Making bioinformatics training FAIR: the EMBL-EBI training portal.

EMBL-EBI provides a broad range of training in data-driven life sciences. To improve awareness and access to training course listings and to make digital learning materials findable and simple to use, the EMBL-EBI Training website, www.ebi.ac.uk/training, was redesigned and restructured. To provide a framework for the redesign of the website, the FAIR (findable, accessible, interoperable, reusable) principles were applied to both the listings of live training courses and the presentation of on-demand training content. Each of the FAIR principles guided decisions on the choice of technology used to develop the website, including the details provided about training and the way in which training was presented. Since its release the openly accessible website has been accessed by an average of 58,492 users a month. There have also been over 12,000 unique users creating accounts since the functionality was added in March 2022, allowing these users to track their learning and record completion of training. Development of the website was completed using the Agile Scrum project management methodology and a focus on user experience. This framework continues to be used now that the website is live for the maintenance and improvement of the website, as feedback continues to be collected and further ways to make training FAIR are identified. Here, we describe the process of making EMBL-EBI's training FAIR through the development of a new website and our experience of implementing Agile Scrum.

The effect of surgical complications on long-term prognosis following oesophagectomy.

INTRODUCTION: Complications are frequent after oesophagectomy, and there is evidence these adversely impact long-term prognosis. However, the effect of multiple complications, and the absolute magnitude of effect on survival is unclear. This study aimed to examine these effects in a single high-volume UK unit. METHODS: Patients undergoing oesophagectomy for cancer and who survived to 90 days post-oesophagectomy were analysed. Complications were graded according to the Clavien-Dindo (CD) classification and the Comprehensive Complication Index (CCI). The effect and magnitude of effect of complications on survival were assessed using multivariable cox regression and the risk-adjusted population attributable fraction. RESULTS: In total, 380 patients were included. Complications occurred in 251 (66.1%). Suffering ≥3 complications (HR 1.89, 95%CI 1.13-3.16, p = 0.015) or an unplanned escalation in care (HR 2.22, 95%CI 1.43-3.45, p < 0.001) significantly reduced survival whereas pulmonary complications and anastomotic leak did not. Patients with a CCI>30 had worse overall survival (HR 1.91, 95%CI 1.32-2.76, p < 0.001) and CCI>30 due to multiple minor complications gave a worse prognosis compared to CCI>30 due to major complications (HR 2.44, 95%CI 1.14-5.20, p = 0.022). An estimated 9.1% (95%CI 3.4-14.4%) of deaths at 5 years were attributable to a CCI>30. CONCLUSION: Long-term survival following oesophagectomy for cancer is significantly affected by complications and the cumulative effect of multiple complications. Interestingly, multiple minor complications had a worse effect on survival than major complications. The absolute magnitude of effect is substantial: minimising all types of postoperative complications could have significant benefit to overall outcomes.

Characteristics of patients with diabetes hospitalised for COVID-19 infection-a brief case series report.

OBJECTIVES: Diabetes has been shown to be a risk factor for corona virus disease-2019 (COVID-19) infection. The characteristics of patients with diabetes vulnerable to this infection are less specified. We aim to present the characteristics of patients with diabetes admitted to hospital with COVID-19. DESIGN: A retrospective case series. SETTING: A single clinical centre in the UK. METHODS: We have retrospectively collected the demographics, medical characteristics and outcome of all patients with diabetes admitted to hospital over two-week period with COVID-19 infection. All cases were diagnosed by a reverse transcription polymerase chain reaction (RT-PCR) of pharyngeal and nasal swabs. RESULTS: A total of 71 COVID-19 patients were admitted during the study period of whom 16 (22.5%) patients had diabetes and were included in this case series. There was no significant difference between patients with compared to those without diabetes regarding age, gender or clinical presentation. However, comorbidities were more common in patients with diabetes specially hypertension {75% v 36.4%, a difference of 38.6%, 95% confidence interval (CI) 6.5-58.3} and chronic kidney disease (37.5 v 5.5, a difference of 32% (1.6-51.6). Patients with diabetes were significantly more obese than those without diabetes (56.2% v 21.8% a difference of 34.4%, 95% CI 7.7-61.1). About one third (31.3%) of patients with diabetes were frail. Mean {standard deviation (SD)} duration of diabetes was 10 (2.8) years and mean (SD) HbA1c was 60.3 (15.6) mmol/mol. The use of angiotensin converting enzyme (ACE) inhibitors, angiotensin receptor blockers (ARBs) and non-steroidal anti-inflammatory drugs (NSAIDs) was common (37.5%, 25% and 18.8% respectively). There was no significant difference in the outcomes between patients with compared to those without diabetes. CONCLUSION: Patients with diabetes hospitalised for COVID-19 were significantly more obese and had high prevalence of comorbidities than those without diabetes. Other features of patients with diabetes and COVID-19 infection included long duration of diabetes, less tight glycaemic control and common use of ACE inhibitors, ARBs and NSAIDs.

Chinese and British Hospitalised Patients with COVID-19-a Comparative Case Series Analysis.

The COVID-19 pandemic initially started in China then spread to Europe. It is not known whether COVID-19 affects patients differently across the two continents. We aimed to describe our cohort of patients admitted to a single British centre with COVID-19 in comparison to a Chinese cohort of similar size and admitted over a similar time period to Chinese centres. We present a comparison of 62 Chinese and 71 British cases hospitalised for COVID-19. Cases in both sites were confirmed by a positive RT-PCR of nasopharyngeal swabs. Comparison analysis highlighted some differences between both populations. The most striking difference is the significantly older age of the British population (72% of the British ≥ 66 years compared to only 3% of the Chinese patients, difference of 69%, 95% confidence interval (CI) 68.3% to 69.7%, respectively) and the associated significant premorbid conditions (85% of patients vs 32%, difference of 53%, 95% CI 52 to 54%, respectively). Gastrointestinal and general symptoms were more common clinical presentation in the British while respiratory symptoms were more prominent in the Chinese cohort. Mortality was significantly higher in the British cohort 14% compared to none in the Chinese cohort (difference of 14%, 95% CI 13.7 to 14.3%). We conclude that COVID-19 does present differently in these two cohorts, but the apparent differences in the clinical presentations could be explained by the inherent differences in the demographics and case mix between both countries.

Soil net nitrogen mineralisation across global grasslands.

Soil nitrogen mineralisation (Nmin), the conversion of organic into inorganic N, is important for productivity and nutrient cycling. The balance between mineralisation and immobilisation (net Nmin) varies with soil properties and climate. However, because most global-scale assessments of net Nmin are laboratory-based, its regulation under field-conditions and implications for real-world soil functioning remain uncertain. Here, we explore the drivers of realised (field) and potential (laboratory) soil net Nmin across 30 grasslands worldwide. We find that realised Nmin is largely explained by temperature of the wettest quarter, microbial biomass, clay content and bulk density. Potential Nmin only weakly correlates with realised Nmin, but contributes to explain realised net Nmin when combined with soil and climatic variables. We provide novel insights of global realised soil net Nmin and show that potential soil net Nmin data available in the literature could be parameterised with soil and climate data to better predict realised Nmin.

Phase-space matching between bent Laue and flat Bragg crystals.

Through phase-space analysis of Dumond diagrams for a flat Bragg crystal, a single bent Laue crystal and a monochromator consisting of double-bent Laue crystals, this work shows that it is possible to match the flat Bragg crystal to both the single-crystal and double-crystal Laue monochromators. The matched system has the advantage that the phase space of the bent crystal's output beam is much larger than that of the flat crystal, making the combined system stable. Here it is suggested that such a matched system can be used at synchrotron facilities to realize X-ray dark-field imaging, analyzer-based imaging and diffraction-enhanced imaging at beamlines using double-Laue monochromators.

Quantum computing on encrypted data.

The ability to perform computations on encrypted data is a powerful tool for protecting privacy. Recently, protocols to achieve this on classical computing systems have been found. Here, we present an efficient solution to the quantum analogue of this problem that enables arbitrary quantum computations to be carried out on encrypted quantum data. We prove that an untrusted server can implement a universal set of quantum gates on encrypted quantum bits (qubits) without learning any information about the inputs, while the client, knowing the decryption key, can easily decrypt the results of the computation. We experimentally demonstrate, using single photons and linear optics, the encryption and decryption scheme on a set of gates sufficient for arbitrary quantum computations. As our protocol requires few extra resources compared with other schemes it can be easily incorporated into the design of future quantum servers. These results will play a key role in enabling the development of secure distributed quantum systems.

Evidence for an isobutylamide associated with host-plant resistance to western flower thrips, Frankliniella occidentalis, in chrysanthemum.

Bioassay-directed fractionation of extracts of chrysanthemum leaves using a choice test permitted isolation of a fraction that exhibited repellent activity against the western flower thrips (WFT). Analysis of this fraction from cultivars exhibiting varying degrees of host-plant resistance to WFT by high performance liquid chromatography revealed a distinctive peak, the height of which correlated with the degree of resistance of those cultivars to WFT. The peak was attributed to a novel unsaturated isobutylamide, N-isobutyl-(E, E, E, Z)-2,4,10,1 2-tetradecatetraen-8-ynamide.

ENCORE: the effect of nutrient enrichment on coral reefs. Synthesis of results and conclusions.

Coral reef degradation resulting from nutrient enrichment of coastal waters is of increasing global concern. Although effects of nutrients on coral reef organisms have been demonstrated in the laboratory, there is little direct evidence of nutrient effects on coral reef biota in situ. The ENCORE experiment investigated responses of coral reef organisms and processes to controlled additions of dissolved inorganic nitrogen (N) and/or phosphorus (P) on an offshore reef (One Tree Island) at the southern end of the Great Barrier Reef, Australia. A multi-disciplinary team assessed a variety of factors focusing on nutrient dynamics and biotic responses. A controlled and replicated experiment was conducted over two years using twelve small patch reefs ponded at low tide by a coral rim. Treatments included three control reefs (no nutrient addition) and three + N reefs (NH4Cl added), three + P reefs (KH2PO4 added), and three + N + P reefs. Nutrients were added as pulses at each low tide (ca twice per day) by remotely operated units. There were two phases of nutrient additions. During the initial, low-loading phase of the experiment nutrient pulses (mean dose = 11.5 microM NH4+; 2.3 microM PO4(-3)) rapidly declined, reaching near-background levels (mean = 0.9 microM NH4+; 0.5 microM PO4(-3)) within 2-3 h. A variety of biotic processes, assessed over a year during this initial nutrient loading phase, were not significantly affected, with the exception of coral reproduction, which was affected in all nutrient treatments. In Acropora longicyathus and A. aspera, fewer successfully developed embryos were formed, and in A. longicyathus fertilization rates and lipid levels decreased. In the second, high-loading, phase of ENCORE an increased nutrient dosage (mean dose = 36.2 microM NH4+; 5.1 microM PO4(-3)) declining to means of 11.3 microM NH4+ and 2.4 microM PO4(-3) at the end of low tide) was used for a further year, and a variety of significant biotic responses occurred. Encrusting algae incorporated virtually none of the added nutrients. Organisms containing endosymbiotic zooxanthellae (corals and giant clams) assimilated dissolved nutrients rapidly and were responsive to added nutrients. Coral mortality, not detected during the initial low-loading phase, became evident with increased nutrient dosage, particularly in Pocillopora damicornis. Nitrogen additions stunted coral growth, and phosphorus additions had a variable effect. Coral calcification rate and linear extension increased in the presence of added phosphorus but skeletal density was reduced, making corals more susceptible to breakage. Settlement of all coral larvae was reduced in nitrogen treatments, yet settlement of larvae from brooded species was enhanced in phosphorus treatments. Recruitment of stomatopods, benthic crustaceans living in coral rubble, was reduced in nitrogen and nitrogen plus phosphorus treatments. Grazing rates and reproductive effort of various fish species were not affected by the nutrient treatments. Microbial nitrogen transformations in sediments were responsive to nutrient loading with nitrogen fixation significantly increased in phosphorus treatments and denitrification increased in all treatments to which nitrogen had been added. Rates of bioerosion and grazing showed no significant effects of added nutrients. ENCORE has shown that reef organisms and processes investigated in situ were impacted by elevated nutrients. Impacts were dependent on dose level, whether nitrogen and/or phosphorus were elevated and were often species-specific. The impacts were generally sub-lethal and subtle and the treated reefs at the end of the experiment were visually similar to control reefs. Rapid nutrient uptake indicates that nutrient concentrations alone are not adequate to assess nutrient condition of reefs. Sensitive and quantifiable biological indicators need to be developed for coral reef ecosystems. The potential bioindicators identified in ENCORE should be tested in future research on coral reef/nutrient interactions. Synergistic and cumulative effects of elevated nutrients and other environmental parameters, comparative studies of intact vs. disturbed reefs, offshore vs. inshore reefs, or the ability of a nutrient-stressed reef to respond to natural disturbances require elucidation. An expanded understanding of coral reef responses to anthropogenic impacts is necessary, particularly regarding the subtle, sub-lethal effects detected in the ENCORE studies.

A seven-day Helicobacter pylori treatment regimen using clarithromycin, omeprazole and tripotassium dicitrato bismuthate.

AIM: To evaluate clarithromycin 500 mg t.d.s., tripotassium dicitrato bismuthate 240 mg b.d. and omeprazole 20 mg b.d. for 7 days as a Helicobacter pylori treatment regimen. METHODS: The H. pylori status of dyspeptic patients undergoing endoscopy was assessed by histology, culture and rapid urease testing of biopsies and by 13C-urea breath test. Fifty patients who were H. pylori-positive were treated with the above treatment regimen for 7 days. Those patients with active duodenal ulcers present at endoscopy were given omeprazole 20 mg nocte for a further 21 days. Not less than 28 days after completing treatment, all tests were repeated to reassess H. pylori status. Bacterial sensitivity of H. pylori cultures was determined and patients recorded any side-effects. RESULTS: On an intention-to-treat basis, H. pylori infection was cured in 90% (95% CI: 78-96%) of patients. Taste disturbance was experienced by 35% patients. Compliance was excellent, with 96% patients taking more than 95% of tablets. Metronidazole resistance was 41% but all cultures were sensitive to clarithromycin. CONCLUSIONS: This 7-day treatment achieved a high level of cure of H. pylori infection with relatively minor side-effects. It may have a role to play, particularly where there is a high level of metronidazole resistance.

Population development and reproduction of fungus- and bacterium feeding nematodes in the presence of insect growth regulators.

The insect growth regulators (IGRs), diflubenzuron and BAY SIR 8514, at 300 and 1,000 ppm a.i. in potato dextrose agar (PDA) inhibited the radial growth of the fungus Rhizoctonia solani host of Aphelenchus avenae. The IGRs had no effect on the growth of the bacterium Pseudomonas pseudoalcaligenes host of Acrobeloides nanus and Diplogaster iheritieri. At 59 ppm a.i., neither IGR inhibited the population development of A. nanus and D. iheritieri on P. pseudoalcaligenes; however, diflubenzuron stimulated the population development of D. iheritieri. At 300 ppm, both IGRs inhibited the population development of A. nanus and D. iheritieri; however, BAY SIR 8514 was more effective than diflubenzuron except on A. nanus L's. At 300 ppm, only BAY SIR 8514 affected the population development of A. avenae, except the L's. At 1,000 ppm, both IGRs inhibited development, except diflubenzuron for L and L's. Again, BAY SIR 8514 was more effective than diflubenzuron. With single females of A. nanus and D. iheritieri, both IGRs at 300 ppm reduced egg laying, inhibited embryonation, and slowed larval development.