109 research outputs found
Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery
Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. In this paper, a new clustering paradigm is proposed. In this paradigm, all three eventualities of a gene being exclusively assigned to a single cluster, being assigned to multiple clusters, and being not assigned to any cluster are possible. These possibilities are realised through the primary novelty of the introduction of tunable binarization techniques. Results from multiple clustering experiments are aggregated to generate one fuzzy consensus partition matrix (CoPaM), which is then binarized to obtain the final binary partitions. This is referred to as Binarization of Consensus Partition Matrices (Bi-CoPaM). The method has been tested with a set of synthetic datasets and a set of five real yeast cell-cycle datasets. The results demonstrate its validity in generating relevant tight, wide, and complementary clusters that can meet requirements of different gene discovery studies.National Institute for Health Researc
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Use of probiotics in preventing antibiotic associated diarrhoea and Clostridium difficile associated diarrhoea in spinal injury centres: An international survey of four western European countries
Probiotics may prevent antibiotic-associatedand Clostridium difficile-associated- diarrhoea (AAD/CDAD). Many spinal cord injury centres (SCICs) practitioners consider probiotics generically and may not realise that efficacy can be strain-, dose-, and disease-specific. One to four SCICs per country (depending on population size) were contacted (UK:4; the Netherlands:3; Belgium: I; Republic of Ireland: 1) to (a) determine if they stocked probiotics; (b) determine whether the use of those probiotics was evidence-based; and (c) document their C. difficile infection (CDI) practices. All nine SCICs responded to the survey (7 physicians, 3 microbiologists, 1 nurse and 2 dietitians). Five (55.5%) stocked probiotics; five different probiotics were identified. Four probiotics were preferred choice prevention o f AAD/CDAD were Lactobacillus casei Shirota (44.4%), L. casei D N -114001 (22.2%), L. acidophilus (22.2%) and a mixed-strains probiotic (Ecologic Pro-AD) (11.1%). Only one evidence base study was identified supporting the use of probiotic for prevention of AAD in SCI patients. Mean CDI cases per 10,000 patient-days were 0.307 (s.d: 0.486, range 0.00 to 1.08). Definitions of diarrhoea and CDI varied among SCICs. Stocking probiotics for the prevention of AAD / CDAD is not common. There is only one single study showing efficiency of a particular strain in SCI populations. The study highlighted the importance of using a standardised definition o f diarrhoea when conducting AAD/CDAD research
Web services composition for concurrent plan using artificial intelligence planning
Automatic planning of web services composition is a challenging problem both in academia and real-world application. Artificial Intelligence (AI) planning can be applied to automate web services composition by depicting composition problem as AI planning problem. Web services composition would combine multiple services whenever some requirements cannot be fulfilled by a single service. Subsequently, many of the planning algorithms to detect and generate composition plan would focus only on sequence composition thus, neglecting concurrent composition. The aim of this paper is to develop an approach to generate a concurrent plan for web services composition based on semantic web services (OWL-S) and Hierarchical Task Network (HTN) Planning. A Bioinformatics case study for pathway data retrieval is used to validate the effectiveness of proposed approach. The planning algorithm extend Hierarchical Task Network (HTN) algorithm to solve the problem of automatic web service composition in the context of concurrent task planning. Experimental analysis showed that the proposed algorithms are capable of detecting and generating concurrent plan when compared with existing algorithms
Adopting a portfolio of ultrasonic and advanced bipolar electrosurgery devices from a single manufacturer compared to currently used ultrasonic and advanced bipolar devices: a probabilistic budget impact analysis from a Spanish hospital perspective
Aims: Advanced energy devices are commonly used in electrosurgery, including ultrasonic and advanced bipolar (ABP) devices. Smoke evacuation and reusable dispersive electrodes are also utilized during electrosurgery to improve staff and patient safety. This study assessed the budget impact of adopting a portfolio of Ethicon energy devices compared to devices from other manufacturers from a Spanish hospital perspective.
Methods: The main analysis compared the Ethicon advanced energy device portfolio (ultrasonic and ABP devices) to Non-Ethicon advanced energy devices. It was assumed that 4,000 procedures using one advanced energy device each were performed annually, and the cost impact of operating room time, length of stay, and transfusions were considered. A probabilistic budget impact analysis with 10,000 iterations was conducted for generalizability to other hospitals in Spain and Europe. Secondary analysis assessed whether cost savings from the Ethicon advanced energy device portfolio could offset costs of adopting smoke evacuation and reusable dispersive electrodes (Full Ethicon energy portfolio). Results: In the main analysis, the annual budget impact of introducing the Ethicon advanced energy device portfolio was cost saving in 79.8% of probabilistic iterations (mean: -€945,214; 95% credible interval [CrI]: -€3,242,710; €1,285,942) with a mean budget impact per procedure of -€236 (95% CrI: -€811; €321). In the secondary analysis, adding smoke evacuation and reusable dispersive electrodes was still cost saving in 75.3% of iterations compared to Non-Ethicon advanced energy devices (mean: -€778,208; 95% CrI: -€3,075,086; €1,464,728) with a mean budget impact per procedure of -€97 (95% CrI: -€384; €183). Savings resulted from differences in operating room time, length of hospital stay, and volume of disposable electrodes.
Conclusions: Adopting Ethicon advanced energy devices demonstrated economic benefits compared to non-Ethicon devices. Introducing the advanced portfolio may improve surgical care quality and the full portfolio was cost saving while improving OR safety for staff and patients
Linear and nonlinear optical properties of trigonal borate crystals K7MIn2-xYbx(B5O10)3 (M = Ca, Sr, Ba; x=0…2) with isolated B5O10 units
Noncentrosymmetric borates K7MIn2−xYbx(B5O10)3 (M = Ca, Sr, Ba; x = 0…2) were synthesized by the solid state reaction and the crystals were successfully grown by the top seeded solution growth method using the K2O-B2O3-MF2 flux. According to Rietveld refinement, the crystal structure belongs to the noncentrosymmetric R32 space group. Also, the octahedrally coordinated In atoms are located at wide ranges ∼8 Å which may be promising for phosphor and laser applications. Samples with ytterbium show a characteristic emission band in the range of 950–1050 nm related to the 2F5/2 → 2F7/2 transition of Yb3+ ions that is commonly used for laser generation. IR, Raman and absorption spectra were obtained for the samples as well. The short cut edge of UV absorption, SHG intensity comparable with KDP and low concentration quenching of luminescence suggest that the K7MIn2−xYbx(B5O10)3 borates are promising self-frequency doubling materials
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Lactobacillus casei Shirota probiotic drinks reduce antibiotic associated diarrhoea in patients with spinal cord injuries who regularly consume proton pump inhibitors: a subgroup analysis of the ECLISP multicentre RCT
Study design
This was a sub-group analysis of a multicentre, randomised, placebo-controlled, double-blind trial (ECLISP trial)
Objectives
To assess the efficacy of a probiotic containing at least 6.5 x 109 live Lactobacillus casei Shirota (LcS) in preventing antibiotic associated diarrhoea (AAD) in patients with spinal cord injury (SCI) who consumed proton pump inhibitor (PPI) regularly. LcS or placebo was given once daily for the duration of an antibiotic course and continued for 7 days thereafter. The trial was registered with ISRCTN:13119162.
Setting
Three SCI centres (National Spinal Injuries Centre, Midland Centre for Spinal Injuries and Princess Royal Spinal Cord Injuries Centre) in the United Kingdom
Methods
Between November 2014, and November 2019, 95 eligible consenting SCI patients (median age: 57; IQ range: 43-69) were randomly allocated to receive LcS (n = 50) or placebo (n = 45). The primary outcome is the occurrence of AAD up to 30 days after finishing LcS/placebo.
Results
The LcS group had a significantly lower incidence of AAD at 30 days after finishing the antibiotic course (28.0 v 53.3%, RR: 95% CI:0.53, 0.31-0.89; z = 2.5, p = 0.01). Multivariate logistic regression analysis identified that LcS can reduce the risk of AAD at 30 days (OR: 0.36, 95% CI 0.13, 0.99,p < 0.05). No intervention-related adverse events were reported during the study.
Conclusions
LcS has the potential to prevent AAD in what could be considered a defined vulnerable group of SCI patients on regular PPL A confirmatory, randomised, placebo-controlled study is needed to confirm this apparent therapeutic success to translate it into appropriate clinical outcomes
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Use of antibiotics and the prevalence of antibiotic-associated diarrhoea in patients with spinal cord injuries: an international, multi-centre study
BACKGROUND: Little is known about the use of antibiotics and the extent of antibiotic-associated diarrhoea (AAD) in patients with spinal cord injuries (SCIs).
AIMS: To record the use of antibiotics, establish the prevalence of AAD and Clostridium difficile infection (CDI), and assess if there was any seasonal variation in antibiotic use and incidence of AAD in patients with SCIs.
METHODS: A retrospective study was conducted in six European SCI centres between October 2014 and June 2015. AAD was defined as two or more watery stools (Bristol Stool Scale type 5, 6 or 7) over 24 h.
FINDINGS: In total, 1267 adults (median age 54 years, 30.7% female) with SCIs (52.7% tetraplegia, 59% complete SCI) were included in this study. Among the 215 (17%) patients on antibiotics, the top three indications for antibiotics were urinary tract infections (UTIs), infected pressure ulcers and other skin infections. Thirty-two of these 215 (14.9%) patients developed AAD and two patients out of the total study population (2/1267; 0.16%) developed CDI. AAD was more common in summer than in spring, autumn or winter (30.3% vs 3.8%, 7.4% and 16.9%, respectively; P<0.01). AAD was associated with age ≥65 years, tetraplegia, higher body mass index, hypoalbuminaemia, polypharmacy, multiple antibiotic use and high-risk antibiotic use. Summer and winter seasons and male sex were identified as independent predictors for the development of AAD.
CONCLUSION: This survey found that AAD is common in patients with SCIs, and UTI is the most common cause of infection. Summer and winter seasons and male sex are unique predictors for AAD. Both AAD and UTIs are potentially preventable; therefore, further work should focus on preventing the over-use of antibiotics, and developing strategies to improve hospital infection control measures
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A study into the effect of Lactobacillus casei Shirota in preventing antibiotic associated diarrhoea including Clostridioides difficile infection in patients with spinal cord injuries: a multicentre randomised, double-blind, placebo-controlled trial.
Background
Antibiotic Associated Diarrhoea (AAD) and Clostridioides Difficile Infection (CDI) are of major concern in spinal cord injury (SCI) rehabilitation.
Methods
A multi-centre, randomized, double-blind, placebo-controlled (the ECLISP) trial, was conducted in three tertiary spinal cord injury centre in the UK to assess the efficacy of consuming a probiotic beverage containing at least 6.5 × 109 live Lactobacillus casei Shirota (LcS) in preventing AAD and CDI and in patients with SCI and to determine whether proton pump inhibitors (PPI) and under nutrition-risk are risk factors for AAD/CDI. LcS or placebo was given once daily for the duration of an antibiotic course and continued for 7 days thereafter. Follow up was set at 7 and 30 days after the antibiotic course finished. The primary outcome was occurrence of AAD up to 30 days after finishing LcS/placebo. This trial is completed and registered (ISRCTN:13119162).
Findings
Between November 2014, and November 2019, 359 consenting adult SCI patients (median age: 53.3; range: 18–88 years), from 3 SCI centres responsible for providing approximate 45–50% of UK SCI service, with a requirement for antibiotics due to infection were randomly allocated to receive LcS (n = 181) or placebo (n = 178). Overall, no statistical difference was seen in occurrence of the primary outcomes of AAD at 30 days follow up (45% v 42.1%, RR: 1.071, 0.8-1.4, p = 0.639). In the secondary analyses LcS was associated with a lower risk of AAD at 7 (19% v 35.7%, RR: 0.53, 0.29–0.99, p = 0.040) and 30 days follow up (28% v 52.2%, RR: 0.54, 0.32–0.91, p = 0.015) in the participants who took PPI regularly. Under nutrition-risk was associated with an increased risk of AAD at 7 (RR: 1.76, 1.28–2.44) and 30 days follow up (RR: 1.69, 1.30–2.0). No intervention-related adverse events were reported during the study.
Interpretation
The present study indicates that LcS could not prevent AAD/CDI in unselected SCI patients. LcS might have the potential to prevent AAD in the higher risk group of patients on regular PPI. Confirmatory studies are needed to allow translation of this apparent therapeutic success into improved clinical outcomes
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