JNets: Exploring networks by integrating annotation

<p>Abstract</p> <p>Background</p> <p>A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published network visualizations are static representations that do not support user interaction.</p> <p>Results</p> <p>JNets was designed as a network visualization tool that incorporates annotation to explore the underlying features of interaction networks. The software is available as an application and a configurable applet that can provide a flexible and dynamic online interface to many types of network data. As a case study, we use JNets to investigate approved drug targets present within the HIV-1 Human protein interaction network. Our software highlights the intricate influence that HIV-1 has on the host immune response.</p> <p>Conclusion</p> <p>JNets is a software tool that allows interaction networks to be visualized and studied remotely, from within a standard web page. Therefore, using this free software, network data can be presented in an enhanced, interactive format. More information about JNets is available at <url>http://www.manchester.ac.uk/bioinformatics/jnets</url>.</p

JNets: Exploring networks by integrating annotation

<p>Abstract</p> <p>Background</p> <p>A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published network visualizations are static representations that do not support user interaction.</p> <p>Results</p> <p>JNets was designed as a network visualization tool that incorporates annotation to explore the underlying features of interaction networks. The software is available as an application and a configurable applet that can provide a flexible and dynamic online interface to many types of network data. As a case study, we use JNets to investigate approved drug targets present within the HIV-1 Human protein interaction network. Our software highlights the intricate influence that HIV-1 has on the host immune response.</p> <p>Conclusion</p> <p>JNets is a software tool that allows interaction networks to be visualized and studied remotely, from within a standard web page. Therefore, using this free software, network data can be presented in an enhanced, interactive format. More information about JNets is available at <url>http://www.manchester.ac.uk/bioinformatics/jnets</url>.</p

Seeing with sound? Exploring different characteristics of a visual-to-auditory sensory substitution device

Sensory substitution devices convert live visual images into auditory signals, for example with a web camera (to record the images), a computer (to perform the conversion) and headphones (to listen to the sounds). In a series of three experiments, the performance of one such device (‘The vOICe’) was assessed under various conditions on blindfolded sighted participants. The main task that we used involved identifying and locating objects placed on a table by holding a webcam (like a flashlight) or wearing it on the head (like a miner’s light). Identifying objects on a table was easier with a hand-held device, but locating the objects was easier with a head-mounted device. Brightness converted into loudness was less effective than the reverse contrast (dark being loud), suggesting that performance under these conditions (natural indoor lighting, novice users) is related more to the properties of the auditory signal (ie the amount of noise in it) than the cross-modal association between loudness and brightness. Individual differences in musical memory (detecting pitch changes in two sequences of notes) was related to the time taken to identify or recognise objects, but individual differences in self-reported vividness of visual imagery did not reliably predict performance across the experiments. In general, the results suggest that the auditory characteristics of the device may be more important for initial learning than visual associations

MicroRNAs from the same precursor have different targeting properties

UnlabelledBackgroundThe processing of a microRNA results in an intermediate duplex of two potential mature products that derive from the two arms (5' and 3') of the precursor hairpin. It is often suggested that one of the sequences is degraded and the other is incorporated into the RNA-induced silencing complex. However, both precursor arms may give rise to functional levels of mature microRNA and the dominant product may change from species to species, from tissue to tissue, or between developmental stages. Therefore, both arms of the precursor have the potential to produce functional mature microRNAs.ResultsWe have investigated the relationship between predicted mRNA targets of mature sequences derived from the 5' and 3' arms of the same pre-microRNAs. Using six state-of-the-art target prediction algorithms, we find that 5'/3' microRNA pairs target different sites in 3' untranslated regions of mRNAs. We also find that these pairs do not generally target overlapping sets of genes, or functionally related genes.ConclusionsWe show that alternative mature products produced from the same precursor microRNAs have different targeting properties and therefore different biological functions. These data strongly suggest that developmental or evolutionary changes in arm choice will have significant functional consequences

Research Data Management in the Atlantic Provinces

Research Data Management (RDM) is becoming an increasingly important issue for post-secondary institutions. The Tri-Agencies (SSHRC, NSERC, CIHR) are expected to release a new policy that will stipulate that institutions have an institutional strategy for dealing with research data. Part of the responsibility will lie with researchers and the management of their research data. Three Atlantic universities are aiming to discover how researchers are storing, using and sharing their data through administering a survey using an instrument that has been used at many Canadian universities. Surveys will be administered in Winter 2019. Data from the surveys will be analyzed separately by each institution and may be combined to identify commonalities and possibilities for collaboration in the region. The results of these surveys will help librarians, IT specialists, data managers, and others interested in data management to understand current practices and attitudes. The results will also be used to contribute of the development of RDM services and resources across Atlantic post-secondary institutions with the aim of being prepared for the Tri-Agency policy once it comes into effect

A Case of Identity: John Adams and Massachusettensis

This article undertakes an interdisciplinary reexamination of the claims of American revolutionary John Adams (1735–1826) that Jonathan Sewall (1729–96) was a lead author of the influential Loyalist tracts Massachusettensis (Dec. 12, 1774–April 3, 1775). The Massachusettensis letters constitute the most cogent articulation of Loyalist ideology on the eve of the American Revolution. Adams replied with his Novanglus letters (Jan. 23–April 17, 1775). While Adams believed that Sewall was the author or coauthor of Massachusettensis, scholars subsequently attributed sole authorship to Daniel Leonard (1740–1829), a Loyalist refugee who claimed authorship whilst in exile in England. After reviewing the historical and literary evidence and the results of authorship attribution tests, we proffer four historiographical conclusions. First, Massachusettensis was probably coauthored by Leonard and Sewall with Sewall exercising editorial direction over this and other Loyalist propaganda. This validates Adams’s contention that Sewall had a principal role in Massachusettensis’s composition. Second, Adams’s presumption of Sewall’s authorship shaped the writing of both Massachusettensis and Novanglus, as revealed in a critical reading of the debate. Third, Adams biographers and Revolution scholars have underestimated the extent to which the literary contest with “Massachusettensis” was instrumental in John Adams’s radicalization. Fourth, the Novanglus-Massachusettensis debate was shrouded in friendship: publicly it encapsulated the signal ideological differences between Patriots and Loyalists while privately crowning a friendly rivalry between Adams and Sewall of fifteen years’ standing. Their friendship may have facilitated communication between British headquarters and the American rebels in the weeks preceding the outbreak of military hostilities. In sum, this article demonstrates the vitality of friendship as an analytical category for political history. Friendship has been under studied by historians of the American Revolutionary Era but the Revolution was at its most revolutionary in the division of intimate friends like Adams and Sewall

Child oral health and preventive dental service access among children with intellectual disabilities, autism and other educational additional support needs: a population-based record linkage cohort study

Objective: Inequalities in child oral health are a global challenge and the intersection of socioeconomic factors with educational additional support needs (ASN), including children with intellectual disabilities or autism, have thus far received limited attention in relatively small clinical studies. We aimed to address this evidence gap by investigating oral health and access to preventive dental services among children with ASN compared to the general child population. Methods: Cohort study linking data from six Scotland-wide health and education databases compared: dental caries experience and tooth extraction via general anaesthetic; receipt of school-based dental inspection; access to primary care and hospital dental services; and access to the Childsmile national oral health improvement programme between children with a range of ASN (intellectual disabilities, autism, social and other) and their peers for the school years 2016/17–2018/19 (n = 166 781). Results: Children with any ASN had higher rates of caries experience than those with no ASN, however, after adjustment for socioeconomic deprivation, sex, year, and school type only those with a social or other ASN remained at increased risk. Rates of tooth extraction under general anaesthesia in hospital were higher among children with intellectual disabilities (aRR = 1.67;95% CI = [1.16–2.37]). School-based dental inspection access improved for children with intellectual disability and/or autism from 2016/17 onwards, although higher rates of child refusal on the day were observed in these groups (no ASN refusal: 5.4%; intellectual disability: 35.8%; autism: 40.3%). Children with any ASN were less likely to attend primary dental-care regularly, and in those who attended, children with intellectual disability or autism were less likely than their peers to receive prevention (fluoride varnish, oral-hygiene instruction, or dietary advice). Childsmile nursery-supervised toothbrushing programme access among children with any ASN was similar to children with no ASN and children with intellectual disability (aRR = 1.27;95% CI = [1.12–1.45]) or autism (aRR = 1.32;95% CI = [1.19–1.45]) were more likely to receive support from Childsmile dental health support worker. Conclusions: We have identified inequalities in oral health and dental care for children with different ASN in Scotland with both a greater burden of disease among some groups and higher complexity of care; compounded by reduced and variable access to preventive dental services. Further efforts are needed to develop and improve preventive care pathways for children with ASN and integrate oral health to wider healthcare systems for these children to mitigate against oral health inequalities

Evaluation of a national complex oral health improvement programme: a population data linkage cohort study in Scotland

Objectives Child dental caries is a global public health challenge with high prevalence and wide inequalities. A complex public health programme (Childsmile) was established. We aimed to evaluate the reach of the programme and its impact on child oral health. Setting Education, health and community settings, Scotland-wide. Interventions Childsmile (national oral health improvement programme) interventions: nursery-based fluoride varnish applications (FVAs) and supervised daily toothbrushing, community-based Dental Health Support Worker (DHSW) contacts and primary care dental practice visits—delivered to the population via a proportionate universal approach. Participants: 50 379 children (mean age=5.5 years, SD=0.3) attending local authority schools (2014/2015). Design: Population-based individual child-level data on four Childsmile interventions linked to dental inspection survey data to form a longitudinal cohort. Logistic regression assessed intervention reach and the independent impact of each intervention on caries experience, adjusting for age, sex and area-based Scottish Index of Multiple Deprivation (SIMD). Outcome measures: Reach of the programme is defined as the percentage of children receiving each intervention at least once by SIMD fifth. Obvious dental caries experience (presence/absence) is defined as the presence of decay (into dentine), missing (extracted) due to decay or filled deciduous teeth. Results: 15 032 (29.8%) children had caries experience. The universal interventions had high population reach: nursery toothbrushing (89.1%), dental practice visits (70.5%). The targeted interventions strongly favoured children from the most deprived areas: DHSW contacts (SIMD 1: 29.5% vs SIMD 5: 7.7%), nursery FVAs (SIMD 1: 75.2% vs SIMD 5: 23.2%). Odds of caries experience were markedly lower among children participating in nursery toothbrushing (&gt;3 years, adjusted OR (aOR)=0.60; 95% CI 0.55 to 0.66) and attending dental practice (≥6 visits, aOR=0.55; 95% CI 0.50 to 0.61). The findings were less clear for DHSW contacts. Nursery FVAs were not independently associated with caries experience. Conclusions: The universal interventions, nursery toothbrushing and regular dental practice visits were independently and most strongly associated with reduced odds of caries experience in the cohort, with nursery toothbrushing having the greatest impact among children in areas of high deprivation

A systems approach using the functional resonance analysis method to support fluoride varnish application for children attending general dental practice

Background All children attending General Dental Practice in Scotland are recommended to receive twice-yearly applications of sodium fluoride varnish to prevent childhood caries, yet application is variable. Development of complex interventions requires theorizing and modelling to understand context. This study applies the Functional Resonance Analysis Method (FRAM) to produce a sociotechnical systems model and identify opportunities for intervention to support application. Methods The FRAM was used to synthesise data which were: routine monitoring of fluoride varnish application in 2015/16; a longitudinal survey with practitioners (n = 1090); in-depth practitioner and key informant interviews (n = 43); and a ‘world café’ workshop (n = 56). Results We describe a detailed model of functions linked to application, and use this to make recommendations for system-wide intervention. Conclusions Rigorous research is required to produce accessible models of complex systems in healthcare. This novel paper shows how careful articulation of the functions associated with fluoride varnish application can support future improvement efforts