Icing: Large-scale inference of immunoglobulin clonotypes

Immunoglobulin (IG) clonotype identification is a fundamental open question in modern immunology. An accurate description of the IG repertoire is crucial to understand the variety within the immune system of an individual, potentially shedding light on the pathogenetic process. Intrinsic IG heterogeneity makes clonotype inference an extremely challenging task, both from a computational and a biological point of view. Here we present icing, a framework that allows to reconstruct clonal families also in case of highly mutated sequences. icing has a modular structure, and it is designed to be used with large next generation sequencing (NGS) datasets, a technology which allows the characterisation of large-scale IG repertoires. We extensively validated the framework with clustering performance metrics on the results in a simulated case. icing is implemented in Python, and it is publicly available under FreeBSD licence at https://github.com/slipguru/icing

Neuromotor tolerability and behavioural characterisation of cannabidiolic acid, a phytocannabinoid with therapeutic potential for anticipatory nausea

Rationale: Anticipatory nausea (AN) is a poorly controlled side-effect experienced by chemotherapy patients. Currently, pharmacotherapy is restricted to benzodiazepine anxiolytics, which have limited efficacy, significant sedative effects, and induce dependency. The non-psychoactive phytocannabinoid, cannabidiolic acid (CBDA), has shown considerable efficacy in pre-clinical AN models, however determination of its neuromotor tolerability profile is crucial to justify clinical investigation. Provisional evidence for appetite-stimulating properties also requires detailed investigation. Objectives: To assess the tolerability of CBDA in locomotor activity, motor coordination and muscular strength tests, and additionally for ability to modulate feeding behaviours. Methods: Male Lister hooded rats administered CBDA (0.05-5 mg/kg; p.o.) were assessed in habituated open field (for locomotor activity), static beam and grip strength tests. A further study investigated whether these CBDA doses modulated normal feeding behaviour. Finally, evidence of anxiolytic-like effects in the habituated open field prompted testing of 5 mg/kg CBDA for anxiolytic-like activity in unhabituated open field, light/dark box and novelty-supressed feeding (NSF) tests. Results: CBDA had no adverse effects upon performance in any neuromotor tolerability test, however anxiolytic-like behaviour was observed in the habituated open field. Normal feeding behaviours were unaffected by any dose. CBDA (5 mg/kg) abolished the increased feeding latency in the NSF test induced by the 5-HT1AR antagonist, WAY-100,635, indicative of anxiolytic-like effects, but had no effect on anxiety-like behaviour in the novel open field or light/dark box. Conclusions: CBDA is very well tolerated and devoid of the sedative side-effect profile of benzodiazepines, justifying its clinical investigation as a novel AN treatment

Tapes, transcripts and trials:The routine contamination of police interview evidence

This article addresses a serious, but currently unacknowledged, problem of evidential consistency regarding police-suspect interview evidence. It sheds light on flaws in current criminal procedure through the lens of linguistics, focusing on key stages of currently accepted practice which fly in the face of what linguists have long known about language. It demonstrates that, in stark contrast to the strict principles of preservation applied to physical evidence, interview data go through significant transformation between their creation in the interview room and their presentation in the courtroom, especially through changes in format between written and spoken text. It argues that, despite the safeguards provided by PACE 1984, there is nonetheless a level of routine distortion and contamination unintentionally built in to the current system of presenting police interviews as evidence in England & Wales

Comparisons of food intake between breast cancer patients and controls in Korean women

The purpose of this study was to compare food intakes between Korean breast cancer patients and a healthy control group. We compared the intake of nutrients of 117 food items between Korean breast cancer patients (n=97) and age matched healthy controls (n=97). Nutrient intake was estimated using a quantitative food frequency questionnaire. The mean caloric intake of breast cancer patients and healthy controls was not significantly different. Breast cancer patients consumed significantly less fat and antioxidant nutrients such as vitamin A, retinol, β-carotene, vitamin C and vitamin E when compared to the control subjects. Among the food items, the intake of eggs (p<0.01), legumes (p<0.05), vegetables (p<0.05), seasonings (p<0.001), and oils and fats (p<0.01) in breast cancer patients was significantly lower than that in the controls. These results suggest that Korean breast cancer patients consumed less amount of soy and vegetables, which are rich source of antioxidant nutrients and phytosterols. Thus, dietary guidance to increase intake of these foods may be beneficial in the prevention of breast cancer

Tissue Microenvironments Define and Get Reinforced by Macrophage Phenotypes in Homeostasis or during Inflammation, Repair and Fibrosis

Current macrophage phenotype classifications are based on distinct in vitro culture conditions that do not adequately mirror complex tissue environments. In vivo monocyte progenitors populate all tissues for immune surveillance which supports the maintenance of homeostasis as well as regaining homeostasis after injury. Here we propose to classify macrophage phenotypes according to prototypical tissue environments, e.g. as they occur during homeostasis as well as during the different phases of (dermal) wound healing. In tissue necrosis and/or infection, damage- and/or pathogen-associated molecular patterns induce proinflammatory macrophages by Toll-like receptors or inflammasomes. Such classically activated macrophages contribute to further tissue inflammation and damage. Apoptotic cells and antiinflammatory cytokines dominate in postinflammatory tissues which induce macrophages to produce more antiinflammatory mediators. Similarly, tumor-associated macrophages also confer immunosuppression in tumor stroma. Insufficient parenchymal healing despite abundant growth factors pushes macrophages to gain a profibrotic phenotype and promote fibrocyte recruitment which both enforce tissue scarring. Ischemic scars are largely devoid of cytokines and growth factors so that fibrolytic macrophages that predominantly secrete proteases digest the excess extracellular matrix. Together, macrophages stabilize their surrounding tissue microenvironments by adapting different phenotypes as feed-forward mechanisms to maintain tissue homeostasis or regain it following injury. Furthermore, macrophage heterogeneity in healthy or injured tissues mirrors spatial and temporal differences in microenvironments during the various stages of tissue injury and repair. Copyright (C) 2012 S. Karger AG, Base

The role of the right temporoparietal junction in perceptual conflict: detection or resolution?

The right temporoparietal junction (rTPJ) is a polysensory cortical area that plays a key role in perception and awareness. Neuroimaging evidence shows activation of rTPJ in intersensory and sensorimotor conflict situations, but it remains unclear whether this activity reflects detection or resolution of such conflicts. To address this question, we manipulated the relationship between touch and vision using the so-called mirror-box illusion. Participants' hands lay on either side of a mirror, which occluded their left hand and reflected their right hand, but created the illusion that they were looking directly at their left hand. The experimenter simultaneously touched either the middle (D3) or the ring finger (D4) of each hand. Participants judged, which finger was touched on their occluded left hand. The visual stimulus corresponding to the touch on the right hand was therefore either congruent (same finger as touch) or incongruent (different finger from touch) with the task-relevant touch on the left hand. Single-pulse transcranial magnetic stimulation (TMS) was delivered to the rTPJ immediately after touch. Accuracy in localizing the left touch was worse for D4 than for D3, particularly when visual stimulation was incongruent. However, following TMS, accuracy improved selectively for D4 in incongruent trials, suggesting that the effects of the conflicting visual information were reduced. These findings suggest a role of rTPJ in detecting, rather than resolving, intersensory conflict

Children struggle beyond preschool-age in a continuous version of the ambiguous figures task

Children until the age of five are only able to reverse an ambiguous figure when they are informed about the second interpretation. In two experiments, we examined whether children’s difficulties would extend to a continuous version of the ambiguous figures task. Children (Experiment 1: 66 3- to 5-year olds; Experiment 2: 54 4- to 9-year olds) and adult controls saw line drawings of animals gradually morph—through well-known ambiguous figures—into other animals. Results show a relatively late developing ability to recognize the target animal, with difficulties extending beyond preschool-age. This delay can neither be explained with improvements in theory of mind, inhibitory control, nor individual differences in eye movements. Even the best achieving children only started to approach adult level performance at the age of 9, suggesting a fundamentally different processing style in children and adults

Chalk-steel Interface testing for marine energy foundations

The Energy Technology Partnership (ETP) and Lloyd’s Register EMEA are gratefully acknowledged for the funding of this project. The authors would also like to acknowledge the support of the European Regional Development Fund (ERDF) SMART Centre at the University of Dundee that allowed purchase of the equipment used during this study. The views expressed are those of the authors alone, and do not necessarily represent the views of their respective companies or employing organizations.Peer reviewedPostprin

Precisely timed oculomotor and parietal EEG activity in perceptual switching

Blinks and saccades cause transient interruptions of visual input. To investigate how such effects influence our perceptual state, we analyzed the time courses of blink and saccade rates in relation to perceptual switching in the Necker cube. Both time courses of blink and saccade rates showed peaks at different moments along the switching process. A peak in blinking rate appeared 1,000 ms prior to the switching responses. Blinks occurring around this peak were associated with subsequent switching to the preferred interpretation of the Necker cube. Saccade rates showed a peak 150 ms prior to the switching response. The direction of saccades around this peak was predictive of the perceived orientation of the Necker cube afterwards. Peak blinks were followed and peak saccades were preceded by transient parietal theta band activity indicating the changing of the perceptual interpretation. Precisely-timed blinks, therefore, can initiate perceptual switching, and precisely-timed saccades can facilitate an ongoing change of interpretation