Meeting Curation Challenges in a Neuroimaging Group

The SCARP project is a series of short studies with two aims; firstly to discover more about disciplinary approaches and attitudes to digital curation through ‘immersion’ in selected cases; secondly to apply known good practice, and where possible, identify new lessons from practice in the selected discipline areas. The study summarised here is of the Neuroimaging Group in the University of Edinburgh’s Division of Psychiatry, which plays a leading role in eScience collaborations to improve the infrastructure for neuroimaging data integration and reuse. The Group also aims to address growing data storage and curation needs, given the capabilities afforded by new infrastructure. The study briefly reviews the policy context and current challenges to data integration and sharing in the neuroimaging field. It then describes how curation and preservation risks and opportunities for change were identified throughout the curation lifecycle; and their context appreciated through field study in the research site. The results are consistent with studies of neuroimaging eInfrastructure that emphasise the role of local data sharing and reuse practices. These sustain mutual awareness of datasets and experimental protocols through sharing peer to peer, and among senior researchers and students, enabling continuity in research and flexibility in project work. This “human infrastructure” is taken into account in considering next steps for curation and preservation of the Group’s datasets and a phased approach to supporting data documentation

Agronomic biofortification: Uncovering the evidence. A seminar organized by the Excellence in Agronomy Agronomic Initiative

Human Zn and Fe deficiencies can be reduced through agronomic biofortification, but information on factors influencing maize grain-Zn and -Fe levels remains scant

Correlations between fMRI activation and individual psychotic symptoms in un-medicated subjects at high genetic risk of schizophrenia

<p>Abstract</p> <p>Background:</p> <p>It has been proposed that different types of psychopathology in schizophrenia may reflect distinguishable pathological processes. In the current study we aimed to address such associations in the absence of confounders such as medication and disease chronicity by examining specific relationships between fMRI activation and individual symptom severity scores in un-medicated subjects at high genetic risk of schizophrenia.</p> <p>Methods:</p> <p>Associations were examined across two functional imaging paradigms: the Hayling sentence completion task, and an encoding/retrieval task, comprising encoding (at word classification) and retrieval (old word/new word judgement). Symptom severity was assessed using the positive and negative syndrome scale (PANSS). Items examined were hallucinations, delusions, and suspiciousness/persecution.</p> <p>Results:</p> <p>Associations were seen in the anterior middle temporal gyrus in relation to hallucination scores during the sentence completion task, and in the medial temporal lobe in association with suspiciousness/persecution scores in the encoding/retrieval task. Cerebellar activation was associated with delusions and suspiciousness/persecution scores across both tasks with differing patterns of laterality.</p> <p>Conclusion:</p> <p>These results support a role for the lateral temporal cortex in hallucinations and medial temporal lobe in positive psychotic symptoms. They also highlight the potential role of the cerebellum in the formation of delusions. That the current results are seen in un-medicated high risk subjects indicates these associations are not specific to the established illness and are not related to medication effects.</p

Connecting Food Inequities Through Relational Territories

This paper explores how food inequities manifest at a territorial level, and how food territories are experienced, understood, and navigated by stakeholders to address those inequities. We interpret ‘food territory’ as a relational and transcalar concept, connected through geography, culture, history, and governance. We develop our exploration through four empirical cases: (i) the Cerrado, a disputed Brazilian territory that has been framed and reframed as a place for industrial production of global commodities, to the detriment of local communities and nature; (ii) urban agroecology networks seeking space and recognition to enable food production in the city of Rio de Janeiro, Brazil; (iii) informal food networks forming a complex web of intersecting local and global supply chains in Worcester, a secondary South African city; and (iv) periodic food markets in Ghana that synchronise trade systems across space and time to provide limited profit-making opportunities, but nonetheless accessible livelihood options, for poorer people. Examining these four cases, we identify commonalities and differences between them, in terms of the nature of their inequities and how different territories are connected on wider scales. We discuss how territories are perceived and experienced differently by different people and groups. We argue that a territorial perspective offers more than a useful lens to map how food inequities are experienced and interconnected; it also offers a tool for action.IDS Strategic Research Initiativ

Machine learning of neuroimaging for assisted diagnosis of cognitive impairment and dementia: A systematic review

pp. 519-535Los métodos avanzados de aprendizaje automático pueden ayudar a identificar el riesgo de demencia de la neuroimagen, pero su precisión hasta la fecha no está clara. Revisamos sistemáticamente la literatura, desde 2006 hasta finales de 2016, para los estudios de aprendizaje automático que diferencian el envejecimiento saludable de la demencia de varios tipos, evaluamos la calidad del estudio y comparamos la precisión en diferentes límites de enfermedades. De los 111 estudios relevantes, la mayoría evaluó la enfermedad de Alzheimer en comparación con los controles sanos, utilizando datos de la Iniciativa de neuroimagen AD, máquinas de vectores de soporte y solo secuencias ponderadas en T1. La precisión fue más alta para diferenciar la enfermedad de Alzheimer de los controles sanos y pobre para diferenciar los controles sanos versus deterioro cognitivo leve versus enfermedad de Alzheimer o conversores de deterioro cognitivo leve versus no conversores. La precisión aumentó con los tipos de datos combinados, pero no con la fuente de datos, el tamaño de la muestra o el método de aprendizaje automático. El aprendizaje automático todavía no distingue categorías de enfermedades clínicamente relevantes. Los conjuntos de datos más diversos, las combinaciones de diferentes tipos de datos y la estrecha integración clínica del aprendizaje automático ayudarían a avanzar en este campo.S

The impact of substance use on brain structure in people at high risk of developing schizophrenia

Ventricular enlargement and reduced prefrontal volume are consistent findings in schizophrenia. Both are present in first episode subjects and may be detectable before the onset of clinical disorder. Substance misuse is more common in people with schizophrenia and is associated with similar brain abnormalities. We employ a prospective cohort study with nested case control comparison design to investigate the association between substance misuse, brain abnormality, and subsequent schizophrenia. Substance misuse history, imaging data, and clinical information were collected on 147 subjects at high risk of schizophrenia and 36 controls. Regions exhibiting a significant relationship between level of use of alcohol, cannabis or tobacco, and structure volume were identified. Multivariate regression then elucidated the relationship between level of substance use and structure volumes while accounting for correlations between these variables and correcting for potential confounders. Finally, we established whether substance misuse was associated with later risk of schizophrenia. Increased ventricular volume was associated with alcohol and cannabis use in a dose-dependent manner. Alcohol consumption was associated with reduced frontal lobe volume. Multiple regression analyses found both alcohol and cannabis were significant predictors of these abnormalities when simultaneously entered into the statistical model. Alcohol and cannabis misuse were associated with an increased subsequent risk of schizophrenia. We provide prospective evidence that use of cannabis or alcohol by people at high genetic risk of schizophrenia is associated with brain abnormalities and later risk of psychosis. A family history of schizophrenia may render the brain particularly sensitive to the risk-modifying effects of these substances