Statistical Performance Analysis of an Ant-Colony Optimisation Application in S-NET

Kenneth MacKenzie, Philip K. F. Hölzenspies, Kevin Hammond, Raimund Kirner, Vu Thien Nga Nguyen, Iraneus te Boekhorst, Clemens Grelck, Raphael Poss, Merijn Verstraaten, 'Statistical Performance Analysis of an Ant-Colony Optimisation Application in S-NET'. Paper presented at the 2nd Workshop on Feedback-Directed Compiler Optimization for Multi-Core Architectures. Berlin, Germany, 12 January 2013.We consider an ant-colony optimsation problem implemented on a multicore system as a collection of asynchronous stream- processing components under the control of the S-NET coordina- tion language. Statistical analysis and visualisation techniques are used to study the behaviour of the application, and this enables us to discover and correct problems in both the application program and the run-time system underlying S-NET

Working in group living homes for older people with dementia: the effects on job satisfaction and burnout and the role of job characteristics

ABSTRACT Background: Group living homes are a fast-growing form of nursing home care for older people with dementia. This study seeks to determine the differences in job characteristics of nursing staff in group living homes and their influence on well-being. Methods: We examined the Job Demand Control Support (JDCS) model in relation to 183 professional caregivers in group living homes and 197 professional caregivers in traditional nursing homes. Multilevel linear regression analysis was used to study the mediator effect of the three job characteristics of the JDCS-model (demands, control and social support) on job satisfaction and three components of burnout (emotional exhaustion, depersonalization and decreased personal accomplishment). Results: Demands were lower in group living homes, while control and social support from co-workers were higher in this setting. Likewise, job satisfaction was higher and burnout was lower in group living homes. Analysis of the mediator effects showed that job satisfaction was fully mediated by all three psychosocial job characteristics, as was emotional exhaustion. Depersonalization was also fully mediated, but only by control and social support. Decreased personal accomplishment was partially mediated, again only by job characteristics, control and support. Conclusion: This study indicates that working in a group living home instead of a traditional nursing home has a beneficial effect on the well-being of nursing staff, largely because of a positive difference in psychosocial job characteristic

COVID-19-associated immune thrombocytopenia

Thrombocytopenia is a risk factor for increased morbidity and mortality in patients with the new severe acute respiratory syndrome corona virus, SARS-CoV-2 infection (COVID-19 infection).1 Thrombocytopenia in COVID-19 patients may be caused by disseminated intravascular coagulation (DIC), sepsis or drug-induced. Recently a single case report suggested immune thrombocytopenia (ITP) may be associated with COVID-19 infection.2 ITP is a rare autoimmune disease characterized by a platelet count < 100x109/L, leading to an increased bleeding risk.3 Several risk factors have been described for ITP including environmental (e.g. infection, malignancy and drugs) and genetic predisposition.4 We report here the first case series of three patients with ITP associated with COVID-19 infection

Molecular MRI of Inflammation in Atherosclerosis

Inflammatory activity in atherosclerotic plaque is a risk factor for plaque rupture and atherothrombosis and may direct interventional therapy. Inflammatory activity can be evaluated at the (sub)cellular level using in vivo molecular MRI. This paper reviews recent progress in contrast-enhanced molecular MRI to visualize atherosclerotic plaque inflammation. Various MRI contrast agents, among others ultra-small particles of iron oxide, low-molecular-weight Gd-chelates, micelles, liposomes, and perfluorocarbon emulsions, have been used for in vivo visualization of various inflammation-related targets, such as macrophages, oxidized LDL, endothelial cell expression, plaque neovasculature, MMPs, apoptosis, and activated platelets/thrombus. An enzyme-activatable magnetic resonance contrast agent has been developed to study myeloperoxidase activity in inflamed plaques. Agents creating contrast based on the chemical exchange saturation transfer mechanism were used for thrombus imaging. Transfer of these molecular MRI techniques to the clinic will critically depend on the safety profiles of these newly developed magnetic resonance contrast agents

Bladder irrigation with tap water to reduce antibiotic treatment for catheter-associated urinary tract infections: an evaluation of clinical practice

IntroductionCatheter-associated urinary tract infection (CAUTI) is a common complication among patients with urinary catheters and is often treated with antibiotics. With increasing rates of antibiotic resistance, it is necessary to explore alternative treatment options for CAUTIs. The aims of this study were 1) to assess the efficacy and treatment satisfaction of bladder irrigation (BI) with tap water to prevent and treat CAUTIs, 2) and to evaluate the current use of BI for CAUTIs among Dutch clinicians.MethodsThe first part of this study consisted of a cross-sectional study among patients with intermittent or indwelling catheters who performed BI with tap water between March 2020 and May 2021. Efficacy, treatment satisfaction, and Patient Global Impression of Improvement (PGI-I) were assessed using questionnaires. Outcomes were compared between neurogenic lower urinary tract dysfunction (NLUTD) and non-NLUTD patients. Factors associated with overall treatment satisfaction were determined using logistic regression analysis. Second, a nationwide survey of Dutch clinicians was conducted to evaluate the current use of BI for CAUTIs.ResultsA total of 99 patients who were performing BI for at least three months were included. The median age was 61.9 years, 41.4% had NLUTD, and 72.2% performed BI &gt;1 year. The majority of both NLUTD (65.9%) and non-NLUTD patients (68.4%) were (very) satisfied with BI. Women had higher odds of reporting higher satisfaction and each additional CAUTI decreased the odds. Most NLUTD (85.4%) and non-NLUTD (65.5%) patients reported an improvement on the PGI-I with a difference in favour of NLUTD patients (p=0.002). In addition, 40.4% of the patients had no CAUTI, and 59.6% reported 1.39 (SD 2.06) CAUTIs. Only half of these self-reported CAUTIs were treated with antibiotics. In addition, 33 (58.9%) clinicians used BI for CAUTIs, of which ten used tap water as irrigation agent.DiscussionThis study provides first evidence supporting the efficacy of BI with tap water in the treatment of CAUTIs and reducing the use of antibiotics. Patients are overall satisfied and experience improvement in their condition with BI. In addition, the majority of the surveyed Dutch clinicians use BI for CAUTIs. However, irrigation with tap water is still not widely used

COVID-19 vaccination in patients with immune thrombocytopenia

Immune thrombocytopenia (ITP) is an acquired autoimmune disorder characterized by low platelet count and increased bleeding risk. COVID-19 vaccination has been described as risk factor for de novo ITP, but the effects of COVID-19 vaccination in patients with ITP are unknown. Our aims were to investigate the effects of COVID-19 vaccination in ITP patients on platelet count, bleeding complications and ITP exacerbation (any of: ≥50% decline in platelet count; or nadir platelet count 20% decrease from baseline; or use of rescue therapy). Platelet counts of ITP patients and healthy controls were collected immediately before, 1 and 4 weeks after first and second vaccination. Linear mixed-effects modelling was applied to analyze platelet counts over time. We included 218 ITP patients (50.9% female, mean age 55 years and median platelet count of 106x109/L) and 200 healthy controls (60.0% female, mean age 58 years and median platelet count of 256x109/L). Platelet counts decreased by 6.3% after vaccination. We observed no difference in decrease between the groups. Thirty ITP patients (13.8%, 95%CI 9.5%-19.1%) had an exacerbation and 5 (2.2%, 95%CI 0.7%-5.3%) suffered from a bleeding event. Risk factors for ITP exacerbation were platelet count <50x109/L (OR 5.3, 95%CI 2.1-13.7), ITP treatment at time of vaccination (OR 3.4, 95%CI 1.5-8.0) and age (OR 0.96 per year, 95%CI 0.94-0.99). Our study highlights safety of COVID-19 vaccination in ITP patients and importance of close monitoring platelet counts in a subgroup of ITP patients. ITP patients with exacerbation responded well on therapy

Phospho.ELM: a database of phosphorylation sites—update 2011

The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42 574 serine, threonine and tyrosine non-redundant phosphorylation sites. Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases

Computational problems of analysis of short next generation sequencing reads

Short read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many more applications. However, NGS are prone for errors which complicate scientific conclusions. NGS technologies consist of shearing DNA molecules into collection of numerous small fragments, called a ‘library’, and their further extensive parallel sequencing. These sequenced overlapping fragments are called ‘reads’, they are assembled into contiguous strings. The contiguous sequences are in turn assembled into genomes for further analysis. Computational sequencing problems are those arising from numerical processing of sequenced samples. The numerical processing involves procedures such as: quality-scoring, mapping/assembling, and surprisingly, error-correction of a data. This paper is reviewing post-processing errors and computational methods to discern them. It also includes sequencing dictionary. We present here quality control of raw data, errors arising at the steps of alignment of sequencing reads to a reference genome and assembly. Finally this work presents identification of mutations (“Variant calling”) in sequencing data and its quality control