Opinion Exploiting genomics to improve the benefits of wheat: Prospects and limitations

Conventional breeding has been immensely successful in increasing crop production to meet the demands of the growing global population, particularly for wheat where production has increased by over threefold over the last 60 years without a significant increase in the area of land used. However, the pace of improvement by conventional breeding is slow and limited by the range of variation present in wheat and species with which it can be crossed. Genomics can be defined as “an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes” (Wikipedia). As such it has the potential to revolutionise crop improvement, by accelerating the rate of progress and increasing the range of variation that is available. Despite this potential, progress in the application of biotechnology to improve wheat has been slow, particularly when applied to the quality of the grain for processing and nutrition. We will therefore consider the reasons for this and identify priorities for future research

Fusing Structural and Functional MRIs using Graph Convolutional Networks for Autism Classification

Geometric deep learning methods such as graph convolutional networks have recently proven to deliver generalized solutions in disease prediction using medical imaging. In this paper, we focus particularly on their use in autism classification. Most of the recent methods use graphs to leverage phenotypic information about subjects (patients or healthy controls) as additional contextual information. To do so, metadata such as age, gender and acquisition sites are utilized to define intricate relations (edges) between the subjects. We alleviate the use of such non-imaging metadata and propose a fully imaging-based approach where information from structural and functional Magnetic Resonance Imaging (MRI) data are fused to construct the edges and nodes of the graph. To characterize each subject, we employ brain summaries. These are 3D images obtained from the 4D spatiotemporal resting-state fMRI data through summarization of the temporal activity of each voxel using neuroscientifically informed temporal measures such as amplitude low frequency fluctuations and entropy. Further, to extract features from these 3D brain summaries, we propose a 3D CNN model. We perform analysis on the open dataset for autism research (full ABIDE I-II) and show that by using simple brain summary measures and incorporating sMRI information, there is a noticeable increase in the generalizability and performance values of the framework as compared to state-of-the-art graph-based models

The role of habit in compulsivity.

Compulsivity has been recently characterized as a manifestation of an imbalance between the brain׳s goal-directed and habit-learning systems. Habits are perhaps the most fundamental building block of animal learning, and it is therefore unsurprising that there are multiple ways in which the development and execution of habits can be promoted/discouraged. Delineating these neurocognitive routes may be critical to understanding if and how habits contribute to the many faces of compulsivity observed across a range of psychiatric disorders. In this review, we distinguish the contribution of excessive stimulus-response habit learning from that of deficient goal-directed control over action and response inhibition, and discuss the role of stress and anxiety as likely contributors to the transition from goal-directed action to habit. To this end, behavioural, pharmacological, neurobiological and clinical evidence are synthesised and a hypothesis is formulated to capture how habits fit into a model of compulsivity as a trans-diagnostic psychiatric trait.CM Gillan is supported by a Sir Henry Wellcome Postdoctoral Fellowship (101521/Z/12/Z).This is the final version of the article. It was first available from Elsevier via https://doi.org/10.1016/j.euroneuro.2015.12.03

Analysis of Array-CGH Data Using the R and Bioconductor Software Suite

Background. Array-based comparative genomic hybridization (array-CGH) is an emerging high-resolution and high-throughput molecular genetic technique that allows genome-wide screening for chromosome alterations. DNA copy number alterations (CNAs) are a hallmark of somatic mutations in tumor genomes and congenital abnormalities that lead to diseases such as mental retardation. However, accurate identification of amplified or deleted regions requires a sequence of different computational analysis steps of the microarray data. Results. We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs. Conclusion. The implemented option for the determination of minimal altered regions (MARs) from a series of tumor samples is a step forward in the identification of new tumor suppressor genes or oncogenes

Predicting the naturalistic course in anxiety disorders using clinical and biological markers:a machine learning approach

BackgroundDisease trajectories of patients with anxiety disorders are highly diverse and approximately 60% remain chronically ill. The ability to predict disease course in individual patients would enable personalized management of these patients. This study aimed to predict recovery from anxiety disorders within 2 years applying a machine learning approach.MethodsIn total, 887 patients with anxiety disorders (panic disorder, generalized anxiety disorder, agoraphobia, or social phobia) were selected from a naturalistic cohort study. A wide array of baseline predictors (N = 569) from five domains (clinical, psychological, sociodemographic, biological, lifestyle) were used to predict recovery from anxiety disorders and recovery from all common mental disorders (CMDs: anxiety disorders, major depressive disorder, dysthymia, or alcohol dependency) at 2-year follow-up using random forest classifiers (RFCs).ResultsAt follow-up, 484 patients (54.6%) had recovered from anxiety disorders. RFCs achieved a cross-validated area-under-the-receiving-operator-characteristic-curve (AUC) of 0.67 when using the combination of all predictor domains (sensitivity: 62.0%, specificity 62.8%) for predicting recovery from anxiety disorders. Classification of recovery from CMDs yielded an AUC of 0.70 (sensitivity: 64.6%, specificity: 62.3%) when using all domains. In both cases, the clinical domain alone provided comparable performances. Feature analysis showed that prediction of recovery from anxiety disorders was primarily driven by anxiety features, whereas recovery from CMDs was primarily driven by depression features.ConclusionsThe current study showed moderate performance in predicting recovery from anxiety disorders over a 2-year follow-up for individual patients and indicates that anxiety features are most indicative for anxiety improvement and depression features for improvement in general

Negative cognitive schema modification as mediator of symptom improvement after electroconvulsive therapy in major depressive disorder

Background: Electroconvulsive therapy (ECT) is a potent option for treatment-resistant major depressive disorder (MDD). Cognitive models of depression posit that negative cognitions and underlying all-or-nothing negative schemas contribute to and perpetuate depressed mood. This study investigates whether ECT can modify negative schemas, potentially via memory reactivation, and whether such changes are related to MDD symptom improvement. Method: Seventy-two patients were randomized to either an emotional memory reactivation electroconvulsive therapy (EMR-ECT) or control memory reactivation electroconvulsive therapy (CMR-ECT) intervention prior to ECT-sessions in a randomized controlled trail. Emotional memories associated with patients' depression were reactivated before ECT-sessions. At baseline and after the ECT-course, negative schemas and depression severity were assessed using the Dysfunctional Attitude Scale (DAS) and Hamilton Depression Rating Scale HDRS. Mediation analyses were used to examine whether the effects of ECT on HDRS-scores were mediated by changes in DAS-scores or vice versa. Results: Post-ECT DAS-scores were significantly lower compared to baseline. Post-ECT, the mean HDRS-score of the whole sample (15.10 ± 8.65 [SD]; n = 59) was lower compared to baseline (24.83 ± 5.91 [SD]). Multiple regression analysis showed no significant influence of memory reactivation on schema improvement. Path analysis showed that depression improvement was mediated by improvement of negative cognitive schemas. Conclusion: ECT is associated with improvement of negative schemas, which appears to mediate the improvement of depressive symptoms. An emotional memory intervention aimed to modify negative schemas showed no additional effect