An improved ontological representation of dendritic cells as a paradigm for all cell types

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’

Randomised Comparison of the AMBU AuraOnce Laryngeal Mask and the LMA Unique Laryngeal Mask Airway in Spontaneously Breathing Adults

We conducted a randomised single-blind controlled trial comparing the LMA-Unique (LMAU) and the AMBU AuraOnce (AMBU) disposable laryngeal mask in spontaneously breathing adult patients undergoing general anaesthesia. Eighty-two adult patients (ASA status I–IV) were randomly allocated to receive the LMAU or AMBU and were blinded to device selection. Patients received a standardized anesthetic and all airway devices were inserted by trained anaesthetists. Size selection was guided by manufacturer recommendations. All data were collected by a single, unblinded observer. When compared with the LMAU, the AMBU produced significantly higher airway sealing pressures (AMBU 20 ± 6; LMAU 15 ± 7 cm H2O; P = 0.001). There was no statistical difference between the two devices for overall success rate, insertion time, number of adjustments, laryngeal alignment, blood-staining, and sore throat (P ≥ 0.05). The AMBU AuraOnce disposable laryngeal mask provided a higher oropharyngeal leak pressure compared to the LMA Unique in spontaneously breathing adult patients

Squirrels Do the Math: Flight Trajectories in Eastern Gray Squirrels (Sciurus carolinensis)

Animals are under strong selective pressures to make correct decisions when attempting to escape an approaching predator, and not surprisingly many studies have shown that animals adjust their flight initiation behavior in response to risk. However, we have a poor understanding of animals' capability to select an appropriate flight trajectory. We investigated whether eastern gray squirrels would adjust their flight trajectory based on the relative locations of the squirrel, the approaching threat, and potential refuges. We used a person running toward a focal squirrel (N = 122) as the threat and considered the three trees nearest the squirrel and taller than 8 m to be potential refuges. Squirrels were strongly affected by the angle (θ) formed by the locations of person, squirrel, and the three nearest trees. A squirrel was less likely to run to the nearest tree (Tree 1) when θ1 was relatively acute, but also less likely to run to Tree 1 when θ2 was obtuse, making Tree 2 a more attractive refuge. A squirrel was more likely to run to Tree 1 if it was close and if Tree 2 was relatively far. Subtle differences in the effects of θ1 vs. θ2 on squirrel refuge choice support the idea that squirrels prefer a nearby refuge. Squirrels were more likely to select Trees 2 and 3 rather than Tree 1 only when θ2 was obtuse (105°). In contrast, most squirrels chose to run to Tree 1 when θ1 was >65°; thus squirrels were more likely to choose Tree 1 even when doing so required running at least partly toward the approaching threat. The decisions made by focal squirrels provide evidence that this species' assessment of risk is highly nuanced. A great deal of variation has been reported in responses to predators within species. While part of the variation may be due to strategic unpredictability on the part of the prey, part of it may also be due to differences in flight trajectory and refuge preferences that have not been well-studied

An improved ontological representation of dendritic cells as a paradigm for all cell types

<p>Abstract</p> <p>Background</p> <p>Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal rigor of ontologies to better support computation. Currently, the CL employs multiple <it>is_a </it>relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration.</p> <p>Results</p> <p>To enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. We avoid multiple uses of <it>is_a </it>by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as <it>has_function</it>.</p> <p>Conclusion</p> <p>This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from <url>http://www.obofoundry.org</url>.</p

Joint analysis of stressors and ecosystem services to enhance restoration effectiveness

With increasing pressure placed on natural systems by growing human populations, both scientists and resource managers need a better understanding of the relationships between cumulative stress from human activities and valued ecosystem services. Societies often seek to mitigate threats to these services through large-scale, costly restoration projects, such as the over one billion dollar Great Lakes Restoration Initiative currently underway. To help inform these efforts, we merged high-resolution spatial analyses of environmental stressors with mapping of ecosystem services for all five Great Lakes. Cumulative ecosystem stress is highest in near-shore habitats, but also extends offshore in Lakes Erie, Ontario, and Michigan. Variation in cumulative stress is driven largely by spatial concordance among multiple stressors, indicating the importance of considering all stressors when planning restoration activities. In addition, highly stressed areas reflect numerous different combinations of stressors rather than a single suite of problems, suggesting that a detailed understanding of the stressors needing alleviation could improve restoration planning. We also find that many important areas for fisheries and recreation are subject to high stress, indicating that ecosystem degradation could be threatening key services. Current restoration efforts have targeted high-stress sites almost exclusively, but generally without knowledge of the full range of stressors affecting these locations or differences among sites in service provisioning. Our results demonstrate that joint spatial analysis of stressors and ecosystem services can provide a critical foundation for maximizing social and ecological benefits from restoration investments. www.pnas.org/lookup/suppl/doi:10.1073/pnas.1213841110/-/DCSupplementa

Structural, item, and test generalizability of the psychopathology checklist - revised to offenders with intellectual disabilities

The Psychopathy Checklist–Revised (PCL-R) is the most widely used measure of psychopathy in forensic clinical practice, but the generalizability of the measure to offenders with intellectual disabilities (ID) has not been clearly established. This study examined the structural equivalence and scalar equivalence of the PCL-R in a sample of 185 male offenders with ID in forensic mental health settings, as compared with a sample of 1,212 male prisoners without ID. Three models of the PCL-R’s factor structure were evaluated with confirmatory factor analysis. The 3-factor hierarchical model of psychopathy was found to be a good fit to the ID PCL-R data, whereas neither the 4-factor model nor the traditional 2-factor model fitted. There were no cross-group differences in the factor structure, providing evidence of structural equivalence. However, item response theory analyses indicated metric differences in the ratings of psychopathy symptoms between the ID group and the comparison prisoner group. This finding has potential implications for the interpretation of PCL-R scores obtained with people with ID in forensic psychiatric settings

Hematopoietic stem cell therapy for autoimmune diseases - Clinical experience and mechanisms

With accumulating evidence and improved outcomes along with recognition that modern biological therapies are not universally effective, require chronic administration and have high acquisition costs, hematopoietic stem cell transplantation (HSCT) has become an emerging direction for cell therapy in autoimmune diseases (ADs). The goal of this therapy is to induce medication-free remissions by resetting the immune system into a naïve and self-tolerant state through eradication of the autoreactive immunologic memory and profound re-configuration of the immune system induced by the transplant procedure. Safety of HSCT has generally improved by implementing internal quality management and external accreditation. Inter-disciplinary guidelines for patient selection, transplant technique and supportive care along with greater center experience should optimize safe and appropriate delivery of HSCT in specific ADs. In this review, we discuss the current role and future perspectives of HSCT in AD, focusing on recent published clinical and scientific studies and recommendations in the field