Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

Peer reviewe

The barley pan-genome reveals the hidden legacy of mutation breeding

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Correction to: Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

The original version of this article unfortunately contained a mistake

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Dislodgement Forces and Cost Effectiveness of Dressings and Securement for Peripheral Intravenous Catheters: A Randomized Controlled Trial

Objectives: Peripheral intravenous catheters (PIVC) are the most frequently used invasive devices in medicine. PIVC failure before treatment completion is a significant concern and occurs in 33–69% of patients. Partial dislodgement and accidental removal are some of the reasons for PIVC failure. The most effective dressing and securement method for preventing accidental removal remains unclear. It was the aim of this study to compare the force required to dislodge a PIVC with four commonly used dressing and securement methods. Additionally, costs were calculated. Methods: Truncated 18-gauge i.v. cannulas were attached onto the forearm of 209 volunteers using four different dressings and securements (sterile absorbent wound dressing covered by two different types of elastic polyester fleece, bordered and non-bordered polyurethane). The force during continuously stronger pulling until dislodgement was recorded. Results: The highest resistance against dislodgement forces could be observed with a sterile absorbent wound dressing covered by two incised elastic polyester fleece dressings. Commercially-manufactured bordered and non-bordered polyurethan film dressings were 20% to 75% more expensive than sterile absorbent wound dressings covered by elastic polyester fleece dressing. Conclusions: Elastic polyester fleece secured a PIVC against accidental removal by external force best, compared to commercially-manufactured bordered and non-bordered polyurethane film dressing

Protocol based evaluation for feasibility of extubation compared to clinical scoring systems after major oral cancer surgery safely reduces the need for tracheostomy: a retrospective cohort study

Abstract Background Despite risks, complications and negative impact to quality of life, tracheostomy is widely used to bypass upper airway obstruction after major oral cancer surgery (MOCS). Decision to tracheostomy is frequently based on clinical scoring systems which mainly have not been validated by different cohorts. Delayed extubation in the Intensive Care Unit (ICU) may be a suitable alternative in selected cases. We hypothesize that delayed routine ICU extubation after MOCS instead of scoring system based tracheostomy is safe, feasible and leads to lower tracheostomy rates. Methods We retrospectively analyzed our clinical protocol which provides routine extubation of patients after MOCS in the ICU. The primary outcome measure was a composite of early reintubation within 24 h or secondary tracheostomy. Secondary outcome measures included airway obstruction related morbidity and mortality. Predictor variables included tumor localisation, surgical procedure and reconstruction method, length of operation and pre-existing morbidity. Furthermore we assessed the ability of four clinical scoring systems to identify patients requiring secondary tracheostomy. Statistical processing includes basic descriptive statistics, Chi-squared test and multivariate logistic regression analysis. Results Two hundred thirty four cases were enclosed to this retrospective study. Fourteen patients (6%) required secondary tracheostomy, Ten patients (4%) required reintubation within 24 h after extubation. No airway obstruction associated mortality, morbidity and cannot intubate cannot ventilate situation was observed. Seventy five percent of the patients were extubated within 17 h after ICU admission. All evaluated scores showed a poor positive predictive value (0.08 to 0.18) with a sensitivity ranged from 0.13 to 0.63 and specificity ranged from 0.5 to 0.93. Conclusions Our data demonstrate that common clinical scoring systems fail to prevent tracheostomy in patients after MOCS. Application of scoring systems may lead to a higher number of unnecessary tracheostomies. Delayed routine extubation in the ICU after MOCS seems an appropriate and safe approach to avoid tracheostomy and the related morbidity

An easy-to-build, low-budget point-of-care ultrasound simulator: from Linux to a web-based solution

Abstract Background Hands-on training in point-of-care ultrasound (POC-US) should ideally comprise bedside teaching, as well as simulated clinical scenarios. High-fidelity phantoms and portable ultrasound simulation systems are commercially available, however, at considerable costs. This limits their suitability for medical schools. A Linux-based software for Emergency Department Ultrasound Simulation (edus2TM) was developed by Kulyk and Olszynski in 2011. Its feasibility for POC-US education has been well-documented, and shows good acceptance. An important limitation to an even more widespread use of edus2, however, may be due to the need for a virtual machine for WINDOWS® systems. Our aim was to adapt the original software toward an HTML-based solution, thus making it affordable and applicable in any simulation setting. Methods We created an HTML browser-based ultrasound simulation application, which reads the input of different sensors, triggering an ultrasound video to be displayed on a respective device. RFID tags, NFC tags, and QR Codes™ have been integrated into training phantoms or were attached to standardized patients. The RFID antenna was hidden in a mock ultrasound probe. The application is independent from the respective device. Results Our application was used successfully with different trigger/scanner combinations and mounted readily into simulated training scenarios. The application runs independently from operating systems or electronic devices. Conclusion This low-cost, browser-based ultrasound simulator is easy-to-build, very adaptive, and independent from operating systems. It has the potential to facilitate POC-US training throughout the world, especially in resource-limited areas