, sonographic changes of pulmonary miliary TB have not yet been reported. Here, we describe B-lines and comet-tail artifacts disseminated throughout multiple lung areas and a pattern of sub-pleural granularity as consistent changes seen in lung ultrasound of ten patients with pulmonary miliary TB diagnosed by chest radiography.

Analysis of anonymized pooled urine in nine UK cities: variation in classical recreational drug, novel psychoactive substance and anabolic steroid use

BACKGROUND

Analysis of anonymous pooled urine samples from street urinals has been used to demonstrate time-trends in the detection of classical recreational drugs and novel psychoactive substances (NPS).

AIM

This study aimed to expand this to undertake a geographical trend analysis of classical recreational drugs/NPS across UK.

METHODS

Samples of anonymous pooled urine were collected from street urinals that had been in place for one night in April 2014 in nine cities across the UK. Collected samples were then analysed for the presence of recreational drugs, NPS anabolic steroids using high-performance liquid chromatography coupled to high-resolution accurate mass full-scan mass spectrometry and gas chromatography coupled to electron impact ionization mass spectrometry operating in selected ion monitoring and full-scan modes.

RESULTS

Ten classical recreational drugs, nine NPS and four anabolic steroids were detected across the nine cities; the range of detection was from 1 in Leeds to 14 in London. The most common classical drugs were cocaine (9 cities) and 3,4-methylenedioxy-methamphetamine (8 cities); the most common NPS was 4-methylmethcathinone (5 cities). In addition there was variation in the detection of NPS, with methylhexaneamine detected only in Bristol and London, piperazines (3-trifluoromethylphenylpiperazine and 1-benzylpiperazine) and pentedrone only detected in Birmingham and the cathinone methylone only detected in London.

CONCLUSIONS

There is variability in the detection of classical recreational drugs, NPS and anabolic steroids across UK, likely reflecting variation in their use. This technique can be used to supplement drug use surveys to determine geographical and time trends in the use of these substances. This is important to ensure appropriate targeting of drug-related interventions.

Natural-orifice transluminal endoscopic surgery

BACKGROUND

Natural-orifice transluminal endoscopic surgery (NOTES) represents one of the most significant innovations in surgery to emerge since the advent of laparoscopy. A decade of progress with this approach has now been catalogued, and yet its clinical application remains controversial.

METHODS

A PubMed search was carried out for articles describing NOTES in both the preclinical and the clinical setting. Public perceptions and expert opinion regarding NOTES in the published literature were analysed carefully.

RESULTS

Two hundred relevant articles on NOTES were studied and the outcomes reviewed. A division between direct- and indirect-target NOTES was established. The areas with the most promising clinical application included direct-target NOTES, such as transanal total mesorectal excision and peroral endoscopic myotomy. The clinical experience with distant-target NOTES, such as for appendicectomy and cholecystectomy, showed feasibility; however, NOTES-specific morbidity was introduced and this represents an important limitation.

CONCLUSION

NOTES experimentation in the preclinical setting has increased substantially. There has also been a significant increase in the application of NOTES in humans in the past decade. Enthusiasm for NOTES should be tempered by the risk of incurring NOTES-specific morbidity. Surgeons should carefully consider patient preferences regarding this new minimally invasive option, as opinions are not unanimously supportive of NOTES. As technical limitations are overcome, the clinical application of NOTES is predicted to increase. It is paramount that, when this complex technique is performed on humans, it is applied judiciously by appropriately trained experts with outcomes recorded in a registry.

Prenatal echocardiographic diagnosis of double aortic arch

A double aortic arch is a congenital anomaly associated with the formation of a vascular ring, which can cause varying degrees of airway compression. This can be subclinical or clinical, manifesting as acute stridor, severe respiratory compromise or symptoms of chronic airway compression. An accurate diagnosis of double aortic arch can be made prenatally by fetal echocardiography. In this report, we describe two infants with normal karyotypes in whom a prenatal diagnosis of double aortic arch was made at our fetal cardiology center, between July 2012 and August 2013. The diagnosis was confirmed postnatally by two-dimensional echocardiography and cardiac magnetic resonance imaging (MRI). The presence of a right aortic arch should prompt more careful evaluation to exclude a double aortic arch. Postnatal assessment should comprise echocardiography and cross-sectional imaging in the form of cardiac MRI/computed tomography. Bronchoscopy may be considered to exclude subclinical airway compression and reduce potential long-term respiratory sequelae.

Negotiating a Text Mining License for Faculty Researchers

<p>This case study examines strategies used to leverage the library’s existing journal licenses to obtain a large collection of full-text journal articles in extensible markup language (XML) format; the right to text mine the collection; and the right to use the collection and the data mined from it for grant-funded research to develop biomedical natural language processing (BNLP) tools. Researchers attempted to obtain content directly from PubMed Central (PMC). This attempt failed due to limits on use of content in PMC. Next researchers and their library liaison attempted to obtain content from contacts in the technical divisions of the publishing industry. This resulted in an incomplete research data set. Then researchers, the library liaison, and the acquisitions librarian collaborated with the sales and technical staff of a major science, technology, engineering, and medical (STEM) publisher to successfully create a method for obtaining XML content as an extension of the library’s typical acquisition process for electronic resources. Our experience led us to realize that text mining rights of full-text articles in XML format should routinely be included in the negotiation of the library’s licenses.</p>

A systematic review of transanal minimally invasive surgery (TAMIS) from 2010 to 2013

Transanal minimally invasive surgery (TAMIS) was introduced as an alternative to transanal endoscopic microsurgery in 2010. Over the past 4 years, considerable international experience has been gained with this approach. Most published reports focus on TAMIS for local excision of rectal neoplasia, but there are other important applications such as transanal mesorectal excision for rectal cancer. This comprehensive review details the progress with TAMIS since its inception. Robotic transanal surgery is a natural evolution of TAMIS still in its early infancy, which is also reviewed. A comprehensive search of PubMed, EMBASE, the Cochrane Library, and Web of Knowledge was performed. Since the inception of TAMIS in 2009, 33 retrospective studies and case reports, and 3 abstracts have been published on TAMIS for local excision of rectal neoplasms, which represents a combined n = 390 TAMIS procedures performed worldwide using eight different types of TAMIS platforms. A total of 152 lesions were excised for benign disease including adenomas and high-grade dysplasias (39 %), 209 for malignancy for carcinomas in situ and adenocarcinomas (53.5 %). Twenty-nine (7.5 %) of TAMIS resections were for other pathology, of which the majority (23/29) were neuroendocrine lesions. The remaining resections were for mucocele, gastrointestinal stromal tumor, melanoma, and fibrosis. Robotic-TAMIS has also been reported, however, data are extremely limited as there are only 7 case reports (combined n = 11) in the published literature. Success with Robotic-TAMIS has been demonstrated with various patient positions and by use of a special glove port. Transanal total mesorectal excision using the TAMIS platform has also been demonstrated is several small series, and the feasibility of performing pure transanal total mesorectal excision has also been reported. Combined, n = 78 cases of transanal total mesorectal excision have been performed using TAMIS. The advantages of TAMIS-assisted transanal total mesorectal excision are discussed.

Transanal minimally invasive surgery for total mesorectal excision (TAMIS-TME): results and experience with the first 20 patients undergoing curative-intent rectal cancer surgery at a single institution

BACKGROUND

Transanal TME is a new approach to performing minimally invasive rectal resection. It is particularly well suited for patients with locally advanced distal rectal cancer and obesity, where the abdominal approach is challenging. Transanal TME can be performed with either TAMIS or TEM. Here, we report our initial experience with transanal TME using TAMIS (TAMIS-TME).

METHODS

Patients were selected to undergo transanal TME using the TAMIS platform (TAMIS-TME) primarily for malignant disease, but also for select cases of benign disease. Transanal TME defines a "bottom-up" approach to en bloc rectal cancer resection. Transanal TME requires abdominal access for proximal colonic mobilization and is often done in conjunction with a laparoscopic approach.

RESULTS

During a 32-month period, 20 patients underwent TAMIS-TME with curative intent. The primary indication for transanal TME was distal, locally advanced rectal cancer. The median age of rectal cancer patients at the time of surgery was 57 years (range 36-73 years) with 30% (6) female and 70% (14) male. The median body mass index (BMI) measured was 24 kg/m(2) (range 18-41 kg/m(2)); this included six patients (30%) with obesity (BMI ≥ 30 kg/m(2)). Mean operating time was 243 min (range 140-495 min) with blood loss averaging 153 ml. Postoperative length of stay averaged 4.5 days (range 3-24 days). There was no 30-day postoperative mortality. Surgical complications included wound infection (n = 2), pelvic abscess (n = 4), and prolonged ileus (n = 4). The anastomotic leak rate was 6.7% (1/15). Of the 20 patients who underwent resection, 90% (18/20) had negative margins. Pathologic grading of the TME specimen revealed that 85% (17/20) of transanal TME specimens were found to have "completely" or "near-completely" intact mesorectal envelopes. Data collected during the 6-month median follow-up period revealed that only one patient had developed distant metastasis. There was no locoregional recurrence in any of the patients.

CONCLUSIONS

Transanal TME is a feasible method for oncologic resection of locally advanced mid- and distal-rectal cancer with curative intent. It has special application for patients with obesity and anatomic constraints such as a narrow male pelvis.

Teaching research ethics better: focus on excellent science, not bad scientists

A recent report of the United States' Presidential Commission for the Study of Bioethical Issues highlights how important it is for the research community to enjoy the "earned confidence" of the public and how creating a "culture of responsibility" can contribute to that confidence. It identifies a major role for "creative, flexible, and innovative" ethics education in creating such a culture. Other recent governmental reports from various nations similarly call for a renewed emphasis on ethics education in the sciences. We discuss why some common approaches to ethics education in the graduate sciences fail to meet the goals envisioned in the reports and we describe an approach, animated by primary attention on excellent science as opposed to bad scientists, that we have employed in our ethics teaching that we think is better suited for inspiring and sustaining responsible, trustworthy science.

Approximate subgraph matching-based literature mining for biomedical events and relations

The biomedical text mining community has focused on developing techniques to automatically extract important relations between biological components and semantic events involving genes or proteins from literature. In this paper, we propose a novel approach for mining relations and events in the biomedical literature using approximate subgraph matching. Extraction of such knowledge is performed by searching for an approximate subgraph isomorphism between key contextual dependencies and input sentence graphs. Our approach significantly increases the chance of retrieving relations or events encoded within complex dependency contexts by introducing error tolerance into the graph matching process, while maintaining the extraction precision at a high level. When evaluated on practical tasks, it achieves a 51.12% F-score in extracting nine types of biological events on the GE task of the BioNLP-ST 2011 and an 84.22% F-score in detecting protein-residue associations. The performance is comparable to the reported systems across these tasks, and thus demonstrates the generalizability of our proposed approach.

Regional differences in subcutaneous adipose tissue gene expression

Adipose tissue (AT) located in the viscera is considered to be functionally and metabolically different from that found in the subcutaneous depot. However, subcutaneous AT (SAT) in generalized regions is considered to be homogeneous in nature. Affymetrix GeneChip Human Exon 1.0 ST Arrays were used to determine differential gene expression in four subcutaneous adipose depots (upper abdomen, lower abdomen, flank and hip) in normal weight women. A total of 2,890/24,409 transcripts were differentially expressed between all sites. When comparing the hip and flank to the lower abdomen, 248 and 83 genes were differentially expressed, respectively. When comparing the hip and flank to the upper abdomen, 2,480 and 79 genes were differentially expressed, respectively. No genes were significantly different when the lower abdomen was compared to the upper abdomen and the hip to the flank. Genes involved in the complement and coagulation cascades and immune responses showed increased expression in the lower abdomen compared to the flank. In addition, two genes involved in the complement and coagulation cascade, CR1 and C7, were expressed more highly in the lower abdomen compared to the hip. Genes involved in basic biochemical metabolism including insulin signaling, the urea cycle, glutamate metabolism, arginine and proline metabolism and aminosugar metabolism had higher expression in the lower abdomen compared to the hip. These results in normal weight healthy women provide a new perspective on regional differences in SAT biology that may have pathophysiologic implications when adiposity increases.

Limited use of novel psychoactive substances in South London nightclubs

BACKGROUND

There has been significant media interest in the use of novel psychoactive substances (also known as 'legal highs') and reports in the medical literature of toxicity associated with their use. However, most surveys of recreational drug use focus on classical drugs such as cocaine and ecstasy, and there is limited information on how commonly emerging novel psychoactive substances are used.

AIM

To collect data on use prevalence patterns of a wider range of novel psychoactive substances in South London gay nightclubs.

DESIGN

Questionnaire survey.

METHODS

Individuals attending gay-friendly nightclubs in South East London (July 2011) were asked about life-time use, last month use and/or use on the night of the survey/planned use later that night of novel psychoactive substances, cocaine and MDMA/ecstasy.

RESULTS

A total of 313 individuals were surveyed over 4 nights; 206 (65.8%) had previously used a 'legal high'. Mephedrone had the highest prevalence of last month use (53.2%) and use on the night of the survey (41.0%). This was greater than both cocaine (44.6% and 16.7%, respectively) and MDMA/ecstasy (26.9% and 5.8%). There was limited on the night use of the non-mephedrone 'legal highs': methoxetamine (1.6%) and 1-benzylpiperazine (0.6%), Spice/K2 (0.6%) and pipradrols (0.6%).

CONCLUSION

Although a significant proportion of individuals report previous use of novel psychoactive substances, it seems that only mephedrone has become an established part of the recreational drug scene. It is important that there is a considered approach to determining the utilization of drug prevention/education and enforcement budgets to ensure that this is appropriately targeted to drugs that are used recreationally.

Evidence-based prevention: a comparison of oral hygiene advice given by dental and dental care professional students

AIM

This study aimed to examine the oral hygiene advice given by student dentists and dental care professionals (DCPs), focussing on adherence to evidence-based recommendations provided by the Department of Health and the Scottish Intercollegiate Guidelines Network.

METHOD

A self-administered questionnaire was distributed to 121 fourth- and fifth-year dental undergraduates and 38 hygiene/combined dental hygiene and dental therapy students at a UK dental school.

RESULTS

Completed questionnaires were returned by 39/64 fourth-year and 36/57 fifth-year dental students and 23/38 student DCPs, an overall response rate of 61.6%. Only 48% (36) of dental undergraduates in comparison with 95.7% (22) of DCP students stated that they would give oral hygiene advice to every adult patient (P<0.001). In addition, only 24 (32%) responding dental students were able to accurately state the recommended fluoride toothpaste concentration for adult use; this contrasts with 18 (78.3%) student DCPs. Dental undergraduates tended to accord less importance to oral hygiene advice when compared with student DCPs, only providing it when they felt it was clinically necessary.

CONCLUSIONS

The role of the dental practitioner in providing oral health education requires greater emphasis in the undergraduate curriculum. Given the unfavourable comparison between the attitude and knowledge of dental students and that of DCPs, prequalification training for the dental team should be integrated wherever possible. The apparent lack of awareness of current guidelines is of concern.

SU-E-J-186: CT Textures Can be Predictive for Tumor Shrinkage

PURPOSE

To determine if NSCLC GTV CT textures can be predictive for tumor shrinkage after proton therapy with concurrent chemotherapy.

METHODS

Simulation and weekly 4DCTs were obtained from 25 patients with locally advanced NSCLC treated by proton therapy at a 74 Gy dose level with concurrent chemotherapy. In-house deformable image registration software based on the demons algorithm propagated the physician-generated planning GTV onto each weekly image set. GTV soft tissue volumes were then extracted from CT images by in-house software which pruned out voxels below a cutoff HU threshold. Patients whose normalized end-treatment pruned GTV was less than the group median were classified as 'strong responders.'The remaining patients were classified as 'weak responders.' For each pruned GTV, the MaZda texture analysis software generated quantitative 3D texture features based on the image histogram, absolute gradient, co-occurrence matrix, and run-length matrix. Using the Fisher coefficient, a subset of these texture features that were relevant to distinguishing the two response groups was obtained. In-house software and MaZda were then used to perform neural network data classification with leave-one-out cross-validation based on this texture feature subset. The true positive rate (TPR), false positive rate (FPR), classification accuracy, and one-sided p-values were recorded.

RESULTS

Six classification models were tested. Each model had a unique combination of feature extraction and analysis parameters. Taking 'strong responders' to be the 'positive' class, the average TPR was 0.66 (0.60 - 0.75), the average FPR was 0.36 (0.31 - 0.40), the average classification accuracy was 64.8% (60.0% - 68.0%), and the average one-sided p-value was 0.118 (0.055 - 0.215).

CONCLUSIONS

There is some evidence showing that NSCLC GTV CT textures can be predictive for tumor shrinkage after proton therapy. Further work should be done to include more patients, texture metrics, and data analysis techniques. The presenting author receives funding support from a Hertz Foundation Applied Science Fellowship.

Adipose tissue-derived adiponectin expression is significantly associated with increased post operative mortality in horses undergoing emergency abdominal surgery

REASONS FOR PERFORMING STUDY

Adipose tissue is an important source of inflammatory cytokines (adipokines) and adiposity has been identified as having a significant effect on human morbidity and mortality. Obesity is also an emerging welfare problem in the UK horse population, but the role that it plays in secondary diseases is unclear.

OBJECTIVES

To examine the expression of inflammation-related adipokine genes in retroperitoneal adipose tissue of horses undergoing emergency abdominal surgery and to explore associations with adiposity and post operative survival.

METHODS

Retroperitoneal adipose tissue samples were obtained from 76 horses undergoing emergency abdominal surgery. Real-time PCR was used to measure gene expression for leptin, adiponectin, tumour necrosis factor-alpha, macrophage chemoattractant protein-1, macrophage inhibitory factor, serum amyloid A, haptoglobin and interleukin-1. Multivariate patterns of adipokine expression were explored with principal component analysis (PCA), whilst univariable associations with post operative survival were tested in a Cox proportional hazards model.

RESULTS

Leptin gene expression was higher in overweight and obese horses than in lean animals. Expression of mRNA encoding adiponectin mRNA in visceral adipose tissue was positively associated with increased post operative mortality (hazard ratio 1.31, 95% CI 1.05-1.65). However, PCA did not demonstrate multivariable patterns of adipokine gene expression from visceral adipose tissue associated with body mass index or with survival.

CONCLUSIONS

In horses presented with acute intestinal disease, increased adiponectin gene expression from retroperitoneal adipose tissue is associated with an increased risk of mortality. Obesity assessed by BMI had no association with increased post operative mortality in horses with primary gastrointestinal disease.

POTENTIAL RELEVANCE

Further study is warranted on the expression and effects of adipokines, particularly adiponectin, and correlation with postoperative outcome.

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA

We approached the problems of event detection, argument identification, and negation and speculation detection in the BioNLP'09 information extraction challenge through concept recognition and analysis. Our methodology involved using the OpenDMAP semantic parser with manually written rules. The original OpenDMAP system was updated for this challenge with a broad ontology defined for the events of interest, new linguistic patterns for those events, and specialized coordination handling. We achieved state-of-the-art precision for two of the three tasks, scoring the highest of 24 teams at precision of 71.81 on Task 1 and the highest of 6 teams at precision of 70.97 on Task 2. We provide a detailed analysis of the training data and show that a number of trigger words were ambiguous as to event type, even when their arguments are constrained by semantic class. The data is also shown to have a number of missing annotations. Analysis of a sampling of the comparatively small number of false positives returned by our system shows that major causes of this type of error were failing to recognize second themes in two-theme events, failing to recognize events when they were the arguments to other events, failure to recognize nontheme arguments, and sentence segmentation errors. We show that specifically handling coordination had a small but important impact on the overall performance of the system. The OpenDMAP system and the rule set are available at http://bionlp.sourceforge.net.

11-Hydroxy-β-steroid dehydrogenase gene expression in canine adipose tissue and adipocytes: stimulation by lipopolysaccharide and tumor necrosis factor α

The enzyme 11β-hydroxysteroid dehydrogenase 1 (11β-HSD-1) is expressed in a number of tissues in rodents and humans and is responsible for the reactivation of inert cortisone into cortisol. Its gene expression and activity are increased in white adipose tissue (WAT) from obese humans and may contribute to the adverse metabolic consequences of obesity and the metabolic syndrome. The extent to which 11β-HSD-1 contributes to adipose tissue function in dogs is unknown; the aim of the present study was to examine 11β-HSD-1 gene expression and its regulation by proinflammatory and anti-inflammatory agents in canine adipocytes. Real-time PCR was used to examine the expression of 11β-HSD-1 in canine adipose tissue and canine adipocytes differentiated in culture. The mRNA encoding 11β-HSD-1 was identified in all the major WAT depots in dogs and also in liver, kidney, and spleen. Quantification by real-time PCR showed that 11β-HSD-1 mRNA was least in perirenal and falciform depots and greatest in subcutaneous, omental, and gonadal depots. Greater expression was seen in the omental depot in female than in male dogs (P=0.05). Gene expression for 11β-HSD-1 was also seen in adipocytes, from both subcutaneous and visceral depots, differentiated in culture; expression was evident throughout differentiation but was generally greatest in preadipocytes and during early differentiation, declining as cells progressed to maturity. The inflammatory mediators lipopolysaccharide and tumor necrosis factor α had a main stimulatory effect on 11β-HSD-1 gene expression in canine subcutaneous adipocytes, but IL-6 had no significant effect. Treatment with dexamethasone resulted in a significant time- and dose-dependent increase in 11β-HSD-1 gene expression, with greatest effects seen at 24 h (2 nM: approximately 4-fold; 20 nM: approximately 14-fold; P=0.010 for both). When subcutaneous adipocytes were treated with the peroxisome proliferator activated receptor γ agonist rosiglitazone, similar dose- and time-dependent effects were noted. However, no effects were seen when adipocytes from the gonadal WAT depot were treated with rosiglitazone. The induction of 11β-HSD-1 expression, by the pro-inflammatory cytokine tumor necrosis factor α and by lipopolysaccharide may have implications for the pathogenesis of obesity and its associated diseases in the dog.