A comparative analysis of algorithms for somatic SNV detection in cancer

Motivation: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer–normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer–normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm. Results: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates.Nicola D. Roberts, R. Daniel Kortschak, Wendy T. Parker, Andreas W. Schreiber, Susan Branford, Hamish S. Scott, Garique Glonek and David L. Adelso

The antisaccade task as an index of sustained goal activation in working memory: modulation by nicotine

The antisaccade task provides a laboratory analogue of situations in which execution of the correct behavioural response requires the suppression of a more prepotent or habitual response. Errors (failures to inhibit a reflexive prosaccade towards a sudden onset target) are significantly increased in patients with damage to the dorsolateral prefrontal cortex and patients with schizophrenia. Recent models of antisaccade performance suggest that errors are more likely to occur when the intention to initiate an antisaccade is insufficiently activated within working memory. Nicotine has been shown to enhance specific working memory processes in healthy adults. MATERIALS AND METHODS: We explored the effect of nicotine on antisaccade performance in a large sample (N = 44) of young adult smokers. Minimally abstinent participants attended two test sessions and were asked to smoke one of their own cigarettes between baseline and retest during one session only. RESULTS AND CONCLUSION: Nicotine reduced antisaccade errors and correct antisaccade latencies if delivered before optimum performance levels are achieved, suggesting that nicotine supports the activation of intentions in working memory during task performance. The implications of this research for current theoretical accounts of antisaccade performance, and for interpreting the increased rate of antisaccade errors found in some psychiatric patient groups are discussed

Vaccines against toxoplasma gondii : challenges and opportunities

Development of vaccines against Toxoplasma gondii infection in humans is of high priority, given the high burden of disease in some areas of the world like South America, and the lack of effective drugs with few adverse effects. Rodent models have been used in research on vaccines against T. gondii over the past decades. However, regardless of the vaccine construct, the vaccines have not been able to induce protective immunity when the organism is challenged with T. gondii, either directly or via a vector. Only a few live, attenuated T. gondii strains used for immunization have been able to confer protective immunity, which is measured by a lack of tissue cysts after challenge. Furthermore, challenge with low virulence strains, especially strains with genotype II, will probably be insufficient to provide protection against the more virulent T. gondii strains, such as those with genotypes I or II, or those genotypes from South America not belonging to genotype I, II or III. Future studies should use animal models besides rodents, and challenges should be performed with at least one genotype II T. gondii and one of the more virulent genotypes. Endpoints like maternal-foetal transmission and prevention of eye disease are important in addition to the traditional endpoint of survival or reduction in numbers of brain cysts after challenge

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Glycosaminoglycan profiles of repair tissue formed following autologous chondrocyte implantation differ from control cartilage

Currently, autologous chondrocyte implantation (ACI) is the most commonly used cell-based therapy for the treatment of isolated femoral condyle lesions of the knee. A small number of centres performing ACI have reported encouraging long-term clinical results, but there is currently a lack of quantitative and qualitative biochemical data regarding the nature of the repair tissue. Glycosaminoglycan (GAG) structure influences physiological function and is likely to be important in the long-term stability of the repair tissue. The objective of this study was to use fluorophore-assisted carbohydrate electrophoresis (FACE) to both quantitatively and qualitatively analyse the GAG composition of repair tissue biopsies and compare them with age-matched cadaveric controls. We used immunohistochemistry to provide a baseline reference for comparison. Biopsies were taken from eight patients (22 to 52 years old) 1 year after ACI treatment and from four cadavers (20 to 50 years old). FACE quantitatively profiled the GAGs in as little as 5 μg of cartilage. The pattern and intensity of immunostaining were generally comparable with the data obtained with FACE. In the ACI repair tissue, there was a twofold reduction in chondroitin sulphate and keratan sulphate compared with age-matched control cartilage. By contrast, there was an increase in hyaluronan with significantly shorter chondroitin sulphate chains and less chondroitin 6-sulphate in repair tissue than control cartilage. The composition of the repair tissue thus is not identical to mature articular cartilage

Emotional Intelligence as Assessed by Situational Judgment and Emotion Recognition Tests: Building the Nomological Net

Recent research on emotion recognition ability (ERA) suggests that the capacity to process emotional information may differ for disparate emotions. However, little research has examined whether this findings holds for emotional understanding and emotion management, as well as emotion recognition. Moreover, little research has examined whether the abilities to recognize emotions, understand emotions, and manage emotions form a distinct emotional intelligence (EI) construct that is independent from traditional cognitive ability factors. The current study addressed these issues. Participants (N=118) completed two ERA measures, two situational judgment tests assessing emotional understanding and emotion management, and three cognitive ability tests. Exploratory and confirmatory factor analyses of both the understanding and management item parcels showed that a three-factor model relating to fear, sadness, and anger content was a better fit than a one-factor model, supporting an emotion-specific view of EI. In addition, an EI factor composed of emotion recognition, emotional understanding, and emotion management was distinct from a cognitive ability factor composed of a matrices task, general knowledge test, and reading comprehension task. Results are discussed in terms of their potential implications for theory and practice, as well as the integration of EI research with known models of cognitive ability

The BRICS (Bronchiectasis Radiologically Indexed CT Score)- a multi-center study score for use in idiopathic and post infective bronchiectasis

OBJECTIVES: The goal of this study was to develop a simplified radiological score that could assess clinical disease severity in bronchiectasis. METHODS: The Bronchiectasis Radiologically Indexed CT Score (BRICS) was devised based on a multivariable analysis of the Bhalla score and its ability in predicting clinical parameters of severity. The score was then externally validated in six centers in 302 patients. RESULTS: A total of 184 high-resolution CT scans were scored for the validation cohort. In a multiple logistic regression model, disease severity markers significantly associated with the Bhalla score were percent predicted FEV1, sputum purulence, and exacerbations requiring hospital admission. Components of the Bhalla score that were significantly associated with the disease severity markers were bronchial dilatation and number of bronchopulmonary segments with emphysema. The BRICS was developed with these two parameters. The receiver operating-characteristic curve values for BRICS in the derivation cohort were 0.79 for percent predicted FEV1, 0.71 for sputum purulence, and 0.75 for hospital admissions per year; these values were 0.81, 0.70, and 0.70, respectively, in the validation cohort. Sputum free neutrophil elastase activity was significantly elevated in the group with emphysema on CT imaging. CONCLUSIONS: A simplified CT scoring system can be used as an adjunct to clinical parameters to predict disease severity in patients with idiopathic and postinfective bronchiectasis

Characterising the volume and variation of multiple urgent suspected cancer referrals in England, April 2013–March 2018: a national cohort study

Objectives: To establish a methodology to categorise urgent suspected cancer (USC) referrals in England and use these categories to understand individual patient referral patterns by demographic characteristics, financial year and referral pathway. Design: Cross-sectional population-based cohort study. Setting: From Cancer Waiting Times data, linked to demographic information held by the National Disease Registration Service, referral-level data on all USC referrals in England between 1 April 2013 and 31 March 2018. Participants: After restricting records to those with an English postcode at referral and with complete demographic information, 9 524 435 referrals were identified for 7 542 592 patients. Primary and secondary outcome measures: USC referrals were categorised into first and subsequent USC referrals, based primarily on intervals between referral dates. Our primary outcome was to describe the distribution of referral categories by financial year, suspected cancer referral type and four demographic variables. Our secondary aim was to understand which suspected cancer referral types were found in combination within the first 4 months. Results: During the study period, 7.5 million people had an USC referral, with one in five having more than one referral, with 9.5 million referrals in total. Referrals were categorised as first (91.1%) and subsequent (8.9%) USC referrals. The relative increase in the number of referrals across the study period was largest (78.2%) for subsequent USC referrals. Subsequent referrals were most common in the gynaecological (10%), lung (10%) and haematological cancer pathways (12%). Suspected lower gastrointestinal referrals were most frequently included in a pair of USC referrals; it was one of the five most common pairings for 14 out of 16 referral type pathways, contributing to 30% of upper gastrointestinal USC referral pairings. Conclusion: Multiple USC referrals increased in the study period, particularly within a year of the first referral. Common referral pairings suggest opportunities for pathway reorganisation where common non-specific symptoms result in multiple USC referrals