bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of an artificial surfactant release on air‐sea gas fluxes during Deep Ocean Gas Exchange Experiment II
Authors: Salter M. E. , Upstill‐Goddard R. C. , Nightingale P. D. , Archer S. D. , Blomquist B. , Ho D. T. , Huebert B. , Schlosser P. , Yang M.
Published: September 2011

During the 2007 UK SOLAS Deep Ocean Gas Exchange Experiment in the northeast Atlantic Ocean, we conducted the first ever study of the effect of a deliberately released surfactant (oleyl alcohol) on gas transfer velocities (kw) in the open ocean. Exchange rates were estimated with the 3He/SF6 dual tracer technique and from measured sea‐to‐air DMS fluxes and surface water concentrations. A total of seven kw estimates derived from 3He/SF6 were made, two of which were deemed to be influenced by the surfactant. These exhibited suppression from ∼5% to 55% at intermediate wind speeds (U10) in the range 7.2–10.7 m s−1. Similarly, kw determined from DMS data (kDMS) was also depressed by the surfactant; suppression ranged from ∼39% at 5.0 m s−1 to ∼24% at 10.8 m s−1. Surfactant thus has the potential to measurably suppress gas exchange rates even at moderate to high wind speeds.
Estimation of solar energetic proton mission‐integrated fluences and peak intensities for missions traveling close to the Sun
Authors: Lario D. , Decker R. B.
Published: September 2011

A method to estimate both solar energetic particle mission‐integrated fluences and solar energetic particle peak intensities for missions traveling through the innermost part of the heliosphere (r < 1 AU) is presented. By using (1) an extensive data set of particle intensities measured at 1 AU over the last three solar cycles, (2) successive launch dates for the mission traveling close to the Sun over the time interval spanned by our data set, and (3) appropriate radial dependences to extrapolate fluences and peak intensities measured at 1 AU to the heliocentric radial distance of the mission at each specific time, we generate distributions of both mission‐integrated fluences and maximum peak intensities. From these distributions we extract the values of mission‐integrated fluence and maximum peak intensity at a required confidence level. Results of this method applied to the specific case of the nominal prime mission of Solar Probe Plus are shown.
Basin width control of faulting in the Naryn Basin, south‐central Kyrgyzstan
Authors: Goode Joseph K. , Burbank Douglas W. , Bookhagen Bodo
Published: September 2011

In Central Asia's Tien Shan, deformation is distributed across the wide orogen, a characteristic of intracontinental mountain building. Active faults are commonly found within intramontane basins that separate its constituent ranges. In order to explore the controls on this intramontane basin deformation, we study the Naryn Basin of south‐central Kyrgyzstan. A series of five balanced cross‐sections reveals a transition in patterns of faulting from faults confined to basin margins to faults focused within the basin center. The 20‐km‐wide eastern Naryn Basin displays deformation attributed to low‐angle splays of the northern, basin‐bounding fault. In the 40‐km‐wide western Naryn Basin, the pattern of deformation linked to the northern range remains, but is accompanied by steeper faults that dip both south and north without being directly linked to the basin‐bounding fault. We compare these cross‐sections to synthetic aperture radar interferometry (InSAR) measurements of surface deformation. Profiles of InSAR‐derived surface deformation rates across the Naryn Basin reveal that in the west, deformation is distributed across the broad basin interior, whereas in the east, rapid uplift is concentrated at the margin of the narrower basin. From the geodetic and structural data, we infer that in the western Naryn Basin, deformation has migrated away from the northern basin margin and into the interior. Deformation of the eastern basin interior, however, remains linked to the basin‐bounding fault. A simple mechanical model demonstrates that basin width may control basin deformation whereby basin‐interior faulting in the narrow, eastern Naryn Basin is inhibited by the overburden of adjacent ranges.
Determining longitudinal dispersion coefficients for submerged vegetated flow
Authors: Shucksmith J. D. , Boxall J. B. , Guymer I.
Published: September 2011

Prediction of the physical transport and mixing of pollutants or other soluble material is crucial for effective river management. Although well established methods exist which describe mixing processes in open channel flow, the presence of vegetation has a significant impact on mixing and few existing techniques account for this. To date, existing models which predict longitudinal dispersion coefficients in vegetated open channel flow have been derived and verified based on experiments conducted in simulated vegetation. This paper presents observations of longitudinal dispersion coefficients in a channel featuring living vegetation and tests against both an existing and a newly proposed model for longitudinal dispersion coefficient in submerged vegetated open channel flow. A model based on a mathematical technique of predicting dispersion in plain shear flow is shown to be capable of predicting longitudinal dispersion coefficients to within 20%.
Water cycle dynamics in a changing environment: Improving predictability through synthesis
Authors: Sivapalan M. , Thompson S. E. , Harman C. J. , Basu N. B. , Kumar P.
Published: September 2011

Key Points

There is much to learn from comparative hydrology

We need a synthesis of Newtonian and Darwinian approaches to science

Hydrologic change predictions require a broadening of hydrology
Mechanisms of Glutamate Efflux at the Blood—Brain Barrier: Involvement of Glial Cells
Authors: Cohen-Kashi-Malina Katayun , Cooper Itzik , Teichberg Vivian I
Published: September 2011

At high concentrations, glutamate (Glu) exerts potent neurotoxic properties, leading to irreversible brain damages found in numerous neurological disorders. The accepted notion that Glu homeostasis in brain interstitial fluid is maintained primarily through the activity of Glu transporters present on glial cells does not take into account the possible contribution of endothelial cells constituting the blood-brain barrier (BBB) to this process. Here, we present evidence for the presence of the Glu transporters, excitatory amino-acid transporters (EAATs) 1 to 3, in porcine brain endothelial cells (PBECs) and show their participation in Glu uptake into PBECs. Moreover, transport of Glu across three in vitro models of the BBB is investigated for the first time, and evidence for Glu transport across the BBB in both directions is presented. Our results provide evidence that the BBB can function in the efflux mode to selectively remove Glu, via specific transporters, from the abluminal side (brain) into the luminal compartment (blood). Furthermore, we found that glial cells lining the BBB have an active role in the efflux process by taking up Glu and releasing it, through hemichannels, anion channels, and possibly the reversal of its EAATs, in close proximity to ECs, which in turn take up Glu and release it to the blood.
Traitement précoce des classes III
Authors: Le Gall Michel , Philip Camille , Salvadori André
Published: September 2011

Choisir le moment adéquat pour initier un traitement d’orthodontie est une question
essentielle qui reste des plus controversées actuellement. Particulièrement face à des
dysmorphies de classe III, un certain consensus existe quant au moment et au type
d’appareil à mettre en œuvre afin d’obtenir la correction des pathologies présentes.
L’approche orthopédique réalisée en période de croissance doit se limiter au sujet qui
s’inscrit dans un schéma non héréditaire. Elle débute en phase de denture temporaire ou de
denture mixte, la prévention et l’interception en font partie. Les moyens mis en œuvre
doivent soit empêcher l’apparition d’une dysmorphose soit être un acte thérapeutique
simple permettant d’obtenir une correction partielle ou totale d’une dysmorphose et
d’empêcher son aggravation. Si la malocclusion s’inscrit en période adolescente, un
traitement orthodontique avec appareil multi-bague, basé sur le mécanisme des
compensations, assurera une occlusion équilibrée. Dans le cas contraire, si la
malocclusion est trop sévère, il sera alors nécessaire de reporter la décision
thérapeutique pour qu’elle s’inscrive dans une approche combinée
orthodontico-chirurgicale. Le but de ce travail est de décrire les différents plans de
traitement et appareils, en fonction de l’âge et du diagnostic initial. La gestion de la
malocclusion de classe III reste encore actuellement un défi pour l’orthodontiste.
Planification des soins bucco-dentaires et des traitements ODF
chez les enfants atteints d’une hémopathie maligne
Authors: Mercier Marie , Bocquet Emmanuelle , Danguy Michel , Rousset Monique-Marie
Published: September 2011

Problématique : la maladie cancéreuse concerne en France 1 à 3 % des
enfants et représente la deuxième cause de mortalité la plus fréquente chez les moins de
15 ans. Les hémopathies malignes sont les plus nombreuses et, si la mortalité tend à
diminuer, elle survient le plus souvent à la suite d’une infection dite « opportuniste ».
Celle-ci se développe à partir de foyers latents non éradiqués, délétères chez ces
patients et dont l’origine peut être dentaire. Ce risque infectieux est insuffisamment
diagnostiqué à l’hôpital et concerne chirurgiens-dentistes et orthodontistes.
Objectifs : les chirurgiens-dentistes et orthodontistes ont chacun un
rôle qui doit être précisé dans la mise en place précoce d’une éducation à la santé
bucco-dentaire de ces enfants, dans la recherche et l’éradication des risques infectieux
ainsi que dans le suivi des enfants à risque. Discussion :
l’établissement d’un suivi régulier et les soins de lésions carieuses concernent les
chirurgiens-dentistes. Les orthodontistes, parfois amenés à voir l’enfant souvent, doivent
être conscients de l’importance du dépistage des lésions carieuses et de la surveillance
des appareils posés afin de limiter toute inflammation ou blessure possible. Ils sont l’un
et l’autre responsables de l’enseignement des conseils d’hygiène alimentaire et
bucco-dentaire. Ils peuvent intervenir à la fois dans la mise en place des soins locaux
des lésions aiguës survenant au cours des traitements par chimiothérapie, et dans la
suppression des appareils irritatifs.
Utilisation des mini-vis corticales courtes en
orthodontie
Authors: Chillès Jean-Gabriel , Riemenschneider-Chillès Sylvia
Published: September 2011

Cet article réalise une synthèse des connaissances actuelles sur les mini-vis corticales
courtes utilisées comme ancrage squelettique. Enfouies en fond de vestibule, elles se
révèlent être une excellente alternative aux mini-vis transgingivales classiques et aux
mini-plaques. Elles allient la simplicité d’utilisation des premières à la fiabilité des
secondes et leur polyvalence leur permet d’être utilisées dans de très nombreuses
situations cliniques difficiles. Le matériel utilisé, les connectiques existantes, les
indications ainsi que les procédures cliniques sont abordés et illustrés par des cas
représentatifs.
Gender Effect on the Relation between Diabetes and Hospitalization for Heart Failure
Authors: Seghieri C. , Francesconi P. , Cipriani S. , Rapanà M. , Anichini R. , Franconi F. , Del Prato S. , Seghieri G.
Published: September 2011

Cardiovascular risk among diabetic patients is at least twice as much the one for non-diabetic individuals and even greater when diabetic women are considered. Heart failure (HF) is a common unfavorable outcome of cardiovascular disease in diabetes. However, since the comparison among sexes of heart failure prevalence in diabetic patients remains limited, this study is aimed at expanding the information about this point.

We have evaluated the association between diabetes and HF by reviewing the medical records of all subjects discharged from the Internal Medicine and Cardiology Units of all hospitals in the Tuscany region, Italy, during the period January 2002 through December 2008. In particular we sought concomitance of ICD-9-CM codes for diabetes and HF.

Patients discharged by Internal Medicine were on average older, more represented by women, and had a lesser number of individuals coded as diabetic (p<0.05 for all). Relative risk for HF (95% CI) was significantly higher in patients with diabetes, irrespective of gender 1.39 (1.36–1.41) in males; 1.40 (1.37–1.42) in females. When the diabetes-HF association was analyzed according to decades of age, a “horse-shoe” pattern was apparent with an increased risk in 40–59 years old in female patients discharged by Internal Medicine.

Although there is not a difference in the overall HF risk between hospitalized male and female diabetic patients, women have an excess risk at perimenopausal age.
Distal Symmetric Polyneuropathy in Diabetes. Differences between Patients with and without Neuropathic Pain
Authors: Mondelli M. , Aretini A. , Baldasseroni A.
Published: September 2011

To demonstrate whether in distal symmetric polyneuropathy (DSPN) in diabetes there are differences between patients with and without neuropathic pain and whether pain is associated with demographic, clinical and electrophysiological variables.

We prospectively enrolled 154 consecutive patients (mean age 67 years, 64% men) in an electromyography (EMG) lab. The differences were calculated between DSPN patients with (no.78) and without neuropathic pain (no.76) relating to age, sex, BMI, type, duration, treatment and complications of diabetes, HbA1c, type and duration of DSPN symptoms, DSPN clinical severity score (with Diabetic Neuropathic Index-DNI), electrophysiological findings of lower limb muscles and nerves.

The differences between DSPN patients with and without pain included the presence of symptoms (burning and weakness), DNI score and neurographic findings of all nerves and neurogenic EMG. But in the logistic regression models enter only the following variables: DNI score, neurogenic EMG, and among symptoms “burning-.

The presence of pain in DSPN is associated with DSPN clinical severity, neurogenic EMG and presence of “burning- symptom but not with demographic or neurographic findings, or diabetes related variables. Therefore, the neuropathic pain in DSPN does not associate with the degree of involvement of large diameter sensory fibres or diabetes severity.
Improving the nutrition of Merino ewes during pregnancy and lactation increases weaning weight and survival of progeny but does not affect their mature size
Authors: Thompson A. N. , Ferguson M. B. , Campbell A. J. D. , Gordon D. J. , Kearney G. A. , Oldham C. M. , Paganoni B. L.
Published: September 2011

Lamb growth to weaning, and during the period immediately following weaning, influences post-weaning mortality and may affect mature size. The hypothesis tested in the experiments reported in this paper was that changes in the maternal liveweight of Merino ewes during pregnancy and lactation could predict the weight at weaning, post-weaning survival and mature size of their progeny. At two sites (Vic. and WA) in each of two years, a wide range in the liveweight profiles of ewes was generated during pregnancy and lactation by varying the amount of supplements fed and feed on offer grazed. Across the four experiments this resulted in progeny weights ranging from 13.8 to 28.3 kg just before weaning. Lamb growth was primarily related to the amount of feed on offer during lactation, but was also related to the liveweight change of the ewe during pregnancy. These relationships were consistent in both experiments at each site. Weaning weight was strongly associated with post-weaning survival at the Vic. site. Survival rates decreased significantly when weaning weights were below 20 kg. These results indicate that management of ewe and lamb nutrition to maximise growth of lambs before weaning and growing weaners at 30 g/day or more after weaning are important for optimal post-weaning survival. The findings also suggest that the mature size of offspring is unlikely to be adversely affected by pre-weaning nutrition within the range of nutritional scenarios during pregnancy and lactation that are likely to be experienced within the Australian sheep industry.
The merit of condition score and fat score as alternatives to liveweight for managing the nutrition of ewes
Authors: van Burgel A. J. , Oldham C. M. , Behrendt R. , Curnow M. , Gordon D. J. , Thompson A. N.
Published: September 2011

The liveweight profile of Merino ewes is related to the production and profitability of the sheep enterprise, but few producers measure liveweight to manage the nutrition of Merino ewes. In this paper we examine the relationship between changes in liveweight and condition score using data from the Lifetimewool project and compare condition score and fat score as alternative monitoring tools. Analyses of liveweight and condition score data from 15 flocks of Merino ewes representing a range of different genotypes and environments showed that the relationship between change in liveweight and condition score was on average 9.2 kg per unit change in condition score or 0.19 times the standard reference weight of the flock. In two experiments experienced operators were used to estimate the condition score and fat score in over 200 ewes and accredited ultrasound scanners measured the eye muscle and fat depth at the C site in the same ewes. All assessments were repeated several times in random order. Within 24 h of the assessments the sheep were slaughtered at local abattoirs where the tissue depth at the GR site was measured on the hot carcasses. Both condition score and fat score were highly repeatable though subject to operator bias. They were related to each other and to the objective measures of fat and eye muscle depth at the C site. However, 95% of sheep below condition score 2.5 had a tissue depth (muscle and fat) at the GR site ≤3 mm, by definition equal to fat score 1. As the condition score of ewes on commercial properties often fluctuates between scores 2 and 3, and small changes in condition score within this range can have large effects on welfare and profit, we conclude that condition score is the most appropriate alternative to liveweight for managing the nutritional profile of ewes.
Managing the nutrition of twin-bearing ewes during pregnancy using Lifetimewool recommendations increases production of twin lambs
Authors: Edwards J. E. Hocking , Copping K. J. , Thompson A. N.
Published: September 2011

The effect on ewe and lamb production by differential management of single- and twin-bearing Merino ewes during pregnancy and lactation was examined. The hypothesis that the survival and productivity of single- and twin-born progeny is not affected by differential management of single- and twin-bearing ewes was tested. To test this hypothesis, two ewe flocks were monitored on a commercial property in the south-east of South Australia. The body condition score of one flock of ewes was managed according to Lifetimewool recommendations for southern Australian (Lifetimewool flock; n = 464). Lifetimewool recommendations are that body condition score should be 3.0 at mating and then allowed to decline to an average of 2.7, which is maintained until lambing. Twin- and single-bearing ewes were managed as separate mobs after pregnancy scanning to meet their energy requirements. The second flock was managed similarly to the commercial ewe flock and was representative of ewe management practices in the region (normal-practice flock; n = 464). At lambing, the condition score of the Lifetimewool flock was 0.7 condition scores units greater than the normal-practice flock. Ewe clean fleece weight and fibre diameter were greater in the Lifetimewool flock and their lambs had higher survival rates to weaning. Over three shearings, progeny from Lifetimewool ewe flocks produced more clean wool (P < 0.0001) but there was no consistent effect on fibre diameter, staple length or staple strength. Twin-born lambs from ewes managed to Lifetimewool guidelines had a similar liveweight and produced similar quantity and quality of wool to single-born lambs managed to Lifetimewool guidelines, but still suffered higher rates of mortality to weaning. This suggests that it is possible to manage ewes pregnant with twins to ensure that their surviving progeny perform at a level similar to single-born progeny managed under similar targets.
The wool production and reproduction of Merino ewes can be predicted from changes in liveweight during pregnancy and lactation
Authors: Ferguson M. B. , Thompson A. N. , Gordon D. J. , Hyder M. W. , Kearney G. A. , Oldham C. M. , Paganoni B. L.
Published: September 2011

Defining the nature of the relationship between change in liveweight throughout a breeding cycle and ewe wool production and reproduction would be useful for developing management guidelines for Merino ewes. In this paper we tested the hypotheses that (1) feed on offer has variable effects on liveweight profiles of individual ewes; and (2) liveweight profiles of individual ewes can be used to predict their fleece wool production and reproductive performance. At sites in Victoria and Western Australia in 2001 and 2002, pregnant Merino ewes were exposed to 10 nutritional treatments. In each of the four experiments, ewes in average condition score 3 at artificial insemination were fed to achieve either maintenance or loss of a condition score over the first 100 days of pregnancy before grazing one of five levels of feed on offer between Day 100 and lamb weaning. Across all four experiments, the average difference in ewe liveweight between extreme treatments was: 7.0 kg (range 4.7–8.7 kg) at Day 100 of pregnancy; 11.9 kg (range 4.9–17.8 kg) at lambing; and by weaning was 13.9 kg (range 8.8–22.7 kg). Liveweight at joining and liveweight change during pregnancy and lactation of individual Merino ewes were significantly related to their clean fleece weight, fibre diameter and staple length and thus the second hypothesis was supported. Heavier ewes at joining produced more wool that was longer and broader and this effect was consistent across both sites and years. A 10-kg loss in ewe liveweight between joining and mid pregnancy, mid pregnancy and lambing or during lactation reduced clean fleece weight by 0.4–0.7 kg and fibre diameter by 0.5–1.4 um. At the Victorian site, where ewes were shorn in summer, a loss of 10 kg in liveweight between joining and Day 100 of pregnancy reduced staple strength by 5 N/ktex. As expected the influence of food on offer on changes in ewe liveweight was different between years and sites and between late pregnancy and lactation due to a complex group of pasture and animal factors. Therefore, managing changes in ewe liveweight itself rather than feed on offer will achieve more predictable outcomes. A higher liveweight at joining resulted in a predictable improvement in ewe reproductive rate and liveweight at joining was more important than the liveweight profile leading up to joining. This paper has shown that it is possible to predict the differences in wool production and reproductive rate of flocks of Merino ewes if ewe liveweight records at key times are known.
Participation in Lifetime Ewe Management results in changes in stocking rate, ewe management and reproductive performance on commercial farms
Authors: Trompf J. P. , Gordon D. J. , Behrendt R. , Curnow M. , Kildey L. C. , Thompson A. N.
Published: September 2011

Lifetime Ewe Management is an extension program designed to assist sheep producers to improve their understanding of ewe nutrition and to develop the skills and confidence to improve their management. The course is based on a small-group extension model and was developed by the Lifetimewool project as a way to incorporate the research findings, economic modelling and producer guidelines developed by the project. Lifetime Ewe Management commenced in Victoria in the spring of 2006 and by the end of 2010, 221 producers had completed the 2-year program. The changes in knowledge, attitudes, skills, aspirations and management practices of 182 of these participants were examined. Participants of the Lifetime Ewe Management program increased their whole-farm stocking rates by 14%, increased lamb marking percentages by 11–13% depending on enterprise type, and decreased ewe mortality rates by 43%. These improvements resulted from a significant change in the perceived importance of managing ewes to condition-score targets to improve profitability and increases in the ability of participants to condition score ewes, assess pasture quantity and quality and feed budget. These changes were consistent regardless of how innovative the participants were at the beginning of the program. The appeal and success of the program was attributed largely to the small-group model where producers worked with their own flock under the guidance of a skilled facilitator and with access to effective decision-making tools. The Lifetime Ewe Management program design provides a blueprint for future extension programs striving to achieve widespread practice change.
Successful adoption of new guidelines for the nutritional management of ewes is dependent on the development of appropriate tools and information
Authors: Curnow M. , Oldham C. M. , Behrendt R. , Gordon D. J. , Hyder M. W. , Rose I. J. , Whale J. W. , Young J. M. , Thompson A. N.
Published: September 2011

Low rates of adoption of innovations in sheep management have been blamed on the poor targeting of messages, low relative advantage of the innovation, a focus on awareness-raising activities rather than adoption activities, poor ‘packaging’ of information and few effective tools to aid decision making. Lifetimewool, a national project that developed management guidelines for Merino ewes specific to regions and different times of lambing, used a ‘review and improve’ process to identify areas of interest, level of knowledge and the skills required by different sectors of the audience to adopt the new recommendations for ewe management. To match these needs and to effectively communicate information from Lifetimewool, a combination of simple and complex tools were produced which were practical, effective, regionally specific and credible. All of the products were designed as a ‘family’ in terms of design and content, allowing a recognition by the producer that they complemented each other and led producers through logical steps for making decisions on managing and feeding ewes. The average awareness of all tools by consultants and extensionists was almost 90% and average usage rates were above 50%. However, the usage rates varied dramatically between tools and users, for example, 46% of consultants used the feed budget tables compared with 76% of extensionists for a similar awareness. Of 1353 producers surveyed more than 55% were aware of the Lifetimewool tools and average usage within this group was 19% and related to the length of time the tool had been available. An estimated 14 000 producers were aware of tools produced by Lifetimewool. The uptake and use of these tools by the target audiences support our hypothesis that tools of differing complexities are required to cater for individual needs.
Why a Global Carbon Policy Could Have a Dramatic Impact on the Pattern of the Worldwide Livestock Production
Authors: Avetisyan Misak , Golub Alla , Hertel Thomas , Rose Steven , Henderson Benjamin
Published: September 2011

The taxation of Greenhouse Gases (GHG) represents an efficient means of achieving climate change mitigation, and this is often the starting point in any discussion of long run global GHG reduction. However, the direct effects of such a tax, or equivalently, an emissions trading scheme, will vary across countries and sectors according to the emissions intensity of the sector. We report, for the first time, estimates of such livestock emissions intensities for all regions of the world and decompose the intensities to understand the sources of regional variation. Our findings indicate that most of the variation is due to differences in the value of output per animal in different regions, which in turn is due to regional differences in output per animal (yield) and dollar per unit output (price). Animals with relatively low annual output values tend to be characterized by higher economic emissions intensities. We find this to be the case in many developing countries. Livestock activity in these high emissions intensity regions are hit especially hard by an emissions tax, resulting in disproportionate reductions in output and consumption in many regions already suffering from malnutrition.
High-dimensional bolstered error estimation
Authors: Sima Chao , Braga-Neto Ulisses M. , Dougherty Edward R.
Published: September 2011

Motivation: In small-sample settings, bolstered error estimation has been shown to perform better than cross-validation and competitively with bootstrap with regard to various criteria. The key issue for bolstering performance is the variance setting for the bolstering kernel. Heretofore, this variance has been determined in a non-parametric manner from the data. Although bolstering based on this variance setting works well for small feature sets, results can deteriorate for high-dimensional feature spaces.

Results: This article computes an optimal kernel variance depending on the classification rule, sample size, model and feature space, both the original number and the number remaining after feature selection. A key point is that the optimal variance is robust relative to the model. This allows us to develop a method for selecting a suitable variance to use in real-world applications where the model is not known, but the other factors in determining the optimal kernel are known.

Availability: Companion website at http://compbio.tgen.org/paper_supp/high_dim_bolstering

Contact:  edward@mail.ece.tamu.edu
Inducible Maize Defense Mechanisms Against the Corn Borer Sesamia nonagrioides: A Transcriptome and Biochemical Approach
Authors: Rodríguez Víctor M. , Santiago Rogelio , Malvar Rosa Ana , Butrón Ana
Published: September 2011

In spite of multiple studies elucidating individual defense mechanisms against stalk borer feeding, little information is available about the plant response to these members of Lepidoptera. Four maize inbred lines were cultivated in a greenhouse and challenged with larvae of the corn borer Sesamia nonagrioides. Transcriptome and biochemical analyses were performed to elucidate the maize response mechanisms to this insect. General plant defense mechanisms were activated, including the jasmonic acid biosynthetic pathway, proteinase inhibitors, and four defense-related transcription factors. Interestingly, gene ontology analysis shows that maize plants undergo cell-wall reorganization after being attacked. These results were confirmed through biochemical analyses showing that the concentration of some cell-wall-related compounds significantly changed after plant infestation in a genotype-dependent way. In conclusion, maize plants respond to the attack of the corn borer S. nonagrioides through cell-wall fortification, activating genes involved in cell-wall organization, which finally is reflected in a higher concentration of some cell-wall components, especially in resistant genotypes.
Infection Dynamics in Viral Spread and Interference Under the Synergism Between Cucumber mosaic virus and Turnip mosaic virus
Authors: Takeshita Minoru , Koizumi Emiko , Noguchi Makiko , Sueda Kae , Shimura Hanako , Ishikawa Noriko , Matsuura Hideyuki , Ohshima Kazusato , Natsuaki Tomohide , Kuwata Shigeru , Furuya Naruto , Tsuchiya Kenichi , Masuta Chikara
Published: September 2011

Mixed infection of Cucumber mosaic virus (CMV) and Turnip mosaic virus (TuMV) induced more severe symptoms on Nicotiana benthamiana than single infection. To dissect the relationships between spatial infection patterns and the 2b protein (2b) of CMV in single or mixed infections, the CMV vectors expressing enhanced green fluorescent or Discosoma sp. red fluorescent proteins (EGFP [EG] or DsRed2 [Ds], respectively were constructed from the same wild-type CMV-Y and used for inoculation onto N. benthamiana. CMV2-A1 vector (C2-A1 [A1]) has a functional 2b while CMV-H1 vector (C2-H1 [H1]) is 2b deficient. As we expected from the 2b function as an RNA silencing suppressor (RSS), in a single infection, A1Ds retained a high level of accumulation at initial infection sites and showed extensive fluorescence in upper, noninoculated leaves, whereas H1Ds disappeared rapidly at initial infection sites and could not spread efficiently in upper, noninoculated leaf tissues. In various mixed infections, we found two phenomena providing novel insights into the relationships among RSS, viral synergism, and interference. First, H1Ds could not spread efficiently from vasculature into nonvascular tissues with or without TuMV, suggesting that RNA silencing was not involved in CMV unloading from vasculature. These results indicated that 2b could promote CMV to unload from vasculature into nonvascular tissues, and that this 2b function might be independent of its RSS activity. Second, we detected spatial interference (local interference) between A1Ds and A1EG in mixed infection with TuMV, between A1Ds (or H1Ds) and TuMV, and between H1Ds and H1EG. This observation suggested that local interference between two viruses was established even in the synergism between CMV and TuMV and, again, RNA silencing did not seem to contribute greatly to this phenomenon.
Distribution of Viruses Infecting Cucurbit Crops and Isolation of Potential New Virus-Like Sequences from Weeds in Oklahoma
Authors: Ali Akhtar , Mohammad Osama , Khattab Abeer
Published: September 2011

Field surveys were conducted from 2008 to 2010 to detect and determine the incidence of viruses in the major cucurbit-growing areas of Oklahoma. In total, 1,049 symptomatic leaf samples (890 from cucurbits, 109 from weed species, and 50 from crop plants [agricultural crops]) were collected from 90 fields in four counties (Atoka, Blaine, Jefferson, and Tulsa) of Oklahoma. Samples were tested against seven viruses, including Cucumber mosaic virus (CMV), Cucumber green mottle mosaic virus (CGMMV), Melon necrotic spot virus (MNSV), Papaya ringspot virus-watermelon strain (PRSV-W, formerly known as Watermelon mosaic virus-1), Squash mosaic virus (SqMV), Watermelon mosaic virus-2 (WMV-2), and Zucchini yellow mosaic virus (ZYMV), using dot-immunobinding assay (DIBA). Results showed the highest incidence for PRSV (51%), followed by WMV-2 (14%) and ZYMV (10%) among the collected samples. SqMV, MNSV, and CMV were detected in 3.8, 3.3, and 1.1% of the samples, respectively. None of the samples collected during surveys reacted positively against the antiserum of CGMMV. Mixed virus infections were common involving two (5.18%) or three (4.61%) viruses in various combinations. New weed host species were found to be infected with PRSV when confirmed by both DIBA and reverse-transcription polymerase chain reaction (RT-PCR). Some weed species contained possible new viruses when analyzed by random RT-PCR, followed by cloning, sequencing, and BLAST analysis with sequences in GenBank.
Characterization of a Virus Infecting Citrus volkameriana with Citrus Leprosis-Like Symptoms
Authors: Melzer Michael J. , Sether Diane M. , Borth Wayne B. , Hu John S.
Published: September 2011

A Citrus volkameriana tree displaying symptoms similar to citrus leprosis on its leaves and bark was found in Hawaii. Citrus leprosis virus C (CiLV-C)-specific detection assays, however, were negative for all tissues tested. Short, bacilliform virus-like particles were observed by transmission electron microscopy in the cytoplasm of symptomatic leaves but not in healthy controls. Double-stranded (ds) RNAs ≈8 and 3 kbp in size were present in symptomatic leaf tissue but not in healthy controls. Excluding poly(A) tails, the largest molecule, RNA1, was 8,354 bp in length. The ≈3 kbp dsRNA band was found to be composed of two distinct molecules, RNA2 and RNA3, which were 3,169 and 3,113 bp, respectively. Phylogenetic analyses indicated that the RNA-dependent RNA polymerase (RdRp) domain located in RNA1 was most closely related to the RdRp domain of CiLV-C. A reverse-transcription polymerase chain reaction assay developed for the detection of this virus was used to screen nearby citrus trees as well as Hibiscus arnottianus plants with symptoms of hibiscus green spot, a disease associated with infection by Hibiscus green spot virus (HGSV). All nearby citrus trees tested negative with the assay; however, symptomatic H. arnottianus plants were positive. All three RNAs were present in symptomatic H. arnottianus and were >98% identical to the RNAs isolated from C. volkameriana. We contend that the virus described in this study is HGSV, and propose that it be the type member of a new virus genus, Higrevirus.
Horizontally transferred fungal carotenoid genes in the two-spotted spider mite
Tetranychus urticae
Authors: Altincicek Boran , Kovacs Jennifer L. , Gerardo Nicole M.
Published: September 2011

Carotenoids are organic pigments commonly synthesized by plants, algae and some micro-organisms. Through absorption of light energy, carotenoids facilitate photosynthesis and provide protection against photo-oxidation. While it was presumed that all carotenoids in animals were sequestered from their diets, aphids were recently shown to harbour genomic copies of functional carotenoid biosynthesis genes that were acquired via horizontal gene transfer from fungi. Our search of available animal transcripts revealed the presence of two related genes in the two-spotted spider mite
Tetranychus urticae
. Phylogenetic analyses suggest that the
T. urticae
genes were transferred from fungi into the spider mite genome, probably in a similar manner as recently suggested for aphids. The genes are expressed in both green and red morphs, with red morphs exhibiting higher levels of gene expression. Additionally, there appear to be changes in the expression of these genes during diapause. As carotenoids are associated with diapause induction in these animals, our results add to recent findings highlighting the importance of eukaryotic horizontal gene transfer in the ecology and evolution of higher animals.
Corvids can decide if a future exchange is worth waiting for
Authors: Dufour Valerie , Wascher Claudia A. F. , Braun Anna , Miller Rachael , Bugnyar Thomas
Published: September 2011

Evidence for time-dependent calculations about future rewards is scarce in non-human animals. In non-human primates, only great apes are comparable with humans. Still, some species wait for several minutes to obtain a better reward in delayed exchange tasks. Corvids have been shown to match with non-human primates in some time-related tasks. Here, we investigate a delay of gratification in two corvid species, the carrion crow (Corvus corone) and the common raven (Corvus corax), in an exchange task. Results show that corvids success decreases quickly as delay increases, with a maximal delay of up to 320 s (more than 5 min). The decision to wait rests both on the quality of the prospective reward and the time required to obtain it. Corvids also apply tactics (placing the reward on the ground or caching it) that probably alleviate costs of waiting and distract their attention during waiting. These findings contrast previous results on delayed gratification in birds and indicate that some species may perform comparably to primates.
Derek Robinson. 27 May 1941 — 2 December 2002
Authors: Connor John , Windsor Colin
Published: September 2011

Derek Robinson was a leading UK plasma physicist of his generation. After an early success in measuring the electron temperature in the ZETA plasma through the Thomson scattering of laser light, he became a key member of the team from Culham Laboratory sent to Moscow in 1968 to verify the high temperatures claimed by the Russians for their T3 tokamak. On returning to Culham his research activities continued to broaden and he became an acknowledged expert on a range of fusion devices. His management responsibilities grew in parallel and eventually he became Director of Culham. With his strong support, Culham explored the novel spherical tokamak devices START and MAST, and he promoted this concept as an alternative route to the conventional tokamak for developing fusion power. His energetic leadership and his mastery of theory, experiment and fusion politics brought fusion power nearer to reality. His vision of the ‘way forward’ for the international fusion programme remains with us after his life was so sadly cut short by the unexpected development of lung cancer in a non-smoker.
The epigenome and top-down causation
Authors: Davies P. C. W.
Published: September 2011

Genes store heritable information, but actual gene expression often depends on many so-called epigenetic factors, both physical and chemical, external to DNA. Epigenetic changes can be both reversible and heritable. The genome is associated with a physical object (DNA) with a specific location, whereas the epigenome is a global, systemic, entity. Furthermore, genomic information is tied to specific coded molecular sequences stored in DNA. Although epigenomic information can be associated with certain non-DNA molecular sequences, it is mostly not. Therefore, there does not seem to be a stored ‘epigenetic programme’ in the information-theoretic sense. Instead, epigenomic control is—to a large extent—an emergent self-organizing phenomenon, and the real-time operation of the epigenetic ‘project’ lies in the realm of nonlinear bifurcations, interlocking feedback loops, distributed networks, top-down causation and other concepts familiar from the complex systems theory. Lying at the heart of vital eukaryotic processes are chromatin structure, organization and dynamics. Epigenetics provides striking examples of how bottom-up genetic and top-down epigenetic causation intermingle. The fundamental question then arises of how causal efficacy should be attributed to biological information. A proposal is made to implement explicit downward causation by coupling information directly to the dynamics of chromatin, thus permitting the coevolution of dynamical laws and states, and opening up a new sector of dynamical systems theory that promises to display rich self-organizing and self-complexifying behaviour.
Macro-scale phenomena of arterial coupled cells: a massively parallel simulation
Authors: Shaikh Mohsin Ahmed , Wall David J. N. , David Tim
Published: September 2011

Impaired mass transfer characteristics of blood-borne vasoactive species such as adenosine triphosphate in regions such as an arterial bifurcation have been hypothesized as a prospective mechanism in the aetiology of atherosclerotic lesions. Arterial endothelial cells (ECs) and smooth muscle cells (SMCs) respond differentially to altered local haemodynamics and produce coordinated macro-scale responses via intercellular communication. Using a computationally designed arterial segment comprising large populations of mathematically modelled coupled ECs and SMCs, we investigate their response to spatial gradients of blood-borne agonist concentrations and the effect of micro-scale-driven perturbation on the macro-scale. Altering homocellular (between same cell type) and heterocellular (between different cell types) intercellular coupling, we simulated four cases of normal and pathological arterial segments experiencing an identical gradient in the concentration of the agonist. Results show that the heterocellular calcium (Ca
2+
) coupling between ECs and SMCs is important in eliciting a rapid response when the vessel segment is stimulated by the agonist gradient. In the absence of heterocellular coupling, homocellular Ca
2+
 coupling between SMCs is necessary for propagation of Ca
2+
 waves from downstream to upstream cells axially. Desynchronized intracellular Ca
2+
 oscillations in coupled SMCs are mandatory for this propagation. Upon decoupling the heterocellular membrane potential, the arterial segment looses the inhibitory effect of ECs on the Ca
2+
 dynamics of the underlying SMCs. The full system comprises hundreds of thousands of coupled nonlinear ordinary differential equations simulated on the massively parallel Blue Gene architecture. The use of massively parallel computational architectures shows the capability of this approach to address macro-scale phenomena driven by elementary micro-scale components of the system.
Robustness, fidelity and prediction-looseness of models
Authors: Ben-Haim Yakov , Hemez François M.
Published: September 2011

Assessment of the credibility of a mathematical or numerical model of a complex system must combine three components: (i) the fidelity of the model to test data, e.g. as quantified by a mean-squared error; (ii) the robustness, of model fidelity, to lack of understanding of the underlying processes; and (iii) the prediction-looseness of the model. ‘Prediction-looseness’ is the range of predictions of models that are equivalent in terms of fidelity. The main result of this paper asserts that fidelity, robustness and prediction-looseness are mutually antagonistic. A change in the model that enhances one of these attributes will cause deterioration of another. In particular, increasing thefidelityto test data will decrease therobustnessto imperfect understanding of the process. Likewise, increasing therobustnesswill increase thepredictive looseness. The conclusion is that focusing only on fidelity-to-data is not a sound decision-making strategy for model building and validation. A better strategy is to explore the trade-offs between robustness-to-uncertainty, fidelity to data and tightness of predictions. Our analysis is based on info-gap models of uncertainty, which can be applied to cases of severe uncertainty and lack of knowledge.
Understanding the ecological drivers of avian influenza virus infection in wildfowl: a continental-scale study across Africa
Authors: Gaidet N. , Caron A. , Cappelle J. , Cumming G. S. , Balança G. , Hammoumi S. , Cattoli G. , Abolnik C. , Servan de Almeida R. , Gil P. , Fereidouni S. R. , Grosbois V. , Tran A. , Mundava J. , Fofana B. , Ould El Mamy A. B. , Ndlovu M. , Mondain-Monval J. Y. , Triplet P. , Hagemeijer W. , Karesh W. B. , Newman S. H. , Dodman T.
Published: September 2011

Despite considerable effort for surveillance of wild birds for avian influenza viruses (AIVs), empirical investigations of ecological drivers of AIV prevalence in wild birds are still scarce. Here we used a continental-scale dataset, collected in tropical wetlands of 15 African countries, to test the relative roles of a range of ecological factors on patterns of AIV prevalence in wildfowl. Seasonal and geographical variations in prevalence were positively related to the local density of the wildfowl community and to the wintering period of Eurasian migratory birds in Africa. The predominant influence of wildfowl density with no influence of climatic conditions suggests, in contrast to temperate regions, a predominant role for inter-individual transmission rather than transmission via long-lived virus persisting in the environment. Higher prevalences were found in
Anas
species than in non-
Anas
species even when we account for differences in their foraging behaviour (primarily dabbling or not) or their geographical origin (Eurasian or Afro-tropical), suggesting the existence of intrinsic differences between wildfowl taxonomic groups in receptivity to infection. Birds were found infected as often in oropharyngeal as in cloacal samples, but rarely for both types of sample concurrently, indicating that both respiratory and digestive tracts may be important for AIV replication.