What fraction of the human genome is functional?

Many evolutionary studies over the past decade have estimated α(sel), the proportion of all nucleotides in the human genome that are subject to purifying selection because of their biological function. Most of these studies have estimated the nucleotide substitution rates from genome sequence alignments across many diverse mammals. Some α(sel) estimates will be affected by the heterogeneity of substitution rates in neutral sequence across the genome. Most will also be inaccurate if change in the functional sequence repertoire occurs rapidly relative to the separation of lineages that are being compared. Evidence gathered from both evolutionary and experimental analyses now indicate that rates of "turnover" of functional, predominantly noncoding, sequence are, indeed, high. They are sufficiently high that an estimated 50% of mouse constrained noncoding sequence is predicted not to be shared with rat, a closely related rodent. The rapidity of turnover results in, at least, a twofold underestimate of α(sel) by analyses that measure constraint across the eutherian phylogeny. Approaches that take account of turnover estimate that the steady-state value of α(sel) lies between 10% and 15%. Experimental studies corroborate the predicted rates of loss and gain of noncoding functional sites. These studies show the limitations inherent in the use of deep sequence conservation for identifying functional sequence. Experimental investigations focusing on lineage-specific, noncoding, and functional sequence are now essential if we are to appreciate the complete functional repertoire of the human genome.     

Natural genetic variation caused by small insertions and deletions in the human genome

Human genetic variation is expected to play a central role in personalized medicine. Yet only a fraction of the natural genetic variation that is harbored by humans has been discovered to date. Here we report almost 2 million small insertions and deletions (INDELs) that range from 1 bp to 10,000 bp in length in the genomes of 79 diverse humans. These variants include 819,363 small INDELs that map to human genes. Small INDELs frequently were found in the coding exons of these genes, and several lines of evidence indicate that such variation is a major determinant of human biological diversity. Microarray-based genotyping experiments revealed several interesting observations regarding the population genetics of small INDEL variation. For example, we found that many of our INDELs had high levels of linkage disequilibrium (LD) with both HapMap SNPs and with high-scoring SNPs from genome-wide association studies. Overall, our study indicates that small INDEL variation is likely to be a key factor underlying inherited traits and diseases in humans.     

Study protocol: optimization of complex palliative care at home via telemedicine. A cluster randomized controlled trial

Background

Due to the growing number of elderly with advanced chronic conditions, healthcare services will come under increasing pressure. Teleconsultation is an innovative approach to deliver quality of care for palliative patients at home. Quantitative studies assessing the effect of teleconsultation on clinical outcomes are scarce. The aim of this present study is to investigate the effectiveness of teleconsultation in complex palliative homecare.

Methods/Design

During a 2-year recruitment period, GPs are invited to participate in this cluster randomized controlled trial. When a GP refers an eligible patient for the study, the GP is randomized to the intervention group or the control group. Patients in the intervention group have a weekly teleconsultation with a nurse practitioner and/or a physician of the palliative consultation team. The nurse practitioner, in cooperation with the palliative care specialist of the palliative consultation team, advises the GP on treatment policy of the patient. The primary outcome of patient symptom burden is assessed at baseline and weekly using the Edmonton Symptom Assessment Scale (ESAS) and at baseline and every four weeks using the Hospital Anxiety and Depression Scale (HADS). Secondary outcomes are self-perceived burden from informal care (EDIZ), patient experienced continuity of medical care (NCQ), patient and caregiver satisfaction with the teleconsultation (PSQ), the experienced problems and needs in palliative care (PNPC-sv) and the number of hospital admissions.

Discussion

This is one of the first randomized controlled trials in palliative telecare. Our data will verify whether telemedicine positively affects palliative homecare.

Trial registration

The Netherlands National Trial Register NTR2817     

Genome assembly quality: Assessment and improvement using the neutral indel model

We describe a statistical and comparative-genomic approach for quantifying error rates of genome sequence assemblies. The method exploits not substitutions but the pattern of insertions and deletions (indels) in genome-scale alignments for closely related species. Using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters of nucleotides that were wrongly inserted or deleted during sequencing or assembly. Thus, the method is well-suited to assessing fine-scale sequence quality within single assemblies, between different assemblies of a single set of reads, and between genome assemblies for different species. When applying this approach to four primate genome assemblies, we found that average gap error rates per base varied considerably, by up to sixfold. As expected, bacterial artificial chromosome (BAC) sequences contained lower, but still substantial, predicted numbers of errors, arguing for caution in regarding BACs as the epitome of genome fidelity. We then mapped short reads, at approximately 10-fold statistical coverage, from a Bornean orangutan onto the Sumatran orangutan genome assembly originally constructed from capillary reads. This resulted in a reduced gap error rate and a separation of error-prone from high-fidelity sequence. Over 5000 predicted indel errors in protein-coding sequence were corrected in a hybrid assembly. Our approach contributes a new fine-scale quality metric for assemblies that should facilitate development of improved genome sequencing and assembly strategies.Genome sequence assemblies form the bedrock of genome research. Any errors within them directly impair genomic and comparative genomic predictions and inferences based upon them. The prediction of functional elements or the elucidation of the evolutionary provenance of genomic sequence, for example, relies on the fidelity and completeness of these assemblies. Imperfections, such as erroneous nucleotide substitutions, insertions or deletions, or larger-scale translocations, may misinform genome annotations or analyses (Salzberg and Yorke 2005; Choi et al. 2008; Phillippy et al. 2008). Insertion and deletion (indel) errors are particularly hazardous to the prediction of protein-coding genes since many introduce frame-shifts to otherwise open reading frames. Noncoding yet functional sequence can be identified from a deficit of indels (Lunter et al. 2006), but only where this evolutionary signal has not been obscured by indel errors. Several high-quality reference genomes currently exist, and many errors in initial draft genome sequence assemblies have been rectified in later more finished assemblies. However, because of the substantial costs involved, among the mammals only the genomes of human, mouse, and dog have been taken (or are being taken) toward “finished” quality, defined as fewer than one error in 10⁴ bases and no gaps (International Human Genome Sequencing Consortium 2004; Church et al. 2009). It is likely that other draft genome assemblies will remain in their unfinished states until technological improvements substantially reduce the cost of attaining finished genome quality.Genome assemblies have been constructed from sequence data produced by different sequencing platforms and strategies, and using a diverse array of assembly algorithms (e.g., PCAP [Huang et al. 2003], ARACHNE [Jaffe et al. 2003], Atlas [Havlak et al. 2004], PHUSION [Mullikin and Ning 2003], Jazz [Aparicio et al. 2002], and the Celera Assembler [Myers et al. 2000]). The recent introduction of new sequencing technologies (Mardis 2008) further complicates genome assemblies, as each platform exhibits read lengths and error characteristics very different from those of Sanger capillary sequencing reads. These new technologies have also spawned additional assembly and mapping algorithms, such as Velvet (Zerbino and Birney 2008) and MAQ (Li et al. 2008). Considering the methodological diversity of sequence generation and assembly, and the importance of high-quality primary data to biologists, there is a clear need for an objective and quantitative assessment of the fine-scale fidelity of the different assemblies.One frequently discussed property of genome assemblies is the N50 value (Salzberg and Yorke 2005). This is defined as the weighted median contig size, so that half of the assembly is covered by contigs of size N50 or larger. While the N50 value thus quantifies the ability of the assembler algorithm to combine reads into large seamless blocks, it fails to capture all aspects of assembly quality. For example, artefactually high N50 values can be obtained by lowering thresholds for amalgamating smaller blocks of—often repetitive—contiguous reads, resulting in misassembled contigs, although approaches to ameliorate such problems are being developed (Bartels et al. 2005; Dew et al. 2005; Schatz et al. 2007). Some validation of the global assembly accuracy, as summarized by N50, can be achieved by comparison with physical or genetic maps or by alignment to related genomes. Contiguity can also be quantified from the alignment of known cDNAs or ESTs. More regional errors can be indicated by fragmentation, incompleteness, or exon noncollinearity of gene models, or by unexpectedly high read depths that often reflect collapse of virtually identical segmental duplications.In addition to these problems, N50 values fail to reflect fine-scale inaccuracies, such as substitution and indel errors. Quality at the nucleotide level is summarized as a phred score, with scores exceeding 40 indicating finished sequence (Ewing and Green 1998) and corresponding to an error rate of less than one base in 10,000. Once assembled, a base is assigned a consensus quality score (CQS) depending on its read depth and the quality of each base contributing to that position (Huang and Madan 1999). Finally, assessing sequence error has traditionally relied on comparison with bacterial artificial chromosome (BAC) sequence. Discrepancies between assembly and BAC sequences are assumed to reflect errors in the draft sequence, although a minority may remain in the finished BAC sequence.Here, we introduce a statistical and comparative genomics method that quantifies the fine-scale quality of a genome assembly and that has the merit of being complementary to the aforementioned approaches. Instead of considering rates of nucleotide substitution errors in an assembly, which are already largely indicated by CQSs, the method quantifies genome assembly quality by the rate of insertion and deletion errors in alignments. This approach estimates the abundance of indel errors between aligned genome pairs, by separating these from true evolutionary indels.Previously, we demonstrated that in the absence of selection, indel mutations leave a precise and determinable fingerprint on the distribution of ungapped alignment block lengths (Lunter et al. 2006). These block lengths, which represent distances between successive indel mutations (represented as gaps within genome alignments), we refer to as intergap segment (IGS) lengths. Under the neutral indel model, these IGS lengths are expected to follow a geometric frequency distribution whenever sequence has been free of selection. There is substantial evidence that the large majority of mammalian genome sequence has evolved neutrally (Mouse Genome Sequencing Consortium 2002; Lunter et al. 2006). More specifically, virtually all transposable elements (TEs) have, upon insertion, subsequently been free of purifying selection (Lunter et al. 2006; Lowe et al. 2007). This absence of selection manifests itself in IGS in ancestral repeats (those TEs that were inserted before the common ancestor of two species), closely following the geometric frequency distribution expected of neutral sequence (Fig. 1A).Open in a separate windowFigure 1.Genomic distribution of intergap segment lengths in mouse-rat alignments for ancestral repeats (A) and whole-genome sequences (B). Frequencies of IGS lengths are shown on a natural log scale. The black line represents the prediction of the neutral indel model, a geometric distribution of IGS lengths; observed counts (blue circles) are accumulated in 5 bp bins of IGS lengths. Within mouse-rate ancestral repeat sequence, the observations fit the model accurately for IGS between 10 bp and 300 bp. For whole-genome data, a similarly close fit is observed for IGS between 10 bp and 100 bp. Beyond 100 bp, an excess of longer IGSs (green) above the quantities predicted by the neutral indel model can be observed, representing functional sequence that has been conserved with regards to indel mutations. The depletion of short (<10 bp) IGS reflects a “gap attraction” phenomenon (Lunter et al. 2008).Within conserved functional sequence, on the other hand, deleterious indels will tend to have been purged, hence IGS lengths frequently will be more extended compared with neutral sequence. This results in a departure of the observed IGS length distribution from the geometric distribution (Fig. 1B), the extent of which allows the amount of functional sequence shared between genome pairs to be estimated accurately (for further details, see Lunter et al. 2006).In any alignment, a proportion of gaps will represent true evolutionary events, whereas the remainder represent “gap errors” that inadvertently have been introduced during sequencing and assembly. Causes of assembly errors, such as insufficient read coverage or mis-assembly, are often regional and thus may be expected to result in clustering of errors. In contrast, from the results of comparisons between species such as human and mouse, true evolutionary indel events appear to be only weakly clustered, for instance, through a dependence of indel rate on G+C content (Lunter et al. 2006). Indels may cluster because of recurrent and regional positive selection of nucleotide insertions and/or deletions. Nevertheless, these effects are unlikely to be sufficiently widespread to explain the high rates of indel clustering (up to one indel per 4 kb) that we discuss later. Indels may also cluster because of mutational biases that are independent of G+C, although we know of no such short-distance effects (see Discussion). This reasoning provided the rationale for seeking to exploit the neutral indel model to estimate the number of gap errors in alignments of two assemblies. Purifying selection on indels and clustered indel errors contribute to largely distinct parts of the observed IGS histogram: The former increases the representation of long IGS (Fig. 1B), whereas the latter cause short IGS to become more prevalent than expected.Nevertheless, owing to the considerable divergence between human and mouse, the probability of a true indel greatly exceeds assembly indel error rates (5 × 10⁻² versus 10⁻³ to 10⁻⁴ per nucleotide) (see below) (Lunter et al. 2006). In short, the large number of true indel events renders the proportion of gap errors so low as to be inestimable. Even for more closely related species, such as mouse and rat (Fig. 1A), neutral sequence is estimated to contain one true indel per 50 bases, which is also approximately 100-fold higher than the frequency of indel errors we will report later. Consequently, indel errors will be most easily discerned between genome assemblies from yet more closely related species. Few species pairs, whose divergence within neutral sequence is low (<5%), have yet been sequenced. Nevertheless, recent reductions in sequencing costs are likely to result in substantial numbers of closely related genomes being sequenced in the near future.For this analysis, we took advantage of the newly available genome assembly of the Sumatran orangutan (Pongo pygmaeus abelii), sequenced using a conventional capillary sequencing approach (Orangutan Genome Sequencing Consortium, in prep.; D Locke, pers. comm.), and its alignment to other closely related great ape genome assemblies, namely, those of human (Homo sapiens) and chimpanzee (Pan troglodytes). The latter two genomes have been sequenced to finished quality and sixfold coverage, respectively (see Methods) (International Human Genome Sequencing Consortium 2004; The Chimpanzee Sequencing and Analysis Consortium 2005), whereas the effective coverage of the Sumatran orangutan is lower at approximately fourfold (Orangutan Genome Sequencing Consortium, in prep.).We were able to take advantage of a data set of short reads at approximately 10-fold statistical coverage from a single Bornean orangutan (Pongo pygmaeus pygmaeus) that was shotgun-sequenced using the Illumina short read platform as part of the orangutan sequencing project (Orangutan Genome Sequencing Consortium, in prep.). This substantial read depth afforded us an opportunity to quantify the improvement to traditional capillary-read assemblies from the mapping of short sequence reads. Using a sequence mapper (Stampy) that was specifically designed for high sensitivity and accuracy in the presence of indels as well as substitution mutations (see Methods) (GA Lunter and M Goodson, in prep.), we placed these reads onto the Sumatran orangutan genome assembly. Using this assembly as a template, we called indels and substitutions and, from these, derived a templated assembly of the Bornean individual. This assembly is expected to contain polymorphisms specific to the Bornean individual and also to correct many fine-scale substitution and indel errors present in the Sumatran capillary-read assembly. The assembly will be syntenic with the Sumatran assembly, rather than following the Bornean genome where structural variants exist. Moreover, in regions where the Sumatran genome is divergent or contains many errors, reads will not be mapped; such regions will be excluded from the templated assembly. Using our indel error statistics, we show that this templated assembly improves on the original assembly in terms of accuracy by effectively separating low-fidelity from high-fidelity sequence.     

Massive turnover of functional sequence in human and other mammalian genomes

Despite the availability of dozens of animal genome sequences, two key questions remain unanswered: First, what fraction of any species'' genome confers biological function, and second, are apparent differences in organismal complexity reflected in an objective measure of genomic complexity? Here, we address both questions by applying, across the mammalian phylogeny, an evolutionary model that estimates the amount of functional DNA that is shared between two species'' genomes. Our main findings are, first, that as the divergence between mammalian species increases, the predicted amount of pairwise shared functional sequence drops off dramatically. We show by simulations that this is not an artifact of the method, but rather indicates that functional (and mostly noncoding) sequence is turning over at a very high rate. We estimate that between 200 and 300 Mb (∼6.5%–10%) of the human genome is under functional constraint, which includes five to eight times as many constrained noncoding bases than bases that code for protein. In contrast, in D. melanogaster we estimate only 56–66 Mb to be constrained, implying a ratio of noncoding to coding constrained bases of about 2. This suggests that, rather than genome size or protein-coding gene complement, it is the number of functional bases that might best mirror our naïve preconceptions of organismal complexity.What fraction of a genome confers biological function, as opposed to the remaining proportion that has had no biological effect and thus has not been subject to selection? While the complement of (functional) protein-coding sequence has been estimated in many organisms (e.g., 1.06% of the human genome; Church et al. 2009), it has been more challenging to identify functional sequence that fails to encode protein (Mouse Genome Sequencing Consortium 2002). Even the more simple task of estimating the size of this fraction, or more precisely, the genomic fraction that is under evolutionary constraint and is thereby inferred to confer function to the organism, has proven particularly contentious (Chiaromonte et al. 2003; Pheasant and Mattick 2007).Methods to detect constraint do so by comparing genomic sequence and therefore show greatest power to identify “shared” constrained sequence, and lower power to reveal sequence whose function is “lineage-specific.” Analyzing species at various divergences thus offers an opportunity to investigate the dynamics of genome evolution: Is the functional fraction largely shared and evolving slowly by accumulating a low rate of point mutations, or does, instead, rapid sequence turnover of lineage-specific functional sequence play an important role? While protein-coding genes appear to evolve predominantly in the first mode, it is readily apparent that lineage-specific sequence occurs abundantly in most genomes. Instances where functional sequence has been gained, and erstwhile functional sequence has been lost, have been identified in mammals (Dermitzakis and Clark 2002; Smith et al. 2004; Odom et al. 2007; Kunarso et al. 2010), flies (Ludwig et al. 2000; Bergman and Kreitman 2001; Moses et al. 2006), and yeast (Borneman et al. 2007). Although convincing, these examples represent a very small fraction of the functional complement of each genome, and argue neither for nor against the ubiquity of functional sequence turnover.A second key question is whether the genomes of different species contain different amounts of functional sequence, and whether this measure is related to organismal complexity. For example, it is clear that both the genome size and the number of genes present in a genome fail to reflect at least naïve preconceptions of organismal complexity (Gregory 2005; Ponting 2008). While varying proportions of nonfunctional (“junk”) DNA, often in the form of transposed repetitive elements (TEs), may explain the large variation in genome size across species, the relatively stable number of protein-coding genes suggests the possibility that our naïve notion of complexity is fundamentally incorrect, and that many species are in fact of comparable complexity, in a sense yet to be defined. Alternatively, it may be that much of the apparent differences in complexity between species are encoded by a varying amount of noncoding regulatory sequence, regulating a fairly stable core of protein-coding genes.Addressing these two questions requires accurate estimates of the amount of functional, yet noncoding, sequence in genomes from across the metazoan subkingdom. Several groups have developed comparative genomic methods to estimate this quantity. For example, an early estimate of the genomic fraction of human constrained sequence was obtained from alignments of human and mouse genome assemblies, and suggested that approximately α_sel = 5% of the human genome has been subject to selective constraint (Chiaromonte et al. 2003). (Here, we adopt from Chiaromonte et al. the symbol α_sel as the estimated fraction of a genome that has been subject to selective constraint and thus may be considered functional. In addition, we define g as the full extent of the euchromatic sequence of a genome, and g_sel = g × α_sel as the amount of sequence that has been subject to purifying selection.) This estimate of α_sel was obtained by contrasting nucleotide conservation inside and outside of ancestral repeats (ARs, TEs whose insertion predates the species'' last common ancestor) while taking account of the known regional variation in nucleotide substitution rates. Subsequently, other substitution-based approaches, taking advantage of multiple genome sequence alignments, yielded similar results (Margulies et al. 2003; Cooper et al. 2005; Siepel et al. 2005).All such estimates of α_sel have shown a strong dependence on the parameterization of the underlying neutral substitution model, and as neutral substitutions are difficult to model (Clark 2006), the resulting estimates have wide confidence intervals. For example, the initial approach by Chiaromonte et al. (2003) indicated α_sel as being between 2.3% and 7.9% of the human genome, depending on which values of model parameters were chosen. The attendant uncertainty in the final estimates makes it difficult to use this or similar methods to quantify lineage-specific constrained sequence.More recently, three analyses have estimated α_sel by taking advantage of the 1% of the human genome that has been scrutinized within the pilot phase of the ENCODE project (The ENCODE Project Consortium 2007). These yielded higher α_sel estimates of between 5% and 12% (Asthana et al. 2007; Garber et al. 2009; Parker et al. 2009) with the spread of α_sel values being again dependent upon the values of model parameters that were chosen. With one algorithm constraint was identified within 45% of ARs (Parker et al. 2009). Estimates of α_sel in ENCODE regions may also be upwardly biased, since only some of ENCODE''s regions were randomly selected, while others were chosen because of their functional content.For invertebrates estimates of α_sel have also been imprecise, in the main because their small genomes often contain only a meager amount of neutrally evolving sequence on which to tune a neutral model (Peterson et al. 2009). Estimates of α_sel for Drosophila range between ∼40% and 70% (Andolfatto 2005; Siepel et al. 2005; Halligan and Keightley 2006; Keith et al. 2008), while one study indicated that 18%–37% of the Caenorhabditis elegans genome is under selective constraint (Siepel et al. 2005).As alluded to above, methods for inferring quantities of functional DNA rest upon the hypothesis that in functional sequence most nucleotide changes are detrimental, causing such changes to be purged from the species'' populations, which results in evolutionarily conserved sequence. Methods for quantifying constrained sequence typically contrast interspecies levels of sequence conservation within a sequence of interest and within matched putatively neutrally evolved sequence, typically ARs. While the deletion of conserved sequence identified in this manner does not always result in an overt phenotype (Ahituv et al. 2007; Visel et al. 2009), it has been shown that selection rather than mutational cold-spots are responsible for the low rate of mutation accumulation (Drake et al. 2006). The outlined approach has been further criticized for overlooking sequence that is lineage-specific or that exhibits only weak conservation (Dermitzakis and Clark 2002), for tacitly assuming, rather than demonstrating, the neutrality of ARs, and for overlooking sequence that has evolved by positive, rather than negative, selection (Pheasant and Mattick 2007).Here, we estimate the quantities of functional DNA that are shared between species pairs at various divergences. This allows us to investigate the dependence of this quantity on species divergence, thus partially addressing lineage specificity. An earlier study using the same method demonstrated that ARs are predominantly neutrally evolving (Lunter et al. 2006), thereby addressing the second concern, and the present study confirms these findings. By continuing to overlook potentially positively selected sequence our estimates of the amount of functional sequence are expected to remain slightly conservative.The approach presented here (based on the neutral indel model; Lunter et al. 2006) uses indel mutations, rather than single-nucleotide substitutions, to estimate α_sel. Although indel events occur approximately eightfold less often than substitution mutations (Lunter 2007; Cartwright 2009), their impact upon functional sequence may well be more profound than that exerted by single-nucleotide substitutions. Indels may induce, for example, frame shifts in coding regions and secondary structure changes in RNAs, suggesting that stronger purifying selection may often act upon them. This will compensate for their lower mutation rate when indels are exploited in approaches to detecting evolutionary constraint. In contrast to many substitution-based methods that require fitting an explicit background model to neutrally evolving sequence, the present method has a single free parameter (the indel rate) which can be trained from the full data, without the requirement of first identifying the neutral fraction.Here, we estimate α_sel values for diverse mammalian species and for birds, teleost fish, and fruit flies. We show that the neutral indel model estimates g_sel for closely related pairs as being up to threefold higher than for more distantly related species, a result that is a feature of the data rather than being an inherent bias of the method. This suggests a substantial rate of “turnover” of otherwise constrained sequence. Finally, we show that, despite their comparable protein-coding gene complement, vertebrate (mammalian or avian) genomes harbor substantially more functional sequence than invertebrate (Drosophila and C. elegans) genomes, as a result of a larger complement of functional noncoding sequence.     

Comparing lignocaine-adrenaline-tetracaine gel with lignocaine infiltration for anesthesia during repair of lacerations: A randomized trial

BACKGROUND:

This study aimed to compare the topical anesthetic lignocaine, adrenaline, and tetracaine (LAT) (4% lignocaine, 1:2 000 adrenaline, 1% tetracaine) with the conventional lignocaine infiltration(LI) for repair of minor lacerations, for the comfort of anesthetic administration, efficacy, adverse effects and cost.

METHODS:

This was a prospective randomized clinical trial. Forty Asian patients who required toilet and suture for minor lacerations in the emergency department of the Singapore General Hospital over a 4-month period. The patients were assigned randomly to 2 arms of treatment. The first was the LAT gel group who had LAT gel applied to the laceration prior to suturing. The second was the control group in whom the anesthetic administered was lignocaine infiltration (LI) via a syringe. The pain of the process of administering anesthetic and efficacy of anesthesia were scored using the visual pain scale included within. The efficacy of LAT vs. lignocaine infiltration as an anesthetic prior to the toilet and suture of minor lacerations and complications of therapy.

RESULTS:

Twenty patients were randomized to LAT gel and 16 to LI on an intention to treat analysis. The mean pain score by patients in the LAT gel group was 2.5 (0.52 SE), and 2.5 (0.58 SE) in the LI group. The pain score for pain during application of the anesthetic was 1.5 (0.40) in the LAT gel group, and 3.5 (0.46) in the LI group. There was no difference in complications between the LAT and LI groups

CONCLUSION:

LAT gel prior to the toilet and suture of minor lacerations is proven to be as efficacious as LI in terms of patient comfort and effectiveness of anesthesia. The complications are also comparable to those treated with LI.KEY WORDS: Lignocaine infiltration, Lacerations, Emergency department, Pain score     

9The TANTALUSTM System for obesity: effect on gastric emptying of solids

Background: Gastric electrical stimulation (GES) is currently investigated for the treatment of obesity. The TANTALUS System delivers gastric contractility modulation (GCM) signals in synchrony with gastric slow waves, resulting in significant augmentation of gastric contractions during food intake. We hypothesized that such modulation of contractile activity may affect gastric emptying and plasma ghrelin levels. Aim: To test the effect of GCM of the gastric antrum on gastric emptying of solids and ghrelin levels. Methods: 12 obese subjects were implanted with 2 pairs of antral electrodes and an implantable pulse generator (IPG, TANTALUS ^TM) Gastric emptying test (GE) for solids was performed twice, on separate days, in each subject, starting few weeks after implantation: 1) control, before the start of stimulation, and 2) with stimulation, after device was turned on. Blood samples for ghrelin, were taken at baseline, and at 15, 30, 60 and 120 min after the test meal. Results as mean + SD, analysis by t‐test and p < 0.05. Results: 11 females, 1 male, age: 39.1 ± 8.9 years, BMI: 41.6 ± 3.4, 3 subjects with type 2 diabetes. One diabetic patient did not complete GE test because of technical issues. GCM significantly accelerated gastric emptying: retention at 2 hours 18.7 ± 12.2% vs. 31.9 ± 16.4%, stimulation vs. control respectively, p = 0.008. T ^1/2 78.3 ± 23.5 vs. 95 ± 31.7 min, stimulation vs. control respectively, p = 0.04. Mean results for gastric emptying were within normal at both baseline and stimulation. Meal ingestion induced only minimal, insignificant reduction in ghrelin levels. There was no significant difference in AUC of ghrelin between control and stimulation. Conclusions: After GCM stimulation, there is significant acceleration of gastric emptying of solids in obese patients, without affect on ghrelin levels. The obese subjects did not exhibit the significant, meal‐induced reduction in ghrelin.      

Eliciting Young People’s Views on Wellbeing Through Contemporary Science Debates in Wales

Renewed vigour in wellbeing measurement combined with a shift towards a ‘new sociology of childhood’ has resulted in growing emphasis on incorporating the voices and perspectives of young people in discussions of what matters to them and how this can feed into broader indicator development. This has led to a more sustained effort to ask young people directly about what contributes to their wellbeing. This raises important questions about how young people should be engaged in discussions about what wellbeing means to them. This paper provides an account of an innovative approach to eliciting young people’s views on wellbeing in Wales, United Kingdom, using the vehicle of ‘contemporary science debates’ (CSD). CSD is designed to engage young people in innovative and participative discussions on social and ethical issues associated with contemporary science. Here, it is used to provide young people with the opportunity to debate the relevance of wellbeing to their every-day lives and give them an opportunity to make their opinions heard. The paper explores the value of using this approach as a methodology for gathering information on what young people understand about wellbeing and provides an initial analysis of which aspects of wellbeing were identified as important for them. It situates this within the broader context of giving voice to young people in the development of subjective wellbeing measures.     

The active components of effective training in obstetric emergencies

Confidential enquiries into poor perinatal outcomes have identified deficiencies in team working as a common factor and have recommended team training in the management of obstetric emergencies. Isolated aviation-based team training programmes have not been associated with improved perinatal outcomes when applied to labour ward settings, whereas obstetric-specific training interventions with integrated teamwork have been associated with clinical improvements. This commentary reviews obstetric emergency training programmes from hospitals that have demonstrated improved outcomes to determine the active components of effective training. The common features identified were: institution-level incentives to train; multi-professional training of all staff in their units; teamwork training integrated with clinical teaching and use of high fidelity simulation models. Local training also appeared to facilitate self-directed infrastructural change.