bluuebunny/crossref_metadata_2025 huggingface dataset:
Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport
Authors: Baker Lewis A. , Habershon Scott
Published: May 2017

Photosynthetic pigment-protein complexes (PPCs) are a vital component of the light-harvesting machinery of all plants and photosynthesizing bacteria, enabling efficient transport of the energy of absorbed light towards the reaction centre, where chemical energy storage is initiated. PPCs comprise a set of chromophore molecules, typically bacteriochlorophyll species, held in a well-defined arrangement by a protein scaffold; this relatively rigid distribution leads to a viewpoint in which the chromophore subsystem is treated as a network, where chromophores represent vertices and inter-chromophore electronic couplings represent edges. This graph-based view can then be used as a framework within which to interrogate the role of structural and electronic organization in PPCs. Here, we use this network-based viewpoint to compare excitation energy transfer (EET) dynamics in the light-harvesting complex II (LHC-II) system commonly found in higher plants and the Fenna-Matthews-Olson (FMO) complex found in green sulfur bacteria. The results of our simple network-based investigations clearly demonstrate the role of network connectivity and multiple EET pathways on the efficient and robust EET dynamics in these PPCs, and highlight a role for such considerations in the development of new artificial light-harvesting systems.
Defaunation effects on plant recruitment depend on size matching and size trade-offs in seed-dispersal networks
Authors: Donoso Isabel , Schleuning Matthias , García Daniel , Fründ Jochen
Published: May 2017

Defaunation by humans causes a loss of large animals in many ecosystems globally. Recent work has emphasized the consequences of downsizing in animal communities for ecosystem functioning. However, no study so far has integrated network theory and life-history trade-offs to mechanistically evaluate the functional consequences of defaunation in plant–animal networks. Here, we simulated an avian seed-dispersal network and its derived ecosystem function seedling recruitment to assess the relative importance of different size-related mechanisms. Specifically, we considered size matching (between bird size and seed size) and size trade-offs, which are driven by differences in plant or animal species abundance (negative size–quantity relationship) as well as in recruitment probability and disperser quality (positive size–quality relationship). Defaunation led to impoverished seedling communities in terms of diversity and seed size, but only if models accounted for size matching. In addition, size trade-off in plants, in concert with size matching, provoked rapid decays in seedling abundance in response to defaunation. These results underscore a disproportional importance of large animals for ecosystem functions. Downsizing in ecological networks will have severe consequences for ecosystem functioning, especially in interaction networks that are structured by size matching between plants and animals.
Ecological drift and the distribution of species diversity
Authors: Gilbert Benjamin , Levine Jonathan M.
Published: May 2017

Ecological drift causes species abundances to fluctuate randomly, lowering diversity within communities and increasing differences among otherwise equivalent communities. Despite broad interest in ecological drift, ecologists have little experimental evidence of its consequences in nature, where competitive forces modulate species abundances. We manipulated drift by imposing 40-fold variation in the size of experimentally assembled annual plant communities and holding their edge-to-interior ratios comparable. Drift over three generations was greater than predicted by neutral models, causing high extinction rates and fast divergence in composition among smaller communities. Competitive asymmetries drove populations of most species to small enough sizes that demographic stochasticity could markedly influence dynamics, increasing the importance of drift in communities. The strong effects of drift occurred despite stabilizing niche differences, which cause species to have greater population growth rates when at low local abundance. Overall, the importance of ecological drift appears greater in non-neutral communities than previously recognized, and varies with community size and the type and strength of density dependence.
Tragedy of the Commons in the Chemostat
Authors: Schuster Martin , Foxall Eric , Finch David , Smith Hal , De Leenheer Patrick
Published: May 2017

We present a proof of principle for the phenomenon of the tragedy of the commons that is at the center of many theories on the evolution of cooperation. We establish the tragedy in the context of a general chemostat model with two species, the cooperator and the cheater. Both species have the same growth rate function and yield constant, but the cooperator allocates a portion of the nutrient uptake towards the production of a public good -the “Commons” in the Tragedy-which is needed to digest the externally supplied nutrient. The cheater on the other hand does not produce this enzyme, and allocates all nutrient uptake towards its own growth. We prove that when the cheater is present initially, both the cooperator and the cheater will eventually go extinct, hereby confirming the occurrence of the tragedy. We also show that without the cheater, the cooperator can survive indefinitely, provided that at least a low level of public good or processed nutrient is available initially. Our results provide a predictive framework for the analysis of cooperator-cheater dynamics in a powerful model system of experimental evolution.
Age-specific prevalence of anti-Pgp3 antibodies and severe conjunctival scarring in the Solomon Islands
Authors: Butcher Robert , Sokana Oliver , Jack Kelvin , Martin Diana L , Burton Matthew J , Solomon Anthony W , Mabey David CW , Roberts Chrissy h.
Published: May 2017

Background

Trachomatous trichiasis (TT) and ocularChlamydia trachomatis (Ct)infection in the Solomon Islands are scarce, whereas trachomatous inflammation–follicular (TF) is prevalent.

Methods

We enrolled 1511 people aged ≥1 year from randomly selected households in 13 villages in which >10% of the population had TF prior to a single round of azithromycin MDA undertaken six months previously. Blood was collected from people of all ages to be screened for anti-Pgp3 antibodies. Photographs were collected from people of all ages for analysis of scarring severity.

Results

Conjunctival scars were visible in 13.1% of photographs. Mild (p<0.0001) but not severe (p=0.149) scars increased in prevalence with age. Anti-Pgp3 antibody seroprevalence was 18% in 1–9 year olds, increased sharply around the age of sexual debut, and reached 69% in those over 25 years. Anti-Pgp3 seropositivity did not increase significantly between the ages of 1–9 years, and was not associated with scarring in children (p=0.472) or TF in children (p=0.581).

Conclusions

Signs of trachoma are common in the Solomon Islands but occur frequently in individuals who have no serological evidence of prior ocular infection withCt.WHO recommendations for directing MDA provision based on signs alone may not be suitable in this context.
Advancing a Science for Sustaining Health: Establishing a Model Health District in Madagascar
Authors: Bonds Matthew H. , Garchitorena Andres , Cordier Laura , Miller Ann C. , McCarty Margaret , Andriamihaja Benjamin , Ratsirarson Josea , Randrianambinina Andriamihaja , Rabeza Victor R. , Finnegan Karen , Gillespie Thomas , Wright Patricia A. , Farmer Paul E. , Loyd Tara , Murray Megan B. , Herrnstein Robin M. , Herrnstein James R. ,   PIVOT Impact Team, Gikic Djordje , Ouenzar Mohammed A. , Hall Lara , Rich Michael L.
Published: May 2017

Objective

We demonstrate a replicable model health district for Madagascar. The governments of many low-income countries have adopted health policies that follow international standards, and yet there are four hundred million people without basic access to primary care. Closing this global health delivery gap is typically framed as an issue of scale-up, accomplished primarily through integrating international donor funds with broad-based health system strengthening (HSS) efforts. However, there is no established process by which healthcare systems measure improvements at the point of service and how those, in turn, impact population health. There is no gold standard, equivalent to randomized trials of individual-level interventions, for health systems research. Here, we present a framework for a model district in Madagascar where national policies are implemented along with additional health system interventions to allow for bottom-up adaptation.

Setting

The intervention takes place in a government district in Madagascar, which includes 1 district hospital, 20 primary care health centers, and a network of community health workers.

Intervention

The program simultaneously strengthens the WHO’s six building blocks of HSS at all levels of the health system within a government district and pioneers a data platform that includes 1) strengthening the district’s health management information systems; 2) monitoring and evaluation dashboards; and 3) a longitudinal cohort demographic and health study of over 1,500 households, with a true baseline in intervention and comparison groups.

Conclusion

The integrated intervention and data platform allows for the evaluation of system output indicators as well as population-level impact indicators, such as mortality rates. It thus supports field-based implementation and policy research to fill the know-do gap, while providing the foundation for a new science of sustaining health.

Data Sharing Statement

Data can be made available upon request by emailingresearch@pivotworks.org.
Estimating epidemic incidence and prevalence from genomic data
Authors: Vaughan Timothy G. , Leventhal Gabriel E. , Rasmussen David A. , Drummond Alexei J. , Welch David , Stadler Tanja
Published: May 2017

Modern phylodynamic methods interpret an inferred phylogenetic tree as a partial transmission chain providing information about the dynamic process of transmission and removal (where removal may be due to recovery, death or behaviour change). Birth-death and coalescent processes have been introduced to model the stochastic dynamics of epidemic spread under common epidemiological models such as the SIS and SIR models, and are successfully used to infer phylogenetic trees together with transmission (birth) and removal (death) rates. These methods either integrate analytically over past incidence and prevalence to infer rate parameters, and thus cannot explicitly infer past incidence or prevalence, or allow such inference only in the coalescent limit of large population size. Here we introduce a particle filtering framework to explicitly infer prevalence and incidence trajectories along with phylogenies and epidemiological model parameters from genomic sequences and case count data in a manner consistent with the underlying birth-death model. After demonstrating the accuracy of this method on simulated data, we use it to assess the prevalence through time of the early 2014 Ebola outbreak in Sierra Leone.
Obesity/ Type II Diabetes Promotes Function-limiting Changes in Flexor Tendon Extracellular Matrix that are not Reversed by Restoring Normal Metabolic Function
Authors: Studentsova Valentina , Mora Keshia M. , Glasner Melissa F. , Buckley Mark R. , Loiselle Alayna E.
Published: May 2017

Type II Diabetes (T2DM) negatively alters baseline tendon function, including decreased range of motion and mechanical properties; however, the biological mechanisms that promote diabetic tendinopathy are unknown. To facilitate identification of therapeutic targets we developed a novel murine model of diabetic tendinopathy. Mice fed a High Fat Diet (HFD) developed diet induced obesity and T2DM. Obesity/ T2DM resulted in progressive impairments in tendon gliding function and mechanical properties, relative to mice fed a Low Fat Diet (LFD), as well as a decrease in collagen fibril diameter by transmission electron microscopy. We then determined if restoration of normal metabolic function, by switching mice from HFD to LFD, is sufficient to halt the pathological changes in tendon due to obesity/T2DM. However, switching from a HFD to LFD resulted in greater impairments in tendon gliding function than mice maintained on a HFD. Mechanistically, IRβ signaling is decreased in obese/T2DM murine tendons, suggesting altered IRβ signaling as a driver of diabetic tendinopathy. However, knock-down of IRβ expression in S100a4-lineage cells (IRcKOS100a4) was not sufficient to induce diabetic tendinopathy as no impairments in tendon gliding function or mechanical properties were observed in IRcKOS100a4relative to WT. Collectively, these data define a murine model of diabetic tendinopathy, and demonstrate that tendon-specific, rather than systemic treatment approaches are needed.
PI3K activation in neural stem cells drives tumorigenesis which can be suppressed by targeting CREB
Authors: Daniel Paul M. , Filiz Gulay , Brown Daniel V. , Christie Michael , Waring Paul M. , Zhang Yi , Haynes John M. , Pouton Colin , Flanagan Dustin , Vincan Elizabeth , Johns Terrance G. , Montgomery Karen , Phillips Wayne A. , Mantamadiotis Theo
Published: May 2017

Hyperactivation of the PI3K signaling is common in human cancers, including gliomas, but the precise role of the pathway in glioma biology remains to be determined. Some limited understanding of PI3K signaling in brain cancer come from studies on neural stem/progenitor cells (NSPCs) where signals transmitted via the PI3K pathway cooperate with other intracellular pathways and downstream transcription factors to regulate NSPC proliferation. To investigate the role for the PI3K pathway in glioma initiation and development, we generated a mouse model targeting the inducible expression of a Pik3caH1047Aoncogenic mutation and simultaneous deletion of the PI3K negative regulator, Pten, in NSPCs. We show that the expression of a Pik3caH1047Awas sufficient to initiate tumorigenesis but that simultaneous loss of Pten, was required for the development of invasive, high-grade glioma. Mutant NSPCs exhibited enhanced neurosphere forming capacity which correlated with increased Wnt signaling. We also show that loss of CREB inPik3ca-PTENtumors led to a longer symptom-free survival in mice. Taken together, our findings present a novel mouse model for high-grade glioma with which we demonstrate that the PI3K pathway is important for initiation of tumorigenesis and that disruption of downstream CREB signaling attenuates tumor expansion.
Functional preference for object sounds but not for voices in the occipito-temporal cortex of early blind individuals
Authors: Dormal Giulia , Pelland Maxime , Rezk Mohamed , Yakobov Esther , Lepore Franco , Collignon Olivier
Published: May 2017

Sounds activate occipital regions in early blind individuals. How different sound categories map onto specific regions of the occipital cortex remains however debated. We used fMRI to characterize brain responses of early blind and sighted individuals to familiar object sounds, human voices and their respective low-level control sounds. Sighted participants were additionally tested when viewing pictures of faces, objects and phase-scrambled control pictures. In both early blind and sighted, a double dissociation was evidenced in bilateral auditory cortices between responses to voices and object sounds: voices elicited categorical responses in bilateral superior temporal sulci while object sounds elicited categorical responses along the lateral fissure bilaterally, including the primary auditory cortex and planum temporale. Outside of the auditory regions, object sounds additionally elicited categorical responses in left lateral and ventral occipito-temporal regions in both groups. These regions also showed response preference for images of objects in the sighted, thus suggesting a functional specialization in these regions that is independent of sensory input and visual experience. Between-group comparisons revealed that only in the blind group, categorical responses to object sounds extended more posteriorly into the occipital cortex. Functional connectivity analyses evidenced a selective increase in the functional coupling between these reorganized regions and regions of the ventral occipito-temporal cortex in the early blind. In contrast, vocal sounds did not elicit preferential responses in the occipital cortex in either group. Nevertheless, enhanced voice-selective connectivity between the left temporal voice area and the right fusiform gyrus were found in the blind. Altogether, these findings suggest that separate auditory categories are not equipotent in driving selective auditory recruitment of occipito-temporal regions in the absence of developmental vision, highlighting domain-region constraints on the expression of crossmodal plasticity.
High-throughput laboratory evolution ofEscherichia coliunder multiple stress environments
Authors: Horinouchi Takaaki , Suzuki Shingo , Kotani Hazuki , Tanabe Kumi , Sakata Natsue , Shimizu Hiroshi , Furusawa Chikara
Published: May 2017

Bacterial cells have a remarkable capacity to adapt and to evolve to environmental changes. Although many mutations contributing to adaptive evolution have been identified, the relationship between the mutations and the phenotypic changes responsible for fitness gain has yet to be fully elucidated. For a better understanding of phenotype-genotype relationship in evolutionary dynamics, we performed high-throughput laboratory evolution ofEscherichia coliunder various stress conditions using an automated culture system. One measure of phenotype, transcriptome analysis, revealed that the expression changes which occurred during the evolution were generally similar among the strains evolved in the same stress environment. We also found several genes and gene functions for which mutations were commonly fixed in the strains resistant to the same stress, and whose effects on resistance were verified experimentally. We demonstrated that the integration of transcriptome and genome data enables us to extract the mechanisms for stress resistance.

Author summary

Understanding the relationship between phenotypic and genetic changes is a fundamental goal in evolutionary biology, which can provide insights into the past and future evolutionary trajectories. Evolution of microorganisms in a laboratory has been the primary approach to clarify the mappings of phenotypic and genotypic changes. Here, we performed high-throughput laboratory evolution with bacteria using an automated culture system, to quantify phenotypic and genotypic changes occurred under various stress conditions. We identified various stress-specific gene expression changes and mutations, and contributions of them to fitness gain were validated. These results demonstrated that the integration of phenotypic and genotypic changes makes it possible to extract the mechanisms for stress resistance evolution, which will contribute to bioengineering applications.
Genome-wide comparison of toxigenic and non-toxigenicCorynebacterium diphtheriaeisolates identifies differences in the pan genomes between respiratory and cutaneous strains
Authors: Timms Verlaine J , Nguyen Trang , Crighton Taryn , Yuen Marion , Sintchenko Vitali
Published: May 2017

Objectives

Corynebacterium diphtheriaeis the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasiveC. diphtheriaestrains are identified in countries with low prevalence of diphtheria, raising key questions about genomic structures and population dynamics of the species.

Methods

This study examined genomic diversity among 47C. diphtheriaeisolates collected in Australia over a 10-year period using whole genome sequencing. Phylogeny was determined using SNP-based mapping and genome wide analysis.

Results

C. diphtheriaesequence type (ST) 32, a non-toxigenic ST with evidence of enhanced virulence that is also circulating in Europe, appears to be endemic in Australia. Isolates from temporospatially related patients displayed the same ST and similarity in their core genomes. The genome-wide analysis highlighted a role of pilins, adhesion factors and iron utilization in infections caused by toxigenic as well as non-toxigenic strains.

Conclusions

The genomic diversity of toxigenic and non-toxigenic strains ofC. diphtheriaein Australia suggests multiple local and overseas sources of infection and colonisation. Our findings suggest that regular genomic surveillance of co-circulating toxigenic and non-toxigenicC. diphtheriaecan deliver highly nuanced data in order to inform targeted public health actions and policy for predicting the future impact of this highly successful pathogen.
Lamellar junctions in the endolymphatic sac act as a relief valve to regulate inner ear pressure
Authors: Swinburne Ian A. , Mosaliganti Kishore R. , Upadhyayula Srigokul , Liu Tsung-Li , Hildebrand David G. C. , Tsai Tony Y.-C. , Chen Anzhi , Al-Obeidi Ebaa , Fass Anna K. , Malhotra Samir , Engert Florian , Lichtman Jeff W. , Kirchhausen Tom , Betzig Eric , Megason Sean G.
Published: May 2017

The inner ear is a fluid-filled closed-epithelial structure whose normal function requires maintenance of an internal hydrostatic pressure and fluid composition by unknown mechanisms. The endolymphatic sac (ES) is a dead-end epithelial tube connected to the inner ear. ES defects can cause distended ear tissue, a pathology often seen in hearing and balance disorders. Using live imaging of zebrafish larvae, we reveal that the ES undergoes cycles of slow pressure-driven inflation followed by rapid deflation every 1-3 hours. Using serial-section electron microscopy and adaptive optics lattice light-sheet microscopy, we find a pressure relief valve in the ES comprised of thin overlapping basal lamellae that dynamically extend over neighboring cells before rupturing under pressure leading to ES collapse. The unexpected discovery of a physical relief valve in the ear emphasizes the need for further study into how organs control fluid pressure, volume, flow, and ion homeostasis in development and disease.
Both lipopolysaccharide and lipoteichoic acids potently induce anomalous fibrin amyloid formation: assessment with novel Amytracker™stains
Authors: Pretorius Etheresia , Page Martin J , Hendricks Lisa , Nkosi Nondumiso B , Benson Sven R , Kell Douglas B
Published: May 2017

In recent work, we discovered that the presence of highly substoichiometric amounts (10−8molar ratio) of lipopolysaccharide (LPS) from Gram-negative bacteria caused fibrinogen clotting to lead to the formation of an amyloid form of fibrin. We here show that the broadly equivalent lipoteichoic acids (LTAs) from two species of Gram-positive bacteria have similarly (if not more) potent effects. Using thioflavin T fluorescence to detect amyloid as before, the addition of low concentrations of free ferric ion is found to have similar effects. Luminescent conjugated oligothiophene dyes (LCOs), marketed under the trade name AmytrackerTM, also stain classical amyloid structures. We here show that they too give very large fluorescence enhancements when clotting is initiated in the presence of the four amyloidogens (LPS, ferric ions and two LTA types). The staining patterns differ significantly as a function of both the amyloidogens and the dyes used to assess them, indicating clearly that the nature of the clots formed is different. This is also the case when clotting is measured viscometrically using thromboelastography. Overall, the data provide further evidence for an important role of bacterial cell wall products in the various coagulopathies that are observable in chronic, inflammatory diseases. The assays may have potential in both diagnostics and therapeutics.
Global gene repression by Dicer-independent tRNA Fragments
Authors: Kuscu Canan , Kumar Pankaj , Kiran Manjari , Su Zhangli , Malik Asrar , Dutta Anindya
Published: May 2017

tRNA derived RNA fragments (tRFs) is an emerging group of small RNAs as abundant as miRNAs, and yet their roles are not well understood. Here, we focus on endogenous tRFs (18-22 bases) derived from 3’ end of human mature tRNAs (tRF-3) and their functions in gene repression. tRF-3 levels increase upon parental tRNA over-expression or tRNA induction by c-Myc oncogene activation. Elevated tRF-3 levels lead to repression of target genes with a sequence complementary to the tRF-3 in the 3’ UTR. The tRF-3-mediated repression is Dicer-independent, Argonaute-dependent and the targets are recognized by 5’ seed sequence rules similar to miRNAs. Furthermore, tRF-3s associate with GW proteins in P-bodies. RNA-seq identifies the endogenous target genes of tRF-3s that are specifically repressed upon tRF-3 induction. Overall, our analysis shows Dicer-independent tRF-3s, generated upon tRNA upregulation such as c-Myc overexpression, regulate gene expression globally through Argounate via seed sequence matches.
FGF4retrogene on CFA12 is responsible for chondrodystrophy and intervertebral disc disease in dogs
Authors: Brown Emily A. , Dickinson Peter J. , Mansour Tamer , Sturges Beverly K. , Aguilar Miriam , Young Amy E. , Korff Courtney , Lind Jenna , Ettinger Cassandra L. , Varon Samuel , Pollard Rachel , Brown C. Titus , Raudsepp Terje , Bannasch Danika L.
Published: May 2017

Chondrodystrophy in dogs is defined by dysplastic, shortened long bones and premature degeneration and calcification of intervertebral discs. Independent genome-wide association analyses for skeletal dysplasia (short limbs) within a single breed (pBonferroni=0.0072) and intervertebral disc disease (IVDD) across breeds (pBonferroni=4.02×10−10) both identified a significant association to the same region on CFA12. Whole genome sequencing identified a highly expressedFGF4retrogene within this shared region. TheFGF4retrogene segregated with limb length and had an odds ratio of 51.23 (95% CI = 46.69, 56.20) for IVDD. Long bone length in dogs is a unique example of multiple disease-causing retrocopies of the same parental gene in a mammalian species. FGF signaling abnormalities have been associated with skeletal dysplasia in humans, and our findings present opportunities for both selective elimination of a medically and financially devastating disease in dogs and further understanding of the ever-growing complexity of retrogene biology.
Monocyte-lymphocyte cross-communication via soluble CD163 directly links innate immune system activation and adaptive immune system suppression following ischemic stroke
Authors: O’Connell Grant C. , Tennant Connie S. , Lucke-Wold Noelle , Kabbani Yasser , Tarabishy Abdul R. , Chantler Paul D. , Barr Taura L.
Published: May 2017

CD163 is a scavenger receptor expressed on innate immune cell populations which can be shed from the plasma membrane via the metalloprotease ADAM17 to generate a soluble peptide with lympho-inhibitory properties. The purpose of this study was to investigate CD163 as a possible effector of stroke-induced adaptive immune system suppression. Liquid biopsies were collected from ischemic stroke patients (n=39), neurologically asymptomatic controls (n=20), and stroke mimics (n=20) within 24 hours of symptom onset. Peripheral blood ADAM17 activity and soluble CD163 levels were elevated in stroke patients relative to non-stroke control groups, and negatively associated with post-stroke lymphocyte counts. Subsequentin vitroexperiments suggested that this stroke-induced elevation in circulating soluble CD163 likely originates from activated monocytic cells, as serum from stroke patients stimulated ADAM17-dependant CD163 shedding from healthy donor-derived monocytes. Additionalin vitroexperiments demonstrated that stroke-induced elevations in circulating soluble CD163 can elicit direct suppressive effects on the adaptive immune system, as serum from stroke patients inhibited the proliferation of healthy donor-derived lymphocytes, an effect which was attenuated following serum CD163 depletion. Collectively, these observations provide novel evidence that the innate immune system employs protective mechanisms aimed at mitigating the risk of post-stroke autoimmune complications driven by adaptive immune system overactivation, and that CD163 is key mediator of this phenomenon.
Cooperative Contributions of Structural and Functional Connectivity to Successful Memory and Aging
Authors: Davis Simon W , Szymanski Amanda , Boms Homa , Fink Thomas , Cabeza Roberto
Published: May 2017

Understanding the precise relation between functional connectivity and structural (white-matter) connectivity and how these relationships account for cognitive changes in older adults are major challenges for neuroscience. We investigate these issues using a new approach in which structural equation modeling (SEM) is employed to integrate functional and structural connectivity data analyzed with a common framework based on regions connected by canonical tract groups (CTGs). CTGs (e.g., uncinate fasciculus, cingulum, etc.) serve as a common currency between functional and structural connectivity matrices, and ensures that the same amount of data contributing to brain-behavior relationships. We used this approach to investigate the neural mechanisms supporting memory for items and memory for associations, and how they are affected by healthy aging. Our results are threefold. Firstly, structural and functional CTGs made independent contributions to associative memory performance, suggesting that both forms of connectivity underlie age-related changes in associative memory. Secondly, distinct groups of CTGs supported associative versus item memory. Lastly, the relationship between functional and structural connectivity was best explained by the relationship between latent variables describing functional and structural CTGs based on a constrained set of tracts—but no one specific CTG group—suggesting that age effects in connectivity are constrained to specific pathways. These results provide further insights into the interplay between structural and functional connectivity patterns, and help to elucidate their relative contribution to age-related changes in associative memory performance.
R2s for Correlated Data: Phylogenetic Models, LMMs, and GLMMs
Authors: Ives Anthony R.
Published: May 2017

Many researchers want to report anR2to measure the variance explained by a model. When the model includes correlation among data, such as phylogenetic models and mixed models, defining anR2faces two conceptual problems. (i) It is unclear how to measure the variance explained by predictor (independent) variables when the model contains covariances. (ii) Researchers may want theR2to include the variance explained by the covariances by asking questions such as “How much of the variance is explained by phylogeny?” Here, I investigate threeR2s for phylogenetic and mixed models. A least-squaresR2lsis an extension of the ordinary least-squaresR2that weights residuals by variances and covariances estimated by the model; it is closely related toR2glmmproposed by Nakagawa & Schielzeth (2013). The conditional expectationR2ceis based on “predicting” each residual from the remaining residuals of the fitted model. The likelihood ratioR2lrwas first used by Cragg & Uhler (1970) for logistic regression, and here is used with the standardization proposed by Nagelkerke (1991). These threeR2s are formulated as partialR2s, making it possible to compare the contributions of mean components (regression coefficients in phylogenetic models and fixed effects in mixed models) and variance components (phylogenetic correlations and random effects) to the fit of models. The properties of theR2s for phylogenetic models were assessed using simulations for continuous and binary response data (phylogenetic generalized least squares and phylogenetic logistic regression). Because theR2s are designed broadly for any model for correlated data, theR2s were also compared for LMMs and GLMMs.R2ls,R2ce, andR2lrall have good performance, and each has advantages and disadvantages for different applications. TheseR2s are computed in the R package rr2 (https://github.com/arives/rr2). [Binomial regression, coefficient of determination, non-independent residuals, phylogenetic model, pseudo-likelihood]
Determinants of celebrity-owned brands leveraging price premium
Authors: Singh Gaganpreet , Pandey Neeraj
Published: May 2017

Purpose

The purpose of this paper is to investigate the celebrity-brand association from a different perspective.

Design/methodology/approach

This study uses exploratory factor analysis, confirmatory factor analysis, and binary logistic regression.

Findings

This study conceptualizes celebrity-owned brands (COBs). It statistically validates the complimentary and synergistic effects of six inter-related but distinct factors that are likely to influence a buyer’s willingness to pay price premium for COBs.

Originality/value

This study makes a novel attempt by analysing the celebrity-brand relationship from a different perspective. The paper deviates from the traditional and widely researched linkage of a celebrity with a brand through endorsement.
Genetic fusion protein 3×STa‐ovalbumin is an effective coating antigen in ELISA to titrate anti‐STa antibodies
Authors: Duan Qiangde , Zhang Weiping
Published: May 2017

Heat‐stable toxin type I (STa)‐ovalbumin chemical conjugates are currently used as the only coating antigen in ELISA to titrate anti‐STa antibodies for ETEC vaccine candidates. STa‐ovalbumin chemical conjugation requires STa toxin purification, a process that can be carried out by only a couple of laboratories and often with a low yield. Alternative ELISA coating antigens are needed for anti‐STa antibody titration for ETEC vaccine development. In the present study, we genetically fused STa toxin gene (three copies) to a modified chicken ovalbumin gene for genetic fusion 3×STa‐ovalbumin, and examined application of this fusion protein as an alternative coating antigen of anti‐STa antibody titration ELISA. Data showed fusion protein 3×STa‐ovalbumin was effectively expressed and extracted, and anti‐STa antibody titration ELISA using this recombinant protein (25 ng per well) or STa‐ovalbumin chemical conjugates (10 ng/well) showed the same levels of sensitivity and specificity. Furthermore, mice immunized with this fusion protein developed anti‐STa antibodies; induced antibodies showedin vitroneutralization activity against STa toxin. These results indicate that recombinant fusion protein 3×STa‐ovalbumin is an effective ELISA coating antigen for anti‐STa antibody titration, enabling a reliable reagent supply to make standardization of STa antibody titration assay feasible and to accelerate ETEC vaccine development.
Reviewing the quality of discourse information measures in aphasia
Authors: Pritchard Madeleine , Hilari Katerina , Cocks Naomi , Dipper Lucy
Published: May 2017

Background

Discourse is fundamental to everyday communication, and is an increasing focus of clinical assessment, intervention and research. Aphasia can affect the information a speaker communicates in discourse. Little is known about the psychometrics of the tools for measuring information in discourse, which means it is unclear whether these measures are of sufficient quality to be used as clinical outcome measures or diagnostic tools.

Aims

To profile the measures used to describe information in aphasic discourse, and to assess the quality of these measures against standard psychometric criteria.

Methods & Procedures

A scoping review method was employed. Studies were identified using a systematic search of Scopus, Medline and Embase databases. Standard psychometric criteria were used to evaluate the measures’ psychometric properties.

Main contribution

The current review summarizes and collates the information measures used to describe aphasic discourse, and evaluates their quality in terms of the psychometric properties of acceptability, reliability and validity. Seventy‐six studies described 58 discourse information measures, with a mean of 2.28 measures used per study (SD = 1.29, range = 1–7). Measures were classified as ‘functional’ measures (n = 33), which focused on discourse macrostructure, and ‘functional and structural’ measures (n = 25), which focused on micro‐linguistic and macro‐structural approaches to discourse. There were no reports of the acceptability of data generated by the measures (distribution of scores, missing data). Test–retest reliability was reported for just 8/58 measures with 3/8 > 0.80. Intra‐rater reliability was reported for 9/58 measures and in all cases percentage agreement was reported rather than reliability. Per cent agreement was also frequently reported for inter‐rater reliability, with only 4/76 studies reporting reliability statistics for 12/58 measures; this was generally high (>.80 for 11/12 measures). The majority of measures related clearly to the discourse production model indicating content validity. A total of 36/58 measures were used to make 41 comparisons between participants with aphasia (PWA) and neurologically healthy participants (NHP), with 31/41 comparisons showing a difference between the groups. Four comparisons were made between discourse genres, with two measures showing a difference between genres, and two measures showing no difference.

Conclusions

There is currently insufficient information available to justify the use of discourse information measures as sole diagnostic or outcome measurement tools. Yet the majority of measures are rooted in relevant theory, and there is emerging evidence regarding their psychometric properties. There is significant scope for further psychometric strengthening of discourse information measurement tools.
Revisiting revenue contingent loans for drought relief: government as risk manager
Authors: Botterill Linda Courtenay , Chapman Bruce , Kelly Simon
Published: May 2017

It is clear that Australian governments will provide assistance to farmers in drought, which is a rational political judgement supported by recent survey work suggesting strongly the pervasive existence among voters of agrarian sentiment. In this context, a reasonable question relates to what forms of assistance are most equitable for taxpayers and also have desirable properties for farm businesses. In this study it is argued that traditional and current approaches to drought assistance are not equitable and do not provide sufficient protection to farmers from default and thus insolvency risk. But there is an instrument available to government which can be designed to minimise taxpayer subsidies while at the same time delivering insurance for farmers against default: a Revenue Contingent Loan (RCL). Following the principles inherent in the Higher Education Contribution Scheme, a RCL is financial assistance repaid contingent on a farm's capacity to pay, meaning that loan defaults can be avoided. We model the revenue streams associated with a hypothetical loan of this type and illustrate the advantages for a farm business of these kinds of debt.
Ice cream supplemented with grape juice residue as a source of antioxidants
Authors: Vital Ana Carolina Pelaes , Santos Nadine Woruby , Matumoto‐Pintro Paula Toshimi , da Silva Scapim Monica Regina , Madrona Grasiele Scaramal
Published: May 2017

Grape juice residue was incorporated into ice cream at 2.5%, 5.0% and 10.0% to obtain a product with functional characteristics. The chemical composition, colour, total phenolic compounds, antioxidant capacity and sensory acceptance of the ice creams were analysed at day 0 and after 40 days of storage. Ice creams containing grape juice residue had a higher concentration of phenolic compounds and antioxidant activity compared to the control samples. Consumers’ acceptance was similar for all products. At the end of storage, the polyphenol content and antioxidant activity had decreased. Grape juice residue has potential as a natural source of antioxidants to develop new products.
Patient Experience of Chronic Illness Care and Medical Home Transformation in Safety Net Clinics
Authors: Tung Elizabeth L. , Gao Yue , Peek Monica E. , Nocon Robert S. , Gunter Kathryn E. , Lee Sang Mee , Chin Marshall H.
Published: May 2017

Objective

To examine the relationship between medical home transformation and patient experience of chronic illness care.

Study Setting

Thirteen safety net clinics located in five states enrolled in the Safety Net Medical Home Initiative.

Study Design

Repeated cross‐sectional surveys of randomly selected adult patients were completed at baseline (n = 303) and postintervention (n = 271).

Data Collection Methods

Questions from the Patient Assessment of Chronic Illness Care (PACIC) (100‐point scale) were used to capture patient experience of chronic illness care. Generalized estimating equation methods were used to (i) estimate how differential improvement in patient‐centered medical home (PCMH) capability affected differences in modified PACIC scores between baseline and postintervention, and (ii) to examine cross‐sectional associations between PCMH capability and modified PACIC scores for patients at completion of the intervention.

Principal Findings

In adjusted analyses, high PCMH improvement (above median) was only marginally associated with a larger increase in total modified PACIC score (adjusted β = 7.7, 95 percent confidence interval [CI]: −1.1 to 16.5). At completion of the intervention, a 10‐point higher PCMH capability score was associated with an 8.9‐point higher total modified PACIC score (95 percent CI: 3.1–14.7) and higher scores in four of five subdomains (patient activation, delivery system design, contextual care, and follow‐up/coordination).

Conclusions

We report that sustained, 5‐year medical home transformation may be associated with modest improvement in patient experience of chronic illness care for vulnerable populations in safety net clinics.
End‐of‐Life Care Planning in Accountable Care Organizations: Associations with Organizational Characteristics and Capabilities
Authors: Ahluwalia Sangeeta C. , Harris Benjamin J. , Lewis Valerie A. , Colla Carrie H.
Published: May 2017

Objective

To measure the extent to which accountable care organizations (ACOs) have adopted end‐of‐life (EOL) care planning processes and characterize thoseACOs that have established processes related toEOL.

Data Sources

This study uses data from three waves (2012–2015) of the National Survey ofACOs. Respondents were 397ACOs participating in Medicare, Medicaid, and commercialACOcontracts.

Study Design

This is a cross‐sectional survey study using multivariate ordered logit regression models. We measured the extent to which theACOhad adoptedEOLcare planning processes as well as organizational characteristics, including care management, utilization management, health informatics, and shared decision‐making capabilities, palliative care, and patient‐centered medical home experience.

Principal Findings

Twenty‐one percent ofACOs had few or noEOLcare planning processes, 60 percent had some processes, and 19.6 percent had advanced processes.ACOs with a hospital in their system (OR: 3.07;p = .01), andACOs with advanced care management (OR: 1.43;p = .02), utilization management (OR: 1.58,p = .00), and shared decision‐making capabilities (OR: 16.3,p = .000) were more likely to haveEOLcare planning processes than those with no hospital or few to no capabilities.

Conclusions

There remains considerable room for today'sACOs to increase uptake ofEOLcare planning, possibly by leveraging existing care management, utilization management, and shared decision‐making processes.
Characterizing the Extent of Spatially Integrated Floodplain and Wetland Systems in the White River, Indiana, USA
Authors: Lane C. R. , Hall A. , D'Amico E. , Sangwan N. , Merwade V.
Published: May 2017

Floodplain delineation may inform protection of wetland systems under local, state, or federal laws. Nationally available Federal Emergency Management Agency Flood Insurance Rate Maps (FIRMs, “100‐year floodplain” maps) focus on urban areas and higher‐order river systems, limiting utility at large scales. Few other national‐scale floodplain data are available. We acquired FIRMs for a large watershed and compared FIRMs to floodplain and integrated wetland area mapping methods based on (1) geospatial distance, (2) geomorphic setting, and (3) soil characteristics. We used observed flooding events (OFEs) with recurrence intervals of 25‐50 to >100 years to assess floodplain estimate accuracy. FIRMs accurately reflected floodplain areas based on OFEs and covered 32% of river length, whereas soil‐based mapping was not as accurate as FIRMs but characterized floodplain areas over approximately 65% of stream length. Geomorphic approaches included more areas than indicated by OFE, whereas geospatial approaches tended to cover less area. Overall, soil‐based methods have the highest utility in determining floodplains and their integrated wetland areas at large scales due to the use of nationally available data and flexibility for regional application. These findings will improve floodplain and integrated wetland system extent assessment for better management at local, state, and national scales.
Use of microwave ablation in the treatment of patients with multiple primary malignant tumors
Authors: Han Yue , Shao Na , Xi Xiaoming , Hao Xuezhi
Published: May 2017

A 56‐year‐old man was admitted to our hospital in 2007, complaining of an irritating cough. Computed tomography examination demonstrated a mass in the right lung and enlargement of the hilar and mediastinal lymph nodes. Small cell lung cancer was confirmed by pathological examination after fibro‐bronchoscope biopsy. The patient was treated with received sequential chemotherapy and radiotherapy. Preventive radiotherapy of the whole brain was performed after complete remission of the lung disease. Seven years after diagnosis, follow‐up computed tomography revealed masses in both the liver and kidney. Subsequent percutaneous biopsy confirmed hepatocellular carcinoma in the liver and renal clear cell carcinoma in the kidney. The patient received microwave ablation for the treatment of both liver and renal tumors, and is doing well with no recurrence after two years of follow‐up.
Relating Product Prices to Long‐Run Marginal Cost: Evidence from Solar Photovoltaic Modules
Authors: Reichelstein Stefan , Sahoo Anshuman
Published: May 2017

A basic tenet of microeconomics is that for a competitive industry in equilibrium the market price of a product will be equal to its marginal cost. This paper develops a model framework and a corresponding empirical inference procedure for estimating long‐run marginal cost in industries where production costs decline over time. In the context of the solar photovoltaic (PV) module industry, we rely primarily on firm‐level financial accounting data to estimate the long‐run marginal cost of PV modules for the years 2008–2013. During those years, the industry experienced both unprecedented price declines and significant expansions of manufacturing capacity. We compare the trajectory of average sales prices with the estimated long‐run marginal costs in order to quantify the extent to which actual price declines were attributable to reductions in production costs. The trajectory of estimated product costs is then extrapolated to forecast an equilibrium trend line for future PV module prices.