Sequestration of P fractions in the soils of an incipient ferralisation chronosequence on a humid tropical volcanic island

Background: Phosphorus (P) is the limiting nutrient in many mature tropical forests. The ecological significance of declining P stocks as soils age is exacerbated by much of the remaining P being progressively sequestered. However, the details of how and where P is sequestered during the ageing in tropical forest soils remains unclear. Results: We examined the relationships between various forms of the Fe and Al sesquioxides and the Hedley fractions of P in soils of an incipient ferralitic chronosequence on an altitudinal series of gently sloping benches on Green Island, off the southeastern coast of Taiwan. These soils contain limited amounts of easily exchangeable P. Of the sesquioxide variables, only Fe and Al crystallinities increased significantly with bench altitude/soil age, indicating that the ferralisation trend is weak. The bulk of the soil P was in the NaOH and residual extractable fractions, and of low lability. The P fractions that correlated best with the sesquioxides were the organic components of the NaHCO3 and NaOH extracts. Conclusions: The amorphous sesquioxides, Feo and Alo, were the forms that correlated best with the P fractions. A substantial proportion of the labile P appears to be organic and to be associated with Alo in organic-aluminium complexes. The progression of P sequestration appears to be slightly slower than the chemical and mineralogical indicators of ferralisation

Human Comprehensible Active Learning of Genome-Scale Metabolic Networks

An important application of Synthetic Biology is the engineering of the host cell system to yield useful products. However, an increase in the scale of the host system leads to huge design space and requires a large number of validation trials with high experimental costs. A comprehensible machine learning approach that efficiently explores the hypothesis space and guides experimental design is urgently needed for the Design-Build-Test-Learn (DBTL) cycle of the host cell system. We introduce a novel machine learning framework ILP-iML1515 based on Inductive Logic Programming (ILP) that performs abductive logical reasoning and actively learns from training examples. In contrast to numerical models, ILP-iML1515 is built on comprehensible logical representations of a genome-scale metabolic model and can update the model by learning new logical structures from auxotrophic mutant trials. The ILP-iML1515 framework 1) allows high-throughput simulations and 2) actively selects experiments that reduce the experimental cost of learning gene functions in comparison to randomly selected experiments.Comment: Invited presentation for AAAI Spring Symposium Series 2023 on Computational Scientific Discover

Multicolor plate reader fluorescence calibration

Plate readers are commonly used to measure cell growth and fluorescence, yet the utility and reproducibility of plate reader data is limited by the fact that it is typically reported in arbitrary or relative units. We have previously established a robust serial dilution protocol for calibration of plate reader measurements of absorbance to estimated bacterial cell count and for green fluorescence from proteins expressed in bacterial cells to molecules of equivalent fluorescein. We now extend these protocols to calibration of red fluorescence to the sulforhodamine-101 fluorescent dye and blue fluorescence to Cascade Blue. Evaluating calibration efficacy via an interlaboratory study, we find that these calibrants do indeed provide comparable precision to the prior calibrants and that they enable effective cross-laboratory comparison of measurements of red and blue fluorescence from proteins expressed in bacterial cells

A survey of the management of urinary tract infection in children in primary care and comparison with the NICE guidelines

Background: The aim of this study was to establish current practices amongst general practitioners in the West of Ireland with regard to the investigation, diagnosis and management of urinary tract infection (UTI) in children and to evaluate these practices against recently published guidelines from the National Institute for Health and Clinical Excellence (NICE). Methods: A postal survey was performed using a questionnaire that included short clinical scenarios. All general practices in a single health region were sent a questionnaire, cover letter and SAE. Systematic postal and telephone contact was made with non-responders. The data was analysed using SPSS version 15. Results: Sixty-nine general practitioners were included in the study and 50 (72%) responded to the questionnaire. All respondents agreed that it is important to consider diagnosis of UTI in all children with unexplained fever. Doctors accurately identified relevant risk factors for UTI in the majority (87%) of cases. In collecting urine samples from a one year old child, 80% of respondents recommended the use of a urine collection bag and the remaining 20% recommended collection of a clean catch sample. Respondents differed greatly in their practice with regard to detailed investigation and specialist referral after a first episode of UTI. Co-amoxiclav was the most frequently used antibiotic for the treatment of cystitis, with most doctors prescribing a five day course. Conclusions: In general, this study reveals a high level of clinical knowledge amongst doctors treating children with UTI in primary care in the catchment area of County Mayo. However, it also demonstrates wide variation in practice with regard to detailed investigation and specialist referral. The common practice of prescribing long courses of antibiotics when treating lower urinary tract infection is at variance with NICE's recommendation of a three day course of antibiotics for cystitis in children over three months of age when there are no atypical features

Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

Background Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)