bluuebunny/crossref_metadata_2025 huggingface dataset:
A multibody meshfree strategy for the simulation of highly deformable granular materials
Authors: Mollon Guilhem
Published: April 2016

SUmmary

In this paper, a multibody meshfree framework is proposed for the simulation of granular materials undergoing deformations at the grain scale. This framework is based on an implicit solving of the mechanical problem based on a weak form written on the domain defined by all the grains composing the granular sample. Several technical choices, related to the displacement field interpolation, to the contact modelling, and to the integration scheme used to solve the dynamic equations, are explained in details. A first implementation is proposed, under the acronym Multibody ELement‐free Open code for DYnamic simulation (MELODY), and is made available for free download. Two numerical examples are provided to show the convergence and the capability of the method. Copyright © 2016 John Wiley & Sons, Ltd.
Clinical outcome measures for monitoring physical function in pediatric obesity: An integrative review
Authors: Mahaffey Ryan , Morrison Stewart C. , Stephensen David , Drechsler Wendy I.
Published: April 2016

Objective

Measuring physical function in children with obesity is important to provide targets for clinical intervention to reduce impairments and increase participation in activities. The objective of this integrative review was to evaluate measurement properties of performance‐based measures of physical function in children with overweight and obesity.

Design and Methods

An integrative review of literature published in Cochrane Reviews, SPORTDiscus, CINAHL, PLoS, Medline, and Scopus was conducted.

Results

Twenty‐eight studies were eligible and represented 66 performance‐based measures of physical function. Assessments of repeatability and feasibility were not conducted in the majority of performance measures reported; only 6‐min‐timed walk (6MTW) was examined for test‐retest repeatability. Measures of flexibility, strength, aerobic performance, anaerobic performance, coordination, and balance demonstrated construct validity and responsiveness; however, findings were inconsistent across all performance‐based measures. Multi‐item tests of physical function demonstrated acceptable construct validity and responsiveness; however, internal consistency was not determined.

Conclusions

There is moderate evidence that 6MTW is suitable for the measurement of physical function in children with obesity. However, evidence is low for the use of aerobic and anaerobic performance, muscle strength, Movement Assessment Battery for Children, and Bruininks‐Oseretsky Test of Motor Proficiency multi‐item performance instruments and very low for flexibility, coordination, and balance tests. Based on this review, measurement of physical function using 6MTW is recommended.
Broadening Benefits from Natural Resource Extraction: Housing Values and Taxation of Natural Gas Wells as Property
Authors: Weber Jeremy G. , Burnett J. Wesley , Xiarchos Irene M.
Published: April 2016

We study the effects of the property tax base shock caused by natural gas drilling in the Barnett Shale in Texas—a state that taxes oil and gas wells as property. Over the boom and bust in drilling, housing appreciation closely followed the oil and gas property tax base, which expanded the total tax base by 23 percent at its height. The expansion led to a decline in property tax rates while maintaining or increasing revenues to schools. Overall, each $1 per student increase in the oil and gas property tax base increased the value of the typical home by $0.15. Some evidence suggests that the cumulative density of wells nearby may lower housing values, indicating that drilling could reduce local welfare without policies to increase local public revenues.
Prenatal findings in children with early postnatal diagnosis of CHARGE syndrome
Authors: Busa Tiffany , Legendre Marine , Bauge Marie , Quarello Edwin , Bretelle Florence , Bilan Frederic , Sigaudy Sabine , Gilbert‐Dussardier Brigitte , Philip Nicole
Published: April 2016

Background

CHARGE syndrome is a multiple congenital anomaly syndrome caused by mutations in CHD7. Diagnostic criteria have been proposed to improve diagnosis in fetuses at clinicopathological survey, but no criteria exist for fetal diagnosis during pregnancy.

Method

We collected prenatal findings of 12 children with CHARGE syndrome diagnosed in the first 3 months and a CHD7 mutation. We retrieved data on prenatal ultrasound (US) follow‐up, fetal supplementary investigations, and results of postnatal evaluation.

Result

Seven pregnancies were complicated by the identification of isolated or multiple congenital anomalies. CHARGE syndrome was suspected in three fetuses but could not be confirmed despite additional examinations. Retrospectively, several postnatal findings could have been seen if they had been specifically searched. Intrauterine growth restriction, previously proposed as an exclusion criterion, complicated two pregnancies and is thus compatible with the diagnosis.

Conclusion

Diagnosis of CHARGE syndrome remains difficult during pregnancy. If the diagnosis of CHARGE syndrome is raised in utero, we suggest a careful US examination to identify typical external ears, choanal atresia, or microphthalmia. Fetal brain magnetic resonance imaging can be helpful, but a normal result does not exclude the diagnosis. When CHARGE syndrome is highly suspected, CHD7 molecular analysis must be proposed to confirm the diagnosis. © 2016 John Wiley & Sons, Ltd.
Recommendations for Aligning PGY2 Pharmacy Residency Training and Pharmacy Specialist Board Certification
Authors:   American College of Clinical Pharmacy, Sorensen Todd D. , Shapiro Nancy L. , Benedict Neal , Edwards Krystal L. , Chan Alexandre , Covey Douglas , Daniels Charles , Hagemann Tracy , Hemstreet Brian , Miller William , Musselman Megan E.
Published: April 2016

With the increased focus and anticipated growth in specialty training and certification within the profession of pharmacy, it is important for the profession to step back and evaluate the manner in which its adopted education and certification systems interface. As a result of specialty practice development, significant growth is occurring in both postgraduate year two (PGY2) pharmacy residency programs and individuals seeking certification by the Board of Pharmacy Specialties. As the profession continues to evolve its specialty training and credentialing systems, it is important to consider the inherent relationship between these systems. This paper considers the current landscape of specialty training and certification, including issues related to the quality of PGY2 training, consistent application of standards across and within PGY2 programs, credentialing of preceptors and program directors, and alignment of training with specialty certification examination content domains. We outline recommendations across three areas: (1) creating consistency between specialty training and certification, (2) aligning qualifications of PGY2 residency program directors and preceptors with the designated specialty area, and (3) assessing program quality in the context of the expectations of specialists established by the profession. The goal of this paper is to stimulate professional dialogue on these issues. Establishing both formal and informal connections between specialty training and certification can serve as the foundation for a rational approach to professional development and the credentialing that will be recognized by stakeholders outside the pharmacy profession. Establishing these connections will also support and advance the profession's mission of meeting the medication needs of patients.
Influence of incorporation of starch nanoparticles in PBAT/TPS composite films
Authors: González Seligra Paula , Eloy Moura Lídia , Famá Lucia , Druzian Janice Izabel , Goyanes Silvia
Published: April 2016

Films of PBAT/TPS (poly(butylene adipate‐co‐terephthalate)/thermoplastic starch) (starch plasticized with glycerol containing citric and stearic acids) without and with 0.6 wt% starch nanoparticles were produced by extrusion. The presence of nanoparticles during the extrusion process led to a higher degree of starch gelatinization improving starch compatibility with PBAT. Nanoparticles modified the interaction between the different components of the PBAT/TPS composite. The hydroxyl groups of the starch nanoparticles interacted with starch amylose by means of hydrogen bonds. In addition, nanoparticles modified the structure of the PBAT rigid segment (BT): a shift of Tm of BT toward lower temperatures and a slight shift of the relaxation of the BT segment to higher temperatures were observed. The incorporation of nanoparticles also had a reinforcing effect on the PBAT/TPS matrix. The composite presented slight increases of Young's modulus (E) and stress at break (σb) without affecting the strain at break (ϵb). The rate of biodegradability was improved with the use of starch nanoparticles. The composite showed faster deterioration than the matrix, showing the first changes in its tonality and breakdowns at only 6 days of burial in compost. © 2016 Society of Chemical Industry
Aspergillus infection monitored by multimodal imaging in a rat model
Authors: Pluhacek Tomas , Petrik Milos , Luptakova Dominika , Benada Oldrich , Palyzova Andrea , Lemr Karel , Havlicek Vladimir
Published: April 2016

Although myriads of experimental approaches have been published in the field of fungal infection diagnostics, interestingly, in 21st century there is no satisfactory early noninvasive tool for Aspergillus diagnostics with good sensitivity and specificity. In this work, we for the first time described the fungal burden in rat lungs by multimodal imaging approach. The Aspergillus infection was monitored by positron emission tomography and light microscopy employing modified Grocott's methenamine silver staining and eosin counterstaining. Laser ablation inductively coupled plasma mass spectrometry imaging has revealed a dramatic iron increase in fungi‐affected areas, which can be presumably attributed to microbial siderophores. Quantitative elemental data were inferred from matrix‐matched standards prepared from rat lungs. The iron, silver, and gold MS images collected with variable laser foci revealed that particularly silver or gold can be used as excellent elements useful for sensitively tracking the Aspergillus infection. The limit of detection was determined for both 107Ag and 197Au as 0.03 μg/g (5 μm laser focus). The selective incorporation of 107Ag and 197Au into fungal cell bodies and low background noise from both elements were confirmed by energy dispersive X‐ray scattering utilizing the submicron lateral resolving power of scanning electron microscopy. The low limits of detection and quantitation of both gold and silver make ICP‐MS imaging monitoring a viable alternative to standard optical evaluation used in current clinical settings.
Understanding metabolism of arginine in biological systems via MALDI imaging
Authors: Walker Heather J. , Steels Chloe , Bendell Lilias , Clench Malcolm R. , Read David J. , Cameron Duncan D. , Burrell Michael M.
Published: April 2016

Arginine is an important amino acid but has been barely studied in plants. The little research that has been done indicates that the pathways of synthesis are similar to those found in animals and procaryotes. However little is known about the cellular and tissue localization of the amino acid in plants. The research reported in this paper was designed to examine whether MALDI‐MSI was sufficiently sensitive to examine the distribution of this amino acid in plant material, and whether the synthetic pathways were co‐located. In wheat and orchid roots, the amount of arginine in tissues varies greatly and the pathways for its synthesis were not always detected with the amino acid.
Precision ADMET polyolefins containing dithiane: Synthesis, thermal properties, and macromolecular transformation
Authors: Song Shaofei , He Feng , Fu Zhisheng , Xu Junting , Fan Zhiqiang
Published: April 2016

1,3‐Dithiane and its derivatives are widely used as powerful acyl anion equivalent to a range of useful transformations that are needed in the synthesis of natural products. In this work, a series of polyolefins containing pendant dithiane groups have been designed and synthesized via acyclic diene metathesis polymerization (ADMET) polymerization and subsequent hydrogenation. The structures of these polymers were characterized by 1H NMR, 13C NMR, and FT‐IR, and successful incorporation of the dithiane groups was proved. With different contents of the dithiane moieties, these ADMET polymers exhibited distinct thermal properties different from each other as evidenced by differential scanning calorimetry and thermal gravimetric analysis. The dithiane units in the ADMET polymer with 20 methylene carbons between the adjacent dithiane groups were transformed into thiol groups via reaction with Bu3SnH. This work provided a convenient route to synthesize polyethylene with pendant thiol groups that are evenly distributed in the chain. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2468–2475
Inequalities in long term health‐related quality of life between partnered and not partnered breast cancer survivors through the mediation effect of social support
Authors: Leung Janni , Smith Michelle D. , McLaughlin Deirdre
Published: April 2016

Objective

To compare long‐term quality of life outcomes by marital status among women living with breast cancer, and to test the mediation effects of social support as an underlying factor.

Methods

Data are drawn from 1996 to 2010 of the Australian Longitudinal Study on Women's Health. The sample included 505 women with breast cancer with six years of follow‐up data. Social support was measured by the Medical Outcomes Study Social Support Survey (MOS‐SSS). Physical and mental health‐related quality of life (HRQOL) was measured using the Short‐Form Health Survey (SF‐36).

Results

Breast cancer survivors who did not have a partner, compared to those who had a partner, had significantly lower levels of social support, which was associated with poorer HRQOL. Social support mediated the relationship between not having a partner and poorer HRQOL. Results were consistent after taken into consideration socio‐demographic characteristics, which included age, highest level of education, country of birth, and area of residence.

Conclusions

Women recovering from breast cancer who do not have partners have poorer physical and mental HRQOL, than those with partners, with a lack of social support as an underlying inequality. Partners of breast cancer survivors are importance sources in the provision of social support to help them maintain well‐being and quality of life.

Copyright © 2016 John Wiley & Sons, Ltd.
A Bayesian hierarchical surrogate outcome model for multiple sclerosis
Authors: Pozzi Luca , Schmidli Heinz , Ohlssen David I.
Published: April 2016

The development of novel therapies in multiple sclerosis (MS) is one area where a range of surrogate outcomes are used in various stages of clinical research. While the aim of treatments in MS is to prevent disability, a clinical trial for evaluating a drugs effect on disability progression would require a large sample of patients with many years of follow‐up. The early stage of MS is characterized by relapses. To reduce study size and duration, clinical relapses are accepted as primary endpoints in phase III trials. For phase II studies, the primary outcomes are typically lesion counts based on magnetic resonance imaging (MRI), as these are considerably more sensitive than clinical measures for detecting MS activity. Recently, Sormani and colleagues in ‘Surrogate endpoints for EDSS worsening in multiple sclerosis’ provided a systematic review and used weighted regression analyses to examine the role of either MRI lesions or relapses as trial level surrogate outcomes for disability. We build on this work by developing a Bayesian three‐level model, accommodating the two surrogates and the disability endpoint, and properly taking into account that treatment effects are estimated with errors. Specifically, a combination of treatment effects based on MRI lesion count outcomes and clinical relapse was used to develop a study‐level surrogate outcome model for the corresponding treatment effects based on disability progression. While the primary aim for developing this model was to support decision‐making in drug development, the proposed model may also be considered for future validation. Copyright © 2016 John Wiley & Sons, Ltd.
A radiofrequency system for in vivo hyperpolarized 13C MRS experiments in mice with a 3T MRI clinical scanner
Authors: Giovannetti Giulio , Flori Alessandra , Marsigli Fabio , De Marchi Daniele , Frijia Francesca , Giannoni Massimo , Kusmic Claudia , Positano Vincenzo , Aquaro Giovanni Donato , Menichetti Luca
Published: April 2016

Hyperpolarized carbon‐13 magnetic resonance spectroscopy (MRS) is a powerful tool to explore tissue metabolic state, by permitting the study of intermediary metabolism of biomolecules in vivo. However, a number of technological problems still limit this technology and need innovative solutions. In particular, the low molar concentration of derivate metabolites give rise to low signal‐to‐noise ratio (SNR), which makes the design and development of dedicated radiofrequency (RF) coils a fundamental task. In this article, the authors describe the simulation and the design of a RF coils configuration for MR experiments in mice, constituted by a 1H whole body volume RF coil for imaging and a 13C single circular loop surface RF coil for performing 13C acquisitions. After the building, the RF system was employed in an in vivo experiment in a mouse injected with hyperpolarized [1‐13C]pyruvate by using a 3 T clinical MR scanner. SCANNING 38:710–719, 2016. © 2016 Wiley Periodicals, Inc.
Compositional, structural and optical changes of polyimide irradiated by heavy ions
Authors: Mikšová R. , Macková A. , Cutroneo M. , Slepička P. , Matoušek J.
Published: April 2016

Polyimide (PI, (C22H10O5N2)n) foil, 8 µm thick, was irradiated with 9.6‐MeV C4+ and O4+ ions at fluences of 1010–1013 cm−2. Compositional and structural changes related to the ion species, ion irradiation fluence and the type of polymer were studied and discussed in connection with energy‐loss measurement. The knowledge of these changes of polymers after the irradiation is very important for the estimation of the influence of these effects on the experimentally determined ion‐energy losses. Rutherford back‐scattering (RBS) and elastic recoil detection analysis (ERDA) were used for the elemental composition study, atomic force microscopy (AFM) for the detection of the changes in surface roughness and UV–Visible spectral study (UV–Vis) for variation in the absorbance and the optical band gap. The chemical and structural changes, new radical appearance, and polymeric chain crosslinking especially at ion fluencies above 1013 cm−2 were observed and discussed in the frame of energy stopping experimental determination. Copyright © 2016 John Wiley & Sons, Ltd.
Child Adjustment to First Grade as Perceived by the Parents: The Role of Parents' Personal Growth
Authors: Ben Shlomo Shirley , Taubman‐Ben‐Ari Orit
Published: April 2016

The current study aimed at investigating the direct and moderating role of personal growth in a child's adjustment to first grade as perceived by the parents, drawing on Positive Psychology (Seligman & Csikszentmihalyi, ) and the theory of families as systems (Cox & Paley, ). The sample consisted of 280 Israeli parents (213 mothers and 67 fathers) whose children were in first grade. The participants completed questionnaires relating to background variables of the parent and child, as well as parents' perceived stress, emotional intelligence, perceived child's adjustment to school and personal growth.

The findings indicate that a child's entrance into the school system may lead to personal growth in the parents and that variables of both the parent (age and education) and the child (birth order) contribute to this process. Furthermore, among parents with a low level of personal growth, higher emotional intelligence was associated with a more positive assessment of the child's adjustment. The study thus demonstrates that the transition to first grade may serve as a lever for the parents' growth and development, which in turn may affect their perception of their child's adjustment to school. Copyright © 2016 John Wiley & Sons, Ltd.
High‐Efficiency Gene Transfection of Cells through Carbon Nanotube Arrays
Authors: Golshadi Masoud , Wright Leslie K. , Dickerson Ian M. , Schrlau Michael G.
Published: April 2016

Introducing nucleic acids into mammalian cells is a crucial step to elucidate biochemical pathways, and to modify gene expression and cellular development in immortalized cells, primary cells, and stem cells. Current transfection technologies are time consuming and limited by the size of genetic cargo, the inefficient introduction of test molecules into large populations of target cells, and the cytotoxicity of the techniques. A novel method of introducing genes and biomolecules into tens of thousands of mammalian cells has been developed through an array of aligned hollow carbon nanotubes, manufactured by template‐based nanofabrication processes, to achieve rapid high‐efficiency transfer with low cytotoxicity. The utilization of carbon nanotube arrays for gene transfection overcomes molecular weight limits of current technologies and can be adapted to deliver drugs or proteins in addition to nucleic acids.
Improving strength properties of recycled and virgin pulp mixtures with dry strength agents
Authors: Gulsoy Sezgin Koray , Erenturk Saduman
Published: April 2016

In the paper industry, the increasing use of recycled fibers as a substitute for virgin fibers has resulted in decreased strength properties. In this study, old corrugated container fibers were added in different ratios to virgin kraft fibers, and the effects on paper properties were investigated. Furthermore, 0.75% cationic starch and 0.75% Luredur® with respect to oven‐dry fibers were added separately to old corrugated container fiber‐containing/fiber‐free suspensions, and the effects on handsheet strength properties were determined. Starch is the oldest and most common additive for improving the strength of paper. Luredur®, a cationic polymer‐based vinyl amine and N‐vinylformamide, is used for the same purpose in papermaking. Results indicated that, except for the tear index, old corrugated container fiber addition decreased handsheet strength properties in the agent‐free samples. The cationic starch addition was more efficient than the Luredur® with regard to tensile index, stretch, tensile energy absorption, and burst index. However, the effect of Luredur® on the tear index was more pronounced compared to that of the cationic starch. Consequently, comparable handsheets strength was achieved in the 100% virgin and dry strength additive‐free fibers with the addition of 0.75% cationic starch to a suspension containing 20% old corrugated containers and 80% virgin fiber.
National Security Export Control Regimes: Determinants and Effects on International Business
Authors: Seyoum Belay
Published: April 2016

Countries restrict exports for a number of reasons ranging from national security, foreign policy to the preservation of scarce resources. Most of the restrictions are imposed on military and high‐technology products. This article focuses on national security controls exercised on dual‐use goods, that is, commercial products with current or potential military applications. The article develops a typology of paradigms for national export control regimes: high state–low business, low state–high business, high state–high business, and low state–low business. It then introduces a theoretical model of the economic and political determinants and effects of such paradigms. The study presents national case studies and examines the effects of the four paradigms on international business. The article fills important gaps in our understanding of national export control regimes and their implications for managers of international business firms. © 2016 Wiley Periodicals, Inc.
Selective intrauterine growth restriction in monochorionic twins: changing patterns in umbilical artery Doppler flow and outcomes
Authors: Rustico M. A. , Consonni D. , Lanna M. , Faiola S. , Schena V. , Scelsa B. , Introvini P. , Righini A. , Parazzini C. , Lista G. , Barretta F. , Ferrazzi E.
Published: April 2016

Objectives

To describe changes in umbilical artery (UA) Doppler flow in monochorionic diamniotic (MCDA) twins affected by selective intrauterine growth restriction (sIUGR), to correlate Doppler findings with pregnancy course and perinatal outcome, and to report postnatal follow‐up.

Methods

This was a retrospective study of 140 MCDA twins with sIUGR. UA end‐diastolic flow, defined as Doppler waveform pattern Type I (persistently positive), Type II (persistently absent or persistently reversed) or Type III (intermittently absent or intermittently reversed), was recorded at first examination and monitored weekly until double or single intrauterine fetal death (IUFD), bipolar cord coagulation or delivery. All neonates had an early neonatal brain scan, magnetic resonance imaging, when indicated, and neurological assessment during infancy. Rates (per 100 person‐weeks) and hazard ratios (HR) of IUFD in the IUGR twin in each pregnancy were calculated considering UA Doppler pattern as a time‐dependent variable.

Results

At first examination, there were 65 cases with UA Doppler waveform pattern Type I, 62 with Type II and 13 with Type III. Of the 65 Type‐I cases, 48 (74%) remained stable, while 17 (26%) changed to either Type II absent (14%), Type II reversed (9%) or Type III (3%). Of 62 Type‐II cases (47 with absent and 15 with reversed flow), 33 (53%) remained stable (18 with absent and all 15 with reversed flow). The 29 Type‐II absent cases which changed became Type II reversed (24/47, 51%) or Type III (5/47, 11%). All 13 Type‐III cases remained stable. Compared with Type I, the risk of IUFD (adjusted for estimated fetal weight discordance and amniotic fluid deepest vertical pocket) was highest when the pregnancy was or became Type II reversed (HR, 9.5; 95% CI, 2.7–32.7) or Type II absent (HR, 4.3; 95% CI, 1.3–14.3). Mild neurological impairment was more prevalent in the IUGR twin than in the large cotwin (7%vs1%,P= 0.02).

Conclusions

Risk stratification based on UA Doppler is useful for planning ultrasound surveillance. However, patterns can change over time, with important consequences for management and outcome. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.
The importance of landscape diversity for carbon fluxes at the landscape level: small‐scale heterogeneity matters
Authors: Premke Katrin , Attermeyer Katrin , Augustin Jürgen , Cabezas Alvaro , Casper Peter , Deumlich Detlef , Gelbrecht Jörg , Gerke Horst H. , Gessler Arthur , Grossart Hans‐Peter , Hilt Sabine , Hupfer Michael , Kalettka Thomas , Kayler Zachary , Lischeid Gunnar , Sommer Michael , Zak Dominik
Published: April 2016

Landscapes can be viewed as spatially heterogeneous areas encompassing terrestrial and aquatic domains. To date, most landscape carbon (C) fluxes have been estimated by accounting for terrestrial ecosystems, while aquatic ecosystems have been largely neglected. However, a robust assessment of C fluxes on the landscape scale requires the estimation of fluxes within and between both landscape components. Here, we compiled data from the literature on C fluxes across the air–water interface from various landscape components. We simulated C emissions and uptake for five different scenarios which represent a gradient of increasing spatial heterogeneity within a temperate young moraine landscape: (I) a homogeneous landscape with only cropland and large lakes; (II) separation of the terrestrial domain into cropland and forest; (III) further separation into cropland, forest, and grassland; (IV) additional division of the aquatic area into large lakes and peatlands; and (V) further separation of the aquatic area into large lakes, peatlands, running waters, and small water bodies These simulations suggest that C fluxes at the landscape scale might depend on spatial heterogeneity and landscape diversity, among other factors. When we consider spatial heterogeneity and diversity alone, small inland waters appear to play a pivotal and previously underestimated role in landscape greenhouse gas emissions that may be regarded as C hot spots. Approaches focusing on the landscape scale will also enable improved projections of ecosystems’ responses to perturbations, e.g., due to global change and anthropogenic activities, and evaluations of the specific role individual landscape components play in regional C fluxes. WIREs Water 2016, 3:601–617. doi: 10.1002/wat2.1147

This article is categorized under:

Water and Life > Nature of Freshwater Ecosystems

Science of Water > Water and Environmental Change

Science of Water > Water Quality
Synthesis, Structure, and Magnetic Properties of a Series of Dinuclear Lanthanide Complexes Assembled by Acetate and a Schiff Base Ligand
Authors: Yang Shanshan , Li Bo , Qin Yongjie , Liu Long , Chen Zilu
Published: April 2016

Five dinuclear lanthanide complexes [Ln2L2(NO3)2(OAc)4]·2CH3CN [Ln = Gd (1), Tb (2), Dy (3), Ho (4), and Er (5)] [L = 2‐((2‐pyridinylmethylene)hydrazine)ethanol] were synthesized from the reactions of Ln(NO3)3·6H2O with L and CH3COOH in the presence of triethylamine. Their crystal structures were determined. They show similar dinuclear cores with the two lanthanide ions bridged by four acetate ligands in the μ2‐η1:η2 and μ2‐η1:η1 bridging modes. Each LnIII ion in complexes 1–5 is further chelated by one L ligand and one nitrate ion, leading to the formation of a nine‐coordinated mono‐capped square antiprism arrangement. The dinuclear molecules in 1–5 are consolidated by hydrogen bonds and π···π stacking interactions to build a two‐dimensional sheet. Their magnetic properties were investigated. It revealed antiferromagnetic interactions between the GdIII ions in 1 and ferromagnetic interactions between the TbIII ions in 2. The profiles of χmT vs. T curves of 3–5 reveal that the magnetic properties of 3–5 are probably dominated by the thermal depopulation of the Stark sublevels of LnIII ions.
Activating stereotypes with brand imagery: The role of viewer political identity
Authors: Angle Justin W. , Dagogo‐Jack Sokiente W. , Forehand Mark R. , Perkins Andrew W.
Published: April 2016

The use of ethnic imagery in visual identities of brands, such as those used by professional sports franchises, has long been a contentious issue in American society. This research investigates the oft‐voiced argument that ethnic brand imagery perpetuates negative stereotypes (a claim that has been subject to very little empirical scrutiny) and identifies conditions under which encountering such brand imagery strengthens both positive and negative implicit stereotypes. Within the context of American Indian brand imagery, two laboratory experiments (Studies 1 and 2) and a quasi‐experimental field study (Study 3) revealed that the effects of ethnic brand imagery on stereotypes depend on the viewer's political identity. Exposure to ethnic brand imagery strengthened implicit stereotypes only among more liberal individuals, consistent with the idea that liberals tend to hold more malleable views. These findings demonstrate measurable negative effects of ethnic brand imagery on implicit stereotypes and support the view that the use of such imagery can carry detrimental societal consequences.
Memdock: an α-helical membrane protein docking algorithm
Authors: Hurwitz Naama , Schneidman-Duhovny Dina , Wolfson Haim J.
Published: April 2016

Motivation: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR spectroscopy analyses. All the more so, there is only a small number of membrane protein–protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial. Numerous methods for docking globular proteins exist, however few have been developed especially for membrane proteins and designed to address docking within the lipid bilayer environment.

Results: We present a novel algorithm, Memdock, for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment for docking as well as for refining and ranking the docking candidates. We show that our algorithm improves both the docking accuracy and the candidates ranking compared to a standard protein–protein docking algorithm.

Availability and Implementation:  http://bioinfo3d.cs.tau.ac.il/Memdock/

Contacts:  namih@tau.ac.il or wolfson@tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Efficient identification and analysis of chemical exchange in biomolecules by R1ρ relaxation dispersion with Amaterasu
Authors: Walinda Erik , Morimoto Daichi , Nishizawa Mayu , Shirakawa Masahiro , Sugase Kenji
Published: April 2016

Summary: We introduce here a novel acquisition and processing methodology for cross-polarization based 1D rotating-frame relaxation dispersion NMR experiments. This easy-to-use protocol greatly facilitates the screening, acquisition, processing and model fitting of large on- and off-resonance R1ρ relaxation dispersion NMR datasets in an automated manner for the analysis of chemical exchange phenomena in biomolecules.

Availability and Implementation: The Amaterasu package including the spreadsheet, Bruker pulse programs and analysis software is available at www.moleng.kyoto-u.ac.jp/∼moleng_01/amaterasu.

Contact: sugase@moleng.kyoto-u.ac.jp
Nucleosome fragility is associated with future transcriptional response to developmental cues and stress inC. elegans
Authors: Jeffers Tess E. , Lieb Jason D.
Published: April 2016

Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone-DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. Here, we explored the functional implications of nucleosome properties on gene expression and development inC. elegansembryos. We performed a time-course of micrococcal nuclease (MNase) digestion, and measured the relative sensitivity or resistance of nucleosomes throughout the genome. Fragile nucleosomes were defined by nucleosomal DNA fragments recoverable preferentially in early MNase-digestion time points. We found fragile nucleosomes at locations where we expected to find destabilized nucleosomes, like transcription factor binding sites where nucleosomes compete with DNA-binding factors. Contrary to our expectation, the presence of fragile nucleosomes in gene promoters was anti-correlated with transcriptional activity. Instead, genes with fragile nucleosomes in their promoters tended to be expressed in a context-specific way, operating in neuronal response, the immune system, and stress response. Nucleosome fragility at these promoters was strongly and positively correlated with the AT content of the underlying DNA. There was not a strong correlation between promoter nucleosome fragility and the levels of histone modifications or histone variants. Our data suggest that inC. eleganspromoters, nucleosome fragility is primarily a DNA-encoded feature that poises genes for future context-specific activation in response to environmental stress and developmental cues.
Analysis of clinicalBordetella pertussisisolates using whole genome sequences reveals novel genomic regions associated with recent outbreaks in the United States of America
Authors: Otero Glen , Althouse Benjamin M. , Scarpino Samuel V.
Published: April 2016

Background:

Despite high-levels of vaccination, whooping cough, primarily caused by Bordetella pertussis (BP), has persisted and resurged. It remains a major cause of infant death worldwide and is the most prevalent vaccine-preventable disease in developed countries. To date, most genomic studies have focused on a small subset of the BP genome, biasing our clinical understanding and public health awareness.

Methods:

We performed a Genome-Wide Association Study (GWAS) on 76 U.S. BP whole genomes, including strains from recent outbreaks.

Results:

A GWAS of the 76 BP isolates revealed a sharp increase in genetic variation associated with the Minnesota 2012 outbreak and identified 52 variants unique to the Minnesota outbreak and 19 unique to the California and Washington outbreaks. None of the identified variants were shared between the outbreaks and the vast majority were previously uncharacterized. We further identified variation associated with pertactin negative strains and acellular vaccination.

Conclusions:

We identified novel genomic regions associated with recent BP outbreaks. Our results underscore the need for increased whole genome sequencing of BP isolates, which can reduce costly misdiagnosis and improve surveillance. The genes containing these variants warrant further investigation into their possible roles in BP pathogenicity and the ongoing resurgence in the U.S.
The role of locally adapted mycorrhizas and rhizobacteria in plant–soil feedback systems
Authors: Revillini Daniel , Gehring Catherine A. , Johnson Nancy Collins
Published: April 2016

The plant–soil feedback (PSF) framework has become an important theory in plant ecology, yet many ecological and evolutionary factors that influence PSFs have yet to be fully considered. Here, we discuss the importance of local adaptation among plants and root‐associated fungi and bacteria. Furthermore, we show how inclusion of the optimal resource allocation (OA) model can help predict the direction and outcome of PSFs under environmental change.

Plants and associated soil microbes have co‐evolved for millennia, generating adaptations to each other and to their local environment. This local co‐adaptation is likely generated by a suite of multidirectional exchanges of goods and services among plants, fungi and bacteria, and the constant changes in above‐ground–below‐ground interactions.

Resource limitation may be a driver of local adaptation among organisms involved in nutritional symbioses. The OA model states that when an essential resource is limited, natural selection will favour taxa that forage optimally by adjusting their biomass and energy allocation such that productivity is equally limited by all resources. Co‐adaptation will therefore respond to the local limiting resource conditions through taxa‐specific resource transfer interactions.

The OA model can help predict the outcomes of PSFs across a range of resource gradients and environmental changes such as increasing drought or atmospheric nitrogen deposition. Positive feedback is predicted in systems where resource exchange among plants and associated soil microbes can ameliorate resource limitation, or in systems where microbes provide another important service such as pathogen defence. Feedback strength is expected to diminish as resources become less limiting. Negative feedback is predicted when resources are in luxury supply and populations of opportunistic plant pathogens increase relative to commensal or mutualist microbes.

Future, field‐based studies that integrate naturally co‐occurring systems of plants, microbes and their local soil are needed to further test the hypothesis that resource availability is an effective predictor of the direction and magnitude of PSFs. A more mechanistic understanding of PSFs will help land managers and farmers to manipulate plant–microbial soil interactions to respond to environmental change and to effectively harness beneficial symbioses for plant nutrition and pathogen control.
Merging evolutionary history into species interaction networks
Authors: Peralta Guadalupe
Published: April 2016

The occurrence of complex networks of interactions among species not only relies on species co‐occurrence, but also on inherited traits and evolutionary events imprinted in species phylogenies. The phylogenetic signal found in ecological networks suggests that evolution plays an important role in determining community assembly and hence could inform about the underpinning mechanisms.

The aim of this study was to review the main findings and methodological approaches used for detecting phylogenetic signal in species interaction networks, particularly in different aspects of network structure: conservatism of interactions, modularity, connectivity and nestedness.

In general, studies show that species phylogenies determine interacting partners, module composition, species roles and nested patterns, although these influences are not always consistent across different interaction types. The relative importance of phylogeny to network structure, as well as the scale dependence of phylogenetic signal, denotes key areas for future research.

Phylogenetically informed network ecology represents a promising field for understanding species interaction patterns, community assembly processes and dynamics. It can also provide important information for predicting community changes and improving management practices.

Alay summaryis available for this article.
Foraging modality and plasticity in foraging traits determine the strength of competitive interactions among carnivorous plants, spiders and toads
Authors: Jennings David E. , Krupa James J. , Rohr Jason R.
Published: April 2016

Foraging modalities (e.g. passive, sit‐and‐wait, active) and traits are plastic in some species, but the extent to which this plasticity affects interspecific competition remains unclear.

Using a long‐term laboratory mesocosm experiment, we quantified competition strength and the plasticity of foraging traits in a guild of generalist predators of arthropods with a range of foraging modalities.

Each mesocosm contained eight passively foraging pink sundews, and we employed an experimental design where treatments were the presence or absence of a sit‐and‐wait foraging spider and actively foraging toad crossed with five levels of prey abundance. We hypothesized that actively foraging toads would outcompete the other species at low prey abundance, but that spiders and sundews would exhibit plasticity in foraging traits to compensate for strong competition when prey were limited.

Results generally supported our hypotheses. Toads had a greater effect on sundews at low prey abundances, and toad presence caused spiders to locate webs higher above the ground. Additionally, the closer large spider webs were to the ground, the greater the trichome densities produced by sundews. Also, spider webs were larger with than without toads and as sundew numbers increased, and these effects were more prominent as resources became limited. Finally, spiders negatively affected toad growth only at low prey abundance.

These findings highlight the long‐term importance of foraging modality and plasticity of foraging traits in determining the strength of competition within and across taxonomic kingdoms. Future research should assess whether plasticity in foraging traits helps to maintain coexistence within this guild and whether foraging modality can be used as a trait to reliably predict the strength of competitive interactions.
Phylogenetic community structure of North American desert bats: influence of environment at multiple spatial and taxonomic scales
Authors: Patrick Lorelei E. , Stevens Richard D.
Published: April 2016

Numerous processes influence community structure. The relative importance of these processes is thought to vary with spatial, temporal and taxonomic scales: density‐dependent interactions are thought to be most important at small scales; at intermediate scales, environmental conditions may be the most influential factor; and biogeographic processes are thought to be of greater importance at larger scales. Additionally, the stress‐dominance hypothesis suggests that communities experiencing harsher environmental conditions will be predominantly structured by habitat filtering, whereas communities experiencing more favourable conditions will be structured predominantly by density‐dependent interactions such as competition.

The aim of this study was to investigate the influence of environmental factors on phylogenetic community structure (PCS) of North American desert bats at multiple spatial and taxonomic scales. We also examined whether the stress‐dominance hypothesis is upheld in desert bats across an environmental gradient.

Phylogenetic community structure metrics were calculated using species pools that differed in spatial (from all deserts to individual deserts) and taxonomic (all bat taxa, a single family and a single genus) scales. We calculated mean temperature, precipitation and seasonality for each site to determine whether environmental gradients were related to degree of community structure.

At the largest spatial and taxonomic scales, communities were significantly phylogenetically clustered while degree of clustering decreased at the smallest spatial and taxonomic scales. Climatic data, particularly mean temperature and temperature seasonality, were important predictors of PCS at larger scales and under harsher conditions, but at smaller scales and in less stressful conditions there was a weaker relationship between PCS and climate.

This suggests that North American deserts, while harsh, are not uniform in the challenges they present to the faunas residing in them. Overall, the relationship between PCS and climatic data at large spatial and taxonomic scales, and in harsher conditions, suggests the influence of habitat filtering has been important in North American desert bat community assembly and that other processes have been important at smaller scales.
Effects of fire on pollinators and pollination
Authors: Brown Julian , York Alan , Christie Fiona , McCarthy Michael
Published: April 2016

Increased incidence of landscape fire and pollinator declines with co‐extinctions of dependent plant species are both globally significant. Fire can alter species distributions, but its effects on plant–pollinator interactions are poorly understood so its present and future role in coupled plant–pollinator declines cannot be assessed.

We develop a conceptual model of fire effects on plant–pollinator interactions. We review the empirical literature in the context of this model to identify important knowledge gaps regarding the processes underlying these effects and the phenotypic traits of flowering plants and pollinators mediating these effects. Fire generates, and plant–pollinator interactions respond to, heterogeneity at multiple spatial scales. There is evidence of local‐scale fire effects on these interactions, but landscape‐scale effects are poorly understood. Nest location and floral resource utilization primarily mediate pollinator survival during and after fire. Voltinism and mobility traits are potentially important, but poorly studied. Plant traits mediating flowering responses to fire include growth form, phenology and potentially bud location, seasonal changes in bud exposure and response to bud damage.

Synthesis and applications. We suggest management actions and an agenda for future research to fill knowledge gaps currently inhibiting predictions of fire effects on plant–pollinator interactions. Fire regimes promoting floral diversity at local scales provide a surrogate means of managing pollinators and pollination while empirical research continues. Above‐ground nesting, univoltine pollinators may be particularly vulnerable under expected fire regime changes. Improved knowledge of traits mediating the exploitation of landscape heterogeneity could be used to enhance the persistence of these species. Ultimately, our conceptual framework could be used as a basis for understanding fire effects on aggregate network properties to inform fire management strategies buffering plant–pollinator networks against secondary species extinctions.