bluuebunny/crossref_metadata_2025 huggingface dataset:
Priorities for the conservation of the pudu (Pudu puda) in southern South America
Authors: Silva-Rodríguez Eduardo A. , Aleuy O. Alejandro , Fuentes-Hurtado Marcelo , Vianna Juliana A. , Vidal Fernando , Jiménez Jaime E.
Published: May 2013

The southern pudu (Pudu puda) is a threatened deer that is endemic to the South American temperate forests. Despite its assumed threatened status, there is relatively little understanding on the ecology and conservation of this species. Considering this situation and the fact that there are some research groups currently working on this species, we organised a symposium to discuss research and management priorities – as well as to coordinate efforts – to move forward on the conservation of the pudu. We agreed that main research priorities should be to increase the understanding of the threats that jeopardize the viability of pudu populations, with a strong emphasis on research questions that will provide information for the management of these threats. The main management recommendations were to implement monitoring of pudu populations at least in protected areas, to implement specific actions to remove threats from protected areas and to start following internationally-accepted guidelines for the management of rescued and confiscated animals.
Liquid-phase denaturant gradient gel electrophoresis profiles of rumen bacteria from Brahman cross steers selected into two groups on the basis of post-weaning liveweight gain on low crude protein pasture
Authors: Martínez E. D. , Turnbull K. E. , Quigley S. P. , Streeter S. J. , Swain A. , Klieve A. V. , Ouwerkerk D. , Poppi D. P.
Published: May 2013

Two experiments were conducted to evaluate the relationship between rumen liquid-associated bacterial community structures and post-weaning liveweight gain (LWG) of Brahman crossbred steers. Bacterial diversity was assessed using denaturant gradient gel electrophoresis (DGGE). In Experiment 1, 16 steers were selected from a group of 100 steers by pairing steers with the same weaning weight, but different LWG 90 days after weaning (n = 8 highest growth, 0.21 ± 0.01 kg/day; and n = 8 lowest growth –0.07 ± 0.01 kg/day). Thereafter, steers were allocated to a 28-day pen study and fed Mitchell grass (Astrebla spp.) hay to examine DM intake and digestibility, rumen parameters and rumen microbial community in these two groups. Rumen fluid samples were taken by stomach tube 3 h after feeding on the last day of the pen phase. In Experiment 2, 12 pairs of weaned steers were selected from a group of 203 steers on the same basis as Experiment 1. The post-weaning LWG were 0.20 ± 0.03 and 0.02 ± 0.03 kg/day for the 12 highest and 12 lowest growth animals selected, respectively. Steers then grazed dry season Sabi grass (Urochloa mosambicensis) dominant pasture for 21 days, before rumen sampling 3 h after morning grazing by stomach tubing on the last day. In Experiment 1, there were no significant differences between the two groups in DM intake, digestibility, ruminal pH, total volatile fatty acid (VFA) concentration or the VFA proportion. In Experiments 1 and 2, rumen ammonia-N concentration was similar between LWG groups and there was no evidence of a relationship between liquid-phase DGGE profiles of rumen bacteria and high or low post-weaning LWG using multivariate analyses. Furthermore, the number of detected DGGE bands, the Shannon–Wiener and evenness indexes were not different between LWG groups. This DGGE analysis of the most abundant groups of rumen fluid-associated bacteria suggests that microbial populations were not related with the differences observed in post-weaning LWG within a group of weaners fed low crude protein diets.
Delving of sandy surfaced soils reduces frost damage in wheat crops
Authors: Rebbeck M. , Lynch C. , Hayman P. T. , Sadras V. O.
Published: May 2013

Delving is a farming practice involving the mixing of a deep clayey subsoil layer with a sandy topsoil. One of the many effects of this practice is to reduce soil albedo and increase water-holding capacity of the topsoil, thus increasing the potential for storage and release of heat and potential attenuation of the effects of radiative frost. At Keith, a frost-prone location of South Australia, we investigated the effect of management practices with putative capacity to reduce frost damage, with emphasis on delving. Three field experiments were established on Brown Sodosols with a water-repellent sand topsoil.
In relation to crops in untreated control soil, delving increased wheat yield from 1.9 to 3.1 t/ha in 2003, and from 0.5 to 1.5 t/ha in 2004. This large delving effect contrasted with the minor effects of other treatments including soil rolling, sowing rate, row spacing, and cultivar mixture. Lack of significant interactions between treatments indicated a robust response to delving across a range of management practices.
Topsoil and canopy-height minimum temperatures were consistently higher in the delved treatment. The average difference in canopy-height minimum temperature between delved and control treatments was 0.3–0.4°C, with a maximum of 1.6°C in 2003 and 1.2°C in 2004. A single, robust relationship between yield and frost damage fitted the data pooled across treatments and seasons. This, together with the temperature differential between treatments, and significant relationships between minimum canopy-height temperature around flowering and frost damage supported the conclusion that a substantial part of the yield gain attributable to delving was related to reduced frost damage.
Novel Synthesis of 2-thienylcarbonyl-cyclohexane-1,3-dione as Building Block for Indazolones and Isoxazolones
Authors: Chans Guillermo M. , Moyano Elizabeth L. , Yranzo Gloria I.
Published: May 2013

A new synthetic methodology using ultrasonic treatment was applied to the C-acylation of 1,3-cyclohexanedione with thiophene-2-carbonyl chloride to afford 3-hydroxy-2-(2-thienylcarbonyl)cyclohex-2-en-1-one (5). This compound was used as a building block to prepare different bicyclic systems: tetrahydro-4H-indazol-4-ones (7a–c and 9a,b,d), and 6,7-dihydrobenzisoxazole (11) by reaction with different hydrazines and hydroxylamine, respectively. Structural elucidation of all compounds was thoroughly achieved by NMR spectroscopy.
Developments in Electrospray Ionization Mass Spectrometry of Non-Covalent DNA–Ligand Complexes
Authors: Beck Jennifer L.
Published: May 2013

Many anti-cancer drugs function by binding non-covalently to double-stranded (ds) DNA. Electrospray ionization mass spectrometry (ESI-MS) has emerged over the past decade as a sensitive technique for the determination of stoichiometries and relative binding affinities of DNA–ligand interactions. The chromosome contains nucleotide sequences, for example, guanosine-rich regions, that predispose them to the formation of higher order structures such as quadruplex DNA (qDNA). Sequences that form qDNA are found in the telomeres. The proposal that ligands that stabilize qDNA might interfere with the activity of telomerase in cancer cells has stimulated the search for ligands that are selective for qDNA over dsDNA. The insights gained from the development of ESI-MS methods for analysis of non-covalent dsDNA–ligand complexes are now being applied in the search for qDNA-selective ligands. ESI-MS is a useful first-pass screening technique for qDNA-binding ligands. This short review describes some experimental considerations for ESI-MS analysis of DNA–ligand complexes, briefly addresses the question of whether non-covalent DNA–ligand complexes are faithfully transferred from solution to the gas phase, discusses ion mobility mass spectrometry as a technique for probing this issue, and highlights some recent ESI-MS studies of qDNA-selective ligands.
New 'Green' Corrosion Inhibitors Based on Rare Earth Compounds
Authors: Forsyth Maria , Seter Marianne , Hinton Bruce , Deacon Glen , Junk Peter
Published: May 2013

A series of rare earth organic compounds pioneered by our group have been shown to provide a viable alternative to the use of chromates as corrosion inhibitors for some steel and aluminium applications. For example we have shown that the lanthanum 4-hydroxy cinnamate offers excellent corrosion mitigation for mild steel in aqueous environments while rare earth diphenyl phosphates offer the best protection in the case of aluminium alloys. In both cases the protection appears to be related to the formation of a nanometre thick interphase occurring on the surface that reduces the electrochemical processes leading to metal loss or pitting. Very recent work has indicated that we may even be able to address the challenging issue of stress corrosion cracking of high strength steels. Furthermore, filiform corrosion can be suppressed when selected rare earth inhibitor compounds are added as pigments to a polymer coating. There is little doubt from the work thus far that a synergy exists between the rare earth and organic inhibitor components in these novel compounds. This paper reviews some of the published research conducted by the senior author and colleagues over the past 10 years in this developing field of green corrosion inhibitors.
Ionic Liquids with Solvatochromatic and Charge-Transfer Functionalities Incorporating the Viologen Moiety
Authors: Gunaratne H. Q. Nimal , Nockemann Peter , Olejarz Sonia , Reid Stephanie M. , Seddon Kenneth R. , Srinivasan Geetha
Published: May 2013

The synthesis of oligoether-functionalised viologen-based dicationic ionic liquids, their electrochemical properties, solvatochromism, and ability to form charge-transfer complexes, are described.
Oxidative and Thermal Routes to Novel Isoxazolopyridines
Authors: Dyall LK , Maloney DW , Harvey JJ , Fulloon BE
Published: May 2013

The novel bicyclic compounds isoxazolo [3,4-b] pyridine (1). 3-phenylisoxazolo [3,4- b] pyridine (2) and 3-phenylisoxazolo[3,4-c]pyridine (3) have been synthesized by oxidative cyclization of the amines 2-aminopyridine-3-carbaldehyde (4), (2-amino-3-pyridyl)phenylmethanone (5) and (3-amino-4-pyridyl)phenylmethanone (6). The oxidant was bis(acetato-O)phenyliodine. 3-Phenylisoxazolo[3,4-c]pyridine (3) was also obtained by thermolysis of 3-azido-4-benzoylpyridine (7). Comparison of the rate of thermolysis of this azide with that of 3-azidopyridine identified a neighbouring group effect (from the benzoyl group) which is about four times as large as in a corresponding 2-azidobenzophenone. COSY and HETCOR techniques have been used to assign the 1H and 13C n.m.r. spectra of isoxazolo[3,4-b]pyridine (1).
Yield stability for cereals in a changing climate
Authors: Powell Nicola , Ji Xuemei , Ravash Rudabe , Edlington Jane , Dolferus Rudy
Published: May 2013

The United Nations Food and Agriculture Organisation (FAO) forecasts a 34% increase in the world population by 2050. As a consequence, the productivity of important staple crops such as cereals needs to be boosted by an estimated 43%. This growth in cereal productivity will need to occur in a world with a changing climate, where more frequent weather extremes will impact on grain productivity. Improving cereal productivity will, therefore, not only be a matter of increasing yield potential of current germplasm, but also of improving yield stability through enhanced tolerance to abiotic stresses. Successful reproductive development in cereals is essential for grain productivity and environmental constraints (drought, cold, frost, heat and waterlogging) that are associated with climate change are likely to have severe effects on yield stability of cereal crops. Currently, genetic gains conferring improved abiotic stress tolerance in cereals is hampered by the lack of reliable screening methods, availability of suitable germplasm and poor knowledge about the physiological and molecular underpinnings of abiotic stress tolerance traits.
Determinants of pelagic metabolism in the Timor Sea during the inter-monsoon period
Authors: McKinnon A. D. , Carleton J. H. , Duggan S.
Published: May 2013

The Timor Sea is a major conduit of the Indonesian Throughflow characterised by large internal waves and tides. To ascertain whether these result in high pelagic productivity, we conducted experiments to determine the metabolic balance between net community production (NCP) and community respiration (CR) on the Sahul Shelf, the Sahul Shoals and the Yampi Shelf, an area of active hydrocarbon seeps. The barrier to vertical mixing of subthermocline nutrients represented by the halocline allowed new production to dominate in March 2004, whereas production in June 2005 depended on recycled nutrients. CR was correlated with dissolved organic carbon (DOC) in 2004, but with chlorophyll in 2005, suggesting that respiration was dominated by microheterotrophs in 2004 but by autotrophs in 2005. Overall, area-specific CR averaged 120 ± 92 (s.d.), 101 ± 52 and 61 ± 6 mmol O2 m–2 day–1, NCP averaged 109 ± 85 (s.d.), 32 ± 41 and 57 ± 10 mmol O2 m–2 day–1, and average gross primary production (= CR+NCP) : R ratios were 1.9, 1.4 and 1.9 on the shelf, at the Sahul Shoals and the Yampi Shelf, respectively. We suggest that differences in water column structure and internal wave activity drive intermittent high production events in a predominantly oligotrophic sea.
Implementation, Effectiveness and Political Context of Comprehensive Primary Health Care: Preliminary Findings of a Global Literature Review
Authors: Labonté Ronald , Pooyak Sherri , Baum Fran , Schaay Nikki , Packer Corinne , Laplante Denise , Vega-Romero Roman , Viswanatha Vinay , Barten Francoise , Hurley Catherine , Tujuba Ali Hayat , Manolakos Halli , Acosta-Ramírez Naydú , Pollard Jennifer , Narayan Thelma , Mohamed Suraya , Peperkamp Lonneke , Johns Julie , Ouldzeidoune Nacerdine , Sinclair Raven , Sanders David
Published: May 2013

Primary health care (PHC) is again high on the international agenda. It was the theme of The World Health Report in 2008, thirty years after the Alma-Ata Declaration, and has been the topic of a series of significant conferences around the world throughout 2008. What have we learnt about its impact in improving population health and health equity? What more do we still need to know? These two questions frame a four-year international research/capacity-building project, 'Revitalizing Health for All' (RHFA), funded by the Canadian Global Health Research Initiative (http://www.idrc.ca/en/ev-108118-201-1-DO_TOPIC.html). The RHFA project is organised under the umbrella of the People?s Health Movement (http://www.phmovement.org/en) and the International People?s Health University (http://phmovement.org/iphu/), and involves researchers from over a dozen countries. Our project team?s understanding of PHC is of a comprehensive approach aimed at reducing health inequities that is based on meaningful community participation, multidisciplinary teams and action across sectors.
Activating patients with chronic disease for self-management: comparison of self-managing patients with those managing by frequent readmissions to hospital
Authors: Kirby Sue E. , Dennis Sarah M. , Bazeley Pat , Harris Mark F.
Published: May 2013

Understanding the factors that activate people to self-manage chronic disease is important in improving uptake levels. If the many frequent hospital users who present with acute exacerbations of chronic disease were to self-manage at home, some hospital admissions would be avoided. Patient interview and demographic, psychological, clinical and service utilisation data were compared for two groups of patients with chronic disease: those attending self-management services and those who managed by using hospital services. Data were analysed to see whether there were differences that might explain the two different approaches to managing their conditions. The two groups were similar in terms of comorbidity, age, sex, home services, home support and educational level. Self-managing patients were activated by their clinician, accepted their disease, changed their identity, confronted emotions and learnt the skills to self-manage and avoid hospital. Patients who frequently used hospital services to manage their chronic disease were often in denial about their chronic disease, hung on to their identity and expressed little emotional response. However, they reported a stronger sense of coherence and rated their health more highly than self-managing patients. This study shed light on the process of patient activation for self-management. A better understanding of the process of patient activation would encourage clinicians who come into contact with frequently readmitted chronic disease patients to be more proactive in supporting self-management.
Inactivated Sendai-virus-mediated fusion improves early development of cloned bovine embryos by avoiding endoplasmic-reticulum-stress-associated apoptosis
Authors: Song Bong-Seok , Kim Ji-Su , Yoon Seung-Bin , Lee Kyu-Sun , Koo Deog-Bon , Lee Dong-Seok , Choo Young-Kug , Huh Jae-Won , Lee Sang-Rae , Kim Sun-Uk , Kim Sang-Hyun , Kim Hwan Mook , Chang Kyu-Tae
Published: May 2013

Somatic cell nuclear transfer (SCNT) is a powerful tool, not only for producing cloned animals, but also in revealing various early developmental events. However, relatively little is known regarding the biological events and underlying mechanism(s) directly associated with early development of SCNT embryos. Here, we show that production of high-quality bovine SCNT blastocysts is dependent on the method used for fusion and the associated reduction in endoplasmic reticulum (ER) stress. During fusion between the donor cell and the enucleated oocyte, electrofusion triggers spontaneous oocyte activation, accompanied by an increase in intracellular Ca2+ and improper nuclear remodelling. These events can be greatly reduced by the use of Sendai virus (SV)-mediated fusion. Moreover, SV-SCNT improves the blastulation rate and blastocyst quality, defined by the number and ratio of inner cell mass and trophectoderm cells in each blastocyst, in comparison with electrofusion-mediated SCNT (E-SCNT). Interestingly, expression of ER-stress-associated genes and blastomere apoptosis were significantly increased in E-SCNT embryos. These increases could be reversed by inhibition of ER stress or by using the SV-mediated fusion method. Collectively, these results indicate that SV-mediated fusion improves the developmental competence and quality of SCNT blastocysts, by reducing ER-stress-associated apoptosis.
Immunisation against inhibin enhances follicular development, oocyte maturation and superovulatory response in water buffaloes
Authors: Li D. R. , Qin G. S. , Wei Y. M. , Lu F. H. , Huang Q. S. , Jiang H. S. , Shi D. S. , Shi Z. D.
Published: May 2013

This study was carried out to test the feasibility of enhancing embryo production in vivo and in vitro by immunoneutralisation against inhibin or follistatin. In Experiment 1, multi-parity buffaloes were assigned into three groups: High group (n = 8), which received one primary (2 mg) and two booster (1 mg) vaccinations (28-day intervals) with a recombinant inhibin α subunit in 1 mL of white oil adjuvant; Low group (n = 8), which received half that dose; and Control group (n = 7), which received only adjuvant. Immunisation against inhibin stimulated development of ovarian follicles. Following superovulation and artificial insemination, inhibin-immunised buffaloes had more developing follicles than the Control buffaloes. The average number of embryos and unfertilised ova (4.5 ± 0.6, n = 6) in the High group was higher (P < 0.05) than in the Control group (2.8 ± 0.6, n = 5) and was intermediate (4.1 ± 0.7, n = 7) in the Low group. The pooled number of transferable embryos of the High and Low groups (3.2 ± 0.5, n = 13) was also higher (P < 0.05) than that (1.6 ± 0.7, n = 5) of the controls. The immunised groups also had higher plasma concentrations of activin, oestradiol and progesterone. In Experiment 2, the addition of anti-inhibin or anti-follistatin antibodies into buffalo oocyte IVM maturation medium significantly improved oocyte maturation and cleavage rates following parthenogenic activation. Treatment with anti-follistatin antibody also doubled the blastocyst yield from activated embryos. These results demonstrated that immunisation against inhibin stimulated follicular development, enhanced oocyte quality and maturation competence, yielded more and better embryos both in vivo and in vitro.
Managing Murray–Darling Basin livestock systems in a variable and changing climate: challenges and opportunities
Authors: Crimp S. J. , Stokes C. J. , Howden S. M. , Moore A. D. , Jacobs B. , Brown P. R. , Ash A. J. , Kokic P. , Leith P.
Published: May 2013

The key biophysical impacts associated with projected climate change in the Murray–Darling Basin (MDB) include: declines in pasture productivity, reduced forage quality, livestock heat stress, greater problems with some pests and weeds, more frequent droughts, more intense rainfall events, and greater risks of soil degradation. The most arid and least productive rangelands in the MDB region may be the most severely impacted by climate change, while the more productive eastern and northern grazing lands in the MDB may provide some opportunities for slight increases in production. In order to continue to thrive in the future, livestock industries need to anticipate these changes, prepare for uncertainty, and develop adaptation strategies now. While climate change will have direct effects on livestock, the dominant influences on grazing enterprises in the MDB will be through changes in plant growth and the timing, quantity and quality of forage availability. Climate change will involve a complex mix of responses to rising atmospheric carbon dioxide levels, rising temperatures, changes in rainfall and other weather factors, and broader issues related to how people collectively and individually respond to these changes. Enhancing the ability of individuals to respond to a changing climate will occur through building adaptive capacity. We have, via secondary data, selected from the Australian Agricultural and Grazing Industries Survey, built a national composite index of generic adaptive capacity of rural households. This approach expresses adaptive capacity as an emergent property of the diverse forms of human, social, natural, physical and financial capital from which livelihoods are derived. Human capital was rated as ‘high’ across the majority of the MDB compared with the rest of Australia, while social, physical and financial capital were rated as ‘moderate’ to ‘low’. The resultant measure of adaptive capacity, made up of the five capitals, was ‘low’ in the northern and central-west regions of the MDB and higher in the central and eastern parts possibly indicating a greater propensity to adapt to climate change in these regions.
Morphometric studies of polyploid Cardamine species (Brassicaceae) from Japan: solving a long-standing taxonomic and nomenclatural controversy
Authors: Lihová Judita , Kudoh Hiroshi , Marhold Karol
Published: May 2013

Polyploidy is an important evolutionary mechanism and speciation mode in plants; however, delimitation of species boundaries in polyploid complexes is often a difficult task. In the present paper, we explore morphological variation in a group of East Asian Cardamine polyploids that have long been shrouded in taxonomic and nomenclatural confusion. We relate the present morphometric data of 41 sampled populations with recently published ploidy-level data, and propose a revised taxonomic treatment, including the designation of several lectotypes. The following species are recognised in Japan: C. schinziana O.E.Schulz (2n = 6x, 8x), C. torrentis Nakai (2n = 8x), C. valida (Takeda) Nakai (2n = 4x) and C. yezoensis Maxim. (2n = 6x−12x). C. amariformis Nakai (2n = 4x) from Korea is also discussed, although it may be conspecific with C. valida, pending further studies. Distribution of these taxa in the Japanese Archipelago is characterised, including comments on their occurrence outside of Japan.
Phylogeny reconstruction of Callitris Vent. (Cupressaceae) and its allies leads to inclusion of Actinostrobus within Callitris
Authors: Piggin Josephine , Bruhl Jeremy J.
Published: May 2013

Relationships between Callitris, Actinostrobus and Neocallitropsis, members of the southern hemisphere ‘callitroid clade’ (Callitroideae sensu Gadek et al. 2000) of Cupressaceae, are estimated using a database of 42 morphological and anatomical characters. Callitris is paraphyletic, with Actinostrobus being closer to a large well supported clade of 15 Australian species of Callitris than are C. baileyi, C. macleayana and the New Caledonian taxa. The New Caledonian unispecific endemic, Neocallitropsis, is sister to the clade comprising all Callitris and Actinostrobus species. There are marked differences between this estimate of the phylogeny and two recent estimates based on nuclear encoded DNA sequence data and non-molecular data, respectively, but some simlarities to the molecular estimate are highlighted and lead us here to formally include Actinostrobus within Callitris. Further molecular data are needed to test these results and explore the cause of the conflict between these estimates of the phylogeny within the group, and the status of Neocallitropsis.
Surface charge characteristics of variable charge soils in Thailand
Authors: Wisawapipat W. , Kheoruenromne I. , Suddhiprakarn A. , Gilkes R. J.
Published: May 2013

Surface charge characteristics were investigated using a charge fingerprinting procedure for 90 samples from 32 profiles of highly weathered Oxisols and Ultisols derived from shale/limestone, basalt, granite, local alluvium, sedimentary, and metasedimentary rocks under tropical savanna and tropical monsoonal climates in Thailand. The charge fingerprints of 5 whole soils, after removal of organic matter and of kaolin and ion oxides from these soils, were also measured to clarify factors contributing to the variable charge behaviour. Phosphate sorption was determined and related to charge properties. Kaolin was the dominant mineral of the clay fraction with moderate amounts of goethite and hematite. Gibbsite was present in Oxisols formed on limestone and basalt under more humid conditions. All soils exhibited variable charge behaviour but the magnitude and rate of change in variable charge with pH varied greatly between Oxisols and Ultisols. Oxisols had higher amounts of variable charge than Ultisols, reflecting the differences in amounts of clay and extractable Fe and Al. Oxisols formed on basalt and limestone under more humid conditions had high values of anion exchange capacity (AEC) due to the contributions of goethite, gibbsite, and boehmite. The relationships of base cation exchange capacity (CECB) and AEC with pH were linear. Rates of change with pH of both negative and positive variable charge (Ac, Aa) were closely related to CEC, specific surface area (SSA), pH(NaF), and various forms of extractable Fe, Al, and Mn. The charge fingerprints of soil after removal of organic matter indicated that organic matter exerted a strong influence on both the magnitude of negative charge and rate of change with pH. Kaolin had permanent and variable charge, with SSA and crystal size (MCD001) being highly predictive of the rate of change in variable negative charge with pH. Iron oxide concentrates exhibited strongly pH-dependent charge and the mean coherently diffracting length (MCD110) of hematite was highly predictive of both the magnitude and rate of change in variable positive charge with pH. Charge coefficients (Ac, Ba) had highly significant (P = 0.005) positive relationships with Langmuir and Freundlich phosphate sorption maximum coefficients (Xm, k), indicating that the surfaces of amorphous, poorly ordered, and crystalline Fe and Al oxides are prime sites for both P sorption and variable charge.
Allowing a wildfire to burn: estimating the effect on future fire suppression costs
Authors: Houtman Rachel M. , Montgomery Claire A. , Gagnon Aaron R. , Calkin David E. , Dietterich Thomas G. , McGregor Sean , Crowley Mark
Published: May 2013

Where a legacy of aggressive wildland fire suppression has left forests in need of fuel reduction, allowing wildland fire to burn may provide fuel treatment benefits, thereby reducing suppression costs from subsequent fires. The least-cost-plus-net-value-change model of wildland fire economics includes benefits of wildfire in a framework for evaluating suppression options. In this study, we estimated one component of that benefit – the expected present value of the reduction in suppression costs for subsequent fires arising from the fuel treatment effect of a current fire. To that end, we employed Monte Carlo methods to generate a set of scenarios for subsequent fire ignition and weather events, which are referred to as sample paths, for a study area in central Oregon. We simulated fire on the landscape over a 100-year time horizon using existing models of fire behaviour, vegetation and fuels development, and suppression effectiveness, and we estimated suppression costs using an existing suppression cost model. Our estimates suggest that the potential cost savings may be substantial. Further research is needed to estimate the full least-cost-plus-net-value-change model. This line of research will extend the set of tools available for developing wildfire management plans for forested landscapes.
Habitat model for baiting foxes in suburban areas to counteract Echinococcus multilocularis
Authors: König Andreas , Janko Christof , Barla-Szabo Bence , Fahrenhold Diana , Heibl Claudius , Perret Eva , Wermuth Stefanie
Published: May 2013

Context
Foxes are carriers of many zoonoses, such as the fox tapeworm. Treating foxes with medication of edible bait is often the only way of protecting people. Whereas bait can be distributed very effectively by aeroplane in rural areas, in settled areas it must be distributed by hand. In doing so it is important to get as close as possible to the foxes.

Aims
In suburban areas it is important to ensure that it is mainly foxes that take the bait and that they do so within a short time. In order to achieve this, a habitat model was developed for the baiting of foxes in suburban areas.

Methods
In Grünwald, a suburb of Munich, 12 foxes were radio-collared and observed to see which gardens they visited more frequently or for longer periods. At the same time, the community area was divided up by a grid. At each point on the grid, two gardens were selected: one garden known to be visited by foxes, and a control garden in which no fox had been observed. In this way the structure of average gardens in the community could be compared with those used by foxes. On this basis a model of garden use by foxes was developed and checked by a program of phototrapping in a separate area.

Key results
Using sources of food, bushes and garden houses as variables, a habitat model was developed with the categories ‘unsuitable’, ‘less suitable’ and ‘very suitable’ for foxes. This correlated closely with the appearance of foxes in gardens (P < 0.001).

Conclusion
The model helps to identify gardens preferred by foxes.

Implications
This study shows us how to reach foxes in suburban environments quickly with bait containing medication and so contributes to improving public health. The method described, of checking a model in an area not used in the development of the model, can also be seen as a contribution towards the universalisation of models.
Detection and stratification approaches for aerial surveys of deer in prairie–parklands
Authors: Habib Thomas J. , Moore David A. , Merrill Evelyn H.
Published: May 2013

Context
For management decisions that require accurate and precise estimates of large mammal population numbers, aerial surveys are considered reliable despite their cost. However, aerial surveys may still suffer from underestimation because of undetected animals and low precision as a result of inefficient sampling designs.

Aims
We assess detection of two species of deer in prairie-parkland communities of western Canada and evaluate a suite of survey design features for improving the accuracy and precision of population estimates from aerial surveys.

Methods
Modelling detection of deer was based on 100 sightability trials involving 54 radio-collared white-tailed and 46 mule deer. We used empirical survey data to simulate surveys under three alternative stratification approaches, schemes for grouping strata, and allocations of survey effort and compared the precision and accuracy of the resulting population estimates.

Key results
We observed deer in 83 of the 100 trials, with detection decreasing with small group size, reduced deer activity, low snow cover, high forest cover and observer fatigue. Survey precision and accuracy were highest when stratification was based on natural breaks, calculated via Jenks optimisation, in the values of resource-selection function (RSF), although improvement was less pronounced for estimates of mule deer abundance. Optimal or equal allocation of sampling effort among strata outperformed proportional allocation of sampling effort. Use of RSF for stratification reduced the coefficient of variation (CV) in estimates of deer numbers from 38% to 23% for white-tailed deer and from 33% to 27% for mule deer compared with past approaches.

Conclusions
Stratification based on RSF values improved precision of deer surveys the most; however, using even simple measures related to habitat selection can improve population estimates. Where deer are highly aggregated, reliably recording all variables needed to implement sightability models can prove problematic; however, survey detection adjustments are nevertheless important to account for the relatively small, but still significant, proportion of missed animals in open prairie–parkland environments.

Implications
Field experiments to assess aerial survey design are impractical because of cost. We illustrate how simulated surveys using empirical data can be useful to evaluate alternative survey designs to improve population estimates in a region when high accuracy or precision are needed to address management questions or to calibrate more cost-effective approaches.
Long-term effects of immunocontraception on wild boar fertility, physiology and behaviour
Authors: Massei Giovanna , Cowan Dave P. , Coats Julia , Bellamy Fiona , Quy Roger , Pietravalle Stéphane , Brash Matthew , Miller Lowell A.
Published: May 2013

Context
Fertility control appears as a publicly acceptable alternative to lethal methods for limiting population growth in wildlife. Recently developed single-dose immunocontraceptive vaccines have induced infertility in several mammals. However, the potential side-effects and the long-term effectiveness of these contraceptives have been poorly investigated.

Aims
We tested the long-term effectiveness and potential side-effects of the single-dose gonadotrophin-releasing hormone (GnRH) vaccine GonaCon™ on captive female wild boar.

Methods
We carried out two sequential trials: Trial 1 (n = 6 GonaCon™-treated and 6 control wild boar) and Trial 2 which started two years later and replicated Trial 1. We assessed the effectiveness of GonaCon™ to cause infertility by measuring GnRH antibody titres, by monitoring the oestrous cycle through the concentration of faecal progesterone and by recording the sows’ reproductive output in the 4–6 years following treatment. We evaluated the potential side-effects by monitoring behaviour, bodyweight and haematological and biochemical variables.

Key results
GnRH-antibody titres decreased with time but were still detectable in all females six years after vaccination with a single dose of GonaCon™. In Trial 1 none of the treated females gave birth in the six years after vaccination. In Trial 2, progesterone indicated that two of the six treated females were cycling. One of the cycling treated females gave birth one year after vaccination; the other five, including the second cycling sow, did not reproduce in the four years following vaccination. We found no differences in bodyweight, haematology, biochemistry and behaviour and no obvious sign of injection site reaction.

Conclusions
GonaCon™ can suppress reproduction in wild boar with no long-term effects on behaviour and physiology. Therefore, GonaCon™ can be regarded as an effective and safe contraceptive for this species.

Implications
The lack of evidence of adverse effects and the longevity of effect of GonaCon™ suggest that this contraceptive could be now tested in field trials and in contexts where culling of overabundant populations of wild boar is unfeasible, illegal or unacceptable. These instances include urban areas, parks, and management of diseases where culling might cause social perturbation and result in increased disease transmission rates.
Natal nest locations of the Asian house rat (Rattus tanezumi) in lowland rice–coconut cropping systems: a coconut penthouse or rice bunds with water frontage?
Authors: Stuart Alexander M. , Prescott Colin V. , Singleton Grant R.
Published: May 2013

Context
Rattus tanezumi is a serious crop pest within the island of Luzon, Philippines. In intensive flood-irrigated rice field ecosystems of Luzon, female R. tanezumi are known to primarily nest within the tillers of ripening rice fields and along the banks of irrigation canals. The nesting habits of R. tanezumi in complex rice–coconut cropping systems are unknown.

Aims
To identify the natal nest locations of R. tanezumi females in rice–coconut systems of the Sierra Madre Biodiversity Corridor (SMBC), Luzon, during the main breeding season to develop a management strategy that specifically targets their nesting habitat.

Methods
When rice was at the booting to ripening stage, cage-traps were placed in rice fields adjacent to coconut habitat. Thirty breeding adult R. tanezumi females were fitted with radio-collars and successfully tracked to their nest sites.

Key results
Most R. tanezumi nests (66.7%) were located in coconut groves, five nests (16.7%) were located in rice fields and five nests (16.7%) were located on the rice field edge. All nests were located above ground level and seven nests were located in coconut tree crowns. The median distance of nest sites to the nearest rice field was 22.5 m. Most nest site locations had good cover of ground vegetation and understorey vegetation, but low canopy cover. Only one nest location had an understorey vegetation height of less than 20 cm.

Conclusions
In the coastal lowland rice–coconut cropping systems of the SMBC, female R. tanezumi showed a preference for nesting in adjacent coconut groves. This is contrary to previous studies in intensive flood-irrigated rice ecosystems of Luzon, where the species nests mainly in the banks of irrigation canals. It is important to understand rodent breeding ecology in a specific ecosystem before implementing appropriate management strategies.

Implications
In lowland rice–coconut cropping systems, coconut groves adjacent to rice fields should be targeted for the management of R. tanezumi nest sites during the main breeding season as part of an integrated ecologically based approach to rodent pest management.
Short-term response of the long-nosed bandicoot, Perameles nasuta, and the southern brown bandicoot, Isoodon obesulus obesulus, to low-intensity prescribed fire in heathland vegetation
Authors: Hope Ben
Published: May 2013

Context
Prescribed burning is routinely performed within the Sydney Basin as a method of fire-hazard mitigation. Despite the widespread use of prescribed fire, knowledge of the impact of prescribed fire on most fauna species remains unclear. This is particularly the case for bandicoot species.

Aims
To determine the impact of a low-intensity prescribed fire on the survival of the long-nosed bandicoot, Perameles nasuta, and the southern brown bandicoot, Isoodon obesulus obesulus (hereafter abbreviated to I. obesulus), immediately after the fire and at 5 weeks, 5 months and 13 months following the fire. To document the spatial ecology and nesting requirements of I. obesulus and P. nasuta before and after fire.

Methods
One I. obesulus and seven P. nasuta (five female and two male) individuals were radio-tracked. Animals were tracked before, during and following a hazard-reduction burn to assess the impact of fire on home range, survival and nesting behaviour.

Key results
Post-fire survival of P. nasuta and I. obesulus was high and the population remained stable up to 5 months following the fire. All animals tracked within the burn area (three female P. nasuta) survived the passage of fire. The home range for one male I. obesulus was found to be 2.35 ha 50% kernel-density estimate (KDE) and 12.35 ha 95% KDE. Female P. nasuta (n = 5) had a home range of 1.3 ha ± 0.2 s.e. 50% KDE and 7.5 ha ± 1.7 s.e. 95% KDE. Male P. nasuta (n = 1) had a home range of 1.1 ha 50% KDE and 6.5ha 95% KDE. Nesting for both species tended to occur in dense vegetation, with a slight shift to non-combustible refuge sites post-fire. Animals tended to maintain exclusive and relatively stable core home ranges, although overlap of non-core home ranges was common.

Conclusions
The survival of bandicoots following a low-intensity hazard-reduction fire was high in the short term; however, further research is required to determine how the components of a fire regime affect native species, in particular peramelids.

Implications
Hazard-reduction fires should be used with caution to manage the isolated and endangered northern Sydney population of I. obesulus, so as to ensure the persistence of this species.
Reciprocal regulation of PKA and Rac signaling
Authors: Bachmann Verena A. , Riml Anna , Huber Roland G. , Baillie George S. , Liedl Klaus R. , Valovka Taras , Stefan Eduard
Published: May 2013

Activated G protein-coupled receptors (GPCRs) and receptor tyrosine kinases relay extracellular signals through spatial and temporal controlled kinase and GTPase entities. These enzymes are coordinated by multifunctional scaffolding proteins for precise intracellular signal processing. The cAMP-dependent protein kinase A (PKA) is the prime example for compartmentalized signal transmission downstream of distinct GPCRs. A-kinase anchoring proteins tether PKA to specific intracellular sites to ensure precision and directionality of PKA phosphorylation events. Here, we show that the Rho-GTPase Rac contains A-kinase anchoring protein properties and forms a dynamic cellular protein complex with PKA. The formation of this transient core complex depends on binary interactions with PKA subunits, cAMP levels and cellular GTP-loading accounting for bidirectional consequences on PKA and Rac downstream signaling. We show that GTP-Rac stabilizes the inactive PKA holoenzyme. However, β-adrenergic receptor-mediated activation of GTP-Rac–bound PKA routes signals to the Raf-Mek-Erk cascade, which is critically implicated in cell proliferation. We describe a further mechanism of how cAMP enhances nuclear Erk1/2 signaling: It emanates from transphosphorylation of p21-activated kinases in their evolutionary conserved kinase-activation loop through GTP-Rac compartmentalized PKA activities. Sole transphosphorylation of p21-activated kinases is not sufficient to activate Erk1/2. It requires complex formation of both kinases with GTP-Rac1 to unleash cAMP-PKA–boosted activation of Raf-Mek-Erk. Consequently GTP-Rac functions as a dual kinase-tuning scaffold that favors the PKA holoenzyme and contributes to potentiate Erk1/2 signaling. Our findings offer additional mechanistic insights how β-adrenergic receptor-controlled PKA activities enhance GTP-Rac–mediated activation of nuclear Erk1/2 signaling.
Probing quantum coherence in qubit arrays
Authors: Almeida J , de Groot P C , Huelga S F , Liguori-Schremp A M , Plenio M B
Published: May 2013

We discuss how the observation of population localization effects in periodically driven systems can be used to quantify the presence of quantum coherence in interacting qubit arrays. Essential for our proposal is the fact that these localization effects persist beyond tight-binding Hamiltonian models. This result is of special practical relevance in those situations where direct system probing using tomographic schemes becomes infeasible beyond a very small number of qubits. As a proof of principle, we study analytically a Hamiltonian system consisting of a chain of superconducting flux qubits under the effect of a periodic driving. We provide extensive numerical support of our results in the simple case of a two-qubit chain. For this system we also study the robustness of the scheme against different types of noise and disorder. We show that localization effects underpinned by quantum coherent interactions should be observable within realistic parameter regimes in chains with a larger number of qubits.
Galectin-3– and phospho-caveolin-1–dependent outside-in integrin signaling mediates the EGF motogenic response in mammary cancer cells
Authors: Boscher Cecile , Nabi Ivan R.
Published: May 2013

In murine mammary epithelial cancer cells, galectin-3 binding to β1,6-acetylglucosaminyltransferase V (Mgat5)–modified N-glycans restricts epidermal growth factor (EGF) receptor mobility in the plasma membrane and acts synergistically with phospho-caveolin-1 to promote integrin-dependent matrix remodeling and cell migration. We show that EGF signaling to RhoA is galectin-3 and phospho-caveolin-1 dependent and promotes the formation of transient, actin-rich, circular dorsal ruffles (CDRs), cell migration, and fibronectin fibrillogenesis via Src- and integrin-linked kinase (ILK)–dependent signaling. ILK, Src, and galectin-3 also mediate EGF stimulation of caveolin-1 phosphorylation. Direct activation of integrin with Mn2+induces galectin-3, ILK, and Src-dependent RhoA activation and caveolin-1 phosphorylation. This suggests that in response to EGF, galectin-3 enables outside-in integrin signaling stimulating phospho-caveolin-1–dependent RhoA activation, actin reorganization in CDRs, cell migration, and fibronectin remodeling. Similarly, caveolin-1/galectin-3–dependent EGF signaling induces motility, peripheral actin ruffling, and RhoA activation in MDA-MB-231 human breast carcinoma cells, but not HeLa cells. These studies define a galectin-3/phospho-caveolin-1/RhoA signaling module that mediates integrin signaling downstream of growth factor activation, leading to actin and matrix remodeling and tumor cell migration in metastatic cancer cells.
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
Authors: Hebestreit Katja , Dugas Martin , Klein Hans-Ulrich
Published: May 2013

Motivation: Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre-processing and alignment software, methods for analyzing the resulting methylation profiles are relatively limited so far. For instance, an appropriate pipeline to detect DNA methylation differences between cancer and control samples is still required.

Results: We propose an algorithm that detects significantly differentially methylated regions in data obtained by targeted bisulfite sequencing approaches, such as reduced representation bisulfite sequencing. In a first step, this approach tests all target regions for methylation differences by taking spatial dependence into account. A false discovery rate procedure controls the expected proportion of incorrectly rejected regions. In a second step, the significant target regions are trimmed to the actually differentially methylated regions. This hierarchical procedure detects differentially methylated regions with increased power compared with existing methods.

Availability: R/Bioconductor package BiSeq.

Contact:  katja.hebestreit@uni-muenster.de

Supplementary information:  Supplementary data are available at Bioinformatics online.