bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity
Authors: Pasetto Matteo , Antignani Antonella , Ormanoglu Pinar , Buehler Eugen , Guha Rajarshi , Pastan Ira , Martin Scott E. , FitzGerald David J.
Published: February 2015

Significance

To increase understanding of how antibody–toxin fusion proteins (immunotoxins) kill cells, we used RNAi, striving to reduce the expression level of all human genes. Some RNAi treatments resulted in resistance to immunotoxins and some caused increased sensitivity. We focused on target genes that caused cells to be more immunotoxin-sensitive. Results highlight genes that naturally protect cells from the action of immunotoxins. Of interest, many of these genes encode proteins that reside in the endoplasmic reticulum and Golgi, and are part of the cell’s secretion system. Should these gene products be amenable to regulation via small molecular drugs, enhancement of killing might be possible via chemical intervention.
Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy
Authors: Deshmukh Lalit , Ghirlando Rodolfo , Clore G. Marius
Published: February 2015

Significance

The late stages of the HIV-1 life cycle are governed by the Gag polyprotein (also known as group specific antigen). Here we use modern solution NMR methods to probe the structure and conformation of Gag. We show that Gag exists in a dynamic monomer–dimer equilibrium in solution and its structured domains reorient semi-independently of one another. We monitor proteolytic processing of Gag by HIV-1 protease in real-time, and show that the conformational transition at the N-terminus of the capsid domain from a random coil to a β-hairpin upon cleavage at the matrix|capsid junction occurs five times faster than cleavage at the capsid|spacer peptide 1 junction. These results provide insights into the HIV-1 life cycle that may lead to the development new antiretroviral strategies.
The Impact of Egg Ozonation on Hatching Success, Larval Growth, and Survival of Atlantic Cod, Atlantic Salmon, and Rainbow Trout
Authors: Fry Jessica , Casanova Juan Pérez , Hamoutene Dounia , Lush Lynn , Walsh Andy , Couturier Cyr
Published: February 2015

The direct exposure of fish eggs to ozonated water has generated interest as a means of ensuring pathogen-free eggs without the use of harsh chemicals. However, there are numerous knowledge gaps, including safe contact times, exposure levels, and potential long-term effects on aquaculture species in both freshwater and seawater. The effect of different ozone (O3) doses (0.5–1.0, 1.5–2.0, and 2.5–3.0 mg of O3/L for 90 s) on recently fertilized eggs of Atlantic Cod Gadus morhua and eyed eggs of Atlantic Salmon Salmo salar and Rainbow Trout Oncorhynchus mykiss was evaluated in comparison with the effects of two commercial disinfectants: Perosan (0.004 mg/L) and Ovadine (100 mg/L). The impact of ozone application was evaluated based on hatching success, larval nucleic acid concentration, larval growth, and survival. Overall, results indicated that ozonation of Atlantic Cod eggs at a dose less than 3.0 mg/L for 90 s produced no negative effect on the larvae up to 30 d posthatch. Furthermore, ozonation of Atlantic Salmon and Rainbow Trout eggs generated no negative effect on the larvae, based on monitoring until 85% yolk sac re-absorption (16 d posthatch).

Received May 6, 2014; accepted October 24, 2014
NICTABA and UDA, two GlcNAc-binding lectins with unique antiviral activity profiles
Authors: Gordts Stephanie C. , Renders Marleen , Férir Geoffrey , Huskens Dana , Van Damme Els J. M. , Peumans Willy , Balzarini Jan , Schols Dominique
Published: February 2015

Objectives

This study aimed to assess the antiviral properties of a unique lectin (NICTABA) produced by the tobacco plant, Nicotiana tabacum.

Methods

Cellular assays were used to investigate the antiviral activity of NICTABA and Urtica dioica agglutinin (UDA). Surface plasmon resonance (SPR) studies were performed to study the sugar specificity and the interactions of both lectins with the envelope glycoproteins of HIV-1.

Results

The N-acetyl-d-glucosamine (GlcNAc)-binding lectins exhibited broad-spectrum activity against several families of enveloped viruses including influenza A/B, Dengue virus type 2, herpes simplex virus types 1 and 2 and HIV-1/2. The IC50 of NICTABA for various HIV-1 strains, clinical isolates and HIV-2 assessed in PBMCs ranged from 5 to 30 nM. Furthermore, NICTABA inhibited syncytium formation between persistently HIV-1-infected T cells and uninfected CD4+ T lymphocytes and prevented DC-SIGN-mediated HIV-1 transmission to CD4+ target T lymphocytes. However, unlike many other antiviral carbohydrate-binding agents (CBAs) described so far, NICTABA did not block HIV-1 capture to DC-SIGN+ cells and it did not interfere with the binding of the human monoclonal antibody 2G12 to gp120. SPR studies with HIV-1 envelope glycoproteins showed that the affinity of NICTABA for gp120 and gp41 was in the low nanomolar range. The specific binding of NICTABA to gp120 could be prevented in the presence of a GlcNAc trimer, but not in the presence of mannose trimers. NICTABA displayed no antiviral activity against non-enveloped viruses.

Conclusions

Since CBAs possess a high genetic barrier for the development of viral resistance and NICTABA shows a broad antiviral activity profile, this CBA may qualify as a potential antiviral candidate with a pleiotropic mode of action aimed at targeting the entry of enveloped viruses.
Solvent-vapour-assisted pathways and the role of pre-organization in solid-state transformations of coordination polymers
Authors: Wright James S. , Vitórica-Yrezábal Iñigo J. , Adams Harry , Thompson Stephen P. , Hill Adrian H. , Brammer Lee
Published: February 2015

A family of one-dimensional coordination polymers, [Ag4(O2C(CF2)2CF3)4(phenazine)2(arene)n]·m(arene),1(arene = toluene or xylene), have been synthesized and crystallographically characterized. Arene guest loss invokes structural transformations to yield a pair of polymorphic coordination polymers [Ag4(O2C(CF2)2CF3)4(phenazine)2],2aand/or2b, with one- and two-dimensional architectures, respectively. The role of pre-organization of the polymer chains of1in the selectivity for formation of either polymorph is explored, and the templating effect of toluene andp-xylene overo-xylene orm-xylene in the formation of arene-containing architecture1is also demonstrated. The formation of arene-free phase2b, not accessible in a phase-pure form through other means, is shown to be the sole product of loss of toluene from1-tol·tol[Ag4(O2C(CF2)2CF3)4(phenazine)2(toluene)]·2(toluene), a phase containing toluene coordinated to Ag(I) in an unusual μ:η1,η1manner. Solvent-vapour-assisted conversion between the polymorphic coordination polymers and solvent-vapour influence on the conversion of coordination polymers1to2aand2bis also explored. The transformations have been examined and confirmed by X-ray diffraction, NMR spectroscopy and thermal analyses, includingin situdiffraction studies of some transformations.
Routine phasing of coiled-coil protein crystal structures withAMPLE
Authors: Thomas Jens M. H. , Keegan Ronan M. , Bibby Jaclyn , Winn Martyn D. , Mayans Olga , Rigden Daniel J.
Published: February 2015

Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The programAMPLEcan solve crystal structures by molecular replacement usingab initiosearch models in the absence of an existent homologous protein structure.AMPLEhas been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable byab initiomethodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both theab initiomodelling and the use of ensemble search models contribute to the success ofAMPLEby comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement withAMPLEshould be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore,AMPLEmay be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.
Corrosion protection of coatings doped with inhibitor-loaded nanocapsules
Authors: Khajouei Ahmad , Jamalizadeh Effat , Hosseini Seyed Mohammad Ali
Published: February 2015

Purpose

– The purpose of this paper was to study the corrosion resistance of AA2024 alloy using surfactant-modified halloysite nanocapsules capable of holding benzotriazole (BTA) as the corrosion inhibitor and discharging it into the solution.

Design/methodology/approach

– The effect of surfactant shells was studied by surfactant-modified halloysite nanotubes fabricated through assembly of two types of cationic surfactants. The zeta potential and size distribution measurements were performed using a Zetasizer Nano. The concentration of BTA during release into the solution was detected by using a UV–vis spectrophotometer. The anti-corrosion activity of nanocapsules as free agents with respect to the AA2024 alloy was investigated using the potentiodynamic scan (PDS) method. An epoxy resin doped with nanocapsules was used as an anti-corrosion coating deposited on the AA2024 alloy. The corrosion protection performance of coatings was studied by using the electrochemical impedance spectroscopy (EIS) method.

Findings

– The results indicate that the release of the inhibitor from nanocapsules depends on the surfactant shell components. The PDS results confirmed the feasibility of developing “smart” corrosion protection by inhibitor-loaded nanocapsules. The results of EIS measurements showed that the coating with the nanocapsules exhibited enhanced corrosion protection in comparison with the undoped coating.

Originality/value

– The findings of this paper indicate that surfactant-modified halloysite nanocapsules can be added to epoxy resin coatings to improve their corrosion protective properties for the AA2024 alloy.
An accelerated testing method for the evaluation of atmospheric corrosion resistance of weathering steels
Authors: Qian Yuhai , Xu Jingjun , Li Meishuan
Published: February 2015

Purpose

– The purpose of this paper is to present a laboratory accelerated periodic immersion wet/dry cyclic corrosion test, reflecting the alternate wet/dry process during the atmospheric exposure of metallic materials, which can be applied to evaluate the atmospheric corrosion resistance (ACR) of weathering steels in a very short period.

Design/methodology/approach

– This test method uses 0.01 M sodium bisulfite aqueous solution with pH 4.4 as the immersion medium, simulating the notable characteristics of sulfur dioxide pollutant in industrially polluted atmospheres. During the test process, the tested specimens are immersed into the solution for 12 minutes, immediately followed by the subsequent drying process for 48 minutes, and such alternate process consists of a cyclic period, i.e. 1 hour. As a result of this procedure, a relative corrosion rate is defined to determine the ACR. To determine a preferred test period, different test periods including 72 and 200 hours were compared.

Findings

– Compared with several other commonly used test methods, it was confirmed that the relative ACR of various steels can be determined after testing for only 72 hours. The constituent of the corrosion products, i.e. the rust layer, was consistent with that formed after long-term exposure in a typical outdoor atmospheric environment.

Originality/value

– The test method enables comparative testing for ranking the ACR of weathering steel during the development of new weathering steels.
Shaping gender inequalities: critical moments and critical places
Authors: Riano Yvonne , Limacher Katharina , Aschwanden André , Hirsig Sophie , Wastl-Walter Doris
Published: February 2015

Purpose

– There is much scientific interest in the connection between the emergence of gender-based inequalities and key biographical transition points of couples in long-term relationships. Little empirical research is available comparing the evolution of a couple’s respective professional careers over space and time. The purpose of this paper is to contribute to filling this gap by addressing the following questions: what are the critical biographical moments when gender (in)equalities within a relationship begin to arise and consolidate? Which biographical decisions precede and follow such critical moments? How does decision making at critical moments impact the opportunities of both relationship partners in gaining equal access to paid employment?

Design/methodology/approach

– These questions are addressed from the perspectives of intersectionality and economic citizenship. Biographical interviewing is used to collect the personal and professional narratives of Swiss-, bi-national and migrant couples. The case study of a Swiss-Norwegian couple illustrates typical processes by which many skilled migrant women end up absently or precariously employed.

Findings

– Analysis reveals that the Scandinavian woman’s migration to Switzerland is a primary and critical moment for emerging inequality, which is then reinforced by relocation (to a small town characterized by conservative gender values) and the subsequent births of their children. It is concluded that factors of traditional gender roles, ethnicity and age intersect to create a hierarchical situation which affords the male Swiss partner more weight in terms of decision making and career advancement.

Practical implications

– The paper’s findings are highly relevant to the formulation of policies regarding gender inequalities and the implementation of preventive programmes within this context.

Originality/value

– Little empirical research is available comparing the evolution of a couple’s respective professional careers over space and time. The originality of this paper is to fill this research gap; to include migration as a critical moment for gender inequalities; to use an intersectional and geographical perspective that have been given scant attention in the literature; to use the original concept of economic citizenship; and to examine the case of a bi-national couple, which has so far not been examined by the literature on couple relationships.
Recent developments in reflective cold protective clothing
Authors: Morrissey Matthew Patrick , Rossi René Michel
Published: February 2015

Purpose

– The purpose of this paper is to present some new results about reflective cold protective clothing (i.e. those featuring metal coatings), and compare and contrast the data with other recent research work.

Design/methodology/approach

– The authors used a thermal manikin and a guarded hot plate to determine the thermal resistance of different textile assemblies and garment featuring plasma-deposited metal-coated insulation and interlayers.

Findings

– Depending on the exact approach, the authors show that metal coatings can increase the thermal resistance of textile assemblies by ∼30-75 per cent.

Practical implications

– New data on reflective cold weather clothing show that metal coatings could be an important addition to cold weather clothing, especially those featuring high air permeability/optical porosity insulation. Plasma-deposited metal coatings cause the lowest increase in weight.

Originality/value

– This paper provides new data about the efficacy, in terms of thermal resistance, of metal coatings for cold weather clothing.
Light-emitting textile display with floats for electronics covering
Authors: Parkova Inese , Parkovs Ivars , Vilumsone Ausma
Published: February 2015

Purpose

– Flexible light-emitting textile display is designed with floats for electronic elements covering and electronic contacts insulation what at the same time provides an opportunity to develop aesthetic design of the display in the single piece construction of material. The paper aims to discuss these issues.

Design/methodology/approach

– Display consists of interwoven electrically conductive yarns, non-conductive yarns and SMD LEDs connected to conductive yarns. Industrial jacquard weaving machine have been used, weave patterns were designed in PC-Edit software.

Findings

– Weave can be used as a tool to build and evolve electrotextile. Exploring weaving techniques and perceiving electronic circuit as a weave pattern, new approaches can be developed in electrotextile design field.

Research limitations/implications

– Connections of electronic elements and conductive textile materials still is actual problem what should be explored in further research.

Practical implications

– Flexible light emitting textile display can be used as output interface integrated into communication clothing by representing different animated images directly on clothing. Display also can be used for accessories, room and auto interior etc. applications.

Originality/value

– Paper describes method of light source integration directly into textile structure, combining functional and visual design of textile display.
Investigating the sustainability of the Korean textile and fashion industry
Authors: Na Youngjoo , Na Dong Kyu
Published: February 2015

Purpose

– Fashion and textile industry has confronted to participate with the sustainable industry and society proactively not by the government regulations, but by the shareholders or consumers driven with corporate social responsibility. The purpose of this paper is to consider methods applied for the sustainability of products according to Korean domestic fashion and textile companies and clothing types and to investigate the limitation of current sustainability methods of companies.

Design/methodology/approach

– The study used document analysis and case studies of 396 companies. The study looked into newspapers, monthly magazines, and publications of fashion companies and internet web sites of almost every possible type that have been issued to date and analyzed the previous studies as well.

Findings

– The companies’ strategies are of three groups, the uses of environmental friendly materials: 36.9 percent (natural fibers, recycled fibers and biodegradable fibers), apparel reuse: 4.5 percent (remodeling/alteration and transform/combination with more materials), and eco-marketing promotions: 58.6 percent. For women’s and casual wear section, the methods used with organic materials and the green-campaign messages appeared frequently, while in the men’s wear section, coolMapsi, 0or warm OnMapsi for business wear did a lot for the low indoor energy consumption, such as no neck-tie in the hot season or wearing underwear in the cold season.

Originality/value

– Fashion and textile products have provided the key solutions for the generation’s happiness, identity, value, self-realization, health and role. There have been the low quality and similarity of fashion products from mass production and high speed and we should consider sustainability for the next generation and society. But the current problem in the industry is that most of eco-product developments are only short term. Also, from the high cost of eco materials and processes, there is a limited portion of sustainability section among total products and low design quality of fashion or the low profit outcomes.
Market response to land auction events: a transaction volume approach
Authors: Chiu Shuk Man , Chau Kwong Wing , Yau Yung
Published: February 2015

Purpose

– The purpose of this paper is to investigate the response of transaction volume in Hong Kong’s housing market to public land auctions.

Design/methodology/approach

– An event study approach with the use of regression analyses was adopted for the empirical study.

Findings

– Fewer pre-event transactions in the secondary housing spot market come with greater dispersion in the pre-event forecasts of land auction outcomes. Unexpected auction outcomes were also found to minify the post-event transaction volume in the secondary housing spot market, with negative unexpected outcomes exerting a stronger downward force.

Research limitations/implications

– These findings are contrary to the empirical evidence commonly found in most financial literature on stock transaction volume around corporate earnings announcements with an assumption of negligible transaction costs. Imperfect market structure, differences in sellers’ and buyers’ characteristics and short-sale restriction may explain the disparity.

Practical implications

– Price in the secondary housing market is more sensitive to negative unexpected land auction outcomes. The analysis results of the current study attest that the impact exerted by the negative unexpected auction outcomes on transaction volume in the housing spot market is stronger than that of positive unexpected auction outcomes.

Originality/value

– Unlike price and return, transaction volume has not received substantial academic attention in property research. In particular, within the existing small body of transaction volume research, the impact of information events on trading activities has been largely ignored.
Interest plurality and institutional work
Authors: Crawford Brett , Branch John
Published: February 2015

Purpose

– The institutional work literature has paid little attention to cognition and interests in the creation, maintenance, and disruption of institutions. The purpose of this paper is to explore the construct of interests as it relates to institutional work projects. The authors frame interests as recognitions situated within broader institutional meaning systems, with a specific focus on interest plurality.

Design/methodology/approach

– The authors conducted an 18-month ethnography exploring institutional work projects within a rural chamber of commerce. The authors aimed to understand how projects contributed to community survival on a micro-level and institutional change on a macro-level. Rural chambers of commerce represent a unique example of emergent public-private partnerships, challenging traditional commercial logics of chambers of commerce. The research design included qualitative data collection, coding, and analysis of field notes, interviews, and archival sources.

Findings

– Purposive action was grounded in the community inhabited by the rural chamber of commerce and not the institution itself. Recognized interests enabled nontraditional workers – public employees with newly founded and legitimate roles within the chamber – to pursue community-focussed projects. Change across the institution of chambers of commerce occurred because of the separated and aggregate projects spanning across rural communities.

Originality/value

– Recognized interests are a social, plural, and malleable phenomenon supporting situated agency and the co-creation activities embodied in institutional work projects. The authors contribute to the institutional work literature by introducing the idea of interest plurality and illustrating how the work of rural chambers of commerce captures contemporary forms of community organizing.
Space‐use behaviour of woodland caribou based on a cognitive movement model
Authors: Avgar Tal , Baker James A. , Brown Glen S. , Hagens Jevon S. , Kittle Andrew M. , Mallon Erin E. , McGreer Madeleine T. , Mosser Anna , Newmaster Steven G. , Patterson Brent R. , Reid Douglas E. B. , Rodgers Art R. , Shuter Jennifer , Street Garrett M. , Thompson Ian , Turetsky Merritt J. , Wiebe Philip A. , Fryxell John M.
Published: February 2015

Movement patterns offer a rich source of information on animal behaviour and the ecological significance of landscape attributes. This is especially useful for species occupying remote landscapes where direct behavioural observations are limited. In this study, we fit a mechanistic model of animal cognition and movement toGPSpositional data of woodland caribou (Rangifer tarandus caribou;Gmelin 1788) collected over a wide range of ecological conditions.

The model explicitly tracks individual animal informational state over space and time, with resulting parameter estimates that have direct cognitive and ecological meaning. Three biotic landscape attributes were hypothesized to motivate caribou movement: forage abundance (dietary digestible biomass), wolf (Canis lupus; Linnaeus, 1758) density and moose (Alces alces; Linnaeus, 1758) habitat. Wolves are the main predator of caribou in this system and moose are their primary prey.

Resulting parameter estimates clearly indicated that forage abundance is an important driver of caribou movement patterns, with predator and moose avoidance often having a strong effect, but not for all individuals. From the cognitive perspective, our results support the notion that caribou rely on limited sensory inputs from their surroundings, as well as on long‐term spatial memory, to make informed movement decisions. Our study demonstrates how sensory, memory and motion capacities may interact with ecological fitness covariates to influence movement decisions by free‐ranging animals.
Agricultural intensification and the functional capacity of soil microbes on smallholder African farms
Authors: Wood Stephen A. , Bradford Mark A. , Gilbert Jack A. , McGuire Krista L. , Palm Cheryl A. , Tully Katherine L. , Zhou Jizhong , Naeem Shahid
Published: February 2015

Fertilization may impact ecosystem processes that sustain agriculture, such as nutrient cycling, by altering the composition of soil microbial communities that regulate such processes. These processes are crucial to low‐input, smallholder tropical agriculture, which supports 900 million of the world's poorest people. Yet little is known about how efforts to increase crop yield on such farms will affect the capacity of soil microbial communities to carry out ecosystem processes.

We studied the diversity and functional capacity of microbial communities on smallholder farms in western Kenya. We measured functional capacity as the abundance of functional genes involved in several components of nutrient cycling as well as catabolism of multiple carbon substrates; taxonomic diversity was measured using metagenomic sequencing. Diversity and functional capacity were measured on short‐term, experimental mineral fertilizer addition plots and on actively managed farms that have maintained for at least seven years a management strategy of low mineral fertilization, high mineral fertilization, or high fertilization combined with legume rotations.

Soil bacterial diversity decreased with mineral fertilizer addition, with a community shift towards taxa that thrive in high‐resource conditions. This taxonomic response did not correspond with decreased microbial functional capacity. Instead, functional capacity was increased, along with yields, when fertilizers were combined with legume rotations that add organic matter to soil.

Policy implications. Mineral fertilizer use is associated with lower soil microbial diversity on smallholder farms, but not associated with changes in microbial functional capacity. Functional capacity is highest, along with yields, when mineral fertilizers are paired with legume rotations. Our findings suggest that this type of agroforestry can be an important strategy for maintaining the long‐term functional capacity of soil microbes as well as increasing crop yields on smallholder farms. These observations support proposals to achieve long‐term food production targets in sub‐Saharan Africa by combining mineral fertilizers with organic inputs.
Generation of a CRISPR database for Yersinia pseudotuberculosis complex and role of CRISPR‐based immunity in conjugation
Authors: Koskela Katja A. , Mattinen Laura , Kalin‐Mänttäri Laura , Vergnaud Gilles , Gorgé Olivier , Nikkari Simo , Skurnik Mikael
Published: February 2015

The clustered regularly interspaced short palindromic repeat – CRISPR‐associated genes (CRISPR‐Cas) system is used by bacteria and archaea against invading conjugative plasmids or bacteriophages. Central to this immunity system are genomic CRISPR loci that contain fragments of invading DNA. These are maintained as spacers in the CRISPR loci between direct repeats and the spacer composition in any bacterium reflects its evolutionary history. We analysed the CRISPR locus sequences of 335 Yersinia pseudotuberculosis complex strains. Altogether 1902 different spacer sequences were identified and these were used to generate a database for the spacer sequences. Only ∼10% of the spacer sequences found matching sequences. In addition, surprisingly few spacers were shared by Yersinia pestis and Y. pseudotuberculosis strains. Interestingly, 32 different protospacers were present in the conjugative plasmid pYptb32953. The corresponding spacers were identified from 35 different Y. pseudotuberculosis strains indicating that these strains had encountered pYptb32953 earlier. In conjugation experiments, pYptb32953‐specific spacers generally prevented conjugation with spacer‐positive and spacer‐free strains. However, some strains with one to four spacers were invaded by pYptb32953 and some spacer‐free strains were fully resistant. Also some spacer‐positive strains were intermediate resistant to conjugation. This suggests that one or more other defence systems are determining conjugation efficiency independent of the CRISPR‐Cas system.
Some ‘ant’swers: Application of a layered barcode approach to problems in ant taxonomy
Authors: Paknia Omid , Bergmann Tjard , Hadrys Heike
Published: February 2015

DNAbarcoding has emerged as a routine tool in modern taxonomy. Although straightforward, this approach faces new challenges, when applied to difficult situation such as defining cryptic biodiversity. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. Here, we test theDNAbarcoding region, cytochrome c oxidase 1 and two supplementary markers, 28S ribosomalDNAand long‐wavelength rhodopsin, commonly used in ant taxonomy, for their potential in a layered, character‐based barcoding approach across different taxonomic levels. Furthermore, we assess performance of the character‐based barcoding approach to determine cryptic species diversity in ants. We found (i) that the barcode potential of a specific genetic marker varied widely among taxonomic levels in ants; (ii) that application of a layered, character‐based barcode for identification of specimens can be a solution to taxonomical challenging groups; (iii) that the character‐based barcoding approach allows us to differentiate specimens even within locations based on pure characters. In summary, (layered) character‐based barcoding offers a reliable alternative for problematic species identification in ants and can be used as a fast and cost‐efficient approach to estimate presence, absence or frequency of cryptic species.
batemanater: a computer program to estimate and bootstrap mating system variables based on Bateman's principles
Authors: Jones Adam G.
Published: February 2015

Bateman's principles continue to play a major role in the characterization of genetic mating systems in natural populations. The modern manifestations of Bateman's ideas include the opportunity for sexual selection (i.e. Is – the variance in relative mating success), the opportunity for selection (i.e. I – the variance in relative reproductive success) and the Bateman gradient (i.e. βss – the slope of the least‐squares regression of reproductive success on mating success). These variables serve as the foundation for one convenient approach for the quantification of mating systems. However, their estimation presents at least two challenges, which I address here with a new Windows‐based computer software package called batemanater. The first challenge is that confidence intervals for these variables are not easy to calculate. batemanater solves this problem using a bootstrapping approach. The second, more serious, problem is that direct estimates of mating system variables from open populations will typically be biased if some potential progeny or adults are missing from the analysed sample. batemanater addresses this problem using a maximum‐likelihood approach to estimate mating system variables from incompletely sampled breeding populations. The current version of batemanater addresses the problem for systems in which progeny can be collected in groups of half‐ or full‐siblings, as would occur when eggs are laid in discrete masses or offspring occur in pregnant females. batemanater has a user‐friendly graphical interface and thus represents a new, convenient tool for the characterization and comparison of genetic mating systems.
A discrete‐beta model for testing gene flow after speciation
Authors: Liu Junfeng , Zhang De‐Xing , Yang Ziheng
Published: February 2015

Due to the polymorphism in the ancestral species and the stochastic fluctuation of the coalescent process, the divergence time between sequences from two closely related species varies throughout the genome. This variation is described by an exponential distribution. Gene flow between the species causes additional variation in the sequence divergence time, beyond the expected variation from the ancestral coalescent process. This prediction can be used to test for gene flow between species using genomic sequence data.

A previous implementation of the model used an empirical beta distribution to describe the variation in species divergence time across the genome, with numerical integration used to calculate the 3D integrals involved in the likelihood function. However, with a huge number of loci, the numerical integration is not accurate enough, so the false‐positive rate of the likelihood ratio test may exceed the significance level.

In this study, we replace the beta model with a discretized version, so that the likelihood calculation involves 2D integrals. We implement the new discrete‐beta model in the program 3s and also extend our previous implementation to accommodate loci with different data configurations. We use computer simulation to examine the false‐positive rate, the power and the robustness of the likelihood ratio test.

The results show that the test had low false‐positive rates and had even higher power in detecting gene flow than a likelihood ratio test based on a proper implementation of the isolation‐with‐migration model. It is, however, not robust to high levels of recombination within locus. Application of the test to two empirical data sets (from the hominoid genomes and from the Drosophila fruit flies) suggests the presence of gene flow for both data sets.
Treatment of Pulmonary Embolism With Rivaroxaban: Outcomes by Simplified Pulmonary Embolism Severity Index Score from a Post Hoc Analysis of the EINSTEIN PE Study
Authors: Fermann Gregory J. , Erkens Petra M. G. , Prins Martin H. , Wells Philip S. , Pap Ákos F. , Lensing Anthonie W. A.
Published: February 2015

Objectives

The objective was to assess adverse outcomes in relation to the simplified Pulmonary Embolism Severity Index (PESI) score in patients treated with rivaroxaban or standard therapy in the phase III EINSTEIN PE study and to evaluate the utility of the simplified PESI score to identify low‐risk pulmonary embolism (PE) patients.

Methods

A post hoc analysis of EINSTEIN PE data was performed to assess the efficacy and safety of rivaroxaban in patients with a range of simplified PESI scores. Recurrent venous thromboembolism, fatal PE, all‐cause mortality, and major bleeding were stratified by simplified PESI scores of 0, 1, or ≥2 and according to treatment period at 7, 14, 30, and 90 days and at the end of the full intended treatment period.

Results

Simplified PESI scores could be calculated in 4,831 of the 4,832 randomized patients; of those, 53.6, 36.7, and 9.7% had PESI scores of 0, 1, and ≥2, respectively. Among patients with simplified PESI scores of 0 or 1, fatal PE, all‐cause mortality, and other adverse outcomes were uncommon within the first 7, 14, and 30 days. Patients with simplified PESI scores of ≥2 had more frequent adverse outcomes. Major bleeding was lower in the rivaroxaban group, particularly in those with simplified PESI scores of 1 or ≥2.

Conclusions

The findings support using risk stratification with the simplified PESI score to identify low‐risk patients with PE.
Semilobar Holoprosencephaly Associated with Multiple Malformations in a Foal
Authors: Pintore M. D. , Cantile C.
Published: February 2015

A full‐term male foal born in a farm holidays in Maremma (Tuscany, Italy) was euthanized shortly after birth due to the presence of several malformations. The rostral maxilla and the nasal septum were deviated to the right (wry nose), and a severe cervico‐thoracic scoliosis and anus atresia were evident. Necropsy revealed ileum atresia and agenesis of the right kidney. The brain showed an incomplete separation of the hemispheres of the rostral third of the forebrain and the olfactory bulbs and tracts were absent (olfactory aplasia). A diagnosis of semilobar holoprosencephaly (HPE) was achieved. This is the first case of semilobar HPE associated with other organ anomalies in horses.
NPOs in China: Capacity‐Building Development Since the 1990s
Authors: Li Changwen , Guo Jing
Published: February 2015

The development of nonprofit organizations (NPOs) in China has experienced unprecedented growth since the 1990s. Capacity‐building is a critical aspect of NPO research. Based on data through document reviews and personal interviews, we conducted a systematic analysis and presented a conceptual framework to examine NPO capacity‐building in China. Three main bodies – government agencies, educational institutions, and supporting NPOs – lead NPO capacity‐building, and its development has experienced four critical stages: starting, localization, standardization, and diversification. A major implication for international literature and policy lies in the discovery of an evolving environmental context of NPO development in China.
Toll‐like receptor 4 contributes to vascular remodelling and endothelial dysfunction in angiotensin II‐induced hypertension
Authors: Hernanz R , Martínez‐Revelles S , Palacios R , Martín A , Cachofeiro V , Aguado A , García‐Redondo L , Barrús M T , de Batista P R , Briones A M , Salaices M , Alonso M J
Published: February 2015

Background and Purpose

Toll‐like receptor 4 (TLR4) signalling contributes to inflammatory cardiovascular diseases, but its role in hypertension and the associated vascular damage is not known. We investigated whether TLR4 activation contributed to angiotensin II (AngII)‐induced hypertension and the associated vascular structural, mechanical and functional alterations.

Experimental Approach

AngII was infused (1.44 mg·kg−1·day−1, s.c.) for 2 weeks in C57BL6 mice, treated with a neutralizing anti‐TLR4 antibody or IgG (1 μg·day−1); systolic BP (SBP) and aortic cytokine levels were measured. Structural, mechanical and contractile properties of aortic and mesenteric arterial segments were measured with myography and histology. RT‐PCR and Western blotting were used to analyse these tissues and cultured vascular smooth muscle cells (VSMC) from hypertensive rats (SHR).

Key Results

Aortic TLR4 mRNA levels were raised by AngII infusion. Anti‐TLR4 antibody treatment of AngII‐treated mice normalised: (i) increased SBP and TNF‐α, IL‐6 and CCL2 levels; (ii) vascular structural and mechanical changes; (iii) altered aortic phenylephrine‐ and ACh‐induced responses; (iv) increased NOX‐1 mRNA levels, superoxide anion production and NAD(P)H oxidase activity and effects of catalase, apocynin, ML‐171 and Mito‐TEMPO on vascular responses; and (v) reduced NO release and effects of L‐NAME on phenylephrine‐induced contraction. In VSMC, the MyD88 inhibitor ST‐2825 reduced AngII‐induced NAD(P)H oxidase activity. The TLR4 inhibitor CLI‐095 reduced AngII‐induced increased phospho‐JNK1/2 and p65 NF‐κB subunit nuclear protein expression.

Conclusions and Implications

TLR4 up‐regulation by AngII contributed to the inflammation, endothelial dysfunction, vascular remodelling and stiffness associated with hypertension by mechanisms involving oxidative stress. MyD88‐dependent activation and JNK/NF‐κB signalling pathways participated in these alterations.
Andrographolide derivative AL‐1 improves insulin resistance through down‐regulation of NF‐κB signalling pathway
Authors: Li Yongmei , Yan Hui , Zhang Zaijun , Zhang Gaoxiao , Sun Yewei , Yu Pei , Wang Yuqiang , Xu Lipeng
Published: February 2015

Background and Purpose

Andrographolide is the most active constituent of the medicinal plant Andrographis paniculata. Previously, we synthesized a novel andrographolide derivative AL‐1, conjugating andrographolide with lipoic acid. Although the antioxidative and/or anti‐inflammatory activity of AL‐1 contributes to its cytoprotective effects, whether AL‐1 can improve insulin resistance and the mechanisms responsible for its action have not been elucidated.

Experimental Approach

We investigated the anti‐hyperlipidaemic and anti‐hyperglycaemic effects of AL‐1 in a high‐fat diet/streptozocin‐induced animal diabetic model. In addition, we investigated the effect of AL‐1 on the NF‐κB signalling pathway in rat islet derived insulinoma cells (RIN‐m cells) with a focus on the link between reactive oxygen species‐associated inflammation and insulin resistance.

Key Results

AL‐1, at doses of 40 and 80 mg·kg−1, had a significant hypoglycaemic effect; it significantly reduced the level of cholesterol and increased HDL. AL‐1 also reduced the homeostasis model assessment of insulin resistance and enhanced insulin sensitivity. In addition, AL‐1 improved the morphology of pancreatic islets and their function. Furthermore, AL‐1 suppressed high glucose‐induced phosphorylation of p65 and IκBα in RIN‐m cells.

Conclusion and Implications

AL‐1 has a hypoglycaemic effect and improves insulin resistance in type 2 diabetic rats. It protected islet from high glucose‐induced oxidative damage by down‐regulating the NF‐κB signalling pathway. Further investigations of AL‐1 as a promising new agent for treatment and/or prevention of diabetes are warranted.
One‐Year Multicenter Prospective Evaluation of Survival Rates and Bone Resorption in One‐Piece Implants
Authors: Ghaleh Golab Kaveh , Balouch Amir , Mirtorabi Shahram
Published: February 2015

Background

Several studies have reported the efficiency of immediate loading techniques.

Purpose

The aim of this multicenter prospective study was to evaluate the clinical efficiency of the one‐piece screw (OPS) implants used by general dentists.

Materials and Methods

A total of 272 patients were treated with 533 implants at five dental clinics by five general dentists. Some implants were provided with provisional restoration. Implants in partially edentulous spaces were splinted with acryl, composite, and intraoral welding. The implant survival rates, bone resorption, plaque accumulation, and soft tissue health were evaluated after 3, 6, and 12 months. The final restorations were cemented in the maxilla after 6 months and in the mandible after 3 months.

Results

Twelve implants failed (98% survival rate) after 12 months. None of the splinted implants failed during the follow‐ups. There were five failures in unsplinted partial cases. The average amounts of bone loss around the implants were 0.40 ± 0.35 mm, 0.56 ± 0.41 mm, and 0.59 ± 0.41 mm after 3, 6, and 12 months, respectively. Visible plaque was registered in 18% of the implants, and bleeding on probing was observed in 17% of the implants after 12 months.

Conclusions

High survival rates and favorable host tissue responses support the clinical performance of OPS implants. This study demonstrated that one‐piece implants can be efficiently used by well‐trained general dentists.
Increased levels of irisin in people with long‐standing Type 1 diabetes
Authors: Espes D. , Lau J. , Carlsson P. O.
Published: February 2015

Background

Irisin stimulates browning of white adipose tissue and improves metabolic control in mice. Betatrophin, another recently described hormone, improves metabolic control in mice by inducing β–cell proliferation. In vitro, irisin stimulates the expression of betatrophin in rat adipocytes. There is a great interest in developing drugs that target or use these hormones for the treatment of obesity and diabetes. We have previously reported on increased levels of betatrophin in people with Type 1 diabetes, but the levels of irisin are currently unknown.

Aim

To characterize the levels of irisin in Type 1 diabetes and investigate a potential correlation with betatrophin.

Methods

Irisin and betatrophin were measured by enzyme‐linked immunosorbant assay (ELISA) in 45 individuals with Type 1 diabetes and in 25 healthy controls.

Results

Irisin levels were increased in people with Type 1 diabetes, and especially in women. Negative correlations between irisin levels and age at onset of Type 1 diabetes and plasma triacylglycerol levels were observed. Interestingly, in women with Type 1 diabetes a negative correlation between irisin and insulin doses was also observed. When computing correlations for all study participants, a positive correlation between irisin and total betatrophin was observed, but not between irisin and full‐length betatrophin.

Conclusion

We report on increased circulating levels of irisin in people with Type 1 diabetes, especially in women. For women with Type 1 diabetes, the levels of irisin correlated with lower insulin requirements. Further studies are clearly needed to determine the role of irisin in Type 1 diabetes.
Efficacy, safety and tolerability of aleglitazar in patients with type 2 diabetes: pooled findings from three randomized phase III trials
Authors: Henry R. R. , Buse J. B. , Wu H. , Durrwell L. , Mingrino R. , Jaekel K. , El Azzouzi B. , Andjelkovic M. , Herz M.
Published: February 2015

Aims

To evaluate the potential efficacy, safety and tolerability of aleglitazar as monotherapy or add‐on therapy to metformin or to a sulphonylurea (either alone or in combination with metformin).

Methods

We conducted a pooled analysis of data from three randomized phase III clinical trials of aleglitazar in patients with type 2 diabetes (n = 591). The three studies focused on: (i) aleglitazar alone; (ii) aleglitazar and metformin; and (iii) aleglitazar and sulphonylurea with or without metformin. Patients were randomized to 26 weeks' treatment with aleglitazar 150 µg/day or placebo. The primary endpoint was change in glycated haemoglobin (HbA1c) concentration from baseline to week 26. Secondary endpoints included changes in lipids, fasting plasma glucose and homeostatic model assessment of insulin resistance (HOMA‐IR) at week 26.

Results

Reductions in HbA1c concentration from baseline to week 26 were statistically significantly greater with aleglitazar than with placebo. Aleglitazar treatment was associated with more beneficial changes in lipid profiles and HOMA‐IR values than was placebo. Aleglitazar was generally well tolerated, with no reports of congestive heart failure. The incidence of peripheral oedema was similar in both groups. Change in body weight was +1.37 kg with aleglitazar and −0.53 kg with placebo. Hypoglycaemia was more frequently reported with aleglitazar (7.8%) than with placebo (1.7%), a result probably driven by the type of background medication.

Conclusions

Development of aleglitazar was halted because of a lack of cardiovascular efficacy and peroxisome proliferator‐activated receptor‐related side effects in patients with type 2 diabetes post‐acute coronary syndrome; however, in the present studies, aleglitazar was well tolerated and effective in improving HbA1c, insulin resistance and lipid variables.