Two rapid assays for screening of patulin biodegradation

Artículo sobre distintos ensayos para comprobar la biodegradación de la patulinaThe mycotoxin patulin is produced by the blue mould pathogen Penicillium expansum in rotting apples during postharvest storage. Patulin is toxic to a wide range of organisms, including humans, animals, fungi and bacteria. Wash water from apple packing and processing houses often harbours patulin and fungal spores, which can contaminate the environment. Ubiquitous epiphytic yeasts, such as Rhodosporidium kratochvilovae strain LS11 which is a biocontrol agent of P. expansum in apples, have the capacity to resist the toxicity of patulin and to biodegrade it. Two non-toxic products are formed. One is desoxypatulinic acid. The aim of the work was to develop rapid, high-throughput bioassays for monitoring patulin degradation in multiple samples. Escherichia coli was highly sensitive to patulin, but insensitive to desoxypatulinic acid. This was utilized to develop a detection test for patulin, replacing time-consuming thin layer chromatography or high-performance liquid chromatography. Two assays for patulin degradation were developed, one in liquid medium and the other in semi-solid medium. Both assays allow the contemporary screening of a large number of samples. The liquid medium assay utilizes 96-well microtiter plates and was optimized for using a minimum of patulin. The semisolid medium assay has the added advantage of slowing down the biodegradation, which allows the study and isolation of transient degradation products. The two assays are complementary and have several areas of utilization, from screening a bank of microorganisms for biodegradation ability to the study of biodegradation pathways

Selection of Wavelet Subbands Using Genetic Algorithm for Face Recognition

Abstract. In this paper, a novel representation called the subband face is proposed for face recognition. The subband face is generated from selected subbands obtained using wavelet decomposition of the original face image. It is surmised that certain subbands contain information that is more significant for discriminating faces than other subbands. The problem of subband selection is cast as a combinatorial optimization problem and genetic algorithm (GA) is used to find the optimum subband combination by maximizing Fisher ratio of the training features. The performance of the GA selected subband face is evaluated using three face databases and compared with other wavelet-based representations.

Multi-objective Optimization by Uncrowded Hypervolume Gradient Ascent

Evolutionary algorithms (EAs) are the preferred method for solving black-box multi-objective optimization problems, but when gradients of the objective functions are available, it is not straightforward to exploit these efficiently. By contrast, gradient-based optimization is well-established for single-objective optimization. A single-objective reformulation of the multi-objective problem could therefore offer a solution. Of particular interest to this end is the recently introduced uncrowded hypervolume (UHV) indicator, which takes into account dominated solutions. In this work, we show that the gradient of the UHV can often be computed, which allows for a direct application of gradient ascent algorithms. We compare this new approach with two EAs for UHV optimization as well as with one gradient-based algorithm for optimizing the well-established hypervolume. On several bi-objective benchmarks, we find that gradient-based algorithms outperform the tested EAs by obtaining a better hypervolume with fewer evaluations whenever exact gradients of the multiple objective functions are available and in case of small evaluation budgets. For larger budgets, however, EAs perform similarly or better. We further find that, when finite differences are used to approximate the gradients of the multiple objectives, our new gradient-based algorithm is still competitive with EAs in most considered benchmarks. Implementations are available at https://github.com/scmaree/uncrowded-hypervolume.Comment: T.M.D. and S.C.M. contributed equally. The final authenticated version is available in the conference proceedings of Parallel Problem Solving from Nature - PPSN XVI. Changes in new version: removed statement about Pareto compliance in abstract; added related work; corrected minor mistake

Why alternative teenagers self-harm: exploring the link between non-suicidal self-injury, attempted suicide and adolescent identity

Background: The term ‘self-harm’ encompasses both attempted suicide and non-suicidal self-injury (NSSI). Specific adolescent subpopulations such as ethnic or sexual minorities, and more controversially, those who identify as ‘Alternative’ (Goth, Emo) have been proposed as being more likely to self-harm, while other groups such as ‘Jocks’ are linked with protective coping behaviours (for example exercise). NSSI has autonomic (it reduces negative emotions) and social (it communicates distress or facilitates group ‘bonding’) functions. This study explores the links between such aspects of self-harm, primarily NSSI, and youth subculture.<p></p> Methods: An anonymous survey was carried out of 452 15 year old German school students. Measures included: identification with different youth cultures, i.e. Alternative (Goth, Emo, Punk), Nerd (academic) or Jock (athletic); social background, e.g. socioeconomic status; and experience of victimisation. Self-harm (suicide and NSSI) was assessed using Self-harm Behavior Questionnaire and the Functional Assessment of Self-Mutilation (FASM).<p></p> Results: An “Alternative” identity was directly (r ≈ 0.3) and a “Jock” identity inversely (r ≈ -0.1) correlated with self-harm. “Alternative” teenagers self-injured more frequently (NSSI 45.5% vs. 18.8%), repeatedly self-injured, and were 4–8 times more likely to attempt suicide (even after adjusting for social background) than their non-Alternative peers. They were also more likely to self-injure for autonomic, communicative and social reasons than other adolescents.<p></p> Conclusions: About half of ‘Alternative’ adolescents’ self-injure, primarily to regulate emotions and communicate distress. However, a minority self-injure to reinforce their group identity, i.e. ‘To feel more a part of a group’

STA, the Space Trajectory Analysis Project

This article describes the objectives of the Space Trajectory Analysis (STA) project. The article also details the birth of STA, and its present configuration. STA is a project to develop an open source astrodynamics software suite involving university science departments and space research institutions. It was initiated by ESA as internal activity in 2005 and now it involves 16 partners. The article explains the partnership into the STA Steering Board. The main purpose of the STA is to allow advanced simulation for the analysis of space trajectories in an open and free environment under the premises of innovation and reliability.Further, the article explains that the STA development is open source and is based on the state of the art astrodynamics routines that are grouped into modules. Finally, the article concludes about the benefits of the STA initiative: the STA project allows a strong link among applied mathematics, space engineering, and informatics disciplines by reinforcing the academic community with requirements and needs coming from real missions

Design considerations for workflow management systems use in production genomics research and the clinic

Abstract The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance

Self-harm in young people with perinatal HIV and HIV negative young people in England: cross sectional analysis.

BACKGROUND: Self-harm in adolescents is of growing concern internationally but limited evidence exists on the prevalence of self-harm in those living with HIV, who may be at higher risk of poor mental health outcomes. Therefore our aim was to determine the prevalence and predictors of self-harm among young people with perinatally-acquired HIV (PHIV) and HIV negative (with sibling or mother living with HIV) young people living in England. METHODS: 303 PHIV and 100 HIV negative young people (aged 12-23 years) participating in the Adolescents and Adults Living with Perinatal HIV cohort study completed an anonymous self-harm questionnaire, as well as a number of standardised mental-health assessments. Logistic regression investigated predictors of self-harm. RESULTS: The median age was 16.7 years in both groups, and 40.9% of the PHIV and 31.0% of the HIV negative groups were male. In total 13.9% (56/403) reported having ever self-harmed, with no difference by HIV status (p = 0.089). Multivariable predictors of self-harm were female sex (adjusted odds ratio (AOR) 5.3, (95% confidence interval 1.9, 14.1), p = 0.001), lower self-esteem (AOR 0.9 (0.8, 0.9) per 1 point increase, p < 0.001) and having ever used alcohol (AOR 3.8 (1.8, 7.8), p < 0.001). Self-esteem z-scores for both PHIV and HIV negative participants were 1.9 standard deviations below the mean for population norms. CONCLUSIONS: Self-harm is common among PHIV and HIV negative adolescents in England. Reassuringly however, they do not appear to be at an increased risk compared to the general adolescent population (15-19% lifetime prevalence). The low level of self-esteem (compared to available normative data) in both groups is worrying and warrants further attention

A proof of principle for using adaptive testing in routine Outcome Monitoring: the efficiency of the Mood and Anxiety Symptoms Questionnaire -Anhedonic Depression CAT

<p>Abstract</p> <p>Background</p> <p>In Routine Outcome Monitoring (ROM) there is a high demand for short assessments. Computerized Adaptive Testing (CAT) is a promising method for efficient assessment. In this article, the efficiency of a CAT version of the Mood and Anxiety Symptom Questionnaire, - Anhedonic Depression scale (MASQ-AD) for use in ROM was scrutinized in a simulation study.</p> <p>Methods</p> <p>The responses of a large sample of patients (<it>N </it>= 3,597) obtained through ROM were used. The psychometric evaluation showed that the items met the requirements for CAT. In the simulations, CATs with several measurement precision requirements were run on the item responses as if they had been collected adaptively.</p> <p>Results</p> <p>CATs employing only a small number of items gave results which, both in terms of depression measurement and criterion validity, were only marginally different from the results of a full MASQ-AD assessment.</p> <p>Conclusions</p> <p>It was concluded that CAT improved the efficiency of the MASQ-AD questionnaire very much. The strengths and limitations of the application of CAT in ROM are discussed.</p

Web-based tools can be used reliably to detect patients with major depressive disorder and subsyndromal depressive symptoms

BACKGROUND: Although depression has been regarded as a major public health problem, many individuals with depression still remain undetected or untreated. Despite the potential for Internet-based tools to greatly improve the success rate of screening for depression, their reliability and validity has not been well studied. Therefore the aim of this study was to evaluate the test-retest reliability and criterion validity of a Web-based system, the Internet-based Self-assessment Program for Depression (ISP-D). METHODS: The ISP-D to screen for major depressive disorder (MDD), minor depressive disorder (MinD), and subsyndromal depressive symptoms (SSD) was developed in traditional Chinese. Volunteers, 18 years and older, were recruited via the Internet and then assessed twice on the online ISP-D system to investigate the test-retest reliability of the test. They were subsequently prompted to schedule face-to-face interviews. The interviews were performed by the research psychiatrists using the Mini-International Neuropsychiatric Interview and the diagnoses made according to DSM-IV diagnostic criteria were used for the statistics of criterion validity. Kappa (κ) values were calculated to assess test-retest reliability. RESULTS: A total of 579 volunteer subjects were administered the test. Most of the subjects were young (mean age: 26.2 ± 6.6 years), female (77.7%), single (81.6%), and well educated (61.9% college or higher). The distributions of MDD, MinD, SSD and no depression specified were 30.9%, 7.4%, 15.2%, and 46.5%, respectively. The mean time to complete the ISP-D was 8.89 ± 6.77 min. One hundred and eighty-four of the respondents completed the retest (response rate: 31.8%). Our analysis revealed that the 2-week test-retest reliability for ISP-D was excellent (weighted κ = 0.801). Fifty-five participants completed the face-to-face interview for the validity study. The sensitivity, specificity, positive, and negative predictive values for major depressive disorder were 81.8% and 72.7%, 66.7%, and 85.7% respectively. The overall accuracy was 76.4%. CONCLUSION: The evidence indicates the ISP-D is a reliable and valid online tool for assessing depression. Further studies should test the ISP-D in clinical settings to increase its applications in clinical environments with different populations and in a larger sample size