Recording advances for neural prosthetics

An important challenge for neural prosthetics research is to record from populations of neurons over long periods of time, ideally for the lifetime of the patient. Two new advances toward this goal are described, the use of local field potentials (LFPs) and autonomously positioned recording electrodes. LFPs are the composite extracellular potential field from several hundreds of neurons around the electrode tip. LFP recordings can be maintained for longer periods of time than single cell recordings. We find that similar information can be decoded from LFP and spike recordings, with better performance for state decodes with LFPs and, depending on the area, equivalent or slightly less than equivalent performance for signaling the direction of planned movements. Movable electrodes in microdrives can be adjusted in the tissue to optimize recordings, but their movements must be automated to be a practical benefit to patients. We have developed automation algorithms and a meso-scale autonomous electrode testbed, and demonstrated that this system can autonomously isolate and maintain the recorded signal quality of single cells in the cortex of awake, behaving monkeys. These two advances show promise for developing very long term recording for neural prosthetic applications

The GNAT library for local and remote gene mention normalization

Summary: Identifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987

Comparison of the expressed experiences of survivors of childhood medulloblastoma with measures of health and quality of life, and with issues identified in consultations

When the study was planned, the Young Oncology Unit at The Christie housed both the adult and paediatric follow-up clinics for patients who have been diagnosed with a tumour of the central nervous system (CNS) in childhood and adolescence or young adult life. Over the past 10 years, the paediatric clinic had developed a true multi-disciplinary team function with input from paediatric oncology, clinical oncology, teenage and young adult oncology, neurosurgery, social work, physiotherapy and clinical psychology. In contrast, the adult clinic (for follow-up of patients diagnosed in childhood and also in late teenage or early adult life) had solely medical input. The clinic for the follow-up of adult survivors of childhood CNS tumours at The Christie had significantly less multidisciplinary team involvement than its paediatric counterpart, and it was postulated that adult patients’ needs might not be addressed as fully by the current provision. This study was designed to develop a process to capture information systematically about patients’ problems in the domains of medical, physical, psychological and social wellbeing in order to compare the extent to which these were recognised and supported in the context of the adult and paediatric clinics. Ultimately, this information was expected to inform planning for improvements in survivorship support in both clinics

Are virtues national, supranational, or universal?

Many studies investigated cultural differences in values, most notably by Hofstede and Schwarz. Relatively few have focused on virtues, a related and important concept in contemporary social science. The present paper examines the similarities and differences between nations, or blocks of - culturally related - nations on the perceived importance of virtues. Adults (N = 2.809 students) from 14 countries were asked to freely mention which virtues they found important to practice in daily life, and next to rate a list of 15 virtues, which reflect the most frequently mentioned categories in The Netherlands, as found in a previous study. The 14 nations included the United States, Mexico, nine European and three Asian nations. For the free-listed virtues, we compared the top-ten lists of most frequently mentioned virtues across the nations. We used a correspondence analysis on the frequency table to assess the relationships between the virtues and nations. For the 15 virtues ratings, a MANOVA, and follow-up ANOVA’s were used to examine effects of nation, age, gender and religion. We found strong evidence for relationships between nations and blocks of culturally related nations and the importance attached to various virtues. There appear to be some country specific virtues, such as generosity in France, but also some relatively universal virtues, most notably honesty, respect, and kindness

Real-world effectiveness, its predictors and onset of action of cholinesterase inhibitors and memantine in dementia: retrospective health record study

Background The efficacy of acetylcholinesterase inhibitors and memantine in the symptomatic treatment of Alzheimer's disease is well-established. Randomised trials have shown them to be associated with a reduction in the rate of cognitive decline. Aims To investigate the real-world effectiveness of acetylcholinesterase inhibitors and memantine for dementia-causing diseases in the largest UK observational secondary care service data-set to date. Method We extracted mentions of relevant medications and cognitive testing (Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) scores) from de-identified patient records from two National Health Service (NHS) trusts. The 10-year changes in cognitive performance were modelled using a combination of generalised additive and linear mixed-effects modelling. Results The initial decline in MMSE and MoCA scores occurs approximately 2 years before medication is initiated. Medication prescription stabilises cognitive performance for the ensuing 2–5 months. The effect is boosted in more cognitively impaired cases at the point of medication prescription and attenuated in those taking antipsychotics. Importantly, patients who are switched between agents at least once do not experience any beneficial cognitive effect from pharmacological treatment. Conclusions This study presents one of the largest real-world examination of the efficacy of acetylcholinesterase inhibitors and memantine for symptomatic treatment of dementia. We found evidence that 68% of individuals respond to treatment with a period of cognitive stabilisation before continuing their decline at the pre-treatment rate

CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid

SOFTWAR

A scalable machine-learning approach to recognize chemical names within large text databases

MOTIVATION: The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. RESULTS: A first-order Markov Model (MM) was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid

A feasibility study of enhanced occupational therapy for children and young people with central nervous system tumours – outcomes for the families and for occupational therapy

A two-year feasibility study was conducted to explore harmonisation of occupation-focused practice between two UK children’s cancer centres. The Short Child Occupational Profile (SCOPE) identified occupational needs of children with brain tumours to inform goal-setting, treatment-planning and intervention. A professional decision-making log was developed to focus reflection and to enhance communication of clinical decisions. The impact of a range of personal and environmental factors on participation beyond performance components was considered, enabling the occupational therapists to incorporate the child’s strengths to overcome daily occupational challenges. Twenty-four children aged 3-14 years with central nervous system tumours received enhanced occupational therapy for six months which families perceived as being helpful in rehabilitating children to participate in life and equipping them with better coping strategies for the future. Individual occupational needs of children were highlighted using the SCOPE which helped to standardise practice. Using the SCOPE harmonised occupational therapists’ unique focus on occupation in their practice with patients with brain tumours. This both evidenced intervention outcomes and strengthened professional identity. The outcome was robust preparation for a multi-centre intervention study. Keywords Occupational therapy, children, brain tumour, harmonised practice, SCOP

Duplications in RB1CC1 are associated with schizophrenia; identification in large European sample sets

Schizophrenia (SCZ) is a severe and debilitating neuropsychiatric disorder with an estimated heritability of ~80%. Recently, de novo mutations, identified by next-generation sequencing (NGS) technology, have been suggested to contribute to the risk of developing SCZ. Although these studies show an overall excess of de novo mutations among patients compared with controls, it is not easy to pinpoint specific genes hit by de novo mutations as actually involved in the disease process. Importantly, support for a specific gene can be provided by the identification of additional alterations in several independent patients. We took advantage of existing genome-wide single-nucleotide polymorphism data sets to screen for deletions or duplications (copy number variations, CNVs) in genes previously implicated by NGS studies. Our approach was based on the observation that CNVs constitute part of the mutational spectrum in many human disease-associated genes. In a discovery step, we investigated whether CNVs in 55 candidate genes, suggested from NGS studies, were more frequent among 1637 patients compared with 1627 controls. Duplications in RB1CC1 were overrepresented among patients. This finding was followed-up in large, independent European sample sets. In the combined analysis, totaling 8461 patients and 112 871 controls, duplications in RB1CC1 were found to be associated with SCZ (P=1.29 × 10−5; odds ratio=8.58). Our study provides evidence for rare duplications in RB1CC1 as a risk factor for SCZ