Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models

Biomedical events describe complex interactions between various biomedical entities. Event trigger is a word or a phrase which typically signifies the occurrence of an event. Event trigger identification is an important first step in all event extraction methods. However many of the current approaches either rely on complex hand-crafted features or consider features only within a window. In this paper we propose a method that takes the advantage of recurrent neural network (RNN) to extract higher level features present across the sentence. Thus hidden state representation of RNN along with word and entity type embedding as features avoid relying on the complex hand-crafted features generated using various NLP toolkits. Our experiments have shown to achieve state-of-art F1-score on Multi Level Event Extraction (MLEE) corpus. We have also performed category-wise analysis of the result and discussed the importance of various features in trigger identification task.Comment: The work has been accepted in BioNLP at ACL-201

Functional Eubacteria Species Along with Trans-domain Gut Inhabitants Favour Dysgenic Diversity in Oxalate Stone Disease

Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p \u3c 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies

Drug-Excipient Compatibility Studies in Formulation Development: Current Trends and Techniques

The safety, efficacy, quality and stability of a formulation are the cornerstones of any new drug development process. In order to consistently maintain these attributes in a finished dosage form, it is important to have a comprehensive understanding of the physico-chemical characteristics of the active pharmaceutical ingredient (API), as well as all other components (e.g. excipients, manufacturing aids, packaging materials) of the drug product. In a new drug development process, a detailed characterization of the API and other formulation components is usually carried out during the preformulation stage. The preformulation stage involves characterization of several aspects of the API including solubility, dissolution, permeability, polymorph/salt screening, stability (solidstate and solution-state), ionization properties, particle size distribution, API-excipient compatibilities etc. [1]. Excipients are ubiquitous to virtually every pharmaceutical formulation, and facilitate the manufacture, stability, administration, delivery of the API, and/or provide other functionalities to the dosage form. Excipients are used to improve processing (e.g. improving powder flow [2, 3], powder compactibility [4-6] etc.), enhance aesthetics (e.g. identification, branding etc. [7]), optimize product performance (e.g. modified drug-release [8-11]), and/or to facilitate patient compliance (e.g. taste masking [12-15]). They may constitute anywhere from 1 to 99 % of the total formulation mass. Due to the intimate contact of the API with one or more excipients in a formulation, there exists a likelihood of physical and/or chemical interactions between them. Any such interactions may result in a negative impact on the physical, stability or performance attributes of the drug product [16, 17]. The choice of excipients is of crucial importance to avoid these negative effects, and to facilitate the development of a robust and an effective formulation [18-20]. Thus, for a rational selection of excipients, screening of excipient-API compatibility is recognized as an important aspect of formulation development. Moreover, the USFDA’s 21st century current Good Manufacturing Practices (cGMP) initiative and International Council on Harmonization (ICH) Q8 guidelines encourage the pharmaceutical manufacturers to apply Quality by Design (QbD) principles in their drug development process [21, 22]. These guidelines include expectations of a clear understanding of any interactions between the formulation components. Moreover, recent advances in various thermal and non-thermal analytical techniques have led to an improved efficiency in the detection, monitoring and prevention of the incompatibilities early in the drug development process [23, 24]. This article aims to provide a brief overview of the nature of drug-excipient incompatibilities; as well as current trends and techniques used to evaluate these compatibilities in formulation development

Star formation in mergers with cosmologically motivated initial conditions

We use semi-analytic models and cosmological merger trees to provide the initial conditions for multi-merger numerical hydrodynamic simulations, and exploit these simulations to explore the effect of galaxy interaction and merging on star formation (SF). We compute numerical realisations of twelve merger trees from z=1.5 to z=0. We include the effects of the large hot gaseous halo around all galaxies, following recent obervations and predictions of galaxy formation models. We find that including the hot gaseous halo has a number of important effects. Firstly, as expected, the star formation rate on long timescales is increased due to cooling of the hot halo and refuelling of the cold gas reservoir. Secondly, we find that interactions do not always increase the SF in the long term. This is partially due to the orbiting galaxies transferring gravitational energy to the hot gaseous haloes and raising their temperature. Finally we find that the relative size of the starburst, when including the hot halo, is much smaller than previous studies showed. Our simulations also show that the order and timing of interactions are important for the evolution of a galaxy. When multiple galaxies interact at the same time, the SF enhancement is less than when galaxies interact in series. All these effects show the importance of including hot gas and cosmologically motivated merger trees in galaxy evolution models.Comment: 19 pages, 15 figures, 6 tables. Accepted for publication in MNRA

A solid dispersion based on milk-micelle as a drug-carrier for the enhancement of the aqueous solubility of ritonavir

The goal of present investigation was to evaluate the feasibility of formulating a solid-dispersion using milk-micelles as drug-carriers, to enhance the aqueous solubility of ritonavir

Formulation of a drug-phospholipid complex (Naturosome) to enhance the aqueous solubility of standardized extract of Centella asiastica (SCE)

Purpose: To evaluate the enhancement of aqueous solubility of standardized extract of Centella asiastica, a natural drug with known anti- Alzheimer’s activity, by formulating its complex (Naturosome) with a phospholipid - Phospholipon® 90H

Stable Electromyographic Sequence Prediction During Movement Transitions using Temporal Convolutional Networks

Transient muscle movements influence the temporal structure of myoelectric signal patterns, often leading to unstable prediction behavior from movement-pattern classification methods. We show that temporal convolutional network sequential models leverage the myoelectric signal's history to discover contextual temporal features that aid in correctly predicting movement intentions, especially during interclass transitions. We demonstrate myoelectric classification using temporal convolutional networks to effect 3 simultaneous hand and wrist degrees-of-freedom in an experiment involving nine human-subjects. Temporal convolutional networks yield significant $(p<0.001)$ performance improvements over other state-of-the-art methods in terms of both classification accuracy and stability.Comment: 4 pages, 5 figures, accepted for Neural Engineering (NER) 2019 Conferenc

From Discs to Bulges: effect of mergers on the morphology of galaxies

We study the effect of mergers on the morphology of galaxies by means of the simulated merger tree approach first proposed by Moster et al. This method combines N-body cosmological simulations and semi-analytic techniques to extract realistic initial conditions for galaxy mergers. These are then evolved using high resolution hydrodynamical simulations, which include dark matter, stars, cold gas in the disc and hot gas in the halo. We show that the satellite mass accretion is not as effective as previously thought, as there is substantial stellar stripping before the final merger. The fraction of stellar disc mass transferred to the bulge is quite low, even in the case of a major merger, mainly due to the dispersion of part of the stellar disc mass into the halo. We confirm the findings of Hopkins et al., that a gas rich disc is able to survive major mergers more efficiently. The enhanced star formation associated with the merger is not localised to the bulge of galaxy, but a substantial fraction takes place in the disc too. The inclusion of the hot gas reservoir in the galaxy model contributes to reducing the efficiency of bulge formation. Overall, our findings suggest that mergers are not as efficient as previously thought in transforming discs into bulges. This possibly alleviates some of the tensions between observations of bulgeless galaxies and the hierarchical scenario for structure formation.Comment: MNRAS Accepted, 17 pages, 11 figures, 3 Table