Semantically linking molecular entities in literature through entity relationships

Background Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attribute to this goal by formally identifying the relations between genes, promoters, complexes and various other molecular entities found in text. More importantly, these studies help to enhance integration of text mining results with database facts. Results We describe, compare and evaluate two frameworks developed for the prediction of non-causal or 'entity' relations (REL) between gene symbols and domain terms. For the corresponding REL challenge of the BioNLP Shared Task of 2011, these systems ranked first (57.7% F-score) and second (41.6% F-score). In this paper, we investigate the performance discrepancy of 16 percentage points by benchmarking on a related and more extensive dataset, analysing the contribution of both the term detection and relation extraction modules. We further construct a hybrid system combining the two frameworks and experiment with intersection and union combinations, achieving respectively high-precision and high-recall results. Finally, we highlight extremely high-performance results (F-score > 90%) obtained for the specific subclass of embedded entity relations that are essential for integrating text mining predictions with database facts. Conclusions The results from this study will enable us in the near future to annotate semantic relations between molecular entities in the entire scientific literature available through PubMed. The recent release of the EVEX dataset, containing biomolecular event predictions for millions of PubMed articles, is an interesting and exciting opportunity to overlay these entity relations with event predictions on a literature-wide scale

Discriminative and informative features for biomolecular text mining with ensemble feature selection

Motivation: In the field of biomolecular text mining, black box behavior of machine learning systems currently limits understanding of the true nature of the predictions. However, feature selection (FS) is capable of identifying the most relevant features in any supervised learning setting, providing insight into the specific properties of the classification algorithm. This allows us to build more accurate classifiers while at the same time bridging the gap between the black box behavior and the end-user who has to interpret the results

Isolating unique variance in mental health outcomes attributable to personality variables and childhood emotional abuse

IntroductionUniversity students are at high risk for anxiety and depression. Our main objective was to tease apart variance in symptom severity that was uniquely attributable to four associated variables that are frequently confounded: exposure to childhood emotional abuse, alexithymia, sensory processing sensitivity (SPS), and anxiety sensitivity (AS).MethodsUniversity students (N = 410) completed an online survey designed to measure our four key study variables along with several other potentially relevant variables including sex, physical activity levels, and perceived COVID-19 impacts.ResultsOver half of the participants reported moderate to extremely severe symptoms of anxiety and depression. Females reported stronger signs of SPS and AS and were more likely than males to have increased their moderate/vigorous exercise since the pandemic began. After controlling for the other variables, the best predictors of perceived COVID-19 impacts were SPS, childhood emotional abuse, and current levels of physical activity. Whereas all three personality variables and childhood emotional abuse emerged as significant predictors of both depression and anxiety, neither COVID-19 impacts nor physical activity levels accounted for unique variance in either model. Unexpectedly, male sex emerged as an additional risk factor for depression, raising the possibility that males experience unique stressors and societal pressures that increase their risk of depression.DiscussionThese findings help to clarify the links between childhood emotional abuse, personality traits implicated in emotional awareness and self-regulation, and mental health. They may have important implications for the development and implementation of individualized treatments for common mental disorders

Statistical profiling of unemployed jobseekers : the increasing availability of big data allows for the profiling of unemployed jobseekers via statistical models

Statistical models can help public employment services to identify factors associated with long-term unemployment and to identify groups at risk. Statistical profiling models will probably even become more prominent as new machine learning techniques in combination with the increasing availability of big data will improve their predictive power. However, a policy maker cannot just define an outcome variable at the start of the project and walk away: a continuous dialogue between data analysts, policy makers and caseworkers is very important. Indeed, throughout the process, normative decisions are to be made: profiling practices misclassify many individuals. They can reinforce but also prevent existing patterns of discrimination

Amplified Sediment waves in the Irish Sea (AmSedIS)

Exceptionally high, straight-crested and trochoidal sediment waves have recently been observed on shelf seas world-wide, and reach heights of up to 36 m in the Irish Sea. It is uncertain how the interplay between geological, biogeochemical and hydrodynamic processes influences the migration and extreme growth of these sediment waves. The AmSedIS project thus sets out to (1) investigate the role of sediment granulometry and sedimentavailability on both “extreme” and “normal” sediment wave development and (2) investigate the potential association of methane derived carbonate formation with extreme sediment wave growth. The preliminary findings are: (1) The crests of unusually high and trochoidal sediment waves still migrate over several meters per year and they consist of coarser, more poorly sorted sediments in comparison to the "normal" sediments waves; (2) Methane seepage is not considered a factor in extreme sediment wave development; (3) The excess of mobile sediment supply seems to allow for "extreme" sediment wave growth, and is linked to palaeo-tunnel valleys and the finer sediments that fill them or with converging sediment transport pathways; (4) The variation in sediment from sediment wave trough to crest to trough will form the basis for more advanced numerical modelling

Intramolecular locking and coumarin insertion: a stepwise approach for TADF design

Three novel TADF (thermally activated delayed fluorescence) emitters based on the well-studied Qx-Ph-DMAC fluorophore are designed and synthesized. The photophysical properties of these materials are studied from a theoretical and experimental point of view, demonstrating the cumulative effects of multiple small modifications that combine to afford significantly improved TADF performance. First, an extra phenyl ring is added to the acceptor part of Qx-Ph-DMAC to increase the conjugation length, resulting in BQx-Ph-DMAC, which acts as an intermediate molecular structure. Next, an electron-deficient coumarin unit is incorporated to fortify the electron accepting ability, affording ChromPy-Ph-DMAC with red-shifted emission. Finally, the conjugated system is further enlarged by ‘locking’ the molecular structure, generating DBChromQx-DMAC with further red-shifted emission. The addition of the coumarin unit significantly impacts the charge-transfer excited state energy levels with little effect on the locally excited states, resulting in a decrease of the singlet–triplet energy gap. As a result, the two coumarin-based emitters show considerably improved TADF performance in 1 w/w% zeonex films when compared to the initial Qx-Ph-DMAC structure. ‘Locking’ the molecular structure further lowers the singlet–triplet energy gap, resulting in more efficient reverse intersystem crossing and increasing the contribution of TADF to the total emission

Cytokine Induction of Tumor Necrosis Factor Receptor 2 Is Mediated by STAT3 in Colon Cancer Cells

The IL-6/STAT3 and TNFα/NFκB pathways are emerging as critical mediators of inflammation-associated colon cancer. TNFR2 expression is increased in inflammatory bowel diseases, the azoxymethane/dextran sodium sulfate (AOM/DSS) model of colitis-associated cancer, and by combined IL-6 and TNFα. The molecular mechanisms that regulate TNFR2 remain undefined. This study used colon cancer cell lines to test the hypothesis that IL-6 and TNFα induce TNFR2 via STAT3 and/or NFκB. Basal and IL-6 + TNFα-induced TNFR2 were decreased by pharmacological STAT3 inhibition. NFκB inhibition had little effect on IL-6 + TNFα-induced TNFR2, but did inhibit induction of endogenous IL-6 and TNFR2 in cells treated with TNFα alone. Chromatin immunoprecipitation (ChIP) revealed cooperative effects of IL-6 + TNFα to induce STAT3 binding to a -1578 STAT response element in the TNFR2 promoter, but no effect on NFκB binding to consensus sites. Constitutively active STAT3 was sufficient to induce TNFR2 expression. Over-expression of SOCS3, a cytokine-inducible STAT3 inhibitor, which reduces tumorigenesis in preclinical models of colitis-associated cancer, decreased cytokine-induced TNFR2 expression and STAT3 binding to the -1578 STAT response element. SOCS3 over-expression also decreased proliferation of colon cancer cells and dramatically decreased anchorage-independent growth of colon cancer cells, even cells over-expressing TNFR2. Collectively, these studies demonstrate that IL-6 and TNFα-induced TNFR2 expression in colon cancer cells is mediated primarily by STAT3, and provide evidence that TNFR2 may contribute to the tumor-promoting roles of STAT3

Extent and retreat history of the Barra Fan Ice Stream offshore western Scotland and northern Ireland during the last glaciation

During the Last Glacial Maximum (LGM) the marine-terminating Barra Fan Ice Stream (BFIS), a major conduit of the British Irish Ice Sheet (BIIS), drained much of western Scotland and northwest Ireland with ice streaming onto the continental shelf of the Malin Sea. The extent and retreat history of this ice stream across the shelf, until now, is not well known. In particular, geochronological constraints on the history of this ice stream have thus far been restricted to deep-sea cores or terrestrial cosmogenic nuclide dating onshore, with ages across the shelf absent. To understand the possible external forcing factors acting on this marine terminating ice stream during retreat, improved geochronological constraint on its deglaciation is necessary. Here, we present new geophysical data, marine sediment cores and over forty radiocarbon dates to provide important constraints on maximum extent of the BFIS, as well as the timing and pattern of retreat back across the Malin Shelf. Dated moraines and grounding-zone wedges (GZW) seen in seafloor sub-bottom profiles provide evidence that the BFIS reached the Malin Shelf edge during the LGM and was at its maximum extent around 26.7 ka BP. The presence of two sets of GZWs suggests that the style of retreat was episodic. The new radiocarbon chronology shows that retreat from the shelf edge was underway by 25.9 ka BP, with the majority of the continental shelf ice free by 23.2 ka BP, and that glacimarine conditions were present in the Sea of Hebrides by 20.2 ka BP at the latest. Collectively, these results indicate that the majority of the Malin Shelf was free of grounded ice by ∼21.5–20 ka BP, which is up to 4000 years earlier than previously reconstructed. We attribute this early deglaciation to high relative sea level caused by glacial isostatic depression when the BIIS reached its maximum extent promoting ice shelf and grounding line instability. Two deep troughs, forming reverse bed slopes, aided the continued retreat of the BFIS. This suggests that local ice loading and bed morphology can be significant controls on the destabilisation of a marine-terminating ice stream and can override the influence of ocean and atmospheric temperatures