A novel framework for biomedical entity sense induction

BACKGROUND

Rapid advancements in biomedical research have accelerated the number of relevant electronic documents published online, ranging from scholarly articles to news, blogs, and user-generated social media content. Nevertheless, the vast amount of this information is poorly organized, making it difficult to navigate. Emerging technologies such as ontologies and knowledge bases (KBs) could help organize and track the information associated with biomedical research developments. A major challenge in the automatic construction of ontologies and KBs is the identification of words with its respective sense(s) from a free-text corpus. Word-sense induction (WSI) is a task to automatically induce the different senses of a target word in the different contexts. In the last two decades, there have been several efforts on WSI. However, few methods are effective in biomedicine and life sciences.

METHODS

We developed a framework for biomedical entity sense induction using a mixture of natural language processing, supervised, and unsupervised learning methods with promising results. It is composed of three main steps: (1) a polysemy detection method to determine if a biomedical entity has many possible meanings; (2) a clustering quality index-based approach to predict the number of senses for the biomedical entity; and (3) a method to induce the concept(s) (i.e., senses) of the biomedical entity in a given context.

RESULTS

To evaluate our framework, we used the well-known MSH WSD polysemic dataset that contains 203 annotated ambiguous biomedical entities, where each entity is linked to 2-5 concepts. Our polysemy detection method obtained an F-measure of 98%. Second, our approach for predicting the number of senses achieved an F-measure of 93%. Finally, we induced the concepts of the biomedical entities based on a clustering algorithm and then extracted the keywords of reach cluster to represent the concept.

CONCLUSIONS

We have developed a framework for biomedical entity sense induction with promising results. Our study results can benefit a number of downstream applications, for example, help to resolve concept ambiguities when building Semantic Web KBs from biomedical text.

Distinctive effects of eicosapentaenoic and docosahexaenoic acids in regulating neural stem cell fate are mediated via endocannabinoid signalling pathways

Emerging evidence suggests a complex interplay between the endocannabinoid system, omega-3 fatty acids and the immune system in the promotion of brain self-repair. However, it is unknown if all omega-3 fatty acids elicit similar effects on adult neurogenesis and if such effects are mediated or regulated by interactions with the endocannabinoid system. This study investigated the effects of DHA and EPA on neural stem cell (NSC) fate and the role of the endocannabinoid signalling pathways in these effects. EPA, but not DHA, significantly increased proliferation of NSCs compared to controls, an effect associated with enhanced levels of the endocannabinoid 2-arachidonylglycerol (2-AG) and p-p38 MAPK, effects attenuated by pre-treatment with CB1 (AM251) or CB2 (AM630) receptor antagonists. Furthermore, in NSCs derived from IL-1β deficient mice, EPA significantly decreased proliferation and p-p38 MAPK levels compared to controls, suggesting a key role for IL-1β signalling in the effects observed. Although DHA similarly increased 2-AG levels in wild-type NSCs, there was no concomitant increase in proliferation or p-p38 MAPK activity. In addition, in NSCs from IL-1β deficient mice, DHA significantly increased proliferation without effects on p-P38 MAPK, suggesting effects of DHA are mediated via alternative signalling pathways. These results provide crucial new insights into the divergent effects of EPA and DHA in regulating NSC proliferation and the pathways involved, and highlight the therapeutic potential of their interplay with endocannabinoid signalling in brain repair.

Angular roughshark Oxynotus centrina (Squaliformes: Oxynotidae) in captivity feeding exclusively on elasmobranch eggs: an overlooked feeding niche or a matter of individual taste?

A specimen of angular roughshark Oxynotus centrina has been kept successfully in captivity for the first time. Over a period of 24 months, the specimen preyed exclusively on the contents of elasmobranch egg cases, suggesting a specialized trophic niche.

Survival in patients with primary liver cancer, gallbladder and extrahepatic biliary tract cancer and pancreatic cancer in Europe 1999-2007: Results of EUROCARE-5

BACKGROUND

The EUROCARE study collects and analyses survival data from population-based cancer registries (CRs) in Europe in order to provide data on between-country differences in survival and time trends in survival.

METHODS

This study analyses data on liver cancer, gallbladder and extrahepatic biliary tract cancers ("biliary tract cancers"), and pancreatic cancer diagnosed in 2000-2007 from 88 CRs in 29 countries. Relative survival (RS) was estimated overall, by region, sex, age and period of diagnosis using the complete approach. Time trends in 5-year RS over 1999-2007 were also analysed using the period approach.

RESULTS

The prognosis of the studied cancers was poor. Age-standardised 5-year RS was 12% for liver cancer, 17% for biliary tract cancers and 7% for pancreatic cancer. There were some between-country differences in survival. In general, RS was low in Eastern Europe and high in Central and Southern Europe. For all sites, 5-year RS was similar in men and women and decreased with advancing age. No substantial changes in survival were reported for pancreatic cancer over the period 1999-2007. On average, there was a crude increase in 5-year RS of 3 percentage points between the periods 1999-2001 and 2005-2007 for liver cancer and biliary tract cancers.

CONCLUSIONS

The major changes in imaging techniques over the study period for the diagnosis of the three studied cancers did not result in an improvement in the prognosis of these cancers. In the near future, new innovative treatments might be the best way to improve the prognosis in these cancers.

[Pathomimia and plastic surgery, a case report]

Pathomimia is defined as a dummy pathology self-induced deliberately and is neither associated with mental confusion nor disturbance of consciousness. This article reports a case of pathomimia in plastic surgery. One of our patients had intentionally injected physiological saline solution into her breast implants in order to increase their volume. Implants removal was necessary because of severe local inflammatory signs. Psychiatric assessment revealed body dysmorphic disorder (BDD) developed on an hysterical personality, which explained the self-induced injuries. This nosologic entity must be promptly identified because it's diagnosis remains problematic and a multidisciplinary medical management is essential.

A role for PPARα in the medial prefrontal cortex in formalin-evoked nociceptive responding in rats

BACKGROUND AND PURPOSE

The nuclear hormone receptor, PPARα, and its endogenous ligands, are involved in pain modulation. PPARα is expressed in the medial prefrontal cortex (mPFC), a key brain region involved in both the cognitive-affective component of pain and in descending modulation of pain. However, the role of PPARα in the mPFC in pain responding has not been investigated. Here, we investigated the effects of pharmacological modulation of PPARα in the rat mPFC on formalin-evoked nociceptive behaviour and the impact of formalin-induced nociception on components of PPARα signalling in the mPFC.

EXPERIMENTAL APPROACH

The effects of intra-mPFC microinjection of a PPARα agonist (GW7647) or a PPARα antagonist (GW6471) on formalin-evoked nociceptive behaviour in rats were studied. Quantitative real-time PCR and LC-MS/MS were used to study the effects of intraplantar injection of formalin on PPARα mRNA expression and levels of endogenous ligands, respectively, in the mPFC.

KEY RESULTS

Intra-mPFC administration of GW6471, but not GW7647, resulted in delayed onset of the early second phase of formalin-evoked nociceptive behaviour. Furthermore, formalin-evoked nociceptive behaviour was associated with significant reductions in mPFC levels of endogenous PPARα ligands (N-palmitoylethanolamide and N-oleoylethanolamide) and a 70% reduction in PPARα mRNA but not protein expression.

CONCLUSIONS AND IMPLICATIONS

These data suggest that endogenous ligands may act at PPARα in the mPFC to play a facilitatory/permissive role in second phase formalin-evoked nociceptive behaviour in rats.

LINKED ARTICLES

This article is part of a themed section on Cannabinoids 2013. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue-6.

The monoacylglycerol lipase inhibitor JZL184 attenuates LPS-induced increases in cytokine expression in the rat frontal cortex and plasma: differential mechanisms of action

BACKGROUND AND PURPOSE

JZL184 is a selective inhibitor of monoacylglycerol lipase (MAGL), the enzyme that preferentially catabolizes the endocannabinoid 2-arachidonoyl glycerol (2-AG). Here, we have studied the effects of JZL184 on inflammatory cytokines in the brain and plasma following an acute immune challenge and the underlying receptor and molecular mechanisms involved.

EXPERIMENTAL APPROACH

JZL184 and/or the CB₁ receptor antagonist, AM251 or the CB₂ receptor antagonist, AM630 were administered to rats 30 min before lipopolysaccharide (LPS). 2 h later cytokine expression and levels, MAGL activity, 2-AG, arachidonic acid and prostaglandin levels were measured in the frontal cortex, plasma and spleen.

KEY RESULTS

JZL184 attenuated LPS-induced increases in IL-1β, IL-6, TNF-α and IL-10 but not the expression of the inhibitor of NFkB (IκBα) in rat frontal cortex. AM251 attenuated JZL184-induced decreases in frontal cortical IL-1β expression. Although arachidonic acid levels in the frontal cortex were reduced in JZL184-treated rats, MAGL activity, 2-AG, PGE₂ and PGD₂ were unchanged. In comparison, MAGL activity was inhibited and 2-AG levels enhanced in the spleen following JZL184. In plasma, LPS-induced increases in TNF-α and IL-10 levels were attenuated by JZL184, an effect partially blocked by AM251. In addition, AM630 blocked LPS-induced increases in plasma IL-1β in the presence, but not absence, of JZL184.

CONCLUSION AND IMPLICATIONS

Inhibition of peripheral MAGL in rats by JZL184 suppressed LPS-induced circulating cytokines that in turn may modulate central cytokine expression. The data provide further evidence for the endocannabinoid system as a therapeutic target in treatment of central and peripheral inflammatory disorders.

Abstract P5-08-07: HER3, MET and immune pathways play important roles in the resistance of triple negative breast cancer (TNBC) after neoadjuvant anti-EGFR (panitumumab) combined with FEC 100

Background: Our group has previously reported (SABCS 2012, abstract 1081) a 2-fold higher pathologic complete response (pCR) rate in TNBC treated with panitumumab+FEC100 (47%) than with the standard therapy alone. However, in a half of the patients (pts) a residual tumor (RT) was detected. Having in mind the detrimental impact of resistant TNBC on patient outcome, we have investigated the tumor tissue factors that might have been important in development of resistance to this treatment.

Methods: 40 TNBC pts, treated with 8 cycles the anti-EGFR antibody panitumumab combined with FEC 100 for the first 4 and with docetaxel only for the last 4 cycles, were eligible. All pts underwent breast surgery after the neoadjuvant chemotherapy (NACT) completion. Formalin-fixed, paraffin-embedded tumor samples were collected before and after NACT for biomarker analysis. EGFR, HER3, IGF-1R, MET and the number of FOXP3+ or CD8+ tumor-infiltrating lymphocytes (TIL) were evaluated by immunohistochemistry (IHC). Expression of the kinases was graded semi-quantitatively (histoscores).

Results: Out of 40 treated pts, 21 demonstrated a RT (53%, according to the Chevallier classification, PMID 8338056). The IHC data were available for 17 pts. Since high EGFR expression was important for pCR achievement in this study (SABC 2012), we first investigated the expressions of EGFR, HER3 and MET in the RT. The results are presented in Table 1.

Table 1post-NACT RTn = 17EGFR down or flatEGFR up143HER3 upHER3 flatHER3 upHER3 flat8512MET upMET down or flatMET upMET down or flatMET upMET down or flatMET upMET down or flat17220120

Overall, among the 9 cases (cs) with increased post-NACT HER3 expression (HER3 up), only 1 had increased MET (MET up), while among the 7 cs with no change in HER3 post-CTNA (HER3 flat), 4 had MET expression increased.

Interestingly, although the pre-NACT IGF-1R expression was a strong predictor of pCR (p = 0.028, SABCS 2012), no significant changes in this kinase expression were observed in the RT, compared to the pre-NACT levels. Most RT had low IGF-1R scores (<100). The only 2 RT in which IGF-1R was increased post-CTNA were small groups of tumor cells either in breast or in the nodes, heavily surrounded by lymphocytes.

The density of TIL post-NACT correlated principally with the% of tumor mass (TM) reduction. Among the 7 pts with average reduction of 20%, there was only 1 cs with a good InSitu Immune Response (ISIR: dense TIL, with CD8+/FOXP3+ > 1.2). On the contrary, among the 9 pts with average TM reduction of 90%, 8 demonstrated a good ISIR.

Conclusion: The results indicate that HER3 and MET play significant roles in development of TNBC resistance to the anti-EGFR agents. Those molecules seem to drive 2 different resistance pathways in TNBC, as it has been shown in other malignancies. As several anti-HER3 or anti-MET drugs are nowadays available, we find very important investigating the expression of HER3 and MET in each TNBC pt pre- and post-NACT, in order to rapidly detect and combat the resistance. The ISIR-stimulating agents may bring an additional therapeutic benefit to those patients.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-08-07.

Altered neuropathic pain behaviour in a rat model of depression is associated with changes in inflammatory gene expression in the amygdala

The association between chronic pain and depression is widely recognized, the comorbidity of which leads to a heavier disease burden, increased disability and poor treatment response. This study examined nociceptive responding to mechanical and thermal stimuli prior to and following L5-L6 spinal nerve ligation (SNL), a model of neuropathic pain, in the olfactory bulbectomized (OB) rat model of depression. Associated changes in the expression of genes encoding for markers of glial activation and cytokines were subsequently examined in the amygdala, a key brain region for the modulation of emotion and pain. The OB rats exhibited mechanical and cold allodynia, but not heat hyperalgesia, when compared with sham-operated counterparts. Spinal nerve ligation induced characteristic mechanical and cold allodynia in the ipsilateral hindpaw of both sham and OB rats. The OB rats exhibited a reduced latency and number of responses to an innocuous cold stimulus following SNL, an effect positively correlated with interleukin (IL)-6 and IL-10 mRNA expression in the amygdala, respectively. Spinal nerve ligation reduced IL-6 and increased IL-10 expression in the amygdala of sham rats. The expression of CD11b (cluster of differentiation molecule 11b) and GFAP (glial fibrillary acidic protein), indicative of microglial and astrocyte activation, and IL-1β in the amygdala was enhanced in OB animals when compared with sham counterparts, an effect not observed following SNL. This study shows that neuropathic pain-related responding to an innocuous cold stimulus is altered in an animal model of depression, effects accompanied by changes in the expression of neuroinflammatory genes in the amygdala.