Beyond blue gene: Intellectual property and bioinformatics

This article considers the challenges posed to intellectual property law by the emerging field of bioinformatics. It examines the intellectual property strategies of established biotechnology companies, such as Celera Genomics, and information technology firms entering into the marketplace, such as IBM. First this paper argues that copyright law is not irrelevant to biotechnology, as some commentators would suggest. It claims that the use of copyright law and contract law is fundamental to the protection of biomedical and genomic databases. Second this article questions whether biotechnology companies are exclusively interested in patenting genes and genetics sequences. Recent evidence suggests that biotechnology companies and IT firms are patenting bioinformatics software and Internet business methods, as well as underlying instrumentation such as microarrays and genechips. Finally, this paper evaluates what impact the privatisation of bioinformatics will have on public research and scientific communication. It raises important questions about integration, interoperability, and the risks of monopoly. It finally considers whether open source software such as the Ensembl Project and peer to peer technology like DSAS will be able to counter this trend of privatisation.

Japonica rice: Intellectual property, scientific publishing and data-sharing

This article examines a series of controversies within the life sciences over data sharing. Part 1 focuses upon the agricultural biotechnology firm Syngenta publishing data on the rice genome in the journal Science, and considers proposals to reform scientific publishing and funding to encourage data sharing. Part 2 examines the relationship between intellectual property rights and scientific publishing, in particular copyright protection of databases, and evaluates the declaration of the Human Genome Organisation that genomic databases should be global public goods. Part 3 looks at varying opinions on the information function of patent law, and then considers the proposals of Patrinos and Drell to provide incentives for private corporations to release data into the public domain.

Capnography monitoring during procedural sedation and analgesia: A systematic review protocol

Background An important potential clinical benefit of using capnography monitoring during procedural sedation and analgesia (PSA) is that this technology could improve patient safety by reducing serious sedation-related adverse events, such as death or permanent neurological disability, which are caused by inadequate oxygenation. The hypothesis is that earlier identification of respiratory depression using capnography leads to a change in clinical management that prevents hypoxaemia. As inadequate oxygenation/ventilation is the most common reason for injury associated with PSA, reducing episodes of hypoxaemia would indicate that using capnography would be safer than relying on standard monitoring alone. Methods/design The primary objective of this review is to determine whether using capnography during PSA in the hospital setting improves patient safety by reducing the risk of hypoxaemia (defined as an arterial partial pressure of oxygen below 60 mmHg or percentage of haemoglobin that is saturated with oxygen [SpO2] less than 90 %). A secondary objective of this review is to determine whether changes in the clinical management of sedated patients are the mediating factor for any observed impact of capnography monitoring on the rate of hypoxaemia. The potential adverse effect of capnography monitoring that will be examined in this review is the rate of inadequate sedation. Electronic databases will be searched for parallel, crossover and cluster randomised controlled trials comparing the use of capnography with standard monitoring alone during PSA that is administered in the hospital setting. Studies that included patients who received general or regional anaesthesia will be excluded from the review. Non-randomised studies will be excluded. Screening, study selection and data extraction will be performed by two reviewers. The Cochrane risk of bias tool will be used to assign a judgment about the degree of risk. Meta-analyses will be performed if suitable. Discussion This review will synthesise the evidence on an important potential clinical benefit of capnography monitoring during PSA within hospital settings. Systematic review registration: PROSPERO CRD42015023740

Quantitative genetic modeling of lateral ventricular shape and volume using multi-atlas fluid image alignment in twins

Despite substantial progress in measuring the 3D profile of anatomical variations in the human brain, their genetic and environmental causes remain enigmatic. We developed an automated system to identify and map genetic and environmental effects on brain structure in large brain MRI databases . We applied our multi-template segmentation approach ("Multi-Atlas Fluid Image Alignment") to fluidly propagate hand-labeled parameterized surface meshes into 116 scans of twins (60 identical, 56 fraternal), labeling the lateral ventricles. Mesh surfaces were averaged within subjects to minimize segmentation error. We fitted quantitative genetic models at each of 30,000 surface points to measure the proportion of shape variance attributable to (1) genetic differences among subjects, (2) environmental influences unique to each individual, and (3) shared environmental effects. Surface-based statistical maps revealed 3D heritability patterns, and their significance, with and without adjustments for global brain scale. These maps visualized detailed profiles of environmental versus genetic influences on the brain, extending genetic models to spatially detailed, automatically computed, 3D maps.

Mapping genetic influences on ventricular structure in twins

Despite substantial progress in measuring the anatomical and functional variability of the human brain, little is known about the genetic and environmental causes of these variations. Here we developed an automated system to visualize genetic and environmental effects on brain structure in large brain MRI databases. We applied our multi-template segmentation approach termed "Multi-Atlas Fluid Image Alignment" to fluidly propagate hand-labeled parameterized surface meshes, labeling the lateral ventricles, in 3D volumetric MRI scans of 76 identical (monozygotic, MZ) twins (38 pairs; mean age = 24.6 (SD = 1.7)); and 56 same-sex fraternal (dizygotic, DZ) twins (28 pairs; mean age = 23.0 (SD = 1.8)), scanned as part of a 5-year research study that will eventually study over 1000 subjects. Mesh surfaces were averaged within subjects to minimize segmentation error. We fitted quantitative genetic models at each of 30,000 surface points to measure the proportion of shape variance attributable to (1) genetic differences among subjects, (2) environmental influences unique to each individual, and (3) shared environmental effects. Surface-based statistical maps, derived from path analysis, revealed patterns of heritability, and their significance, in 3D. Path coefficients for the 'ACE' model that best fitted the data indicated significant contributions from genetic factors (A = 7.3%), common environment (C = 38.9%) and unique environment (E = 53.8%) to lateral ventricular volume. Earlier-maturing occipital horn regions may also be more genetically influenced than later-maturing frontal regions. Maps visualized spatially-varying profiles of environmental versus genetic influences. The approach shows promise for automatically measuring gene-environment effects in large image databases.

Utility of web content blocks in content extraction

Currently we are facing an overburdening growth of the number of reliable information sources on the Internet. The quantity of information available to everyone via Internet is dramatically growing each year [15]. At the same time, temporal and cognitive resources of human users are not changing, therefore causing a phenomenon of information overload. World Wide Web is one of the main sources of information for decision makers (reference to my research). However our studies show that, at least in Poland, the decision makers see some important problems when turning to Internet as a source of decision information. One of the most common obstacles raised is distribution of relevant information among many sources, and therefore need to visit different Web sources in order to collect all important content and analyze it. A few research groups have recently turned to the problem of information extraction from the Web [13]. The most effort so far has been directed toward collecting data from dispersed databases accessible via web pages (related to as data extraction or information extraction from the Web) and towards understanding natural language texts by means of fact, entity, and association recognition (related to as information extraction). Data extraction efforts show some interesting results, however proper integration of web databases is still beyond us. Information extraction field has been recently very successful in retrieving information from natural language texts, however it is still lacking abilities to understand more complex information, requiring use of common sense knowledge, discourse analysis and disambiguation techniques.

Acoustic adaptation in cross database audio visual SHMM training for phonetic spoken term detection

Visual information in the form of lip movements of the speaker has been shown to improve the performance of speech recognition and search applications. In our previous work, we proposed cross database training of synchronous hidden Markov models (SHMMs) to make use of external large and publicly available audio databases in addition to the relatively small given audio visual database. In this work, the cross database training approach is improved by performing an additional audio adaptation step, which enables audio visual SHMMs to benefit from audio observations of the external audio models before adding visual modality to them. The proposed approach outperforms the baseline cross database training approach in clean and noisy environments in terms of phone recognition accuracy as well as spoken term detection (STD) accuracy.

Cross database training of audio-visual hidden Markov models for phone recognition

Speech recognition can be improved by using visual information in the form of lip movements of the speaker in addition to audio information. To date, state-of-the-art techniques for audio-visual speech recognition continue to use audio and visual data of the same database for training their models. In this paper, we present a new approach to make use of one modality of an external dataset in addition to a given audio-visual dataset. By so doing, it is possible to create more powerful models from other extensive audio-only databases and adapt them on our comparatively smaller multi-stream databases. Results show that the presented approach outperforms the widely adopted synchronous hidden Markov models (HMM) trained jointly on audio and visual data of a given audio-visual database for phone recognition by 29% relative. It also outperforms the external audio models trained on extensive external audio datasets and also internal audio models by 5.5% and 46% relative respectively. We also show that the proposed approach is beneficial in noisy environments where the audio source is affected by the environmental noise.

Does the technique employed for skin temperature assessment alter outcomes? A systematic review

Skin temperature is an important physiological measure that can reflect the presence of illness and injury as well as provide insight into the localised interactions between the body and the environment. The aim of this systematic review was to analyse the agreement between conductive and infrared means of assessing skin temperature which are commonly employed in in clinical, occupational, sports medicine, public health and research settings. Full-text eligibility was determined independently by two reviewers. Studies meeting the following criteria were included in the review: 1) the literature was written in English, 2) participants were human (in vivo), 3) skin surface temperature was assessed at the same site, 4) with at least two commercially available devices employed—one conductive and one infrared—and 5) had skin temperature data reported in the study. A computerised search of four electronic databases, using a combination of 21 keywords, and citation tracking was performed in January 2015. A total of 8,602 were returned. Methodology quality was assessed by 2 authors independently, using the Cochrane risk of bias tool. A total of 16 articles (n = 245) met the inclusion criteria. Devices are classified to be in agreement if they met the clinically meaningful recommendations of mean differences within ±0.5 °C and limits of agreement of ±1.0 °C. Twelve of the included studies found mean differences greater than ±0.5 °C between conductive and infrared devices. In the presence of external stimulus (e.g. exercise and/or heat) five studies foundexacerbated measurement differences between conductive and infrared devices. This is the first review that has attempted to investigate presence of any systemic bias between infrared and conductive measures by collectively evaluating the current evidence base. There was also a consistently high risk of bias across the studies, in terms of sample size, random sequence generation, allocation concealment, blinding and incomplete outcome data. This systematic review questions the suitability of using infrared cameras in stable, resting, laboratory conditions. Furthermore, both infrared cameras and thermometers in the presence of sweat and environmental heat demonstrate poor agreement when compared to conductive devices. These findings have implications for clinical, occupational, public health, sports science and research fields.

Effectiveness of electrocardiographic guidance in CVAD tip placement

Background International standard practice for the correct confirmation of the central venous access device is the chest X-ray. The intracavitary electrocardiogram-based insertion method is radiation-free, and allows real-time placement verification, providing immediate treatment and reduced requirement for post-procedural repositioning. Methods Relevant databases were searched for prospective randomised controlled trials (RCTs) or quasi RCTs that compared the effectiveness of electrocardiogram-guided catheter tip positioning with placement using surface-anatomy-guided insertion plus chest X-ray confirmation. The primary outcome was accurate catheter tip placement. Secondary outcomes included complications, patient satisfaction and costs. Results Five studies involving 729 participants were included. Electrocardiogram-guided insertion was more accurate than surface anatomy guided insertion (odds ratio: 8.3; 95% confidence interval (CI) 1.38; 50.07; p=0.02). There was a lack of reporting on complications, patient satisfaction and costs. Conclusion The evidence suggests that intracavitary electrocardiogram-based positioning is superior to surface-anatomy-guided positioning of central venous access devices, leading to significantly more successful placements. This technique could potentially remove the requirement for post-procedural chest X-ray, especially during peripherally inserted central catheter (PICC) line insertion.

The case for the plain packaging of tobacco products

AIMS: The Framework Convention on Tobacco Control (FCTC) requires nations that have ratified the convention to ban all tobacco advertising and promotion. In the face of these restrictions, tobacco packaging has become the key promotional vehicle for the tobacco industry to interest smokers and potential smokers in tobacco products. This paper reviews available research into the probable impact of mandatory plain packaging and internal tobacco industry statements about the importance of packs as promotional vehicles. It critiques legal objections raised by the industry about plain packaging violating laws and international trade agreements. METHODS: Searches for available evidence were conducted within the internal tobacco industry documents through the online document archives; tobacco industry trade publications; research literature through the Medline and Business Source Premier databases; and grey literature including government documents, research reports and non-governmental organization papers via the Google internet search engine. RESULTS: Plain packaging of all tobacco products would remove a key remaining means for the industry to promote its products to billions of the world's smokers and future smokers. Governments have required large surface areas of tobacco packs to be used exclusively for health warnings without legal impediment or need to compensate tobacco companies. CONCLUSIONS: Requiring plain packaging is consistent with the intention to ban all tobacco promotions. There is no impediment in the FCTC to interpreting tobacco advertising and promotion to include tobacco packs.

Aligning and characterising group behaviours using role information

Techniques to align spatio-temporal data for large-scale analysis of human group behaviour have been developed. Application of the techniques to sports databases enable sport team's characteristic styles of play to be discovered and compared for tactical analysis. Applications in surveillance to recognise group activities in real-time for person re-identification from low-resolution video footage have also been developed.

An exploration into younger and older pedestrians' risky behaviours at train level crossings

Background: Younger and older pedestrians are both overrepresented in train-pedestrian injury and fatality collision databases. However, scant research has attempted to determine the factors that influence level crossing behaviours for these high risk groups. Method: Five focus groups were undertaken with a total of 27 younger and 17 older pedestrian level crossing users (N = 44). Due to the lack of research in the area, a focus group methodology was implemented to gain a deeper exploratory understanding into the sample’s decision making processes through a pilot study. The three main areas of enquiry were identifying the: (a) primary reasons for unsafe behaviour; (b) factors that deter this behaviour and (c) proposed interventions to improve pedestrian safety at level crossings in the future. Results: Common themes to emerge from both groups regarding the origins of unsafe behaviours were: running late and a fatalistic perspective that some accidents are inevitable. However, younger pedestrians were more likely to report motivators to be: (a) non-perception of danger; (b) impulsive risk taking; and (c) inattention. In contrast, older pedestrians reported their decisions to cross are influenced by mobility issues and sensory salience. Conclusion: The findings indicate that a range of factors influence pedestrian crossing behaviours. This paper will further outline the major findings of the research in regards to intervention development and future research direction.

Left on the side of the road? A review of deterrence-based theoretical developments in road safety

Deterrence-based initiatives form a cornerstone of many road safety countermeasures. This approach is informed by Classical Deterrence Theory, which proposes that individuals will be deterred from committing offences if they fear the perceived consequences of the act, especially the perceived certainty, severity and swiftness of sanctions. While deterrence-based countermeasures have proven effective in reducing a range of illegal driving behaviours known to cause crashes such as speeding and drink driving, the exact level of exposure, and how the process works, remains unknown. As a result the current study involved a systematic review of the literature to identify theoretical advancements within deterrence theory that has informed evidence-based practice. Studies that reported on perceptual deterrence between 1950 and June 2015 were searched in electronic databases including PsychINFO and ScienceDirect, both within road safety and non-road safety fields. This review indicated that scientific efforts to understand deterrence processes for road safety were most intense during the 1970s and 1980s. This era produced competing theories that postulated both legal and non-legal factors can influence offending behaviours. Since this time, little theoretical progression has been made in the road safety arena, apart from Stafford and Warr's (1993) reconceptualisation of deterrence that illuminated the important issue of punishment avoidance. In contrast, the broader field of criminology has continued to advance theoretical knowledge by investigating a range of individual difference-based factors proposed to influence deterrent processes, including: moral inhibition, social bonding, self-control, tendencies to discount the future, etc. However, this scientific knowledge has not been directed towards identifying how to best utilise deterrence mechanisms to improve road safety. This paper will highlight the implications of this lack of progression and provide direction for future research.

Relationship between living alone and food and nutrient intake

The increase in the number of individuals living alone has implications for nutrition and health outcomes. This review aimed to investigate whether there is a difference in food and nutrient intake between adults living alone and those living with others. Eight electronic databases were searched, using terms related to living alone, nutrition, food, and socioeconomic factors. Forty-one papers met the inclusion criteria, and data of interest were extracted. Results varied but suggested that, compared with persons who do not live alone, persons who live alone have a lower diversity of food intake, a lower consumption of some core foods groups (fruit, vegetables, and fish) and a higher likelihood of having an unhealthy dietary pattern. Associations between living alone and nutrient intake were unclear. Men living alone were more often observed to be at greater risk of undesirable intakes than women. The findings of this review suggest that living alone could negatively affect some aspects of food intake and contribute to the relationship between living alone and poor health outcomes, although associations could vary between socioeconomic groups. Further research is required to help to elucidate these findings.