Bio-Swarm-Pipeline: a light-weight, extensible batch processing system for efficient biomedical data processing

A streamlined scientific workflow system that can track the details of the data processing history is critical for the efficient handling of fundamental routines used in scientific research. In the scientific workflow research community, the information that describes the details of data processing history is referred to as provenance which plays an important role in most of the existing workflow management systems. Despite its importance, however, provenance modeling and management is still a relatively new area in the scientific workflow research community. The proper scope, representation, granularity and implementation of a provenance model can vary from domain to domain and pose a number of challenges for an efficient pipeline design. This paper provides a case study on structured provenance modeling and management problems in the neuroimaging domain by introducing the Bio-Swarm-Pipeline (BSP). This new model, which is evaluated in the paper through real world scenarios, systematically addresses the provenance scope, representation, granularity, and implementation issues related to the neuroimaging domain. Although this model stems from applications in neuroimaging, the system can potentially be adapted to a wide range of bio-medical application scenarios

Altered hippocampal-parahippocampal function during stimulus encoding:A potential indicator of genetic liability for schizophrenia

IMPORTANCE Declarative memory-the ability to learn, store, and retrieve information-has been consistently reported to be altered in schizophrenia, and hippocampal-parahippocampal dysfunction has been implicated in this deficit. To elucidate the possible role of genetic risk factors in such findings, it is necessary to study healthy relatives of patients with schizophrenia who carry risk-associated genes but not the confounding factors related to the disorder. OBJECTIVE To investigate whether altered brain responses, particularly in the hippocampus and parahippocampus, during the encoding phase of a simple declarative memory task are also observed in unaffected siblings who are at increased genetic risk for schizophrenia. DESIGN, SETTING, AND PARTICIPANTS Functional magnetic resonance imaging was used with a simple visual declarative memory paradigm to test for differences in neural activation across normal control participants, patients with schizophrenia, and their healthy siblings. This study was conducted at a research center and included a total of 308 participants (181 normal control participants, 65 healthy siblings, and 62 patients with schizophrenia); all participants were white of European ancestry. MAIN OUTCOMES AND MEASURES All participants completed a declarative memory task involving incidental encoding of neutral visual scenes interleaved with crosshair fixation while undergoing functional magnetic resonance imaging. Differences in hippocampus and parahippocampus activation and coupling across groups and correlations with accuracy were analyzed. Analyses were repeated in pairwise-matched samples. RESULTS Both patients with schizophrenia and their healthy siblings showed reduced parahippocampal activation (bilaterally) and hippocampal-parietal (BA 40) coupling during the encoding of novel stimuli when compared with normal control participants. There was a significant positive correlation between parahippocampal activation during encoding and the visual-memory score. CONCLUSIONS AND RELEVANCE These results suggest that altered hippocampal-parahippocampal function during encoding is an intermediate biologic phenotype related to increased genetic risk for schizophrenia. Therefore, measuring hippocampal-parahippocampal function with neuroimaging represents a potentially useful approach to understanding genetic mechanisms that confer risk for schizophrenia