Metro Habitat Connectivity Toolkit: Bringing Connectivity to an Actionable Scale

Habitat fragmentation is a serious threat to maintaining biodiversity particularly in urbanizing areas. Methods exist to model habitat connectivity, however many of these are applied at large scales and rely on data that may be a decade or older, resulting in inaccuracies when compared to on the ground conditions, particularly in dynamic urban systems that experience rapid change. These issues make taking action to preserve or enhance these connectivity zones difficult, if not impossible. The Metro Regional Habitat Connectivity Toolkit approaches this problem by combining GIS analysis with on the ground assessments at realistic scales for land acquisition, restoration projects and/or barrier mitigation. We employed a surrogate species approach to address connectivity needs in a way that incorporates empirical data. Local information and research was combined with other habitat attributes to focus development of field assessments for habitat quality and barrier permeability. The field assessments allow technicians to verify GIS data, identify barriers and record habitat attributes in a way that is comparable across multiple habitat connectivity zones and for multiple species. Once assessments are concluded the resulting information is used to generate two species specific scores for habitat quality and barrier permeability. These scores identify where on the landscape restoration and/or land acquisitions would provide the most connectivity benefit vs areas where mitigation for barriers such as wildlife passages structures across roads are the priority. This toolkit is in the final stages of development and is currently being testing in pilot areas in the Portland Metro region

Metro Habitat Connectivity Toolkit: Bringing Connectivity to an Actionable Scale

Habitat fragmentation is a serious threat to maintaining biodiversity particularly in urbanizing areas. Methods exist to model habitat connectivity, however many of these are applied at large scales and rely on data that may be a decade or older, resulting in inaccuracies when compared to on the ground conditions, particularly in dynamic urban systems that experience rapid change. These issues make taking action to preserve or enhance these connectivity zones difficult, if not impossible. The Metro Regional Habitat Connectivity Toolkit approaches this problem by combining GIS analysis with on the ground assessments at realistic scales for land acquisition, restoration projects and/or barrier mitigation. We employed a surrogate species approach to address connectivity needs in a way that incorporates empirical data. Local information and research was combined with other habitat attributes to focus development of field assessments for habitat quality and barrier permeability. The field assessments allow technicians to verify GIS data, identify barriers and record habitat attributes in a way that is comparable across multiple habitat connectivity zones and for multiple species. Once assessments are concluded the resulting information is used to generate two species specific scores for habitat quality and barrier permeability. These scores identify where on the landscape restoration and/or land acquisitions would provide the most connectivity benefit vs areas where mitigation for barriers such as wildlife passages structures across roads are the priority. This toolkit is in the final stages of development and is currently being testing in pilot areas in the Portland Metro region

Psychological Flexibility Is Key for Reducing the Severity and Impact of Fibromyalgia

Fibromyalgia has a significant impact on the lives of patients; symptoms are influenced by psychological factors, such as psychological flexibility and catastrophizing. The objective of this study was to determine the importance of these variables in moderating the association between the severity and impact of fibromyalgia symptoms. A total of 187 patients from a general hospital population were evaluated using the Combined Index of Severity of Fibromyalgia (ICAF), the Fibromyalgia Impact Questionnaire (FIQ), the Acceptance and Action Questionnaire-II (AAQ-II), and the Pain Catastrophizing Scale (PCS). A series of multiple regression analyses were carried out using the PROCESS macro and decision tree analysis. The results show that psychological flexibility modulates the relation between severity and the impact of fibromyalgia symptoms. Catastrophism has residual importance and depends on the interaction with psychological flexibility. Interaction occurs if the severity of the disease is in transition from a mild to a moderate level and accounts for 40.1% of the variance in the sample. These aspects should be considered for evaluation and early intervention in fibromyalgia patients

The Chicken Yolk Sac IgY Receptor, a Mammalian Mannose Receptor Family Member, Transcytoses IgY across Polarized Epithelial Cells

In mammals the transfer of passive immunity from mother to young is mediated by the MHC-related receptor FcRn, which transports maternal IgG across epithelial cell barriers. In birds, maternal IgY in egg yolk is transferred across the yolk sac to passively immunize chicks during gestation and early independent life. The chicken yolk sac IgY receptor (FcRY) is the ortholog of the mammalian phospholipase A2 receptor, a mannose receptor family member, rather than an FcRn or MHC homolog. FcRn and FcRY both exhibit ligand binding at the acidic pH of endosomes and ligand release at the slightly basic pH of blood. Here we show that FcRY expressed in polarized mammalian epithelial cells functioned in endocytosis, bidirectional transcytosis, and recycling of chicken FcY/IgY. Confocal immunofluorescence studies demonstrated that IgY binding and endocytosis occurred at acidic but not basic pH, mimicking pH-dependent uptake of IgG by FcRn. Colocalization studies showed FcRY-mediated internalization via clathrin-coated pits and transport involving early and recycling endosomes. Disruption of microtubules partially inhibited apical-to-basolateral and basolateral-to-apical transcytosis, but not recycling, suggesting the use of different trafficking machinery. Our results represent the first cell biological evidence of functional equivalence between FcRY and FcRn and provide an intriguing example of how evolution can give rise to systems in which similar biological requirements in different species are satisfied utilizing distinct protein folds

Clinical validation of the in silico prediction of immunogenicity of a human recombinant therapeutic protein

Antibodies elicited by protein therapeutics can cause serious side effects in humans. We studied immunogenicity of a recombinant fusion protein (FPX) consisting of two identical, biologically active, peptides attached to human Fc fragment. EpiMatrix, an in silico epitope-mapping tool, predicted promiscuous T-cell epitope(s) within the 14-amino-acid carboxy-terminal region of the peptide portion of FPX. On administration of FPX in 76 healthy human subjects, 37% developed antibodies after a single injection. A memory T-cell response against the above carboxy-terminus of the peptide was observed in antibody-positive but not in antibody-negative subjects. Promiscuity of the predicted T-cell epitope(s) was confirmed by representation of all common HLA alleles in antibody-positive subjects. As predicted by EpiMatrix, HLA haplotype DRB1*0701/1501 was associated with the highest T-cell and antibody response. In conclusion, in silico prediction can be successfully used to identify Class II restricted T-cell epitopes within therapeutic proteins and predict immunogenicity thereof in humans

Turbulence and passive scalar transport in a free-slip surface

We consider the two-dimensional (2D) flow in a flat free-slip surface that bounds a three-dimensional (3D) volume in which the flow is turbulent. The equations of motion for the two-dimensional flow in the surface are neither compressible nor incompressible but strongly influenced by the 3D flow underneath the surface. The velocity correlation functions in the 2D surface and in the 3D volume scale with the same exponents. In the viscous subrange the amplitudes are the same, but in the inertial subrange the 2D one is reduced to 2/3 of the 3D amplitude. The surface flow is more strongly intermittent than the 3D volume flow. Geometric scaling theory is used to derive a relation between the scaling of the velocity field and the density fluctuations of a passive scalar advected on the surface.Comment: 11 pages, 10 Postscript figure

Longitudinal Characterization of Atopic Dermatitis Phenotypes in The Children\u27s Respiratory and Environmental Workgroup (CREW) Birth Cohort Consortium

Rationale: Previously identified longitudinal patterns of atopic dermatitis (AD) may lack generalizability and precision due to small sample size and limited time points. We identify and describe longitudinal AD phenotypes in a large consortium study. Methods: Data from 11 birth cohorts across the United States from the CREW (Children’s Respiratory and Environmental Workgroup) consortium were harmonized to determine physician diagnosis of AD in each year of life from 0-7 years of age (N=7,900). AD phenotypes were identified using Longitudinal Latent Class Analysis, and relationships with demographic variables were determined using multinomial logistic regression with a 3-step procedure to account for uncertainty in class membership. Results: We identified 5 classes of AD expression, selected based on model fit, interpretability, and clinical utility: Persistent AD (15.4%), Early AD with Potential Reoccurrence (2.7%), Late-Onset AD (7.0%), Transient Early AD (3.0%), and Minimal/No AD (72.0%). Males had significantly higher odds of Persistent AD (OR [95% CI]=1.47 [1.22, 1.75]) and Early AD with Potential Reoccurrence (OR [95% CI]=1.89 [1.19, 2.94]). Relative to White children, Black children had higher odds of Persistent AD (OR [95% CI]=2.50 [2.05, 3.05]), Early AD with Potential Reoccurrence (OR [95% CI]=3.07 [1.94, 4.85]), and Transient Early AD (OR [95% CI]=4.12 [2.62, 6.48]). Conclusions: Five AD phenotypes exist in a diverse national sample of children. Black children and males are at increased risk of early and persistent AD. These findings illustrate potential risk factors to target AD prevention

Longitudinal assessment of Allergic Outcomes and Atopic Dermatitis Phenotypes in The Children\u27s Respiratory and Environmental Workgroup (CREW) Birth Cohort Consortium

Rationale: Atopic dermatitis (AD) is a heterogenous inflammatory skin disease often associated with other allergic diseases. We characterized AD phenotypes and associated allergic outcomes longitudinally across a multi-site consortium. Methods: AD expression in 11 U.S. birth cohorts from the CREW (Children’s Respiratory and Environmental Workgroup) consortium was assessed in each year of life from age 0-7 years (N=7,900). Longitudinal Latent Class Analysis was performed to identify AD phenotypes. Five classes of AD were identified: Persistent AD (15.4%), Early AD with Potential Reoccurrence (2.7%), Late-Onset AD (7.0%), Transient Early AD (3.0%), and Minimal/No AD (72.0%). Serum allergen sensitization patterns and allergic clinical disease were associated with AD phenotype using multinomial logistic regression with a 3-step procedure to account for uncertainty in class membership. Results: Children with Persistent AD, Early AD with Potential Reoccurrence, and Transient Early AD were more likely to have food allergy compared to those with Minimal/No AD (OR[95% CI]=2.73[2.15, 3.45], 2.69[1.63, 4.45], 2.54[1.55, 4.16], respectively). These groups had similarly higher odds of food sensitization. Persistent AD (OR[95% CI]=1.81[1.48, 2.21]) and Early AD with Potential Reoccurrence (OR[95% CI]=3.66[1.90, 7.05]) had significantly higher odds of ever asthma relative to Minimal/No AD. At both 2-4 years and 5-7 years, persistent AD (OR[95% CI]=1.35[1.04, 1.74], 1.25[1.01, 1.53]) and Late-Onset AD (OR[95% CI]=1.68[1.13, 2.50], 2.22[1.33, 3.70]) relative to Minimal/No AD had higher odds of allergic rhinitis. Conclusions: Longitudinal AD phenotypes had varying associations with allergic sensitization, food allergy, asthma and allergic rhinitis, demonstrating the heterogeneity of allergic comorbidity risk associated with AD

Globally Distributed Drug Discovery of New Antibiotics: Design and Combinatorial Synthesis of Amino Acid Derivatives in the Organic Chemistry Laboratory

An experiment for the synthesis of N-acyl derivatives of natural amino acids has been developed as part of the Distributed Drug Discovery (D3) program. Students use solid-phase synthesis techniques to complete a three-step, combinatorial synthesis of six products, which are analyzed using LC–MS and NMR spectroscopy. This protocol is suitable for introductory organic laboratory students and has been successfully implemented at multiple academic sites internationally. Accompanying prelab activities introduce students to SciFinder and to medicinal chemistry design principles. Pairing of these activities with the laboratory work provides students an authentic and cohesive research project experience

Intermediate Resolution Near-Infrared Spectroscopy of 36 late-M Dwarfs

We present observations of 36 late-M dwarfs obtained with the KeckII/NIRSPEC in the J-band at a resolution of \sim20,000. We have measured projected rotational velocities, absolute radial velocities, and pseudo-equivalent widths of atomic lines. 12 of our targets did not have previous measurements in the literature. For the other 24 targets, we confirm previously reported measurements. We find that 13 stars from our sample have vsini below our measurement threshold (12 km/s) whereas four of our targets are fast rotators (vsini > 30 km/s). As fast rotation causes spectral features to be washed out, stars with low projected rotational velocities are sought for radial velocity surveys. At our intermediate spectral resolution we have confirmed the identification of neutral atomic lines reported in Mclean et al. 2007. We also calculated pseudo-equivalent widths (p-EW) of 12 atomic lines. Our results confirm that the p-EW of K I lines are strongly dependent on spectral types. We observe that the p-EW of Fe I and Mn I lines remain fairly constant with later spectral type. We suggest that those lines are particularly suitable for deriving metallicities for late-M dwarfs.Comment: accepted in Astronomical Journal. 30 pages, 7 tables, and 7 figure