bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased avidity for Dpp/BMP2 maintains the proliferation of eye progenitors inDrosophila
Authors: Neto M. , Casares F.
Published: November 2015

During normal organ development, the progenitor cell state is transient: it depends on specific combinations of transcription factors and extracellular signals, that cooperate to sustain the proliferative potential and undifferentiated status of organ progenitor cells. Not surprisingly, abnormal maintenance of progenitor transcription factors may lead to tissue overgrowth, and the concurrence of specific signals from the local environment is often critical to trigger this overgrowth. Therefore, the identification of the specific combinations of transcription factors and signals that promote or oppose proliferation in progenitor cells is essential to understand normal development and disease. We have investigated this issue by asking what signals may promote the proliferation of eye progenitors inDrosophila. Two transcription factors, the MEIS1 homologuehomothorax (hth)and the Zn-fingerteashirt (tsh)are transiently expressed in eye progenitors causing the expansion of the progenitor pool. However, if their co-expression is maintained experimentally, cell proliferation continues and differentiation is halted. Here we show that Hth+Tsh-induced tissue overgrowth requires the BMP2 ligand Dpp and the activation of its pathway. In Hth+Tsh cells, the Dpp pathway is abnormally hyperactivated. Rather than using autocrine Dpp expression, Hth+Tsh cells increase their avidity for Dpp, produced locally, by upregulating extracellular matrix components. During normal development, Dpp represses hth and tsh ensuring that the progenitor state is transient. However, cells in which Hth+Tsh expression is maintained use Dpp to enhance their proliferation.

Summary Statement

InDrosophila, homothorax, the Meis1 homologue, andteashirtjointly sustain the proliferation of eye progenitor cells by increasing their avidity for BMP produced by the local microenvironment.
A comprehensive analysis of 3’ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation
Authors: Gruber Andreas J. , Schmidt Ralf , Gruber Andreas R. , Martin Georges , Ghosh Souvik , Belmadani Manuel , Keller Walter , Zavolan Mihaela
Published: November 2015

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3’ untranslated region (3’ UTR) isoforms interact with different RNA binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3’ end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3’ UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3’ end sequencing data sets we have uncovered 18 signals, 6 of which novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3’ end processing in both mouse and human. With 3’ end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3’ UTRs are enriched in ELAV-like RNA binding protein 1 (ELAVL1) binding sites and include those of the CD47 molecule (CD47) gene, which participate in the recently discovered mechanism of 3’ UTR-dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3’ end processing sites and poly(A) signals and it uncovers an important role of HNRNPC in regulating 3’ end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript’s life cycle.
AGOUTI: improving genome assembly and annotation using transcriptome data
Authors: Zhang Simo V. , Zhuo Luting , Hahn Matthew W.
Published: November 2015

Current genome assemblies consist of thousands of contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA-seq data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output.

Availability

The software is implemented in python and is available from github.com/svm-zhang/AGOUTI.

Contact

simozhan@indiana.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
An empirical correction for the influence of low-energy contamination
Authors: Krause Lennard , Herbst-Irmer Regine , Stalke Dietmar
Published: November 2015

Low-energy contamination caused by focusing multilayer optics has been known for a long time. So far, the only method to avoid this problem is attenuation by interposition of a low-density material foil into the beam. However, attenuation lowers the intensity, which might be crucial, especially for charge density data collection, and is of course not possible for already measured data. In this article, an empirical correction is proposed as an alternative or addition. The low-energy contamination mainly affects the reflections with indices 3h3k3l. In the programSADABS, a 3λ correction in analogy to the earlier 2/λ correction is now implemented. The correction factor can be determined from the model, but for most cases, a default value depending on the experimental settings is acceptable. Alternatively, the correction can be refined inSHELXL, similarly to a twin refinement. An investigation of several data sets collected with and without attenuation revealed that the empirical correction and attenuation lead to similar improvements. The empirical correction is of special interest for charge density investigations, where the loss of intensity could hinder the data collection up to very high resolution. Here, the improvements in the model, especially for the noise level of the residual density, are even more pronounced.
CDASH: a cloud-enabled program for structure solution from powder diffraction data
Authors: Spillman Mark J. , Shankland Kenneth , Williams Adrian C. , Cole Jason C.
Published: November 2015

The simulated annealing approach to crystal structure determination from powder diffraction data, as implemented in theDASHprogram, is readily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can be achieved by distributing individualDASHruns over a network of computers. TheCDASHprogram delivers this by using scalable on-demand computing clusters built on the Amazon Elastic Compute Cloud service. By way of example, a 360 vCPU cluster returned the crystal structure of racemic ornidazole (Z′ = 3, 30 degrees of freedom)ca40 times faster than a typical modern quad-core desktop CPU. Whilst used here specifically forDASH, this approach is of general applicability to other packages that are amenable to coarse-grained parallelism strategies.
Removing multiple outliers and single-crystal artefacts from X-ray diffraction computed tomography data
Authors: Vamvakeros Antonios , Jacques Simon D. M. , Di Michiel Marco , Middelkoop Vesna , Egan Christopher K. , Cernik Robert J. , Beale Andrew M.
Published: November 2015

This paper reports a simple but effective filtering approach to deal with single-crystal artefacts in X-ray diffraction computed tomography (XRD-CT). In XRD-CT, large crystallites can produce spots on top of the powder diffraction rings, which, after azimuthal integration and tomographic reconstruction, lead to line/streak artefacts in the tomograms. In the simple approach presented here, the polar transform is taken of collected two-dimensional diffraction patterns followed by directional median/mean filtering prior to integration. Reconstruction of one-dimensional diffraction projection data sets treated in such a way leads to a very significant improvement in reconstructed image quality for systems that exhibit powder spottiness arising from large crystallites. This approach is not computationally heavy which is an important consideration with big data sets such as is the case with XRD-CT. The method should have application to two-dimensional X-ray diffraction data in general where such spottiness arises.
Structural aspects of two α-dihydrazones displaying a complete survey of intermolecular interactions
Authors: Bustos Carlos , Alvarez-Thon Luis , Baggio Ricardo
Published: November 2015

The compounds (2′E,2′E)-2,2′-(propane-1,2-diylidene)bis[1-(2-nitrophenyl)hydrazine], C15H14N6O4, (I), and (2Z,3Z)-ethyl 3-[2-(2-nitrophenyl)hydrazinylidene]-2-[2-(4-nitrophenyl)hydrazinylidene]butanoate tetrahydrofuran hemisolvate, C18H18N6O6·0.5C4H8O, (II), are puzzling outliers deviating from a general synthetic route aimed at the preparation of substituted pyrazoles. Possible reasons for this outcome, which is exceptional in an otherwise firmly established synthetic procedure, are analyzed. Compound (I) is unsolvated, while compound (II) crystallizes with a tetrahydrofuran solvent molecule lying on an inversion centre. The ethoxycarbonyl chain of (II), in turn, appears disordered into two equally populated (50%) moieties. In both structures, a plethora of different commonly occurring weak intermolecular interactions [viz. π(phenyl)...π(phenyl), π(C=N)...π(C=N), π(phenyl)...π(C=N), N—H...O and C—H...O] appear responsible for the crystal stability. Much less common are the short O(nitro)...O(nitro) contacts which are observed in the structure of (I), an example of unusual `electron donor–acceptor' (EDA) interactions.
Crystal structure of (E)-13-(pyrimidin-5-yl)parthenolide
Authors: Bommagani Shobanbabu , Penthala Narsimha R. , Parkin Sean , Crooks Peter A.
Published: November 2015

The title compound, C19H22N2O3, {systematic name (1aR,4E,7aS,8E,10aS,10bR)-1a,5-dimethyl-8-[(pyrimidin-5-yl)methylidene]-2,3,6,7,7a,8,10a,10b-octahydrooxireno[2′,3′:9,10]cyclodeca[1,2-b]furan-9(1aH)-one} was obtained from the reaction of parthenolide [systematic name (1aR,7aS,10aS,10bR,E)-1a,5-dimethyl-8-methylene-2,3,6,7,7a,8,10a,10b-octahydrooxireno[2′,3′:9,10]cyclodeca[1,2-b]furan-9(1aH)-one] with 5-bromopyrimidine under Heck reaction conditions, and was identified as anEisomer. The molecule possesses ten-, five- (lactone) and three-membered (epoxide) rings with a pyrimidine group as a substituent. The ten-membered ring displays an approximate chair–chair conformation, while the lactone ring shows a flattened envelope-type conformation. The dihedral angle between the pyrimidine moiety and the lactone ring system is 29.43 (7)°.
Crystal structure of 3,4-dimethyl 2-(tert-butylamino)-5-[2-oxo-4-(thiomorpholin-4-yl)-2H-chromen-3-yl]furan-3,4-dicarboxylate ethyl acetate hemisolvate
Authors: Moriguchi Tetsuji , Jalli Venkataprasad , Krishnamurthy Suvratha , Tsuge Akihiko , Yoza Kenji
Published: November 2015

In the title hemisolvate, C25H28N2O7S·0.5C4H8O2, the thiomorpholine ring adopts a chair conformation, with the exocyclic N—C bond in an equatorial orientation. The dihedral angle between the coumarin ring system (r.m.s. deviation = 0.044 Å) and the furan ring is 64.84 (6)°. An intramolecular N—H...O hydrogen bond closes anS(6) ring. The ethyl acetate solvent molecule is disordered about a crystallographic inversion centre. In the crystal, the components are linked by C—H...O and C—H...S hydrogen bonds, generating a three-dimensional network.
Crystal structure of (E)-5-benzyloxy-2-{[(4-nitrophenyl)imino]methyl}phenol
Authors: Ghichi Nadir , Benaouida Mohamed Amine , Benboudiaf Ali , Merazig Hocine
Published: November 2015

In the title compound, C20H16N2O4, the molecule adopts anEconformation about the N=C bond. There is an intramolecular O—H...N hydrogen bond forming anS(6) ring motif. The nitrobenzene and benzyloxy rings are inclined to the central benzene ring by 4.34 (10) and 27.66 (11)°, respectively, and to one another by 31.40 (12)°. In the crystal, molecules are linkedviaC—H...O hydrogen bonds, forming zigzag chains along [001]. Within the chains there are C—H...π interactions present. The chains are linkedviaπ–π interactions [inter-centroid distance = 3.7048 (15) Å], forming slabs parallel to thebcplane.
Crystal structure of 4-bromo-2-(1H-imidazo[4,5-b]pyridin-2-yl)phenol
Authors: Ouari Kamel
Published: November 2015

In the title compound, C12H8BrN3O, the 4-bromophenol ring is coplanar with the planar imidazo[4,5-b]pyridine moiety (r.m.s deviation = 0.015 Å), making a dihedral angle of 1.8 (2)°. There is an intramolecular O—H...N hydrogen bond forming anS(6) ring motif. In the crystal, molecules are linkedviaN—H...N and O—H...Br hydrogen bonds, forming undulating sheets parallel to (10-2). The sheets are linked by π–π interactions [inter-centroid distance = 3.7680 (17) Å], involving inversion-related molecules, forming a three-dimensional structure.
Crystal structure of 6-deoxy-α-L-psicofuranose
Authors: Yoshihara Akihide , Ishii Tomohiko , Kamakura Tatsuya , Taguchi Hiroaki , Fukada Kazuhiro
Published: November 2015

The title compound, C6H12O5, was crystallized from an aqueous solution of 6-deoxy-L-psicose (6-deoxy-L-allulose, (3S,4S,5S)-1,3,4,5-tetrahydroxyhexan-2-one), and the molecule was confirmed as α-furanose with a3T4(orE4) conformation, which is a predominant tautomer in solution. This five-membered furanose ring structure is the second example in the field of the 6-deoxy-ketohexose family. The cell volume of the title compound [742.67 (7) Å3,Z= 4 at room temperature] is only 1.4% smaller than that of β-D-psicopyranose, C6H12O6(753.056 Å3,Z= 4 at room temperature).
Crystal structure of 4-benzyl-2H-benzo[b][1,4]thiazin-3(4H)-one
Authors: Sebbar N. K. , Ellouz M. , Essassi E. M. , Ouzidan Y. , Mague J. T.
Published: November 2015

In the title compound, C15H13NOS, the thiazine ring adopts a twisted boat conformation and the dihedral angle between the aromatic rings is 86.54 (4)°. In the crystal, molecules are linked by weak C—H...O interactions, resulting in chains along [010].
Crystal structure of racemiccis-2-amino-1,2-diphenylethanol (ADE)
Authors: Fujii Isao
Published: November 2015

In the title racemic compound, C14H15NO, the hydroxy and amino groups form a bent tweezer-like motif towards the phenyl groups. In the crystal, enantiomers aggregate with each other and are linked by O—H...N hydrogen bonds, forming chiral 21-helical columnar structures fromC(5) chains along theb-axis direction. Left- and right-handed 21helices are formed from (1S,2R)-2-amino-1,2-diphenylethanol and (1R,2S)-2-amino-1,2-diphenylethanol, respectively.
Crystal structure of bis(4-acetylanilinium) tetrachloridomercurate(II)
Authors: Thairiyaraja Manickam , Elangovan Arumugam , Arivazhagan Ganesh , Selvaraju Kuthambalam , Thamotharan Subbiah
Published: November 2015

The structure of the title salt, (C8H10NO)2[HgCl4], is isotypic with that of the cuprate(II) and cobaltate(II) analogues. The asymmetric unit contains one 4-acetylanilinium cation and one half of a tetrachloridomercurate(II) anion (point group symmetrym). The Hg—Cl distances are in the range 2.4308 (7)–2.5244 (11) Å and the Cl—Hg—Cl angles in the range of 104.66 (2)–122.94 (4)°, indicating a considerable distortion of the tetrahedral anion. In the crystal, cations are linked by an intermolecular N—H...O hydrogen-bonding interaction, leading to aC(8) chain motif with the chains extending parallel to thebaxis. There is also a π–π stacking interaction with a centroid-to-centroid distance of 3.735 (2) Å between neighbouring benzene rings along this direction. The anions lie between the chains and interact with the cations through intermolecular N—H...Cl hydrogen bonds, leading to the formation of a three-dimensional network structure.
Crystal structure of 7-{[bis(pyridin-2-ylmethyl)amino]methyl}-5-chloroquinolin-8-ol
Authors: Kubono Koji , Kado Kimiko , Kashiwagi Yukiyasu , Tani Keita , Yokoi Kunihiko
Published: November 2015

In the title compound, C22H19ClN4O, the quinolinol moiety is almost planar [r.m.s. deviation = 0.012 Å]. There is an intramolecular O—H...N hydrogen bond involving the hydroxy group and a pyridine N atom forming anS(9) ring motif. The dihedral angles between the planes of the quinolinol moiety and the pyridine rings are 44.15 (9) and 36.85 (9)°. In the crystal, molecules are linkedviaC—H...O hydrogen bonds forming inversion dimers with anR44(10) ring motif. The dimers are linked by C—H...N hydrogen bonds, forming ribbons along [01-1]. The ribbons are linked by C—H...π and π–π interactions [inter-centroid distance = 3.7109 (11) Å], forming layers parallel to (01-1).
The crystal structure of a new polymorph of hexaaquanickel(II) bis(6-oxo-1,6-dihydropyridine-3-carboxylate)
Authors: Pérez-Aguirre Rubén , Pérez-Yáñez Sonia , Beobide Garikoitz , Castillo Oscar , Gutiérrez-Zorrilla Juan Manuel , Luque Antonio
Published: November 2015

In a new polymorph of the title salt, [Ni(H2O)6](C6H4NO3)2, the metal atom of the cationic complex lies on a symmetry centre and is coordinated by six water molecules to provide a quite regular octahedral coordination environment. These cations interact with 6-oxo-1,6-dihydropyridine-3-carboxylate anions through electrostatic interactions and by means of O—H...O and N—H...O hydrogen bonds involving the carboxylate, keto and protonated imine groups of the anion, and the coordinating water molecules from the cationic complex entity to generate a supramolecular three-dimensional architecture. The previously reported polymorph of this compound presents a network of hydrogen bonds, in which the organic anions establish mutual hydrogen-bonding interactions involving their keto and protonated imine groups.
Bedside healthcare rationing dilemmas: a survey from Portugal
Authors: Pinho Micaela , Borges Ana
Published: November 2015

Purpose

– The purpose of this paper is to seek to elicit, in a context of economic crisis, the social preferences for the microallocation of scarce healthcare resources.

Design/methodology/approach

– Data were collected from an online questionnaire which includes a hypothetical rationing choice scenario with four patients differentiated by their personal characteristics and health states competing for treatments and a set of statements that embodies: distributive criteria for prioritizing patients; the authorship of these types of decisions; and the likelihood of these decisions to be taken. Descriptive statistics, factor analysis and non-parametric test were used for describing and validating the data.

Findings

– Findings suggest that respondents: support a pluralism of distributive principles in prioritizing patients with an incident in utilitarianism and the reducing of inequalities in health, translated in the fair-inning and in emotional arguments of fragility; trust in the health professional to make prioritization decisions; and are conscious that rationing decisions will be real in the short term.

Practical implications

– The pursuit of efficiency and the equalizing of a lifetime health seem to be the criteria that should guide any rationing policy at the micro level.

Originality/value

– This study addresses simultaneously several ethical principles inherent to microallocation healthcare resources in a suitable context in which Portugal is facing an economic crisis and where, consequently, rationing healthcare policies gain prominence on the political agenda.
Re-positioning library technology support on Campus-Wilson Library’s journey
Authors: Jiang Amy , Beavers Karen , Cady Jennifer Esteron , McCoy Liberty
Published: November 2015

Purpose

– The purpose of this paper is to discuss the changing role of the academic library, in relation to technology support services. It proposes that library technology services should expand to take a central role in developing student academic technology skills, and shows how moving into non-traditional areas of technology support can expand a library’s operation capabilities to include entrepreneurship and innovation for faculty, staff and students.

Design/methodology/approach

– The paper outlines how our library expanded its technology services to include course management support, technical literacy training and three-dimensional (3D) printing, and details future developments into robotics and software development. It details the authors initial objectives, the issues encountered, the improvements made in response and what the authors hope to do in the future.

Findings

– We are at a time when technology has made innovation and creation available to many. Academic libraries should take on this opportunity of repositioning technology services to provide and promote technical applications, becoming a central point for library users to share ideas and collaborate on projects. As a result of the interdisciplinary nature of academic libraries, the authors are in the best position to make this happen on campus.

Originality/value

– Even though continual change has been a theme in the development of libraries, very little has been written on the role of technology support services. This paper sets the foundation for further exploration in how taking on academic technology support services, 3D printing and makerspaces could be a part of library services.
Motivating language as a mediator between servant leadership and employee outcomes
Authors: Gutierrez-Wirsching Sandra , Mayfield Jacqueline , Mayfield Milton , Wang Wei
Published: November 2015

Purpose

– The purpose of this paper is to propose motivating language as a mediator to increase the positive effects of servant leadership on subordinates’ outcomes. The authors propose that motivating language acts as a mediator to transmit servant leadership traits and enhances the positive impact that servant leadership verbal behavior has on employees’ performance.

Design/methodology/approach

– By developing a conceptual model, the authors propose a connection between servant leadership and motivating language.

Findings

– In the proposed model, motivating language acts as a full and a partial mediator. The authors further categorize three distinct outcome sets that should be improved from this relationship. The first set includes improved worker performance, job satisfaction, absenteeism and worker innovation. The second set is composed of self-efficacy, organizational citizenship behavior and employee commitment. Finally, the third set includes trust, satisfaction with the leader and inspiration to become servant leaders.

Research limitations/implications

– Empirical research needs to be conducted to test this model.

Practical implications

– The positive effects of servant leadership through the use of motivating language could be operationalized in multiple ways. First, potential servant leaders could take the well-established, reliable and valid motivating language scale to diagnostically identify their leader-member communication strengths and weaknesses. Then, tailored motivating language trainings could be implemented which target motivating language weaknesses and key strategic outcomes in the proposed model. Furthermore, motivating language training would be a valuable instrument for transmission of a servant leadership culture.

Social implications

– Servant leadership style responds to the demand for positive ethical behavior that is much needed during these times when emphasis is given to profitability and lack of concern for people is the norm rather than the exception. It is also synchronized with the current benefits of organizational citizenship behaviors that have recently emerged in the field of managerial research.

Originality/value

– This paper aims at addressing a gap in the literature by developing a model of how leader strategic language, namely, motivating language, mediates between servant leadership and worker outcomes.
Effects of mountaintop removal mining and valley filling on the occupancy and abundance of stream salamanders
Authors: Price Steven J. , Muncy Brenee' L. , Bonner Simon J. , Drayer Andrea N. , Barton Christopher D.
Published: November 2015

Human‐induced land‐use changes are among the primary causes of ecosystem degradation and biodiversity loss. Across central Appalachia (USA), mountaintop removal mining and valley filling (MTR/VF) is the prevailing form of land‐use change and represents a stressor to stream ecosystems. Salamanders are the dominant vertebrate in Appalachian headwater streams. Thus, we addressed the question: Is salamander occupancy and conditional abundance reduced in streams impacted by MTR/VF?

We conducted repeated counts of adult and larval salamanders within 10‐m reaches in 11 valley‐filled streams and 12 reference streams in south‐eastern Kentucky. Relationships between occupancy, conditional abundance, and site type (MTR/VF vs. reference) were modelled using the hurdle model (Ecology, 94, 2013 and 1472), where occupancy is modelled separately from abundance while accounting for differences in per‐individual detection probabilities among groups.

We found mean occupancy probabilities were >0·85 for all groups in reference reaches, whereas mean occupancy probabilities were relatively lower in MTR/VF reaches (ranging from 0·23 to 0·66). Posterior means of the difference in occupancy between site types were negative across all groups, although MTR/VF stream reaches were at least 95% less likely to be occupied by spring salamander Gyrinophilus porphyriticus, adult southern two‐lined salamander Eurycea cirrigera and larval dusky salamanders Desmognathus compared to reference reaches.

Posterior means of the difference in conditional abundance between MTR/VF and reference stream reaches were negative across all groups; 95% credible interval for difference in conditional abundance covered zero for only one species (red salamander Pseudotriton ruber). After adjusting for goodness‐of‐fit, point estimates of differences in occupancy and conditional abundance still remained below zero for most species. Additionally, MTR/VF reaches had higher ion concentrations, total organic carbon and specific conductance compared to reference reaches.

Synthesis and applications. Our study concludes that mountaintop removal mining and valley filling (MTR/VF) reduces salamander occupancy and conditional abundance. Although the potential mechanisms responsible for reduction are numerous, our findings suggest a change in the current regulatory framework is needed to offset the impacts of MTR/VF on stream ecosystems and biota. Reclamation techniques that enhance conditions for vegetative succession within catchments may improve habitat on reclaimed surface mines.
When does intraspecific trait variation contribute to functional beta‐diversity?
Authors: Spasojevic Marko J. , Turner Benjamin L. , Myers Jonathan A.
Published: November 2015

Intraspecific trait variation (ITV) is hypothesized to play an important role in community assembly and the maintenance of biodiversity. However, fundamental gaps remain in our understanding of how ITV contributes to mechanisms that create spatial variation in the functional‐trait composition of communities (functional β‐diversity). Importantly, ITV may influence the perceived importance of environmental filtering across spatial scales.

We examined how ITV contributes to functional β‐diversity and environmental filtering in woody plant communities in a temperate forest in the Ozark ecoregion, Missouri, USA. To test the hypothesis that ITV contributes to changes in the perceived importance of environmental filtering across scales, we compared patterns of functional β‐diversity across soil‐resource and topographic gradients at three spatial grains and three spatial extents. To quantify the contribution of ITV to functional β‐diversity, we compared patterns that included ITV in five traits (leaf area, specific leaf area, leaf water content, leaf toughness and chlorophyll content) to patterns based on species‐mean trait values.

Functional β‐diversity that included ITV increased with spatial extent and decreased with spatial grain, suggesting stronger environmental filtering within spatially extensive landscapes that contain populations locally adapted to different habitats. In contrast, functional β‐diversity based on species‐mean trait values increased with spatial extent but did not change with spatial grain, suggesting weaker environmental filtering among larger communities which each contain a variety of habitats and locally adapted populations.

Synthesis. Although studies typically infer community assembly mechanisms from species‐mean trait values, our study suggests that mean trait values may mask the strength of assembly mechanisms such as environmental filtering, especially in landscape‐scale studies that encompass strong environmental gradients and locally adapted populations. Our study highlights the utility of integrating ITV into studies of functional β‐diversity to better understand the ecological conditions under which trait variation within and among species contributes most strongly to patterns of biodiversity across spatial scales.
Soil nutrients influence growth response of temperate tree species to drought
Authors: Lévesque Mathieu , Walthert Lorenz , Weber Pascale
Published: November 2015

Soil properties can buffer forest response to global climate change. However, it is unclear how soil characteristics, water availability and their interactions can affect drought response of trees. The aim of this study was to assess the influence of soil nutrients and physical soil properties on the growth sensitivity ofFagus sylvatica,Quercusspp.,Fraxinus excelsior,Abies alba, Picea abiesandPinus sylvestristo drought in Central Europe.

Yearly growth data from increment cores were obtained from 538 trees and combined with forest inventory and soil data at 52 sites covering a large gradient of water availability and C/N ratios in soil. Linear mixed‐effects models were used to assess the species‐specific growth responses to climate and soil properties for the period 1957–2006. The growth of the species was further projected across the full range of C/N and water availability observed at 1029 sites where soil and species cover‐abundance data were available.

Temperature, water and nutrient availability (C/N) were the most important factors for tree growth. Drought and low nutrient availability significantly reduced the growth of beech, ash, fir and spruce along the gradient. In contrast, the growth of pine and oak was little reduced on poor and dry sites, hence showing their competitive advantage over nutrient‐demanding species under such conditions. The growth of ash and pine was enhanced at sites with high species abundance, whereas an opposite response was found for spruce. No clear relationships between growth and species abundance were found for beech, oak and fir.

Synthesis. Our results suggest that assessing tree responses to climate change without considering simultaneously soil properties and climate may be misleading since soil nutrients can influence growth response of trees to drought. A detailed analysis of the influence of the soil characteristics on growth responses of trees is necessary to understand the sensitivity of tree species to global climate change.
International patterns of the public awareness of aphasia
Authors: Code Chris , Papathanasiou Ilias , Rubio‐Bruno Silvia , de la Paz Cabana María , Villanueva Maria Marta , Haaland‐Johansen Line , Prizl‐Jakovac Tatjana , Leko Ana , Zemva Nada , Patterson Ruth , Berry Richard , Rochon Elizabeth , Leonard Carol , Robert Amelie
Published: November 2015

Background: It has been suggested that public awareness of aphasia is vital for extending services, research support, social inclusion and targeted raising of awareness. Earlier studies show that knowledge of aphasia varies across a range of variables, but is very low compared with other conditions.

Aims: To report a series of surveys of public awareness of aphasia from six countries, the largest study conducted this far.

Methods & Procedures: Surveys were conducted in Argentina (N = 800), Canada (N = 831), Croatia (N = 400), Greece (N = 800), Norway (N = 251) and Slovenia (N = 400) using the same methodology requesting information on age, sex and occupation, asking whether respondents had heard of aphasia and where they had heard of it. Respondents were tested on their levels of knowledge of aphasia.

Outcomes & Results: Results revealed low levels of awareness of aphasia in countries surveyed with marked variability that appeared to interact with occupation, country, age and sex. We surveyed 3483 respondents (mean age = 43.16; SD = 17.68). Between 60% (Croatia) and 16% (Slovenia) said they had heard of aphasia (37.1% overall), but those with actual knowledge ranged from 13.9% (Norway) to 1.0% (Argentina). The combined mean of those with basic knowledge was 9.2%. Those who had heard of aphasia were younger; and females had higher levels of awareness. We also found associations between socio‐economic status and awareness. Those working in health, social and educational spheres had the highest levels. Respondents mainly heard about aphasia through the media and work or personal contact with aphasia.

Conclusions & Implications: Levels of awareness are low everywhere in absolute terms, and relative to the awareness of other conditions, with significant variability between countries, sex and socio‐economic status. We examine how surveys can be utilized to plan ways to increase understanding and discuss the comparison of awareness of aphasia with other conditions.
Evidence of Place: Becoming a Region in Rural Canada
Authors: Markey Sean , Breen Sarah‐Patricia , Vodden Kelly , Daniels Jen
Published: November 2015

The purpose of this article is to investigate whether place is emerging in practice as a critical dimension in the development of Canadian rural regions. Recently, Jones and Paasi set regional researchers the task of better understanding how regions ‘become'. In researching this question, we are particularly interested in the definition and expression of place‐based identity as a mobilizing force for regionalism. Our findings suggest that, while identity plays a critical role in fostering regional development processes, it is either too emergent or actively resisted within our research sites to be a significant force for place‐based regional development.
Effects of Expanded California Health Coverage on Hospitals: Implications for ACA Medicaid Expansions
Authors: Bazzoli Gloria J.
Published: November 2015

Objective

To assess the effects on hospitals of early California actions to expand insurance coverage for low‐income uninsured adults after passage of the Affordable Care Act.

Data Sources/Study Setting

Data from the California Office of Statewide Health Planning and Development and the California Department of Health were merged with U.S. census data for 294 short‐term general hospitals during the period 2009–2012.

Study Design

A difference‐in‐difference analysis was conducted with hospitals in counties that did not implement insurance expansions used as a comparison group. Variables examined included payer mix, costs of unreimbursed care, and hospital operating margin. Sensitivity analyses were conducted as well as a triple difference analysis. Effects were estimated for hospitals overall and by ownership type.

Principal Findings

California insurance expansions primarily benefited for‐profit hospitals, with these facilities experiencing significant decreases in self‐pay patients, increases in county‐covered patients, and reductions in charity care. Most models yielded no significant change in payer mix and conflicting changes in unreimbursed care for nonprofit hospitals.

Conclusions

California hospitals that treated the most uninsured prior to insurance expansions did not as a group experience substantial benefit in terms of reduced uninsured burden or better financial performance after program expansions occurred.
Trust and Reflection in Primary Care Practice Redesign
Authors: Lanham Holly Jordan , Palmer Raymond F. , Leykum Luci K. , McDaniel Reuben R. , Nutting Paul A. , Stange Kurt C. , Crabtree Benjamin F. , Miller William L. , Jaén Carlos Roberto
Published: November 2015

Objective

To test a conceptual model of relationships, reflection, sensemaking, and learning in primary care practices transitioning to patient‐centered medical homes (PCMH).

Data Sources/Study Setting

Primary data were collected as part of the American Academy of Family Physicians' National Demonstration Project of the PCMH.

Study Design

We conducted a cross‐sectional survey of clinicians and staff from 36 family medicine practices across the United States. Surveys measured seven characteristics of practice relationships (trust, diversity, mindfulness, heedful interrelation, respectful interaction, social/task relatedness, and rich and lean communication) and three organizational attributes (reflection, sensemaking, and learning) of practices.

Data Collection/Extraction Methods

We surveyed 396 clinicians and practice staff. We performed a multigroup path analysis of the data. Parameter estimates were calculated using a Bayesian estimation method.

Principal Findings

Trust and reflection were important in explaining the characteristics of practice relationships and their associations with sensemaking and learning. The strongest associations between relationships, sensemaking, and learning were found under conditions of high trust and reflection. The weakest associations were found under conditions of low trust and reflection.

Conclusions

Trust and reflection appear to play a key role in moderating relationships, sensemaking, and learning in practices undergoing practice redesign.
Prebiotic Low Sugar Chocolate Dairy Desserts: Physical and Optical Characteristics and Performance of PARAFAC and PCA Preference Map
Authors: Morais E. C. , Esmerino E. A. , Monteiro R. A. , Pinheiro C. M. , Nunes C. A. , Cruz A.G. , Bolini Helena M.A.
Published: November 2015

The addition of prebiotic and sweeteners in chocolate dairy desserts opens up new opportunities to develop dairy desserts that besides having a lower calorie intake still has functional properties. In this study, prebiotic low sugar dairy desserts were evaluated by 120 consumers using a 9‐point hedonic scale, in relation to the attributes of appearance, aroma, flavor, texture, and overall liking. Internal preference map using parallel factor analysis (PARAFAC) and principal component analysis (PCA) was performed using the consumer data. In addition, physical (texture profile) and optical (instrumental color) analyses were also performed. Prebiotic dairy desserts containing sucrose and sucralose were equally liked by the consumers. These samples were characterized by firmness and gumminess, which can be considered drivers of liking by the consumers. Optimization of the prebiotic low sugar dessert formulation should take in account the choice of ingredients that contribute in a positive manner for these parameters. PARAFAC allowed the extraction of more relevant information in relation to PCA, demonstrating that consumer acceptance analysis can be evaluated by simultaneously considering several attributes. Multiple factor analysis reported Rv value of 0.964, suggesting excellent concordance for both methods.
Calcium–Alginate–Inulin Microbeads as Carriers for Aqueous Carqueja Extract
Authors: Balanč Bojana , Kalušević Ana , Drvenica Ivana , Coelho Maria Teresa , Djordjević Verica , Alves Vitor D , Sousa Isabel , Moldão‐Martins Margarida , Rakić Vesna , Nedović Viktor , Bugarski Branko
Published: November 2015

Carqueja (Pterospartum tridentatum) is an endemic species and various bioactive compounds have been identified in its aqueous extract. The aim of this study was to protect the natural antioxidants from the aqueous extract of carqueja by encapsulation in Ca–alginate microbeads and Ca–alginate microbeads containing 10% and 20% (w/v) of inulin. The microbeads produced by electrostatic extrusion technique had an average diameter from 625 μm to 830 μm depending on the portion of inulin. The sphericity factor of the hydrogel microbeads had values between 0.014 and 0.026, while freeze dried microbeads had irregular shape, especially those with no excipient. The reduction in microbeads size after freeze drying process (expressed as shrinkage factor) ranged from 0.338 (alginate microbeads with 20% (w/v) of inulin) to 0.523 (plain alginate microbeads). The expressed radical scavenging activity against ABTS and DPPH radicals was found to be between 30% and 40% for encapsulated extract, while the fresh extract showed around 47% and 57% of radical scavenging activity for ABTS and DPPH radicals, respectively. The correlation between antioxidant activity and the total phenolic content were found to be positive (in both assay methods, DPPH and ABTS), which indicate that the addition of inulin didn't have influence on antioxidant activity. The presence of inulin reduced stiffness of the hydrogel, and protected bead structure from collapse upon freeze‐drying. Alginate–inulin beads are envisaged to be used for delivery of aqueous P. tridentatum extract in functional food products.
Extending RAD tag analysis to microbial ecology: a comparison between MultiLocus Sequence Typing and 2b‐RAD to investigate Listeria monocytogenes genetic structure
Authors: Pauletto Marianna , Carraro Lisa , Babbucci Massimiliano , Lucchini Rosaria , Bargelloni Luca , Cardazzo Barbara
Published: November 2015

The advent of next‐generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole‐genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time‐consuming, especially for large‐scale analyses. In this study, a genotyping approach based on restriction site‐associated (RAD) tag sequencing, 2b‐RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b‐RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food‐processing sites. The obtained results demonstrate that 2b‐RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large‐scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b‐RAD analysis proposed here.
Efficacy and safety of intravenous fentanyl administered by ambulance personnel
Authors: Friesgaard K. D. , Nikolajsen L. , Giebner M. , Rasmussen C.‐H. , Riddervold I. S. , Kirkegaard H. , Christensen E. F.
Published: November 2015

Background

Management of pain in the pre‐hospital setting is often inadequate. In 2011, ambulance personnel were authorized to administer intravenous fentanyl in the Central Denmark Region. The aim of this study was to evaluate the efficacy and safety of intravenous fentanyl administered by ambulance personnel.

Methods

Pre‐hospital medical charts from 2348 adults treated with intravenous fentanyl by ambulance personnel during a 6‐month period were reviewed. The primary outcome was the change in pain intensity on a numeric rating scale (NRS) from before fentanyl treatment to hospital arrival. Secondary outcomes included the number of patients with reduction in pain intensity during transport (NRS ≥ 2), the number of patients with NRS > 3 at hospital arrival, and potential fentanyl‐related side effects.

Results

Fentanyl reduced pain from before treatment (8, IQR 7–9) to hospital arrival (4, IQR 3–6) (NRS reduction: 3, IQR 2–5; P = 0.001), 79.3% of all patients had a reduction in > 2 on the NRS during transport, and 58.4% of patients experienced pain at hospital arrival (NRS > 3). Twenty‐one patients (0.9%) had oxygen saturation < 90%. A decrease in Glasgow Coma Scale was seen in 31 patients (1.3%) and hypotension observed in 71 patients (3.0%).

Conclusion

Intravenous fentanyl caused clinically meaningful pain reduction in most patients and was safe in the hands of ambulance personnel. Many patients had moderate to severe pain at hospital arrival. As the protocol allowed higher doses of fentanyl, feedback on effect and safety should be part of continuous education of ambulance personnel.
Reduced activity in functional networks during reward processing is modulated by abstinence in cocaine addicts
Authors: Costumero Víctor , Bustamante Juan Carlos , Rosell‐Negre Patricia , Fuentes Paola , Llopis Juan José , Ávila César , Barrós‐Loscertales Alfonso
Published: November 2015

Cocaine addiction is characterized by alterations in motivational and cognitive processes. Recent studies have shown that some alterations present in cocaine users may be related to the activity of large functional networks. The aim of this study was to investigate how these functional networks are modulated by non‐drug rewarding stimuli in cocaine‐dependent individuals. Twenty abstinent cocaine‐dependent and 21 healthy matched male controls viewed erotic and neutral pictures while undergoing a functional magnetic resonance imaging scan. Group independent component analysis was then performed in order to investigate how functional networks were modulated by reward in cocaine addicts. The results showed that cocaine addicts, compared with healthy controls, displayed diminished modulation of the left frontoparietal network in response to erotic pictures, specifically when they were unpredicted. Additionally, a positive correlation between the length of cocaine abstinence and the modulation of the left frontoparietal network by unpredicted erotic images was found. In agreement with current addiction models, our results suggest that cocaine addiction contributes to reduce sensitivity to rewarding stimuli and that abstinence may mitigate this effect.
Conspiracy Endorsement as Motivated Reasoning: The Moderating Roles of Political Knowledge and Trust
Authors: Miller Joanne M. , Saunders Kyle L. , Farhart Christina E.
Published: November 2015

Given the potential political and social significance of conspiracy beliefs, a substantial and growing body of work examines the individual‐level correlates of belief in conspiracy theories and general conspiratorial predispositions. However, although we know much about the psychological antecedents of conspiracy endorsement, we know less about the individual‐level political causes of these prevalent and consequential beliefs. Our work draws from the extant literature to posit that endorsement of conspiracy theories is a motivated process that serves both ideological and psychological needs. In doing so, we develop a theory that identifies a particular type of person—one who is both highly knowledgeable about politics and lacking in trust—who is most susceptible to ideologically motivated conspiracy endorsement. Further, we demonstrate that the moderators of belief in conspiracy theories are strikingly different for conservatives and liberals.