Characterization of hyporheic exchange drivers and patterns within a low-gradient, first-order, river confluence during low and high flow

Confluences are nodes in riverine networks characterized by complex three-dimensional changes in flow hydrodynamics and riverbed morphology, and are valued for important ecological functions. This physical complexity is often investigated within the water column or riverbed, while few studies have focused on hyporheic fluxes, which is the mixing of surface water and groundwater across the riverbed. This study aims to understand how hyporheic flux across the riverbed is organized by confluence physical drivers. Field investigations were carried out at a low gradient, headwater confluence between Baltimore Brook and Cold Brook in Marcellus, New York, USA. The study measured channel bathymetry, hydraulic permeability, and vertical temperature profiles, as indicators of the hyporheic exchange due to temperature gradients. Confluence geometry, hydrodynamics, and morphodynamics were found to significantly affect hyporheic exchange rate and patterns. Local scale bed morphology, such as the confluence scour hole and minor topographic irregularities, influenced the distribution of bed pressure head and the related patterns of downwelling/upwelling. Furthermore, classical back-to-back bend planform and the related secondary circulation probably affected hyporheic exchange patterns around the confluence shear layer. Finally, even variations in the hydrological conditions played a role on hyporheic fluxes modifying confluence planform, and, in turn, flow circulation patterns

Drag Reduction in Wave-Swept Macroalgae: Alternative Strategies and New Predictions

Premise of the study: Intertidal macroalgae must resist extreme hydrodynamic forces imposed by crashing waves. How does frond flexibility mitigate drag, and how does flexibility affect predictions of drag and dislodgement in the field? Methods: We characterized flexible reconfiguration of six seaweed species in a recirculating water flume, documenting both shape change and area reduction as fronds reorient. We then used a high-speed gravity-accelerated water flume to test our ability to predict drag under waves based on extrapolations of drag recorded at slower speeds. We compared dislodgement forces to drag forces predicted from slow- and high-speed data to generate new predictions of survivorship and maximum sustainable frond size along wave-swept shores. Key results: Bladed algae were generally shape changers , limiting drag by reducing drag coefficients, whereas the branched alga Calliarthron was an area reducer , limiting drag by reducing projected area in flow. Drag predictions often underestimated actual drag measurements at high speeds, suggesting that slow- speed data may not reflect the performance of flexible seaweeds under breaking waves. Several seaweeds were predicted to dislodge at similar combinations of velocity and frond size, suggesting common scaling factors of dislodgement strength and drag. Conclusions: Changing shape and reducing projected area in flow are two distinct strategies employed by flexible seaweeds to resist drag. Flexible reconfiguration contributes to the uncertainty of drag extrapolation, and researchers should use caution when predicting drag and dislodgement of seaweeds in the field

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

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

Crusticorallina gen. nov., a nongeniculate genus in the subfamily Corallinoideae (Corallinales, Rhodophyta)

Molecular phylogenetic analyses of 18S rDNA (SSU) gene sequences confirm the placement of Crusticorallina gen. nov. in Corallinoideae, the first non-geniculate genus in an otherwise geniculate subfamily. Crusticorallina is distinguished from all other coralline genera by the following suite of morpho-anatomical characters: 1) sunken, uniporate gametangial and bi/tetrasporangial conceptacles, 2) cells linked by cell fusions, not secondary pit connections, 3) an epithallus of 1 or 2 cell layers, 4) a hypothallus that occupies 50% or more of the total thallus thickness, 5) elongate meristematic cells, 6) trichocytes absent. Four species are recognized based on rbcL, psbA and COI-5P sequences, C. painei sp. nov., the generitype, C. adhaerens sp. nov., C. nootkana sp. nov. and C. muricata comb. nov., previously known as Pseudolithophyllum muricatum. Type material of Lithophyllum muricatum, basionym of C. muricata, in TRH comprises at least two taxa, and therefore we accept the previously designated lectotype specimen in UC that we sequenced to confirm its identity. Crusticorallina species are very difficult to distinguish using morpho-anatomical and/or habitat characters, although at specific sites, some species may be distinguished by a combination of morpho-anatomy, habitat and biogeography. The Northeast Pacific now boasts six coralline endemic genera, far more than any other region of the world. This article is protected by copyright. All rights reserved

G325R GBA mutation in Parkinson's disease: Disease course and long-term DBS outcome

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Interdisciplinary perspectives on the development, integration and application of cognitive ontologies

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data

Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach

An initiative of the NIH Blueprint for neuroscience research, the Neuroscience Information Framework (NIF) project advances neuroscience by enabling discovery and access to public research data and tools worldwide through an open source, semantically enhanced search portal. One of the critical components for the overall NIF system, the NIF Standardized Ontologies (NIFSTD), provides an extensive collection of standard neuroscience concepts along with their synonyms and relationships. The knowledge models defined in the NIFSTD ontologies enable an effective concept-based search over heterogeneous types of web-accessible information entities in NIF’s production system. NIFSTD covers major domains in neuroscience, including diseases, brain anatomy, cell types, sub-cellular anatomy, small molecules, techniques, and resource descriptors. Since the first production release in 2008, NIF has grown significantly in content and functionality, particularly with respect to the ontologies and ontology-based services that drive the NIF system. We present here on the structure, design principles, community engagement, and the current state of NIFSTD ontologies

Differential Requirements for Myeloid Leukemia IFN-γ Conditioning Determine Graft-versus-Leukemio Resistance and Sensitivity

The graft-versus-leukemia (GVL) effect in allogeneic hematopoietic stem cell transplantation (alloSCT) is potent against chronic phase chronic myelogenous leukemia (CP-CML), but blast crisis CML (BC-CML) and acute myeloid leukemias (AML) are GVL resistant. To understand GVL resistance, we studied GVL against mouse models of CP-CML, BC-CML, and AML generated by the transduction of mouse BM with fusion cDNAs derived from human leukemias. Prior work has shown that CD4+ T cell-mediated GVL against CP-CML and BC-CML required intact leukemia MHCII; however, stem cells from both leukemias were MHCII negative. Here, we show that CP-CML, BC-CML, and AML stem cells upregulate MHCII in alloSCT recipients. Using gene-deficient leukemias, we determined that BC-CML and AML MHC upregulation required IFN-γ stimulation, whereas CP-CML MHC upregulation was independent of both the IFN-γ receptor (IFN-γR) and the IFN-α/β receptor IFNAR1. Importantly, IFN-γR-deficient BC-CML and AML were completely resistant to CD4- and CD8-mediated GVL, whereas IFN-γR/IFNAR1 double-deficient CP-CML was fully GVL sensitive. Mouse AML and BC-CML stem cells were MHCI+ without IFN-γ stimulation, suggesting that IFN-γ sensitizes these leukemias to T cell killing by mechanisms other than MHC upregulation. Our studies identify the requirement of IFN-γ stimulation as a mechanism for BC-CML and AML GVL resistance, whereas independence from IFN-γ renders CP-CML more GVL sensitive, even with a lower-level alloimmune response