bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydride vapor phase GaN films with reduced density of residual electrons and deep traps
Authors: Polyakov A. Y. , Smirnov N. B. , Govorkov A. V. , Yugova T. G. , Cox H. , Usikov A. S. , Helava H. , Makarov Yu.
Published: May 2014

Electrical properties and deep electron and hole traps spectra are compared for undoped n-GaN films grown by hydride vapor phase epitaxy (HVPE) in the regular process (standard HVPE samples) and in HVPE process optimized for decreasing the concentration of residual donor impurities (improved HVPE samples). It is shown that the residual donor density can be reduced by optimization from ∼1017 cm−3 to (2–5) × 1014 cm−3. The density of deep hole traps and deep electron traps decreases with decreased donor density, so that the concentration of deep hole traps in the improved samples is reduced to ∼5 × 1013 cm−3 versus 2.9 × 1016 cm−3 in the standard samples, with a similar decrease in the electron traps concentration.
Effect of La3+ substitution with Gd3+ on the resistive switching properties of La0.7Sr0.3MnO3 thin films
Authors: Lee Hong-Sub , Park Chang-Sun , Park Hyung-Ho
Published: May 2014

This study demonstrated that the resistive switching voltage of perovskite manganite material could be controlled by A-site cation substitution in “A” MnO3 perovskite manganite structure. A partial substitution of La3+ in La0.7Sr0.3MnO3 with smaller cation Gd3+ induced A-site vacancy of the largest Sr2+ cation with surface segregation of SrOy due to ionic size mismatch, and the induced vacancies reduced migration energy barrier. The operating voltage decreased from 3.5 V to 2.5 V due to a favorable condition for electrochemical migration and redox of oxygen ions. Moreover, surface-segregated SrOy was enhanced with Gd-substitution and the SrOy reduced Schottky-like barrier height and resistive switching ratio from the potential drop and screening effect. The relationship between A-site vacancy generation resulting in surface segregation of SrOy and resistive switching behavior was also investigated by energy resolved x-ray photoelectron spectroscopy, O 1s near edge x-ray absorption spectroscopy, and current voltage measurement.
Formation of TiO2 nanorods by ion irradiation
Authors: Zheng X. D. , Ren F. , Cai G. X. , Hong M. Q. , Xiao X. H. , Wu W. , Liu Y. C. , Li W. Q. , Ying J. J. , Jiang C. Z.
Published: May 2014

Ion beam irradiation is a powerful method to fabricate and tailor the nanostructured surface of materials. Nanorods on the surface of single crystal rutile TiO2 were formed by N+ ion irradiation. The dependence of nanorod morphology on ion fluence and energy was elaborated. With increasing ion fluence, nanopores grow in one direction perpendicular to the surface and burst finally to form nanorods. The length of nanorods increases with increasing ion energy under same fluence. The development of the nanorod structure is originated from the formation of the nanopores while N2 bubbles and aggregation of vacancies were responsible for the formation of nanopores and nanorods. Combining C+ ion irradiation and post-irradiation annealing experiments, two qualitative models are proposed to explain the formation mechanism of these nanorods.
Cole-cole analysis and electrical conduction mechanism of N+ implanted polycarbonate
Authors: Chawla Mahak , Shekhawat Nidhi , Aggarwal Sanjeev , Sharma Annu , Nair K. G. M.
Published: May 2014

In this paper, we present the analysis of the dielectric (dielectric constant, dielectric loss, a.c. conductivity) and electrical properties (I–V characteristics) of pristine and nitrogen ion implanted polycarbonate. The samples of polycarbonate were implanted with 100 keV N+ ions with fluence ranging from 1 × 1015 to 1 × 1017 ions cm−2. The dielectric measurements of these samples were performed in the frequency range of 100 kHz to 100 MHz. It has been observed that dielectric constant decreases whereas dielectric loss and a.c. conductivity increases with increasing ion fluence. An analysis of real and imaginary parts of dielectric permittivity has been elucidated using Cole-Cole plot of the complex permittivity. With the help of Cole-Cole plot, we determined the values of static dielectric constant (εs), optical dielectric constant (ε∞), spreading factor (α), average relaxation time (τ0), and molecular relaxation time (τ). The I–V characteristics were studied using Keithley (6517) electrometer. The electrical conduction behaviour of pristine and implanted polycarbonate specimens has been explained using various models of conduction.
Extraction of diffuse correlation spectroscopy flow index by integration of Nth-order linear model with Monte Carlo simulation
Authors: Shang Yu , Li Ting , Chen Lei , Lin Yu , Toborek Michal , Yu Guoqiang
Published: May 2014

Conventional semi-infinite solution for extracting blood flow index (BFI) from diffuse correlation spectroscopy (DCS) measurements may cause errors in estimation of BFI (αDB) in tissues with small volume and large curvature. We proposed an algorithm integrating Nth-order linear model of autocorrelation function with the Monte Carlo simulation of photon migrations in tissue for the extraction of αDB. The volume and geometry of the measured tissue were incorporated in the Monte Carlo simulation, which overcome the semi-infinite restrictions. The algorithm was tested using computer simulations on four tissue models with varied volumes/geometries and applied on an in vivo stroke model of mouse. Computer simulations shows that the high-order (N ≥ 5) linear algorithm was more accurate in extracting αDB (errors < ±2%) from the noise-free DCS data than the semi-infinite solution (errors: −5.3% to −18.0%) for different tissue models. Although adding random noises to DCS data resulted in αDB variations, the mean values of errors in extracting αDB were similar to those reconstructed from the noise-free DCS data. In addition, the errors in extracting the relative changes of αDB using both linear algorithm and semi-infinite solution were fairly small (errors < ±2.0%) and did not rely on the tissue volume/geometry. The experimental results from the in vivo stroke mice agreed with those in simulations, demonstrating the robustness of the linear algorithm. DCS with the high-order linear algorithm shows the potential for the inter-subject comparison and longitudinal monitoring of absolute BFI in a variety of tissues/organs with different volumes/geometries.
One-dimensional photonic crystal fishbone hybrid nanocavity with nanoposts
Authors: Lu Tsan-Wen , Lin Pin-Tso , Lee Po-Tsung
Published: May 2014

We propose and investigate a one-dimensional photonic crystal (PhC) fishbone (FB) hybrid nanocavity lying on silver substrate with a horizontal air slot. With very few PhC periods, the confined transverse-magnetic, TM10 hybrid mode concentrated within the air slot shows high quality factor over effective mode volume ratio larger than 105λ−3. Most importantly, this FB hybrid nanocavity allows formation of low-index nanoposts within the air slot without significantly affecting the mode properties. These nanoposts guarantee the structural stabilities under different environmental perturbations. Furthermore, capabilities of our proposed design in serving as optical sensors and tweezers for bio-sized nanoparticles are also investigated.
Band alignment and electrical properties of Al2O3/β-Ga2O3 heterojunctions
Authors: Kamimura Takafumi , Sasaki Kohei , Hoi Wong Man , Krishnamurthy Daivasigamani , Kuramata Akito , Masui Takekazu , Yamakoshi Shigenobu , Higashiwaki Masataka
Published: May 2014

The band alignment of Al2O3/n-Ga2O3 was investigated by x-ray photoelectron spectroscopy (XPS). With a band gap of 6.8 ± 0.2 eV measured for Al2O3, the conduction and valence band offsets at the interface were estimated to be 1.5 ± 0.2 eV and 0.7 ± 0.2 eV, respectively. The conduction band offset was also obtained from tunneling current in Al2O3/n-Ga2O3 (2¯01) metal-oxide-semiconductor (MOS) diodes using the Fowler-Nordheim model. The electrically extracted value was in good agreement with the XPS data. Furthermore, the MOS diodes exhibited small capacitance-voltage hysteresis loops, indicating the successful engineering of a high-quality Al2O3/Ga2O3 interface.
Anomalous photoelectric emission from Ag on zinc-phthalocyanine film
Authors: Tanaka Senku , Otani Tomohiro , Fukuzawa Ken , Ogawa Koji , Azuma Junpei , Yamamoto Isamu , Takahashi Kazutoshi , Kamada Masao , Hiromitsu Ichiro
Published: May 2014

Photoelectric emission from organic and metal thin films is generally observed with irradiation of photon energy larger than 4 eV. In this paper, however, we report photoelectric emission from Ag on a zinc-phthalocyanine (ZnPc) layer at a photon energy of 3.4 eV. The threshold energy for this photoelectric emission is much smaller than the work function of Ag estimated by conventional photoelectron spectroscopy. The photoelectric emission by low-energy photons is significant for Ag thicknesses of less than 1 nm. Photoelectron spectroscopy and morphological study of the Ag/ZnPc suggest that the anomalous photoelectric emission from the Ag surface is caused by a vacuum level shift at the Ag/ZnPc interface and by surface plasmons of the Ag nanoparticles.
An ultra-wideband surface plasmonic filter in microwave frequency
Authors: Gao Xi , Zhou Liang , Liao Zhen , Ma Hui Feng , Cui Tie Jun
Published: May 2014

We propose an ultra-wideband plasmonic waveguide based on designer surface plasmon polaritons (DSPPs) with double gratings. In such plasmonic metamaterials, the DSPP waves in the region of lower frequencies of the dispersion curve can be tightly confined and hence effectively broaden the operating bandwidth. Based on such features, we design and fabricate a high performance DSPP filter, in which a transducer consisting of microstrip, slotline, and gradient corrugations is employed to feed electromagnetic energies into the plasmonic waveguide with high efficiency. The simulated and measured results on reflection and transmission coefficients in the microwave frequency demonstrate the excellent filtering characteristics such as low loss, wide band, and high square ratio. The high performance DSPP waveguide and filter pave a way to develop advanced plasmonic integrated functional devices and circuits in the microwave and terahertz frequencies.
Seeing beyond the Smoke: The Political Ecology of Fire in Horta de Sant Joan (Catalonia)
Authors: González-Hidalgo Marien , Otero Iago , Kallis Giorgos
Published: May 2014

Fires shed light. We revisit a tragic fire which occurred in southern Catalonia in 2009 to uncover tensions and frictions in the ways in which modern societies appreciate and reorganise their relations to nature, by looking at forests and fires in particular. Using a broadly defined political ecology approach, we identify four major contemporary collective discourses and associated visions that underpin humanity's material relations to nature. Our case study shows how these coexist, antagonize, interact, and play out in practices concerning forest-fire prevention and response. The focus is on the emerging discourse of ‘resilience’. In it, nature is seen as socially produced. Resilience embraces and aspires to tinker with the turbulent and unpredictable character of nature. Embodied in GRAF, Catalonia's internationally renowned special fire-fighting unit, this vision faced its hour of judgment in the Horta de Sant Joan fire, when five GRAF firefighters tragically lost their lives. Although the tragedy opened an opportunity for learning, the political processes dealing with the tragedy failed to engage with the fundamental frictions underlying forests and fires. We raise doubts about the possibility for resilience in an increasingly depoliticised public sphere.
Transecting Security and Space in Phnom Penh
Authors: Sidaway James D , Paasche Till F , Woon Chih Yuan , Keo Piseth
Published: May 2014

Our paper examines everyday interactions of money, power, and security in Cambodia's capital city of Phnom Penh, informed by a series of transects and interviews. When Phnom Penh hosted the Association of the Southeast Asian Nations (ASEAN) Summit in April 2012, Prime Minister Hun Sen declared that “Cambodia is not for sale” in an angry exchange with journalists who had quizzed him about China's influence. However, the sale and enclosure of Cambodian land and property have yielded both profit and tensions. These are connected with the meanings and operation of security. The most powerful ‘security’ agency in Phnom Penh is neither wholly ‘public’ nor fully ‘private’, but hybrid; where public police and military personnnel and their equipment are purchased. We argue that this is symptomatic of circulation/operation of state/capital in Cambodia.
Urban Poverty and Regulation, New Spaces and Old: Japan and the US in Comparison
Authors: Hayashi Mahito
Published: May 2014

After the 1970s the new urban poverty (NUP) ballooned in Japan and the US, and it evoked policy responses that produced new, rescaled regulatory spaces to contain the poor on the fringe of social rights and the capital circuit. The paper illuminates this process through the comparison of Japanese and US trajectories, both of which, evolving through economic crises, have established unique pathways. The author first constructs a theoretical framework based on Marxian, Polanyian, and Lefebvrean traditions. Then, he compares national-scale poverty regulation in Japan and the US from the 1950s through the 2000s. Lastly, the author examines how the countries' regulation of a major aspect of the NUP—homelessness—intensified multiscalar rescaling processes. The paper concludes that regulation of the NUP represents a significant instance of uneven spatial development of capitalism mediated by the state that requires synthetic research.
Genetic degeneration of old and young Y chromosomes in the flowering plant
Rumex hastatulus
Authors: Hough Josh , Hollister Jesse D. , Wang Wei , Barrett Spencer C. H. , Wright Stephen I.
Published: May 2014

Significance

Evolutionary theory predicts that in dioecious organisms with sex chromosomes, suppressed X-Y recombination should lead to a loss of Y-chromosome gene content and function. However, the extent to which this process occurs in plants, where sex chromosomes evolved relatively recently, is poorly understood. We tested for Y degeneration in
Rumex hastatulus
, an annual plant that has both XY and XY
1
Y
2
sex chromosome systems. We found that Y-linked genes are undergoing degeneration despite their recent origin; they show a faster accumulation of amino acid substitutions, contain more unpreferred changes in codon usage, and are reduced in expression relative to X-linked alleles. Significantly, the magnitude of these effects depended on sex chromosome age, being greater for genes that have been nonrecombining for longer.
Transactivation of programmed ribosomal frameshifting by a viral protein
Authors: Li Yanhua , Treffers Emmely E. , Napthine Sawsan , Tas Ali , Zhu Longchao , Sun Zhi , Bell Susanne , Mark Brian L. , van Veelen Peter A. , van Hemert Martijn J. , Firth Andrew E. , Brierley Ian , Snijder Eric J. , Fang Ying
Published: May 2014

Significance

Ribosomes synthesize proteins by translating mRNAs into linear chains of amino acids through the decoding of consecutive nucleotide triplets (codons). Specific mRNA signals, however, can stimulate ribosomes to shift into an alternative triplet reading frame (ribosomal frameshifting) resulting in translation of a different protein. Typically, such signals are regions of intramolecular nucleotide base-pairing in the mRNA which form structures that stall ribosome progress. Here we show that the frameshifting signal used to express the nsp2TF and nsp2N proteins of porcine reproductive and respiratory syndrome virus, an important swine pathogen, requires the action of a transacting viral protein rather than a structured RNA. This novel mechanism of gene expression may also be used by other viruses or in cellular gene expression.
Sestrin2 inhibits uncoupling protein 1 expression through suppressing reactive oxygen species
Authors: Ro Seung-Hyun , Nam Myeongjin , Jang Insook , Park Hwan-Woo , Park Haeli , Semple Ian A. , Kim Myungjin , Kim Jeong Sig , Park Haewon , Einat Paz , Damari Golda , Golikov Maya , Feinstein Elena , Lee Jun Hee
Published: May 2014

Significance

Antioxidant therapy was once considered useful for treating metabolic syndrome because excessive accumulation of reactive oxygen species (ROS) was identified as an inducer of diverse metabolic pathologies. However, the effectiveness of dietary antioxidants in treating obesity-associated diseases had been largely controversial in numerous animal and human clinical studies, some of which actually show adverse effects upon antioxidant consumption. Here, we show that Sestrin2 and other antioxidants can interfere with
uncoupling protein 1
(
Ucp1
) expression through suppression of ROS-mediated p38 MAPK activation. Ucp1, a protein responsible for heat generation and energy dissipation, is known to suppress diverse metabolic pathologies associated with obesity and aging. Thus, our results explain why some antioxidant therapies were not successful in treating obesity-associated diseases and extending health and lifespan in mammals.
Oncogenic mutations in intestinal adenomas regulate Bim-mediated apoptosis induced by TGF-β
Authors: Wiener Zoltán , Band Arja M. , Kallio Pauliina , Högström Jenny , Hyvönen Ville , Kaijalainen Seppo , Ritvos Olli , Haglund Caj , Kruuna Olli , Robine Sylvie , Louvard Daniel , Ben-Neriah Yinon , Alitalo Kari
Published: May 2014

Significance

The TGF-β/Smad pathway is mutated in the majority of late-stage colorectal cancers (CRCs), but its role in intestinal adenomas is unclear. We show here that intestinal epithelial cells, including the Lgr5
+
stem cells, are sensitive to the TGF-β–induced apoptosis in adenomas and that this is mediated by the BH3-only protein Bim. Furthermore, the tumor-initiating Apc mutation increases, whereas the KRas oncogene decreases the TGF-β sensitivity. Our results provide important mechanistic insight into how TGF-β regulates intestinal adenoma development and show that drugs mimicking the effects of BH3-only proteins can induce apoptosis also in CRC cells that are resistant to TGF-β.
Conservative harvest habit by harvester ants exploiting fields of bread wheat
Authors: Lev-Yadun Simcha , Grafi Gideon , Grafi Dalia
Published: May 2014

Harvester ants are common and very efficient granivores in many regions of the world. The ants may collect dispersed seeds from the ground or climb on plants to harvest seeds. While collecting or harvesting wild cereal seeds they first trim the long and bulky awns to allow better seed transportation to their nests and through the narrow passages inside their nests. In domesticated free-threshing cereals, flower parts including awns are not adhered to the seeds as in wild-type cereals and cutting open the loose glumes is sufficient to free the seeds. However, when various harvester ant (Messorspp.) species climb on domesticated free-threshing bread wheat in agricultural fields to harvest seeds they keep their ancient habit of beginning harvest by awn trimming of wild-types in spite of the fact that it is not necessary in the domesticated ones. We show and discuss their conservative harvest behavior.
Is the school governing body a determining factor in the under-performance of secondary schools in theWestern Cape province, South Africa? Issues and perspectives
Authors: Bayat Amiena , Louw Wynand , Rena Ravinder
Published: May 2014

In 1996, the Schools Act No. 84 of South Africa was promulgated. In the Schools Act, school governing bodies (SGBs) are mandated to manage the administration and finances of schools. The Act also provides guidelines for the SGB and the principal on their roles and responsibilities in managing the finances and leadership management of the school. However, some members of SGBs and principals either have little knowledge of the Schools Act or simply interpret it incorrectly, which results in many schools experiencing mismanagement which leads to the underperformance of the schools. Although the Western Cape Provincial Department of Education provides financial management training for SGBs, many schools still encounter problems in this area. When financial problems are referred to the department of education, many remain unresolved. The purpose of the study was to determine the perceptions of stakeholders on the financial functions of SGBs, to explore the functions of an SGB in managing a school’s finances and, based on the findings of the research, to develop guidelines for principals and SGBs to enable them to manage their school funds efficiently and effectively. The research design was based on qualitative research because of its exploratory, descriptive and contextual nature.
Vascular Remodeling Process in Pulmonary Arterial Hypertension, with Focus on miR‐204 and miR‐126 (2013 Grover Conference Series)
Authors: Potus François , Graydon Colin , Provencher Steeve , Bonnet Sébastien
Published: May 2014

Pulmonary arterial hypertension (PAH) is a vascular remodeling disease characterized primarily by increased proliferation and resistance to apoptosis in distal pulmonary arteries. Previous literature has demonstrated that the transcription factors NFAT (nuclear factor of activated T cells) and HIF‐1α (hypoxia inducible factor 1α) are extensively involved in the pathogenesis of this disease and, more recently, has implicated STAT3 (signal transducer and activator of transcription 3) in their activation. Novel research shows that miR‐204, a microRNA recently found to be notably downregulated through induction of PARP‐1 (poly [ADP‐ribose] polymerase 1) by excessive DNA damage in PAH, inhibits activation of STAT3. Contemporary research also indicates systemic impairment of skeletal muscle microcirculation in PAH and attributes this to a debilitated vascular endothelial growth factor pathway resulting from reduced miR‐126 expression in endothelial cells. In this review, we focus on recent research implicating miR‐204 and miR‐126 in vascular remodeling processes, data that allow a better understanding of PAH molecular pathways and constitute a new hope for future therapy.
Separation of real algebraic sets and the Łojasiewicz exponent
Authors: Kurdyka Krzysztof , Spodzieja Stanisław
Published: May 2014

We discuss several aspects of Łojasiewicz inequalities, namely local and global versions, and the relations between the gradient inequality and regular separation of real algebraic sets. We give effective estimates for Łojasiewicz’s exponents in the real and complex setting.
SIBIS: a Bayesian model for inconsistent protein sequence estimation
Authors: Khenoussi Walyd , Vanhoutrève Renaud , Poch Olivier , Thompson Julie D.
Published: May 2014

Motivation: The prediction of protein coding genes is a major challenge that depends on the quality of genome sequencing, the accuracy of the model used to elucidate the exonic structure of the genes and the complexity of the gene splicing process leading to different protein variants. As a consequence, today’s protein databases contain a huge amount of inconsistency, due to both natural variants and sequence prediction errors.

Results: We have developed a new method, called SIBIS, to detect such inconsistencies based on the evolutionary information in multiple sequence alignments. A Bayesian framework, combined with Dirichlet mixture models, is used to estimate the probability of observing specific amino acids and to detect inconsistent or erroneous sequence segments. We evaluated the performance of SIBIS on a reference set of protein sequences with experimentally validated errors and showed that the sensitivity is significantly higher than previous methods, with only a small loss of specificity. We also assessed a large set of human sequences from the UniProt database and found evidence of inconsistency in 48% of the previously uncharacterized sequences. We conclude that the integration of quality control methods like SIBIS in automatic analysis pipelines will be critical for the robust inference of structural, functional and phylogenetic information from these sequences.

Availability and implementation: Source code, implemented in C on a linux system, and the datasets of protein sequences are freely available for download at http://www.lbgi.fr/∼julie/SIBIS.

Contact:  thompson@unistra.fr
Family Welfare and Social Work in Post-War England, c.1948–c.1970
Authors: Todd Selina
Published: May 2014

This article examines the transformation in family welfare work precipitated by the post-war expansion of the welfare state. While existing scholarship has suggested that welfare work pathologised working-class families, and particularly working-class mothers, I argue that many family-welfare workers advanced a progressive understanding of poverty’s causes that sympathised with those living in hardship. These workers’ experiences of talking to clients in working-class homes led them to realise that poverty could never be eradicated simply by helping ‘the poor’ to help themselves. Some of these workers came to believe that poverty could be destroyed only by government intervention. Following recent revisionist historiography, I suggest that the 1950s were not a decade of moral conservatism or political consensus, but rather a time of heated debate over the pattern of class and gender relations. However, I offer two caveats to this new direction in scholarship. Firstly, this article suggests that the influence of the psy-sciences in shaping discussion over social relations was more qualified than existing historical studies suggest. Secondly, the impact of this debate on practice and policy was extremely limited until the late 1950s and the 1960s. This indicates that the connection between discourse and experience is far from straightforward, and that more studies of the connections between them would be valuable in helping us to understand the history of post-war Britain.
Externally driven changes in the abundance of summer and winter flounder
Authors: Bell Richard J. , Hare Jonathan A. , Manderson John P. , Richardson David E.
Published: May 2014

Marine organisms that utilize nearshore environments for major components of their life histories are subject to both local-scale forcing such as water quality and estuarine degradation as well as large-scale forcing such as fishing and decadal-scale climate variability. Large-scale forcing has the potential to synchronize the dynamics of subpopulations, while local-level forcing can produce asynchronous subpopulation trends. Summer flounder (Paralichthys dentatus) and winter flounder (Pseudopleuronectes americanus) are important commercial and recreational flatfish along the east coast of North America which spend their first year of life in coastal habitats. We found that the two exhibited significant within-species coherence in commercial landings and fisheries-independent surveys across the northeast shelf of the United States, suggesting large-scale external drivers. In laboratory studies, temperature has been found to be an important factor regulating survival during the egg, larva and settlement phases of both species. We reconstructed a 40-year time-series of coastal water temperature for the major spawning and nursery areas to examine changes in the thermally available habitat. Estimates of winter flounder abundance were negatively correlated with the winter water temperature, but not with fishing mortality. Summer flounder abundance, by contrast, was negatively correlated with fishing mortality, but exhibited no link with temperature. In addition, time-varying stock–recruitment relationships indicated that stock productivity declined for winter flounder over time, while summer flounder productivity has varied without a trend. While both species declined in the 1980s and early 1990s due to heavy fishing pressure, the reduction in fishing over the last two decades has led to rebuilding of the summer flounder stock and an expansion of its age structure. Declining productivity due to warming estuarine conditions has kept the winter flounder stock at low levels despite low fishing pressure. The two stocks illustrate the importance of controlling fishing mortality in the management of natural marine resources while also accounting for changes in productivity due to climate variability and change.
Fold Rise in Antibody Titers by Measured by Glycoprotein-Based Enzyme-Linked Immunosorbent Assay Is an Excellent Correlate of Protection for a Herpes Zoster Vaccine, Demonstrated via the Vaccine Efficacy Curve
Authors: Gilbert Peter B. , Gabriel Erin E. , Miao Xiaopeng , Li Xiaoming , Su Shu-Chih , Parrino Janie , Chan Ivan S. F.
Published: May 2014

Background.  The phase III Zostavax Efficacy and Safety Trial of 1 dose of licensed zoster vaccine (ZV; Zostavax; Merck) in 50–59-year-olds showed approximately 70% vaccine efficacy (VE) to reduce the incidence of herpes zoster (HZ). An objective of the trial was to assess immune response biomarkers measuring antibodies to varicella zoster virus (VZV) by glycoprotein-based enzyme-linked immunosorbent assay as correlates of protection (CoPs) against HZ.

Methods.  The principal stratification vaccine efficacy curve framework for statistically evaluating immune response biomarkers as CoPs was applied. The VE curve describes how VE against the clinical end point (HZ) varies across participant subgroups defined by biomarker readout measuring vaccine-induced immune response. The VE curve was estimated using several subgroup definitions.

Results.  The fold rise in VZV antibody titers from the time before immunization to 6 weeks after immunization was an excellent CoP, with VE increasing sharply with fold rise: VE was estimated at 0% for the subgroup with no rise and at 90% for the subgroup with 5.26-fold rise. In contrast, VZV antibody titers measured 6 weeks after immunization did not predict VE, with similar estimated VEs across titer subgroups.

Conclusions.  The analysis illustrates the value of the VE curve framework for assessing immune response biomarkers as CoPs in vaccine efficacy trials.

Clinical Trials Registration.  NCT00534248.
Axiomatization and Measurement of Quasi-Hyperbolic Discounting *
Authors: Montiel Olea José Luis , Strzalecki Tomasz
Published: May 2014

This article provides an axiomatic characterization of quasi-hyperbolic discounting and a more general class of semi-hyperbolic preferences. We impose consistency restrictions directly on the intertemporal trade-offs by relying on what we call “annuity compensations.” Our axiomatization leads naturally to an experimental design that disentangles discounting from the elasticity of intertemporal substitution. In a pilot experiment we use the partial identification approach to estimate bounds for the distributions of discount factors in the subject pool. Consistent with previous studies, we find evidence for both present and future bias.
Shy birds play it safe: personality in captivity predicts risk responsiveness during reproduction in the wild
Authors: Cole Ella F. , Quinn John L.
Published: May 2014

Despite a growing body of evidence linking personality to life-history variation and fitness, the behavioural mechanisms underlying these relationships remain poorly understood. One mechanism thought to play a key role is how individuals respond to risk. Relatively reactive and proactive (or shy and bold) personality types are expected to differ in how they manage the inherent trade-off between productivity and survival, with bold individuals being more risk-prone with lower survival probability, and shy individuals adopting a more risk-averse strategy. In the great tit (
Parus major
), the shy–bold personality axis has been well characterized in captivity and linked to fitness. Here, we tested whether ‘exploration behaviour’, a captive assay of the shy–bold axis, can predict risk responsiveness during reproduction in wild great tits. Relatively slow-exploring (shy) females took longer than fast-exploring (bold) birds to resume incubation after a novel object, representing an unknown threat, was attached to their nest-box, with some shy individuals not returning within the 40 min trial period. Risk responsiveness was consistent within individuals over days. These findings provide rare, field-based experimental evidence that shy individuals prioritize survival over reproductive investment, supporting the hypothesis that personality reflects life-history variation through links with risk responsiveness.
Sir Edward Penley Abraham CBE. 10 June 1913 — 9 May 1999
Authors: Jones David S. , Jones John H.
Published: May 2014

Edward Penley Abraham (Ted Abraham to intimate friends and family, EPA to his students), was a pioneer in antibiotics who made critical contributions to the purification and structural elucidation of penicillin as a young man in wartime, and led the discovery and development of cephalosporin C in his maturity. A kindly, modest and self-effacing private man, he could have amassed great wealth out of cephalosporin patents, but instead chose the path of philanthropy. He established substantial charitable funds in his lifetime for the benefit of medicine and allied subjects, the Royal Society, King Edward VI School, Southampton, and the University of Oxford, especially the Sir William Dunn School of Pathology and Lincoln College.
Simulated shift work in rats perturbs multiscale regulation of locomotor activity
Authors: Hsieh Wan-Hsin , Escobar Carolina , Yugay Tatiana , Lo Men-Tzung , Pittman-Polletta Benjamin , Salgado-Delgado Roberto , Scheer Frank A. J. L. , Shea Steven A. , Buijs Ruud M. , Hu Kun
Published: May 2014

Motor activity possesses a multiscale regulation that is characterized by fractal activity fluctuations with similar structure across a wide range of timescales spanning minutes to hours. Fractal activity patterns are disturbed in animals after ablating the master circadian pacemaker (suprachiasmatic nucleus, SCN) and in humans with SCN dysfunction as occurs with aging and in dementia, suggesting the crucial role of the circadian system in the multiscale activity regulation. We hypothesized that the normal synchronization between behavioural cycles and the SCN-generated circadian rhythms is required for multiscale activity regulation. To test the hypothesis, we studied activity fluctuations of rats in a simulated shift work protocol that was designed to force animals to be active during the habitual resting phase of the circadian/daily cycle. We found that these animals had gradually decreased mean activity level and reduced 24-h activity rhythm amplitude, indicating disturbed circadian and behavioural cycles. Moreover, these animals had disrupted fractal activity patterns as characterized by more random activity fluctuations at multiple timescales from 4 to 12 h. Intriguingly, these activity disturbances exacerbated when the shift work schedule lasted longer and persisted even in the normal days (without forced activity) following the shift work. The disrupted circadian and fractal patterns resemble those of SCN-lesioned animals and of human patients with dementia, suggesting a detrimental impact of shift work on multiscale activity regulation.
A unifying framework for quantifying the nature of animal interactions
Authors: Potts Jonathan R. , Mokross Karl , Lewis Mark A.
Published: May 2014

Collective phenomena, whereby agent–agent interactions determine spatial patterns, are ubiquitous in the animal kingdom. On the other hand, movement and space use are also greatly influenced by the interactions between animals and their environment. Despite both types of interaction fundamentally influencing animal behaviour, there has hitherto been no unifying framework for the models proposed in both areas. Here, we construct a general method for inferring population-level spatial patterns from underlying individual movement and interaction processes, a key ingredient in building a statistical mechanics for ecological systems. We show that resource selection functions, as well as several examples of collective motion models, arise as special cases of our framework, thus bringing together resource selection analysis and collective animal behaviour into a single theory. In particular, we focus on combining the various mechanistic models of territorial interactions in the literature with step selection functions, by incorporating interactions into the step selection framework and demonstrating how to derive territorial patterns from the resulting models. We demonstrate the efficacy of our model by application to a population of insectivore birds in the Amazon rainforest.
A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin
Authors: Wagner Andreas
Published: May 2014

Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution.
Gene expression changes in the coccolithophoreEmiliania huxleyiafter 500 generations of selection to ocean acidification
Authors: Lohbeck Kai T. , Riebesell Ulf , Reusch Thorsten B. H.
Published: May 2014

Coccolithophores are unicellular marine algae that produce biogenic calcite scales and substantially contribute to marine primary production and carbon export to the deep ocean. Ongoing ocean acidification particularly impairs calcifying organisms, mostly resulting in decreased growth and calcification. Recent studies revealed that the immediate physiological response in the coccolithophoreEmiliania huxleyito ocean acidification may be partially compensated by evolutionary adaptation, yet the underlying molecular mechanisms are currently unknown. Here, we report on the expression levels of 10 candidate genes putatively relevant to pH regulation, carbon transport, calcification and photosynthesis inE. huxleyipopulations short-term exposed to ocean acidification conditions after acclimation (physiological response) and after 500 generations of high CO2adaptation (adaptive response). The physiological response revealed downregulation of candidate genes, well reflecting the concomitant decrease of growth and calcification. In the adaptive response, putative pH regulation and carbon transport genes were up-regulated, matching partial restoration of growth and calcification in high CO2-adapted populations. Adaptation to ocean acidification inE. huxleyilikely involved improved cellular pH regulation, presumably indirectly affecting calcification. Adaptive evolution may thus have the potential to partially restore cellular pH regulatory capacity and thereby mitigate adverse effects of ocean acidification.
Adaptive phylogeography: functional divergence between haemoglobins derived from different glacial refugia in the bank vole
Authors: Kotlík Petr , Marková Silvia , Vojtek Libor , Stratil Antonín , Šlechta Vlastimil , Hyršl Pavel , Searle Jeremy B.
Published: May 2014

Over the years, researchers have used presumptively neutral molecular variation to infer the origins of current species' distributions in northern latitudes (especially Europe). However, several reported examples of genic and chromosomal replacements suggest that end-glacial colonizations of particular northern areas may have involved genetic input from different source populations at different times, coupled with competition and selection. We investigate the functional consequences of differences between two bank vole (
Clethrionomys glareolus
) haemoglobins deriving from different glacial refugia, one of which partially replaced the other in Britain during end-glacial climate warming. This allows us to examine their adaptive divergence and hence a possible role of selection in the replacement. We determine the amino acid substitution Ser52Cys in the major expressed β-globin gene as the allelic difference. We use structural modelling to reveal that the protein environment renders the 52Cys thiol a highly reactive functional group and we show its reactivity
in vitro
. We demonstrate that possessing the reactive thiol in haemoglobin increases the resistance of bank vole erythrocytes to oxidative stress. Our study thus provides striking evidence for physiological differences between products of genic variants that spread at the expense of one another during colonization of an area from different glacial refugia.
Extinction and recolonization of coastal megafauna following human arrival in New Zealand
Authors: Collins Catherine J. , Rawlence Nicolas J. , Prost Stefan , Anderson Christian N. K. , Knapp Michael , Scofield R. Paul , Robertson Bruce C. , Smith Ian , Matisoo-Smith Elizabeth A. , Chilvers B. Louise , Waters Jonathan M.
Published: May 2014

Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctosspp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction–replacement event in penguins (Megadyptesspp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction.
A mechanism for rapid neurosteroidal regulation of parenting behaviour
Authors: Pradhan Devaleena S. , Solomon-Lane Tessa K. , Willis Madelyne C. , Grober Matthew S.
Published: May 2014

While systemic steroid hormones are known to regulate reproductive behaviour, the actual mechanisms of steroidal regulation remain largely unknown. Steroidogenic enzyme activity can rapidly modulate social behaviour by influencing neurosteroid production. In fish, the enzyme 11β-hydroxysteroid dehydrogenase (11β-HSD) synthesizes 11-ketotestosterone (KT, a potent teleost androgen) and deactivates cortisol (the primary teleost glucocorticoid), and both of these steroid hormones can regulate behaviour. Here, we investigated the role of neurosteroidogenesis in regulating parenting in a haremic bidirectionally hermaphroditic fish,
Lythrypnus dalli
, where males provide all requisite parental care. Using an
in vitro
assay, we found that an 11β-HSD inhibitor, carbenoxolone (CBX), reduced brain and testicular KT synthesis by 90% or more. We modulated neurosteroid levels in parenting males via intracerebroventricular injection of CBX. Within only 20 min, CBX transiently eliminated parenting behaviour, but not other social behaviour, suggesting an enzymatic mechanism for rapid neurosteroidal regulation of parenting. Consistent with our proposed mechanism, elevating KT levels rescued parenting when paired with CBX, while cortisol alone did not affect parenting. Females paired with the experimental males opportunistically consumed unattended eggs, which reduced male reproductive success by 15%, but some females also exhibited parenting behaviour and these females had elevated brain KT. Brain KT levels appear to regulate the expression of parenting behaviour as a result of changes in neural 11β-HSD activity.
Evolutionary pressures on primate intertemporal choice
Authors: Stevens Jeffrey R.
Published: May 2014

From finding food to choosing mates, animals must make intertemporal choices that involve fitness benefits available at different times. Species vary dramatically in their willingness to wait for delayed rewards. Why does this variation across species exist? An adaptive approach to intertemporal choice suggests that time preferences should reflect the temporal problems faced in a species's environment. Here, I use phylogenetic regression to test whether allometric factors relating to body size, relative brain size and social group size predict how long 13 primate species will wait in laboratory intertemporal choice tasks. Controlling for phylogeny, a composite allometric factor that includes body mass, absolute brain size, lifespan and home range size predicted waiting times, but relative brain size and social group size did not. These findings support the notion that selective pressures have sculpted intertemporal choices to solve adaptive problems faced by animals. Collecting these types of data across a large number of species can provide key insights into the evolution of decision making and cognition.
Morphology, morphogenesis and molecular phylogeny of a novel soil ciliate, Pseudouroleptus plestiensis n. sp. (Ciliophora, Oxytrichidae), from the uplands of Colfiorito, Italy
Authors: Bharti Daizy , Kumar Santosh , La Terza Antonietta
Published: May 2014

The terrestrial oxytrichid ciliate Pseudouroleptus plestiensis n. sp., isolated from soil samples collected from the uplands of Colfiorito (Umbria region, Italy), was investigated using live observation and protargol impregnation. The morphology, morphogenesis and molecular phylogeny inferred from small-subunit (SSU) rRNA gene sequences were studied. The novel species is mainly characterized by the following: a cell size of about 145×35 µm in vivo; two ellipsoidal macronuclear nodules and two to four micronuclei; adoral zone about 26 % of body length with a mean of 30 membranelles; about 40 cirri in the right marginal row and 38 in the left marginal row; left fronto-ventral row consisting of about 27–40 cirri, right fronto-ventral row of about three to seven cirri forming a short row to the right of the rear portion of the left fronto-ventral row; one parabuccal cirrus ( = III/2), one buccal and one post-peristomial cirrus; and four dorsal kineties with caudal cirri at the end of kineties 1 and 2. The morphogenesis of the novel species is similar to that of Pseudouroleptus caudatus. Phylogenetic analyses based on SSU rRNA gene sequences consistently placed the novel species within the family Oxytrichidae Ehrenberg, 1838, clustering with P. caudatus and the genus Strongylidium. The results from the present study contribute to the expanding knowledge of the diversity of ciliates in Italian soil.