KInNeSS: A Modular Framework for Computational Neuroscience

Making use of very detailed neurophysiological, anatomical, and behavioral data to build biological-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalabiltiy, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multu-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions of ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further developement of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effecitively collaborate using a modern neural simulation platform.

KInNeSS: A Modular Framework for Computational Neuroscience

Making use of very detailed neurophysiological, anatomical, and behavioral data to build biologically-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalability, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multi-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions or ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further development of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effectively collaborate using a modern neural simulation platform.

Variability in frontotemporal brain structure: the importance of recruitment of African Americans in neuroscience research.

BACKGROUND: Variation in brain structure is both genetically and environmentally influenced. The question about potential differences in brain anatomy across populations of differing race and ethnicity remains a controversial issue. There are few studies specifically examining racial or ethnic differences and also few studies that test for race-related differences in context of other neuropsychiatric research, possibly due to the underrepresentation of ethnic minorities in clinical research. It is within this context that we conducted a secondary data analysis examining volumetric MRI data from healthy participants and compared the volumes of the amygdala, hippocampus, lateral ventricles, caudate nucleus, orbitofrontal cortex (OFC) and total cerebral volume between Caucasian and African-American participants. We discuss the importance of this finding in context of neuroimaging methodology, but also the need for improved recruitment of African Americans in clinical research and its broader implications for a better understanding of the neural basis of neuropsychiatric disorders. METHODOLOGY/PRINCIPAL FINDINGS: This was a case control study in the setting of an academic medical center outpatient service. Participants consisted of 44 Caucasians and 33 ethnic minorities. The following volumetric data were obtained: amygdala, hippocampus, lateral ventricles, caudate nucleus, orbitofrontal cortex (OFC) and total cerebrum. Each participant completed a 1.5 T magnetic resonance imaging (MRI). Our primary finding in analyses of brain subregions was that when compared to Caucasians, African Americans exhibited larger left OFC volumes (F (1,68) = 7.50, p = 0.008). CONCLUSIONS: The biological implications of our findings are unclear as we do not know what factors may be contributing to these observed differences. However, this study raises several questions that have important implications for the future of neuropsychiatric research.

Sound the alarm: fraud in neuroscience.

We expect scientists to follow a code of honor and conduct and to report their research honestly and accurately, but so-called scientific misconduct, which includes plagiarism, faked data, and altered images, has led to a tenfold increase in the number of retractions over the past decade. Among the reasons for this troubling upsurge is increased competition for journal placement, grant money, and prestigious appointments. The solutions are not easy, but reform and greater vigilance is needed.

Mapping the semantic structure of cognitive neuroscience.

Cognitive neuroscience, as a discipline, links the biological systems studied by neuroscience to the processing constructs studied by psychology. By mapping these relations throughout the literature of cognitive neuroscience, we visualize the semantic structure of the discipline and point to directions for future research that will advance its integrative goal. For this purpose, network text analyses were applied to an exhaustive corpus of abstracts collected from five major journals over a 30-month period, including every study that used fMRI to investigate psychological processes. From this, we generate network maps that illustrate the relationships among psychological and anatomical terms, along with centrality statistics that guide inferences about network structure. Three terms--prefrontal cortex, amygdala, and anterior cingulate cortex--dominate the network structure with their high frequency in the literature and the density of their connections with other neuroanatomical terms. From network statistics, we identify terms that are understudied compared with their importance in the network (e.g., insula and thalamus), are underspecified in the language of the discipline (e.g., terms associated with executive function), or are imperfectly integrated with other concepts (e.g., subdisciplines like decision neuroscience that are disconnected from the main network). Taking these results as the basis for prescriptive recommendations, we conclude that semantic analyses provide useful guidance for cognitive neuroscience as a discipline, both by illustrating systematic biases in the conduct and presentation of research and by identifying directions that may be most productive for future research.

Ethics in neuroscience graduate training programs:Views and models from Canada

Consideration of the ethical, social, and policy implications of research has become increasingly important to scientists and scholars whose work focuses on brain and mind, but limited empirical data exist on the education in ethics available to them. We examined the current landscape of ethics training in neuroscience programs, beginning with the Canadian context specifically, to elucidate the perceived needs of mentors and trainees and offer recommendations for resource development to meet those needs. We surveyed neuroscientists at all training levels and interviewed directors of neuroscience programs and training grants. A total of 88% of survey respondents reported general interest in ethics, and 96% indicated a desire for more ethics content as it applies to brain research and clinical translation. Expert interviews revealed formal ethics education in over half of programs and in 90% of grants-based programs. Lack of time, resources, and expertise, however, are major barriers to expanding ethics content in neuroscience education. We conclude with an initial set of recommendations to address these barriers which includes the development of flexible, tailored ethics education tools, increased financial support for ethics training, and strategies for fostering collaboration between ethics experts, neuroscience program directors, and funding agencies. © 2010 the Authors. Journal Compilation © 2010 International Mind, Brain, and Education Society and Blackwell Publishing, Inc.

Evaluation of the contribution of theatre attendance to medical undergraduate neuroscience teaching - a pilot study.

Introduction: Medical students often attend the neurosurgical theatre during their clinical neurosciences attachment. However, few studies have been performed to objectively assess the value of this theatre-based learning experience. The main aim of this study was to explore student perceptions on the contribution of neurosurgical theatre attendance to clinical neuroscience teaching.

Materials and Methods: Third-year medical students undergoing their 2-week clinical neurosciences rotation at the Royal Hospitals Belfast were invited to participate in this study. A multi-method strategy was employed using a survey questionnaire comprising of closed and open-ended questions followed by semi-structured interviews to gain a greater 'in-depth' analysis of the potential contribution of neurosurgical theatre attendance to neuroscience teaching.

Results: Based on the completed survey responses of 22 students, the overall experience of neurosurgical theatre-based learning was a positive one. 'In-depth' analysis from semi-structured interviews indicated that students felt that some aspects of their neurosurgical theatre attendance could be improved. Better preparation such as reading up on the case in hand and an introduction to simple theatre etiquette to put the student at ease (in particular, for students who had never attended theatre previously), would improve the learning experience. In addition, having an expectation of what students are expected to learn in theatre making it more learning outcomes-based would probably make it feel a more positive experience by the student.

Conclusions: The vast majority of students acknowledged the positive learning outcomes of neurosurgical theatre attendance and felt that it should be made a mandatory component of the curriculum.

Non-Invasive Human Brain Stimulation in Cognitive Neuroscience: A Primer

The use of non-invasive brain stimulation is widespread in studies of human cognitive neuroscience. This has led to some genuine advances in understanding perception and cognition, and has raised some hopes of applying the knowledge in clinical contexts. There are now several forms of stimulation, the ability to combine these with other methods, and ethical questions that are special to brain stimulation. In this Primer, we aim to give the users of these methods a starting point and perspective from which to view the key questions and usefulness of the different forms of non-invasive brain stimulation. We have done so by taking a critical view of recent highlights in the literature, selected case studies to illustrate the elements necessary and sufficient for good experiments, and pointed to questions and findings that can only be addressed using interference methods

Mental health and neuroscience. A perspective from the magazine market

Mental health awareness has been rising worldwide, motivated by its social and economic costs. Despite the investment in research in neuroscience in the recent years, little is known about the underlying mechanisms in the brain that are correlated with psychiatric conditions. This project, through two feature articles suitable to be published in magazines, provides perspectives onto mental health research. First it presents an example where psychiatry joins forces with neuroscience and computer science in an interdisciplinary effort to improve the life of those affected by mental disorders. The second article gathers opinions which claim that mental health research priorities should be set by patients themselves, or even that people with lived experience of mental health issues should have an active role in that research. This project was planned and researched while I was an Erasmus student at Nottingham Trent University, in the United Kingdom.

Reconsidering the concept of ‘dual-use’ in the context of neuroscience research

Commentaire / Commentary

Impulsivity: A view from the behavioral neuroscience and developmental psychology

Impulsivity has been linked to three main factors: performing without direct involvement of the frontal lobe functions, an increase in the speed of response, and the acquisition of immediate gratification. This behavioral inhibition deficit involves a variety of behaviors including aspects of hyperexcitability, behavioral disinhibition and higher order decision making. Although by tradition, the definition of this executive function has been conceptualized from a psychopathological view, currently, the wide variety of neuropsychological, developmental and animal models assessment techniques encourage us to establish dialogues that integrate the knowledge of these theoretical perspectives for the interpretation and understanding of impulsivity.

Consumer Neuroscience as a reserach issue, concepts and applications. A paradigmatic approach

Consumer neuroscience allows a fullest and objective understanding about desires andactions of consumers, turning itself in a fickle tool to the use of the companies and to improve their Marketing strategies. The use of the Neuroscientific methods to the analysis, description and comprehension of human behavior related to consume open a lot of unknown possibilities to discover. Neuromarketing or The consumer Neuroscience as is known too is the study of mental process been part of the consumer behavior and contexts concerning the marketing as well, apply and follow in the environment of the real life of human been. Its supported by the paradigms and the technological development of Neurosciences whose progress has made possible for the seekers to deep in knowledge abouthow the brain work. Physiological operations of mind are a product of a structural and functional ensemble including the brain, as organ, and mind, emotion and cognition, asfunctions. Mind events just can be understood in the middle of the interaction between the organism and his environment. Neuromarketing paradigm it’s still in his infancy and whatfor it’s full of research possibilities. Inside the consumer neuroscience the ethic building doesn’t collapse, the morality isn’t threaten, inside the normal individual Will it’s alwaysWill. The present paper looking for a place to the consumer neuroscience paradigm over the perspective of research open to the Marketing, from the technological advances and hermeneutical vision offer by Neuroscience; it’s propose some of several possibilities ofresearch and practice been explored actually. To give an example its offer one of methods of research as is the Evoked Potentials.