Reference management software (RMS) in an academic environment: a survey at a research university in Malaysia

Reference Management Software is used by researchers in academics to manage the bibliographic citations they encounter in their research. With these tools, scholars keep track of the scientific literature they read, and to facilitate the editing of the scientific papers they write. This study presents the results of a quantitative survey performed at a research university in Malaysia. The aims of the survey were to observe how much these softwares are used by the scientific community, to see which softwares are most known and used, and to find out the reasons and the approaches behind their usage. Manually questionnaire was distributed to the Master and PhD students at all faculties in Jun 2014. The data collected were analysed through a constant comparative analysis, and the following categories were drawn: a basic practical approach to the instrument, the heavy impact of the time factor, the force of habit in scholars, economic issues, the importance of training and literacy, and the role that the library can have in this stage. Describing the present situation, the study gives final directions to the libraries to better perform effective tasks about the matter. This study presented here is the first survey of the actual distribution and usage of Reference Management Software in a research university in Malaysia. This picture can give an important glance to Reference Management Software as one of the elements in the academic digital librarie

Enhancement of urban pluvial flood risk management and resilience through collaborative modelling: a UK case study

This paper presents the main findings and lessons learned from the development and implementation of a new methodology for collaborative modelling, social learning and social acceptance of flood risk management technologies. The proposed methodology entails three main phases: (1) stakeholder analysis and engagement; (2) improvement of urban pluvial flood modelling and forecasting tools; and (3) development and implementation of web-based tools for collaborative modelling in flood risk management and knowledge sharing. The developed methodology and tools were tested in the Cranbrook catchment (London Borough of Redbridge, UK), an area that has experienced severe pluvial (surface) flooding in the past. The developed methodologies proved to be useful for promoting interaction between stakeholders, developing collaborative modelling and achieving social acceptance of new technologies for flood risk management. Some limitations for stakeholder engagement were identified and are discussed in the present paper

Functional Analysis of the Aspergillus nidulans Kinome

The filamentous fungi are an ecologically important group of organisms which also have important industrial applications but devastating effects as pathogens and agents of food spoilage. Protein kinases have been implicated in the regulation of virtually all biological processes but how they regulate filamentous fungal specific processes is not understood. The filamentous fungus Aspergillus nidulans has long been utilized as a powerful molecular genetic system and recent technical advances have made systematic approaches to study large gene sets possible. To enhance A. nidulans functional genomics we have created gene deletion constructs for 9851 genes representing 93.3% of the encoding genome. To illustrate the utility of these constructs, and advance the understanding of fungal kinases, we have systematically generated deletion strains for 128 A. nidulans kinases including expanded groups of 15 histidine kinases, 7 SRPK (serine-arginine protein kinases) kinases and an interesting group of 11 filamentous fungal specific kinases. We defined the terminal phenotype of 23 of the 25 essential kinases by heterokaryon rescue and identified phenotypes for 43 of the 103 non-essential kinases. Uncovered phenotypes ranged from almost no growth for a small number of essential kinases implicated in processes such as ribosomal biosynthesis, to conditional defects in response to cellular stresses. The data provide experimental evidence that previously uncharacterized kinases function in the septation initiation network, the cell wall integrity and the morphogenesis Orb6 kinase signaling pathways, as well as in pathways regulating vesicular trafficking, sexual development and secondary metabolism. Finally, we identify ChkC as a third effector kinase functioning in the cellular response to genotoxic stress. The identification of many previously unknown functions for kinases through the functional analysis of the A. nidulans kinome illustrates the utility of the A. nidulans gene deletion constructs

An interpretable deep learning model for time-series electronic health records: Case study of delirium prediction in critical care

Deep Learning (DL) models have received increasing attention in the clinical setting, particularly in intensive care units (ICU). In this context, the interpretability of the outcomes estimated by the DL models is an essential step towards increasing adoption of DL models in clinical practice. To address this challenge, we propose an ante-hoc, interpretable neural network model. Our proposed model, named double self-attention architecture (DSA), uses two attention-based mechanisms, including self-attention and effective attention. It can capture the importance of input variables in general, as well as changes in importance along the time dimension for the outcome of interest. We evaluated our model using two real-world clinical datasets covering 22840 patients in predicting onset of delirium 12 h and 48 h in advance. Additionally, we compare the descriptive performance of our model with three post-hoc interpretable algorithms as well as with the opinion of clinicians based on the published literature and clinical experience. We find that our model covers the majority of the top-10 variables ranked by the other three post-hoc interpretable algorithms as well as the clinical opinion, with the advantage of taking into account both, the dependencies among variables as well as dependencies between varying time-steps. Finally, our results show that our model can improve descriptive performance without sacrificing predictive performance

Carvedilol targets beta-arrestins to rewire innate immunity and improve oncolytic adenoviral therapy

Oncolytic viruses are being tested in clinical trials, including in women with ovarian cancer. We use a drug-repurposing approach to identify existing drugs that enhance the activity of oncolytic adenoviruses. This reveals that carvedilol, a β-arrestin-biased β-blocker, synergises with both wild-type adenovirus and the E1A-CR2-deleted oncolytic adenovirus, dl922-947. Synergy is not due to β-adrenergic blockade but is dependent on β-arrestins and is reversed by β-arrestin CRISPR gene editing. Co-treatment with dl922-947 and carvedilol causes increased viral DNA replication, greater viral protein expression and higher titres of infectious viral particles. Carvedilol also enhances viral efficacy in orthotopic, intraperitoneal murine models, achieving more rapid tumour clearance than virus alone. Increased anti-cancer activity is associated with an intratumoural inflammatory cell infiltrate and systemic cytokine release. In summary, carvedilol augments the activity of oncolytic adenoviruses via β-arrestins to re-wire cytokine networks and innate immunity and could therefore improve oncolytic viruses for cancer patient treatment

Modelling H5N1 in Bangladesh across spatial scales : model complexity and zoonotic transmission risk

Highly pathogenic avian influenza H5N1 remains a persistent public health threat, capable of causing infection in humans with a high mortality rate while simultaneously negatively impacting the livestock industry. A central question is to determine regions that are likely sources of newly emerging influenza strains with pandemic causing potential. A suitable candidate is Bangladesh, being one of the most densely populated countries in the world and having an intensifying farming system. It is therefore vital to establish the key factors, specific to Bangladesh, that enable both continued transmission within poultry and spillover across the human–animal interface. We apply a modelling framework to H5N1 epidemics in the Dhaka region of Bangladesh, occurring from 2007 onwards, that resulted in large outbreaks in the poultry sector and a limited number of confirmed human cases. This model consisted of separate poultry transmission and zoonotic transmission components. Utilising poultry farm spatial and population information a set of competing nested models of varying complexity were fitted to the observed case data, with parameter inference carried out using Bayesian methodology and goodness-of-fit verified by stochastic simulations. For the poultry transmission component, successfully identifying a model of minimal complexity, which enabled the accurate prediction of the size and spatial distribution of cases in H5N1 outbreaks, was found to be dependent on the administration level being analysed. A consistent outcome of non-optimal reporting of infected premises materialised in each poultry epidemic of interest, though across the outbreaks analysed there were substantial differences in the estimated transmission parameters. The zoonotic transmission component found the main contributor to spillover transmission of H5N1 in Bangladesh was found to differ from one poultry epidemic to another. We conclude by discussing possible explanations for these discrepancies in transmission behaviour between epidemics, such as changes in surveillance sensitivity and biosecurity practices

Rethinking resilience: home gardening, food sharing and everyday resistance

Resilience and food self-provisioning (FSP), terms that until recently were deployed primarily in the study of livelihoods in the Global South, are now attracting attention from alternative food scholarship in the Global North. Drawing on a large-scale survey conducted in the Czech Republic, this article investigates FSP as a social resilience-enhancing set of practices. In addition to the traditional reading of FSP as a passive, defensive and crisis-deflecting form of resilience, this article puts forward an alternative conceptualisation of resilience as a proactive, preventative, future-oriented and transformation-enabling capacity that runs counter to the tenets of neoliberalism