Enabling RadLex with the Foundational Model of Anatomy Ontology to Organize and Integrate Neuro-imaging Data

In this study we focused on empowering RadLex with an ontological framework and additional content derived from the Foundational Model of Anatomy Ontology1 thereby providing RadLex the facility to correlate the different standards used in annotating neuroradiological image data. The objective of this work is to promote data sharing, data harmonization and interoperability between disparate neuroradiological labeling systems

Intelligent Queries over BIRN Data using the Foundational Model of Anatomy and a Distributed Query-Based Data Integration System

We demonstrate the usefulness of the Foundational Model of Anatomy (FMA) ontology in reconciling different neuroanatomical parcellation schemes in order to facilitate automatic annotation and “intelligent” querying and visualization over a large multisite fMRI study of schizophrenic versus normal controls

Genetic analysis of the spindle checkpoint genes san-1, mdf-2, bub-3 and the CENP-F homologues hcp-1 and hcp-2 in Caenorhabditis elegans

<p>Abstract</p> <p>Background</p> <p>The spindle checkpoint delays the onset of anaphase until all sister chromatids are aligned properly at the metaphase plate. To investigate the role <it>san-1</it>, the MAD3 homologue, has in <it>Caenorhabditis elegans </it>embryos we used RNA interference (RNAi) to identify genes synthetic lethal with the viable <it>san-1(ok1580) </it>deletion mutant.</p> <p>Results</p> <p>The <it>san-1(ok1580) </it>animal has low penetrating phenotypes including an increased incidence of males, larvae arrest, slow growth, protruding vulva, and defects in vulva morphogenesis. We found that the viability of <it>san-1(ok1580) </it>embryos is significantly reduced when HCP-1 (CENP-F homologue), MDF-1 (MAD-1 homologue), MDF-2 (MAD-2 homologue) or BUB-3 (predicted BUB-3 homologue) are reduced by RNAi. Interestingly, the viability of <it>san-1(ok1580) </it>embryos is not significantly reduced when the paralog of HCP-1, HCP-2, is reduced. The phenotype of <it>san-1(ok1580);hcp-1(RNAi) </it>embryos includes embryonic and larval lethality, abnormal organ development, and an increase in abnormal chromosome segregation (aberrant mitotic nuclei, anaphase bridging). Several of the <it>san-1(ok1580);hcp-1(RNAi) </it>animals displayed abnormal kinetochore (detected by MPM-2) and microtubule structure. The survival of <it>mdf-2(RNAi);hcp-1(RNAi) </it>embryos but not <it>bub-3(RNAi);hcp-1(RNAi) </it>embryos was also compromised. Finally, we found that <it>san-1(ok1580) </it>and <it>bub-3(RNAi)</it>, but not <it>hcp-1(RNAi) </it>embryos, were sensitive to anoxia, suggesting that like SAN-1, BUB-3 has a functional role as a spindle checkpoint protein.</p> <p>Conclusion</p> <p>Together, these data suggest that in the <it>C. elegans </it>embryo, HCP-1 interacts with a subset of the spindle checkpoint pathway. Furthermore, the fact that <it>san-1(ok1580);hcp-1(RNAi) </it>animals had a severe viability defect whereas in the <it>san-1(ok1580);hcp-2(RNAi) </it>and <it>san-1(ok1580);hcp-2(ok1757) </it>animals the viability defect was not as severe suggesting that <it>hcp-1 </it>and <it>hcp-2 </it>are not completely redundant.</p

Mixed-mode oscillations and interspike interval statistics in the stochastic FitzHugh-Nagumo model

We study the stochastic FitzHugh-Nagumo equations, modelling the dynamics of neuronal action potentials, in parameter regimes characterised by mixed-mode oscillations. The interspike time interval is related to the random number of small-amplitude oscillations separating consecutive spikes. We prove that this number has an asymptotically geometric distribution, whose parameter is related to the principal eigenvalue of a substochastic Markov chain. We provide rigorous bounds on this eigenvalue in the small-noise regime, and derive an approximation of its dependence on the system's parameters for a large range of noise intensities. This yields a precise description of the probability distribution of observed mixed-mode patterns and interspike intervals.Comment: 36 page

Emigration of hatchery‐reared Pallid Sturgeon, Scaphirhynchus albus (Forbes and Richardson), through a Missouri River dam

The middle Missouri River (MMR; Fort Randall Dam, SD to Gavins Point Dam, NE‐SD) is stocked with hatchery‐reared pallid sturgeon, Scaphirhynchus albus (Forbes and Richardson), from upper Missouri River broodstock to aid recovery of this federally endangered species. Emigration of these fish through Gavins Point Dam restores genetic connectivity that likely existed pre‐impoundment but could lead to outbreeding depression in the future. Recapture data of hatchery‐reared pallid sturgeon stocked in the MMR were evaluated to improve understanding of pallid sturgeon emigration. From 2004 to 2015, 219 emigrants were caught: 4 stocked at age ≥2 years and 215 stocked at age ≤1 year. Emigration of the 2001‐2007 year classes stocked at age 1 was a consistent phenomenon and appeared higher than emigration of year classes stocked at ages 2–3. Little evidence suggested emigration was associated with an unusually high‐water event in 2011. The annual emigration probability of individuals stocked at age 1 estimated from multi‐state mark–recapture models was 0.05 [95% confidence interval = 0.04–0.06] for fish ages ≥1 year. This study suggests that alterations to stocking practices (e.g. stocking age) may affect emigration rates and, therefore, connectivity among pallid sturgeon populations

Overview of NASA Behavioral Health and Performance Standard Measures

NASAs Human Research Program (HRP) is developing a set of Standard Measures for use in spaceflight and spaceflight analog environments to monitor the risks of long-duration missions on human health and performance, including behavioral health, individual and team performance, and social processes. Based on measures selected, developed, and tested under the NASA-funded Behavioral Core Measures project (PI: D.F. Dinges) as well as other projects from NASAs Human Factors & Behavioral Performance research portfolio, NASAs Behavioral Health & Performance (BHP) Laboratory is further evaluating the operational feasibility, acceptability, and validity of a multidisciplinary suite of objective, subjective, behavioral, and biological measures for monitoring monitor behavioral health, individual and team performance, and social processes over time. The inaugural generation of the NASA Behavioral Health & Performance (BHP) Standard Measures includes a neurocognitive test battery, actigraphy, physical proximity sensors, cardiovascular monitors, and subjective self-reports of mood, depression, and various team and social processes and performance outcomes

Rosa hybrid gene GAPC is mutated in the presence of the Rose Rosette Virus

Rose Rosette Disease (RRD) harms the global rose supply by modification of the growth and development in rose cultivar. RRD spreads via a negative-sense RNA plant virus transmitted by eriophyid mites. Importantly, there is no pre-existing knowledge about the biochemistry by which this virus debilitates roses. Here we implicate glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the major metabolic enzymes in plants, as a possible target of the virus. Genomic DNA of the cytosolic form of the protein encoded by GAPC was extracted from both virally-infected and non-infected samples of the Rosa hybrid cultivar Rosa Tropicana. The sequence results provided several distinct differences in the GAPC gene of the non-infected rose compared to the virally-infected rose. Importantly, these modified nucleotide bases resulted in a putative protein sequence containing four unique non-conserved amino acid substitutions in the GAPDH enzyme. This study provides the first evidence of a gene impacted in virally-infected rose plants

Application of Neuroanatomical Ontologies for Neuroimaging Data Annotation

The annotation of functional neuroimaging results for data sharing and re-use is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation schemes. To address this challenge, we extended the Foundational Model of Anatomy Ontology (FMA) to include cytoarchitectural, Brodmann area labels, and a morphological cortical labeling scheme (e.g., the part of Brodmann area 6 in the left precentral gyrus). This representation was also used to augment the neuroanatomical axis of RadLex, the ontology for clinical imaging. The resulting neuroanatomical ontology contains explicit relationships indicating which brain regions are “part of” which other regions, across cytoarchitectural and morphological labeling schemas. We annotated a large functional neuroimaging dataset with terms from the ontology and applied a reasoning engine to analyze this dataset in conjunction with the ontology, and achieved successful inferences from the most specific level (e.g., how many subjects showed activation in a subpart of the middle frontal gyrus) to more general (how many activations were found in areas connected via a known white matter tract?). In summary, we have produced a neuroanatomical ontology that harmonizes several different terminologies of neuroanatomical structures and cortical parcellation schemes. This neuroanatomical ontology is publicly available as a view of FMA at the Bioportal website1. The ontological encoding of anatomic knowledge can be exploited by computer reasoning engines to make inferences about neuroanatomical relationships described in imaging datasets using different terminologies. This approach could ultimately enable knowledge discovery from large, distributed fMRI studies or medical record mining

Comparative effectiveness of endovascular versus open repair of ruptured abdominal aortic aneurysm in the Medicare population

ObjectiveEndovascular aortic repair (EVAR) for abdominal aortic aneurysm (AAA) is increasingly used for emergent treatment of ruptured AAA (rAAA). We sought to compare the perioperative and long-term mortality, procedure-related complications, and rates of reintervention of EVAR vs open aortic repair of rAAA in Medicare beneficiaries.MethodsWe examined perioperative and long-term mortality and complications after EVAR or open aortic repair performed for rAAA in all traditional Medicare beneficiaries discharged from a United States hospital from 2001 to 2008. Patients were matched by propensity score on baseline demographics, coexisting conditions, admission source, and hospital volume of rAAA repair. Sensitivity analyses were performed to evaluate the effect of bias that might have resulted from unmeasured confounders.ResultsOf 10,998 patients with repaired rAAA, 1126 underwent EVAR and 9872 underwent open repair. Propensity score matching yielded 1099 patient pairs. The average age was 78 years, and 72.4% were male. Perioperative mortality was 33.8% for EVAR and 47.7% for open repair (P < .001), and this difference persisted for >4 years. At 36 months, EVAR patients had higher rates of AAA-related reinterventions than open repair patients (endovascular reintervention, 10.9% vs 1.5%; P < .001), whereas open patients had more laparotomy-related complications (incisional hernia repair, 1.8% vs 6.2%; P < .001; all surgical complications, 4.4% vs 9.1%; P < .001). Use of EVAR for rAAA increased from 6% of cases in 2001 to 31% in 2008, whereas during the same interval, overall 30-day mortality for admission for rAAA, regardless of treatment, decreased from 55.8% to 50.9%.ConclusionsEVAR for rAAA is associated with lower perioperative and long-term mortality in Medicare beneficiaries. Increasing adoption of EVAR for rAAA is associated with an overall decrease in mortality of patients hospitalized for rAAA during the last decade

Spatial risk modeling of cattle depredation by black vultures in the midwestern United States

ock operations through depredation of stock are a cause of human‐wildlife conflict. Management of such conflict requires identifying environmental and non‐environmental factors specific to a wildlife species\u27 biology and ecology that influence the potential for livestock depredation to occur. Identification of such factors can improve understanding of the conditions placing livestock at risk. Black vultures (Coragyps atratus) have expanded their historical range northward into the midwestern United States. Concomitantly, an increase in concern among agricultural producers regarding potential black vulture attacks on livestock has occurred. We estimated area with greater or lesser potential for depredation of domestic cattle by black vultures across a 6‐state region in the midwestern United States using an ensemble of small models (ESM). Specifically, we identified landscape‐scale spatial factors, at a zip code resolution, associated with reported black vulture depredation on cattle in midwestern landscapes to predict future potential livestock depredation. We hypothesized that livestock depredation would be greatest in areas with intensive beef cattle production close to preferred black vulture habitat (e.g., areas with fewer old fields and early successional vegetation paired with more direct edge between older forest and agricultural lands). We predicted that the density of cattle within the county, habitat structure, and proximity to anthropogenic landscape features would be the strongest predictors of black vulture livestock‐depredation risk. Our ESM estimated the relative risk of black vulture‐cattle depredation to be between 0.154–0.631 across our entire study area. Consistent with our hypothesis, areas of greatest predicted risk of depredation correspond with locations that are favorable to vulture life‐history requirements and increased potential to encounter livestock. Our results allow wildlife managers the ability to predict where black vulture depredation of cattle is more likely to occur in the future. It is in these areas where extension and outreach efforts aimed at mitigating this conflict should be focused. Researchers and wildlife managers interested in developing or employing tools aimed at mitigating livestock‐vulture conflicts can also leverage our results to select areas where depredation is most likely to occur