BackCLIP: a tool to identify common background presence in PAR-CLIP datasets

MOTIVATION

PAR-CLIP, a CLIP-seq protocol, derives a transcriptome wide set of binding sites for RNA-binding proteins. Even though the protocol uses stringent washing to remove experimental noise, some of it remains. A recent study measured three sets of non-specific RNA backgrounds which are present in several PAR-CLIP datasets. However, a tool to identify the presence of common background in PAR-CLIP datasets is not yet available.

RESULTS

We used the measured sets of non-specific RNA backgrounds to build a common background set. Each element from the common background set has a score that reflects its presence in several PAR-CLIP datasets. We present a tool that uses this score to identify the amount of common backgrounds present in a PAR-CLIP dataset, and we provide the user the option to use or remove it. We used the proposed strategy in 30 PAR-CLIP datasets from nine proteins. It is possible to identify the presence of common backgrounds in a dataset and identify differences in datasets for the same protein. This method is the first step in the process of completely removing such backgrounds.

AVAILABILITY

The tool was implemented in python. The common background set and the supplementary data are available at https://github.com/phrh/BackCLIP.

CONTACT

phreyes@gmail.com

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Hostile attributions in bipolar disorder and schizophrenia contribute to poor social functioning

OBJECTIVE

To compare the profile of attributional style of a group of out-patients with bipolar disorder (BD) and schizophrenia (SZ), and a group of healthy controls - along with other social cognition domains - such as emotion recognition and theory of mind (ToM).

METHOD

A total of 46 out-patients diagnosed with BD, 49 with SZ, and 50 healthy controls were assessed in attributional style (Ambiguous Intentions Hostility Questionnaire), facial emotion recognition (FEIT, FEDT, ER-40), and ToM (Hinting Task). Symptomatology, clinical variables and global functioning were also collected.

RESULTS

Both groups with SZ and BD showed hostile social cognitive biases, compared with the control group. Patients with BD also showed a capacity for emotional recognition similar to those with SZ and worse than control subjects. In contrast, patients with SZ showed poorer ToM. Subthreshold depressive symptoms and an attributional style toward hostility appeared as the factors with a strongest association to global functioning in BD. In SZ, PANSS score and a tendency to aggressiveness were the most relevant factors.

CONCLUSION

Attributional style (along with other domains of social cognition) is altered in out-patients with BD and SZ. The presence of residual symptoms and a hostile social cognitive bias may contribute to the functional impairment of both groups.

Bio-inspired impact-resistant composites

Through evolutionary processes, biological composites have been optimized to fulfil specific functions. This optimization is exemplified in the mineralized dactyl club of the smashing predator stomatopod (specifically, Odontodactylus scyllarus). This crustacean's club has been designed to withstand the thousands of high-velocity blows that it delivers to its prey. The endocuticle of this multiregional structure is characterized by a helicoidal arrangement of mineralized fiber layers, an architecture which results in impact resistance and energy absorbance. Here, we apply the helicoidal design strategy observed in the stomatopod club to the fabrication of high-performance carbon fiber-epoxy composites. Through experimental and computational methods, a helicoidal architecture is shown to reduce through-thickness damage propagation in a composite panel during an impact event and result in an increase in toughness. These findings have implications in the design of composite parts for aerospace, automotive and armor applications.

Untersuchungen zum chemischen Transport von YX3 mit AlX3 und zur Existenz von gasförmigen und festen Komplexen YAl3 X12 (X = Br, I) / Investigations on the Chemical Transport Reaction of YX3 with AlX3 and on the Existence of Gaseous and Solid Complexes YAl3 X12 (X = Br, I) H

The dominant gaseous complexes YAl3Br12 and YAl3I12 were generated in the chemical trans­port reactions of YBr3 with AlBr3 and YI3 with AlI3. The enthalpy of formation

ΔH0 B(YAl3Br12,g,298) = -484,5 ± 6 kcal/mol

and the standard entropy

S°(YA13B12,g,298) = 290,0 ± 7,5 cal/K·mol

have been calculated. It follows from total pressure measurements of mixtures of YBr3,s with AlBr3,1 and YI3,s with AlI3,1 respectively, that complexes YAl3Br12,s and YAl3I12,s do not exist up to the boiling points of the aluminium trihalides.

Abstract PD1-2: PIK3CA mutations and/or low PTEN predict resistance to combined anti-HER2 therapy with lapatinib and trastuzumab and without chemotherapy in TBCRC006, a neoadjuvant trial of HER2-positive breast cancer patients

We have recently reported that in patients with HER2-positive breast cancer, neoadjuvant targeted therapy with lapatinib and trastuzumab to more completely block the HER receptor layer, combined with endocrine therapy (in ER-positive tumors) and without chemotherapy led to a substantial 27% pathologic complete response (pCR) rate in the breast. Activation of downstream signaling pathways may lead to resistance to therapies targeting the HER pathway receptors. Aberrant activation of the PI3K pathway via decreased levels of PTEN and/or the presence of activating PIK3CA mutations has been implicated in resistance to targeted anti-HER2 therapy, but results of clinical trials are all confounded by the co-administration of chemotherapy and are inconsistent. We sought to clarify the role of these variables in predicting pCR, a surrogate for long-term outcome, in patients treated with potent targeted therapy alone in a prospective Phase II neoadjuvant trial in patients with HER2-positive breast cancer.

Patients with large tumors (median 6 cm) were given 12 weeks of lapatinib plus trastuzumab followed by surgery (Rimawi et al. JCO, 2013). Serial tissue biopsies were obtained from study participants. For this study, we focused on baseline pre-treatment characteristics. PTEN protein levels were measured by IHC and scored using the H-score. PIK3CA mutations were identified on extracted DNA using multiplex PCR with targeted next generation sequencing (the Ion Torrent 50-gene cancer mutation panel).

Of 64 evaluable patients, tissue was available on 59 for PTEN IHC, and sufficient DNA was available on 33 for the mutation panel. PTEN median H-score was 100 (range 0-300). PTEN status when dichotomized by the median was correlated with pCR (32% in high PTEN vs. 9% in low PTEN, p = 0.04). Activating PIK3CA mutations were identified in 12 out of 33 tumors (36%; 3 mutations in the helical and 9 in the catalytic domain) and were independent of ER status. None of the patients whose tumors harbored a PIK3CA mutation achieved pCR (p = 0.06). There was no association between PTEN status and PIK3CA mutation suggesting they are independent variables (p = 0.44). When PIK3CA mutations were considered together with PTEN status, there were 31 cases with data on both. The overall pCR rate in this cohort was 16% (lower than pCR rate observed in the overall trial). However, 0/17 cases (0%) with a mutation and/or PTEN low expression (<100 H score) had a pCR compared to 5/14 cases (36%) with PI3KCA wild type and high PTEN levels (p = 0.01).

We conclude that PI3K pathway activation downstream of HER2 as a result of either low PTEN or activating PIK3CA mutation results in resistance to the combination of lapatinib and trastuzumab. This is the first report on patient tissue samples from a neoadjuvant trial using the combination of lapatinib and trastuzumab without chemotherapy. If validated in a larger cohort, our findings suggest that patients with HER2 positive tumors and who also harbor aberrant downstream PI3K pathway activation may benefit from the addition of PI3K/Akt/mTOR inhibitors to potent HER2 blockade.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD1-2.

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

Characterization of large numbers of single-nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. The results from analyses with and without a reference genome supported similar conclusions, further highlighting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals and jellyfishes, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection.

Study of the oscillatory breathing pattern in elderly patients

Some of the most common clinical problems in elderly patients are related to diseases of the cardiac and respiratory systems. Elderly patients often have altered breathing patterns, such as periodic breathing (PB) and Cheyne-Stokes respiration (CSR), which may coincide with chronic heart failure. In this study, we used the envelope of the respiratory flow signal to characterize respiratory patterns in elderly patients. To study different breathing patterns in the same patient, the signals were segmented into windows of 5 min. In oscillatory breathing patterns, frequency and time-frequency parameters that characterize the discriminant band were evaluated to identify periodic and non-periodic breathing (PB and nPB). In order to evaluate the accuracy of this characterization, we used a feature selection process, followed by linear discriminant analysis. 22 elderly patients (7 patients with PB and 15 with nPB pattern) were studied. The following classification problems were analyzed: patients with either PB (with and without apnea) or nPB patterns, and patients with CSR versus PB, CSR versus nPB and PB versus nPB patterns. The results showed 81.8% accuracy in the comparisons of nPB and PB patients, using the power of the modulation peak. For the segmented signal, the power of the modulation peak, the frequency variability and the interquartile ranges provided the best results with 84.8% accuracy, for classifying nPB and PB patients.

Occurrence and persistence of organic emerging contaminants and priority pollutants in five sewage treatment plants of Spain: two years pilot survey monitoring

This work summarized all results obtained during almost two-years of a monitoring programme carried out in five municipal sewage treatment plants (STPs) located in the north, centre and south-east of Spain. The study evaluated the occurrence and persistence of a group of 100 organic compounds belonging to several chemical groups (pharmaceuticals, personal care products, pesticides and metabolites). The average removal efficiencies of the STPs studied varied from 20% (erythromycin) to 99% (acetaminophen). In analysed samples, we identified a large number of compounds at mean range concentrations between 7-59,495 ng/L and 5-32,720 ng/L for influent and effluent samples, respectively. This study also identified 20 of the mostly detected and persistent compounds in wastewater effluent, of which hydrochlorothiazide, atenolol, gemfibrozil, galaxolide and three metabolites (fenofibric acid, 4-AAA and 4-FAA), presented the highest average contribution percentages, in relation to the total load of contaminants for the different STPs effluent studied.

Sense of familiarity and face emotion recognition in schizophrenia

Introduction

Patients with schizophrenia show a deficit in emotion recognition through facial expression. Familiarity means the implicit memory of past affective experiences and it involves fast cognitive processes and it is triggered by certain signals.

Objectives

To assess the emotion recognition in familiar and unfamiliar faces in a sample of schizophrenic patients and healthy controls.

Methods

18 outpatients diagnosed with schizophrenia (DSM-IVTR) and 18 healthy volunteers were assessed with the Ekman Test of emotion recognition in unfamiliar faces. In addition each subject was accompanied by 4 familiar people (parents, siblings or friends), which was photographed by expressing the 6 Ekman’s basic emotions.

Results

Schizophrenic patients recognize worse emotions in their relatives than in neutral faces, a greater extent than controls (Mann-Whitney U = 81, p = .01). The patient group showed a mean score on the Ekman test (neutral faces) lower than control group (16 (SD 2.38) versus 17.82 (2.13; U p = 0.03). Regarding familiar faces, the group patients showed a worse performance than the control group (13.22 (3.8) versus 17.18 (2.82); U p = 0.00). In both tests, the highest number of errors was with emotions of anger and fear. The patients group showed a lower level of familiarity and emotional valence to their families (U = 33, p < 0.01).

Conclusions

The sense of familiarity may be a factor involved in face emotion recognition and it may be disturbed in schizophrenia.

Report of a consultation on the optimization of clinical challenge trials for evaluation of candidate blood stage malaria vaccines, 18-19 March 2009, Bethesda, MD, USA

Development and optimization of first generation malaria vaccine candidates has been facilitated by the existence of a well-established Plasmodium falciparum clinical challenge model in which infectious sporozoites are administered to human subjects via mosquito bite. While ideal for testing pre-erythrocytic stage vaccines, some researchers believe that the sporozoite challenge model is less appropriate for testing blood stage vaccines. Here we report a consultation, co-sponsored by PATH MVI, USAID, EMVI and WHO, where scientists from all institutions globally that have conducted such clinical challenges in recent years and representatives from regulatory agencies and funding agencies met to discuss clinical malaria challenge models. Participants discussed strengthening and harmonizing the sporozoite challenge model and considered the pros and cons of further developing a blood stage challenge possibly better suited for evaluating the efficacy of blood stage vaccines. This report summarizes major findings and recommendations, including an update on the Plasmodium vivax clinical challenge model, the prospects for performing experimental challenge trials in malaria endemic countries and an update on clinical safety data. While the focus of the meeting was on the optimization of clinical challenge models for evaluation of blood stage candidate malaria vaccines, many of the considerations are relevant for the application of challenge trials to other purposes.

Characterization of periodic and non-periodic breathing pattern in chronic heart failure patients

Periodic breathing (PB) has a high prevalence in chronic heart failure (CHF) patients with mild to moderate symptoms and poor ventricular function. This work proposes the analysis and characterization of the respiratory pattern to identify periodic breathing pattern (PB) and non-periodic breathing pattern (nPB) through the respiratory flow signal. The respiratory pattern analysis is based on the extraction and the study of the flow envelope signal. The flow envelope signal is modelled by an autoregressive model (AR) whose coefficients would characterize the respiratory pattern of each group. The goodness of the characterization is evaluated through a linear and non linear classifier applied to the AR coefficients. An adaptive feature selection is used before the linear and non linear classification, employing leave-one-out cross validation technique. With linear classification the percentage of well classified patients (8 PB and 18 nPB patients) is 84.6% using the statistically significant coefficients whereas with non linear classification, the percentage of well classified patients increase to more than 92% applying the best subset of coefficients extracted by a forward selection algorithm.

Nationwide outbreak of Salmonella enterica serotype Kedougou infection in infants linked to infant formula milk, Spain, 2008

On 5 August 2008, the National Reference Laboratory of Salmonella (NRLS) noted an increase in the number of isolates of Salmonella enterica serotype Kedougou. As of 22 August, 29 isolates have been reported during 2008, which is ten times more than the average number of isolates identified by the NRLS during 2002-2007. All isolates have a typical, indistinguishable Pulse Field pattern (SALKEDXB-1, Spanish code) and are fully sensitive to the standard suite of antimicrobials.