bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancement of light extraction efficiency by evanescent wave coupling effect in ridge-shaped AlGaInP/GaInP quantum wells
Authors: Hao Guo-Dong , Wang Xue-Lun
Published: March 2012

The optical properties of a sub-wavelength-sized ridge-shaped AlGaInP/GaInP quantum well structure fabricated by selective-area metal organic vapor phase epitaxy are investigated. The ridge structure exhibits an 8.5 times stronger photoluminescence intensity at room temperature than a planar structure, corresponding to an enhancement of at least 13.6 times in the light extraction efficiency of the ridge sample with respect to the planar sample. Both emission pattern measurements and theoretical simulation demonstrate that the high light extraction efficiency originates from the evanescent wave coupling effect in a narrow ridge structure, which can directly extract the light outside the escape cones to air.
Excitonic diffusion dynamics in ZnO
Authors: Jeong H. , Min K. , Byun S. , Stanton C. J. , Reitze D. H. , Yoo J. K. , Yi G. C. , Jho Y. D.
Published: March 2012

We investigate excitonic carrier diffusion in both bulk ZnO and nanorods (NRs). Using time-resolved differential reflectivity spectroscopy, we observe a fast decaying component together with a longer exponential relaxation. In bulk ZnO, we find that the fast decay term (∼1 ps) originates from excitonic diffusion along the growth direction. By probing at both the A and B excitons, we find different diffusion coefficients for each. In ZnO nanorods, the diffusion contribution is missing. We attribute this to two effects: (1) defects in the nanorods substantially slow the diffusion process and (2) excitons in nanorods are generated more uniformly than in bulk.
Dopant characterization in self-regulatory plasma doped fin field-effect transistors by atom probe tomography
Authors: Takamizawa H. , Shimizu Y. , Nozawa Y. , Toyama T. , Morita H. , Yabuuchi Y. , Ogura M. , Nagai Y.
Published: March 2012

Fin field-effect transistors are promising next-generation electronic devices, and the identification of dopant positions is important for their accurate characterization. We report atom probe tomography (APT) of silicon fin structures prepared by a recently developed self-regulatory plasma doping (SRPD) technique. Trenches between fin-arrays were filled using a low-energy focused ion beam to directly deposit silicon, which allowed the analysis of dopant distribution by APT near the surface of an actual fin transistor exposed to air. We directly demonstrate that SRPD can achieve a boron concentration above 1 × 1020 atoms/cm3 at the fin sidewall.
Optical-force-induced bistability in nanomachined ring resonator systems
Authors: Yu Y. F. , Zhang J. B. , Bourouina T. , Liu A. Q.
Published: March 2012

This paper reports optical-force-induced bistability in a nanomachined ring resonator system. It consists of two ring resonators and a bus waveguide, whereby each ring resonator has a free-hanging arc that is perpendicularly deformable by an optical force and changes the effective refractive index of the system. Therefore, an optical bistability is induced into the nanomachined ring resonator system, in which the bistability band can reach 0.3 nm and 0.68 nm in the ring resonators 1 and 2, respectively. It has potential applications in optical signal processing area, such as all-optical switching and opto-mechanical memory.
Mapping the Tip of the Tongue—Deprivation, Sensory Sensitisation, and Oral Haptics
Authors: Topolinski Sascha , Pereira Philippe Türk
Published: March 2012

We investigated the impact of food deprivation on oral and manual haptic size perception of food and non-food objects. From relevant theories (need-proportional perception, motivated perception, frustrative nonreward, perceptual defence, and sensory sensitisation) at least four completely different competing predictions can be derived. Testing these predictions, we found across four experiments that participants estimated the length of both non-food and food objects to be larger when hungry than when satiated, which was true only for oral haptic perception, while manual haptic perception was not influenced by hunger state. Subjectively reported hunger correlated positively with estimated object size in oral, but not in manual, haptic perception. The impact of food deprivation on oral perception vanished after oral stimulations even for hungry individuals. These results favour a sensory sensitisation account maintaining that hunger itself does not alter oral perception but the accompanying lack of sensory stimulation of the oral mucosa. Both oral and manual haptic perception tended to underestimate actual object size. Finally, an enhancing effect of domain-target matching was found, ie food objects were perceived larger by oral than by manual haptics, while non-food objects were perceived larger by manual than by oral haptics.
Computational Design of Thiourea-based Cyclophane Sensors for Small Anions
Authors: Xie Huifang , Wong Ming Wah
Published: February 2012

The host–guest binding properties of a tri-thiourea cyclophane receptor (1) with several common anions have been investigated using density functional theory (DFT) and molecular dynamics calculations. Receptor 1 is predicted to be an effective receptor for binding small halogen and Y-shaped (NO3– and AcO–) anions in the gas phase, cyclohexane and chloroform. The calculated order of anion binding affinity for the receptor 1 in chloroform is F– > Cl– > AcO– > NO3– >Br– > H2PO4– > HSO4–. The binding free energies are strongly influenced by a dielectric solvent medium. The structures of the receptor–anion complexes are characterized by multiple (typically 6) hydrogen bonds in all cases. The overall binding affinity of various anions is determined by the basicity of anion, size and shape of the binding site, and solvent medium. Explicit chloroform solvent molecular dynamics simulations of selected receptor–anion complexes reveal that the anions are strongly bound within the binding pocket via hydrogen-bonding interactions to all the receptor protons throughout the simulation. A sulfur analogue of receptor 1 (2), with a larger central cavity, is shown to be a more effective sensor than 1 for small anions. Two different approaches to develop the thiourea-based cyclophane receptor into a chromogenic sensor were examined.
Induced mutations in circadian clock regulator
Mat-a
facilitated short-season adaptation and range extension in cultivated barley
Authors: Zakhrabekova Shakhira , Gough Simon P. , Braumann Ilka , Müller André H. , Lundqvist Joakim , Ahmann Katharina , Dockter Christoph , Matyszczak Izabela , Kurowska Marzena , Druka Arnis , Waugh Robbie , Graner Andreas , Stein Nils , Steuernagel Burkhard , Lundqvist Udda , Hansson Mats
Published: February 2012

Time to flowering has an important impact on yield and has been a key trait in the domestication of crop plants and the spread of agriculture. In 1961, the cultivar Mari (
mat-a.8
) was the very first induced early barley (
Hordeum vulgare
L.) mutant to be released into commercial production. Mari extended the range of two-row spring barley cultivation as a result of its photoperiod insensitivity. Since its release, Mari or its derivatives have been used extensively across the world to facilitate short-season adaptation and further geographic range extension. By exploiting an extended historical collection of early-flowering mutants of barley, we identified
Praematurum-a
(
Mat-a
), the gene responsible for this key adaptive phenotype, as a homolog of the
Arabidopsis thaliana
circadian clock regulator
Early Flowering 3
(
Elf3
). We characterized 87 induced
mat-a
mutant lines and identified >20 different
mat-a
alleles that had clear mutations leading to a defective putative ELF3 protein. Expression analysis of
HvElf3
and
Gigantea
in mutant and wild-type plants demonstrated that
mat-a
mutations disturb the flowering pathway, leading to the early phenotype. Alleles of
Mat-a
therefore have important and demonstrated breeding value in barley but probably also in many other day-length-sensitive crop plants, where they may tune adaptation to different geographic regions and climatic conditions, a critical issue in times of global warming.
A cold oceanographic regime with high exploitation rates in the Northeast Pacific forecasts a collapse of the sardine stock
Authors: Zwolinski Juan P. , Demer David A.
Published: February 2012

The oceanographic conditions in the north Pacific have shifted to a colder period, Pacific sardine (
Sardinops sagax
) biomass has declined precipitously in the California Current, the international sardine fishery is collapsing, and mackerel (
Trachurus symmetricus
and
Scomber japonicus
) are thriving. This situation occurred in the mid-1900s, but indices of current oceanographic conditions and the results of our acoustic-trawl surveys indicate it likely is recurring now, perhaps with similar socioeconomic and ecological consequences. Also alarming is the repetition of the fishery's response to a declining sardine stock—progressively higher exploitation rates targeting the oldest, largest, and most fecund fish. Furthermore, our data indicate the recent reproductive condition of sardine is poor, and their productivity is below modeled estimates used to derive the current fishery-exploitation rates. Consequently, the sardine population has been reduced to two cohorts that are unlikely to produce an appreciable new cohort. Thus, a near-term recovery of this important stock is unlikely, depending on the return of warmer oceanographic conditions, reduced pressure from mackerel species, and perhaps the adoption of a more precautionary strategy for managing the residual sardine population.
Critical perspectives on historical collapse
Authors: Butzer Karl W. , Endfield Georgina H.
Published: February 2012

Historical collapse of ancient states or civilizations has raised new awareness about its possible relevance to current issues of sustainability, in the context of global change. This Special Feature examines 12 case studies of societies under stress, of which seven suffered severe transformation. Outcomes were complex and unpredictable. Five others overcame breakdown through environmental, political, or socio-cultural resilience, which deserves as much attention as the identification of stressors. Response to environmental crises of the last millennium varied greatly according to place and time but drew from traditional knowledge to evaluate new information or experiment with increasing flexibility, even if modernization or intensification were decentralized and protracted. Longer-term diachronic experience offers insight into how societies have dealt with acute stress, a more instructive perspective for the future than is offered by apocalyptic scenarios.
Phylogenetic differences in calcium permeability of the auditory hair cell cholinergic nicotinic receptor
Authors: Lipovsek Marcela , Im Gi Jung , Franchini Lucía F. , Pisciottano Francisco , Katz Eleonora , Fuchs Paul Albert , Elgoyhen Ana Belén
Published: February 2012

The α9 and α10 cholinergic nicotinic receptor subunits assemble to form the receptor that mediates efferent inhibition of hair cell function within the auditory sensory organ, a mechanism thought to modulate the dynamic range of hearing. In contrast to all nicotinic receptors, which serve excitatory neurotransmission, the activation of α9α10 produces hyperpolarization of hair cells. An evolutionary analysis has shown that the α10 subunit exhibits signatures of positive selection only along the mammalian lineage, strongly suggesting the acquisition of a unique function. To establish whether mammalian α9α10 receptors have acquired distinct functional properties as a consequence of this evolutionary pressure, we compared the properties of rat and chicken recombinant and native α9α10 receptors. Our main finding in the present work is that, in contrast to the high (pCa
2+
/pMonovalents ∼10) Ca
2+
permeability reported for rat α9α10 receptors, recombinant and native chicken α9α10 receptors have a much lower permeability (∼2) to this cation, comparable to that of neuronal α4β2 receptors. Moreover, we show that, in contrast to α10, α7 as well as α4 and β2 nicotinic subunits are under purifying selection in vertebrates, consistent with the conserved Ca
2+
permeability reported across species. These results have important consequences for the activation of signaling cascades that lead to hyperpolarization of hair cells after α9α10 gating at the cholinergic–hair cell synapse. In addition, they suggest that high Ca
2+
permeability of the α9α10 cholinergic nicotinic receptor might have evolved together with other features that have given the mammalian ear an expanded high-frequency sensitivity.
Higher social class predicts increased unethical behavior
Authors: Piff Paul K. , Stancato Daniel M. , Côté Stéphane , Mendoza-Denton Rodolfo , Keltner Dacher
Published: February 2012

Seven studies using experimental and naturalistic methods reveal that upper-class individuals behave more unethically than lower-class individuals. In studies 1 and 2, upper-class individuals were more likely to break the law while driving, relative to lower-class individuals. In follow-up laboratory studies, upper-class individuals were more likely to exhibit unethical decision-making tendencies (study 3), take valued goods from others (study 4), lie in a negotiation (study 5), cheat to increase their chances of winning a prize (study 6), and endorse unethical behavior at work (study 7) than were lower-class individuals. Mediator and moderator data demonstrated that upper-class individuals’ unethical tendencies are accounted for, in part, by their more favorable attitudes toward greed.
Parallel Versions ofVīdēvdād11
Authors: Andrés-Toledo Miguel Ángel
Published: February 2012

The Pahlavi literature of the Sasanian and post-Sasanian periods preserves not only many fragments of Pahlavi translations of lost Avestan texts, but also parallel versions of those attested in the extant Avestan manuscripts. Their differences are generally interpreted on the assumption of the existence of an underlying common Avestan text. However, the structural comparison between the Pahlavi translation ofVīdēvdād11 in the Pahlavi textZand ī Fragard ī Juddēwdādand its Avestan text in theVīdēvdād Sādeand the PahlaviVīdēvdādmanuscripts could point to the existence of two or even three different Avestan versions of the same chapter (fragard).
A Unique Episode from theKārnāmag ī Ardašīr ī Pābagānin a Nineteenth-Century Illustrated Indian Manuscript of theShāhnāmeh
Authors: Askari Nasrin
Published: February 2012

The episode under discussion in this article comes from the Middle Persian textKārnāmag ī Ardašīr ī Pābagān. It does not appear in any published edition of theShāhnāmeh, nor does it seem to be recorded in any manuscript consulted for these editions. The episode is versified and illustrated in a nineteenth-century manuscript preserved in the Government Museum in Alwar, India. If it is an early interpolation, why is it not found in majorShāhnāmehmanuscripts? And if it is a late interpolation, how did it find its way into an Indian manuscript at such a late date? The article proposes a provenance for the manuscript and draws attention to the possible role of the Zoroastrian community in India in the transmission of Ferdowsi's opus.
TheNiyāyišns Corpus and Its Relationships with theYašts: The Case ofYašts 6 and 7
Authors: Panaino Antonio
Published: February 2012

The present article investigates the relations between the corpus of the five AvestanNiyāyišns and that of theYašts, showing the dependance of the former on the latter. FourNiyāyišns out of five incorporate chapters attested into the corpus of theYašts; only the fifthNiyāyišndepends onYasna62, although it shares some stanzas withYasna27, 33 and 34; in any case this text cannot be considered the source of the parallel passages attested in theYasna. The paragraphs of theNiyāyišns which do not have a direct parallel in other Avestan passages, cannot be considered as original, but probably depend on other original sources or have been made through imitating earlier passages.
Everyday Life in Late Qajar Iran
Authors: Mahdavi Shireen
Published: February 2012

The social history of Iran in general and that of the Qajar era in particular, has been little studied. The subject of this paper, private life in the late Qajar period, has barely been touched upon, probably because it is a subject on which there is not much primary material. There are no comprehensive accounts of people's daily lives of any class or occupation. In this article an attempt is made to give an account of the daily domestic life and activities of the household in the Qajar period. As there were major differences between the daily life and households of urban and rural areas, the discussion is limited to urban areas and Shi'i households. The article discusses the roles of the various members of the household as well as the consumption patterns of the family and those from inside or outside the household who catered to its needs.
The Military of Qajar Iran: The Features of an Irregular Army from the Eighteenth to the Early Twentieth Century
Authors: Rabi Uzi , Ter-Oganov Nugzar
Published: February 2012

The article examines the parameters of the irregular army in Qajar Iran, including its assembly, numbers, and provisions, as well as the army's organizational structure: its administration and the divisions of the ad hoc forces (provincial militia and tribal cavalry) and of the standing forces (the shah's bodyguard and artillery corps). Until the creation of the so-called regular army units in Iran at the beginning of the nineteenth century, the irregular army was regarded as the only military force in the service of the Qajar dynasty. Despite the existence of a “regular army,” irregular forces, particularly tribal cavalry, continued to play a significant role in Iran's military system throughout the nineteenth century. By understanding the features of the irregular army—its role in Qajar society, its organizational and social structures, its ethnic composition, and other characteristics—we can better understand the character of the state itself.
Design, Evolution, and Assessment of a Sea Turtle Deflector Dredge for the U.S. Northwest Atlantic Sea Scallop Fishery: Impacts on Fish Bycatch
Authors: Smolowitz Ronald , Milliken Henry O. , Weeks Matthew
Published: March 2012

Between May 2006 and November 2009 we tested five sequential dredge modifications during 37 trips on 13 different sea scallop fishing vessels. The testing evaluated the impacts of these modifications on the catch of sea scallops Placopecten magellanicus, the bycatch of fish and sea turtles in the families Cheloniidae and Dermochelyidae, and frame durability. We tested the modified dredges and an original New Bedford dredge (control) by conducting paired, side-by-side tows using identical tow parameters. A total of 4,059 paired tows were conducted in which tow data, scallop catch, and bycatch were recorded; data from 44% of the tows were sufficiently sampled for comparisons of bycatch. The dredge catches showed a significant 3% increase in sea scallop catch and significant decreases in the bycatch of many species, including yellowtail flounder Limanda ferruginea (46%), winter flounder Pseudopleuronectes americanus (69%), barndoor skate Dipturus laevis (18%), and winter skate Leucoraja ocellata (20%). The final design, the CFarm turtle deflector dredge, proved effective at guiding turtle carcasses over the top of the dredge by eliminating most of the bale bars and forming a ramp with a forward-positioned cutting bar and closely spaced struts leading back at a 45° angle. The final design also proved effective in reducing bycatch for a number of nontarget fish species. Flow characterizations in a flume tank provided insight into the cutting bar and frame hydrodynamics that may explain the field trial results.

Received February 2, 2011; accepted November 2, 2011
Disruption of an Atlantic Cod Spawning Aggregation Resulting from the Opening of a Directed Gill-Net Fishery
Authors: Dean Micah J. , Hoffman William S. , Armstrong Michael P.
Published: March 2012

Atlantic cod Gadus morhua exhibit multiyear homing to discrete spawning grounds, where they aggregate in dense schools. Within an aggregation, a series of complex mating behaviors takes place before mate selection and successful spawning. Disruption of these behaviors has been suggested as a cause of diminished reproductive success and poor recruitment in some stocks. An area known to support a spawning aggregation in Massachusetts Bay was closed to both commercial and recreational fishing for the months of May and June 2009. During the closure period, 10 Atlantic cod were captured, tagged with acoustic transmitters, and released back to the aggregation. Four stationary acoustic receivers were deployed in the area to record transmissions from the tagged fish. Overlapping detection ranges of the receivers allowed for the reconstruction of fine-scale movements of the tagged fish over several days. The tagged cod showed a consistent pattern of aggregation prior to the fishery, characterized by limited movement and similar space use. With the opening of the fishery, the aggregation behavior was disrupted, resulting in increased horizontal and vertical movements and dissimilar space use among individuals. Half of the tagged fish appeared to have been caught in gill nets within 9 h of the opening, while the remainder left the area within 18 h. Even though the receivers were maintained for 9 d after the opening, none of the tagged fish that left the area returned. These results indicate that the spawning aggregation was completely dispersed by the onset of the fishery. Managers hoping to protect spawning aggregations should be aware that the effects of fishing on a spawning aggregation go beyond the removals from the spawning stock.

Received May 3, 2011; accepted October 13, 2011
HMGB1 promotes recruitment of inflammatory cells to damaged tissues by forming a complex with CXCL12 and signaling via CXCR4
Authors: Schiraldi Milena , Raucci Angela , Muñoz Laura Martínez , Livoti Elsa , Celona Barbara , Venereau Emilie , Apuzzo Tiziana , De Marchis Francesco , Pedotti Mattia , Bachi Angela , Thelen Marcus , Varani Luca , Mellado Mario , Proudfoot Amanda , Bianchi Marco Emilio , Uguccioni Mariagrazia
Published: February 2012

After tissue damage, inflammatory cells infiltrate the tissue and release proinflammatory cytokines. HMGB1 (high mobility group box 1), a nuclear protein released by necrotic and severely stressed cells, promotes cytokine release via its interaction with the TLR4 (Toll-like receptor 4) receptor and cell migration via an unknown mechanism. We show that HMGB1-induced recruitment of inflammatory cells depends on CXCL12. HMGB1 and CXCL12 form a heterocomplex, which we characterized by nuclear magnetic resonance and surface plasmon resonance, that acts exclusively through CXCR4 and not through other HMGB1 receptors. Fluorescence resonance energy transfer data show that the HMGB1–CXCL12 heterocomplex promotes different conformational rearrangements of CXCR4 from that of CXCL12 alone. Mononuclear cell recruitment in vivo into air pouches and injured muscles depends on the heterocomplex and is inhibited by AMD3100 and glycyrrhizin. Thus, inflammatory cell recruitment and activation both depend on HMGB1 via different mechanisms.
Age‐dependent changes in contractile function and passive elastic properties of myocardium from mice lacking muscle LIM protein (MLP)
Authors: Unsöld Bernhard , Schotola Hanna , Jacobshagen Claudius , Seidler Tim , Sossalla Samuel , Emons Julius , Klede Stefanie , Knöll Ralph , Guan Kaomei , El‐Armouche Ali , Linke Wolfgang A. , Kögler Harald , Hasenfuss Gerd
Published: February 2012

Aims

Muscle LIM protein (MLP) null mice are often used as a model for human dilated cardiomyopathy. So far, little is known about the time course and pathomechanisms leading to the development of the adult phenotype.

Methods and results

We systematically analysed the contractile phenotype, myofilament calcium (Ca2+) responsiveness, passive myocardial mechanics, histology, and mRNA expression in mice aged 4 and 12 weeks. In 4‐week‐old animals, there was no significant difference in the force–frequency relationship (FFR) and catecholamine response of intact isolated papillary muscles between wild‐type (WT) and MLP null myocardium. In 12‐week‐old animals, WT myocardium exhibited a significantly positive FFR, while that of MLP null mice was significantly negative, and the inotropic response to catecholamines was significantly reduced in MLP null mice. This time course of decline in contractile function was confirmed in vivo by echocardiography. Whereas at 4 weeks of age MLP null mice and WT littermates showed similar levels of SERCA2a (sarcoplasmic reticulum Ca2+ ATPase) expression, the expression was significantly lower in 12‐week‐old MLP null mice compared with littermate controls. Myofilament Ca2+ responsiveness was not affected by the lack of MLP, irrespective of age. Whereas in 4‐week‐old animals MLP null myocardium showed a trend to an increased compliance compared with the WT, myocardium of 12‐week‐old MLP null mice was significantly less compliant than WT myocardium. Parallel to the decrease in compliance there was an increase in fibrosis in the MLP null animals.

Conclusion

Our data suggest that MLP deficiency does not primarily influence myocardial contractility. A lack of MLP leads to an age‐dependent impairment of excitation–contraction coupling with resulting contractile dysfunction and secondary fibrosis.
Detection of Borrelia burgdorferi sensu lato in endomyocardial biopsy specimens in individuals with recent‐onset dilated cardiomyopathy
Authors: Kubánek Miloš , Šramko Marek , Berenová Dagmar , Hulínská Dagmar , Hrbáčková Hana , Malušková Jana , Lodererová Alena , Málek Ivan , Kautzner Josef
Published: March 2012

Aims

Recent studies in patients with dilated cardiomyopathy (DCM) have detected the genome of Borrelia burgdorferi sensu lato (BBSL) in endomyocardial biopsy (EMB) specimens using a qualitative polymerase chain reaction (PCR), suggesting a causal link between Lyme disease and DCM in areas in which Lyme disease is endemic. We aimed to study this relationship using a comprehensive molecular analysis detecting BBSL in EMB samples.

Methods and results

We performed a comprehensive histopathological, immunohistochemical, ultrastructural, and molecular analysis targeting cardiotropic viruses and BBSL in EMB specimens of 41 individuals with recent‐onset DCM and 15 controls with end‐stage coronary artery disease. Specifically, quantitative PCR and electron microscopy of EMB specimens were employed. In addition, autoantibodies and manifestation of autoimmune diseases were evaluated in both groups. Individuals with recent‐onset DCM presented more frequently with myocardial BBSL persistence as compared with the control group (24% vs. 0%, P = 0.035). In contrast, the prevalence of parvovirus B19 and cytomegalovirus was similar in both groups. Sequence analysis of borrelial DNA revealed the following genospecies: Borrelia burgdorferi sensu stricto in three patients (30%), Borrelia afzelii in two patients (20%), and Borrelia garinii in four patients (40%), the results being inconclusive in one case. BBSL‐positive DCM patients had a higher prevalence of organ‐specific autoimmune diseases in comparison with the remaining DCM patients (50% vs. 16%, P = 0.030).

Conclusion

Myocardial persistence of BBSL may be involved in the pathophysiology of DCM in individuals living in areas in which Lyme disease is endemic.
Why economics matters for understanding the effects of climate change on fisheries
Authors: Haynie Alan C. , Pfeiffer Lisa
Published: February 2012

Haynie, A. C., and Pfeiffer, L. 2012. Why economics matters for understanding the effects of climate change on fisheries. – ICES Journal of Marine Science, 69: . Research attempting to predict the effect of climate change on fisheries often neglects to consider how harvesters respond to changing economic, institutional, and environmental conditions, which leads to the overly simplistic prediction of “fisheries follow fish”. However, climate effects on fisheries can be complex because they arise through physical, biological, and economic mechanisms that interact or may not be well understood. Although most researchers find it obvious to include physical and biological factors in predicting the effects of climate change on fisheries, the behaviour of fish harvesters also matters for these predictions. A general but succinct conceptual framework for investigating the effects of climate change on fisheries that incorporates the biological and economic factors that determine how fisheries operate is presented. The use of this framework will result in more complete, reliable, and relevant investigations of the effects of climate change on fisheries. The uncertainty surrounding long-term projections, however, is inherent in the complexity of the system.
Heat content in the Norwegian Sea, 1995–2010
Authors: Skagseth Øystein , Mork Kjell Arne
Published: February 2012

Skagseth, Ø., and Mork, K. A. 2012. Heat content in the Norwegian Sea, 1995–2010. – ICES Journal of Marine Science, 69: 826–832. Spatio-temporal hydrographic data from the Nordic Seas during spring over the period 1995–2010 were investigated in terms of the relative heat content (RHC) above the density surface σt = 27.9, chosen to capture the changes in Atlantic water (AW). Focusing on the Atlantic (eastern) domain of the Nordic Seas, negative anomalies dominated the early part of the series. There was then a gradual transition towards an absolute maximum in 2003/2004, followed by a small reduction with positive values for the period ending in 2010. The maps clearly reveal the events of propagating signals. The variability is regionally comparable, but the persistence on a year-to-year basis is higher in the Lofoten Basin than in the Norwegian Basin. Compared with other studies, in this study, the estimated trend in the RHC of the Nordic Seas was larger than for the global mean and the North Atlantic. The warming of the Nordic Seas derives mainly from the advection of warmer inflowing AW and less from changes in local air–sea heat fluxes. The importance of advection suggests that the variability of the Norwegian Sea's ocean climate can, to a large extent, be predicted based on the observed hydrographic conditions.
Combined hormonal contraception
Authors: Juttner Isabel
Published: February 2012

Combined hormonal contraception is a convenient, reversible and effective method of contraception. The combined oral contraceptive is the most popular reversible method of contraception in the UK. GPs should be confident in prescribing combined hormonal contraception and counselling women about key points such as the risks and benefits associated with this method of contraception and how to use it correctly.
Modeling the role of IL2 in the interplay between CD4+ helper and regulatory T cells: studying the impact of IL2 modulation therapies
Authors: García-Martínez Karina , León Kalet
Published: February 2012

Several reports in the literature have drawn a complex picture of the effect of treatments aiming to modulate IL2 activity in vivo. They seem to promote indistinctly immunity or tolerance, probably depending on the specific context, dose and timing of their application. Such complexity might derives from the dual role of IL2 on T-cell dynamics. To theoretically address the latter possibility, we develop a mathematical model for helper, regulatory and memory T-cells dynamics, which account for most well-known facts relative to their relationship with IL2. We simulate the effect of three types of therapies: IL2 injections, IL2 depletion using anti-IL2 antibodies and IL2/anti-IL2 immune complexes injection. We focus in the qualitative and quantitative conditions of dose and timing for these treatments which allow them to potentate either immunity or tolerance. Our results provide reasonable explanations for the existent pre-clinical and clinical data and further provide interesting practical guidelines to optimize the future application of these types of treatments. Particularly, our results predict that: (i) Immune complexes IL2/anti-IL2 mAbs, using mAbs which block the interaction of IL2 and CD25 (the alpha chain of IL2 receptor), is the best option to potentate immunity alone or in combination with vaccines. These complexes are optimal when a 1:2 molar ratio of mAb:IL2 is used and the mAbs have the largest possible affinity; (ii) Immune complexes IL2/anti-IL2 mAbs, using mAbs which block the interaction of IL2 and CD122 (the beta chain of IL2 receptor), are the best option to reinforce preexistent natural tolerance, for instance to prevent allograft rejection. These complexes are optimal when a 1:2 molar ratio of mAb:IL2 is used and the mAbs have intermediate affinities; (iii) mAbs anti-IL2 can be successfully used alone to treat an ongoing autoimmune disorder, promoting the re-induction of tolerance. The best strategy in this therapy is to start treatment with an initially high dose of the mAbs (one capable to induce some immune suppression) and then scales down slowly the dose of mAb in subsequent applications.
DOP-PCR Amplification of Probe DNA for Whole-Mount FISH in Drosophila
Authors: Dernburg Abby F.
Published: March 2012

It is sometimes useful to amplify DNA before labeling it. Degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) allows amplification of any complex DNA, regardless of sequence. DOP-PCR is performed using a single primer that has a fixed sequence at its 5′ end and several degenerate bases near its 3′ end that allow it to anneal at low stringency to many sites in complex DNA. Following several PCR cycles with an annealing temperature of only 30°C, the annealing temperature is raised so that only products with the primer sequence at each end are amplified in the reaction. This protocol describes the use of DOP-PCR to amplify probe DNA for whole-mount fluorescent in situ hybridization (FISH) in Drosophila. Primary DOP-PCR amplification may be used for microdissected material, small volumes of melted gel slice, or small quantities of other DNA template. A procedure for secondary DOP-PCR amplification is also provided.
Identifying cis-Acting DNA Elements within a Control Region
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: March 2012

Computational methods can be used to identify DNA sequence motifs that have been conserved through evolution, as well as motifs that correspond to recognition sites for known DNA-binding proteins. These computational methods, when combined with chromatin immunoprecipitation and other basic experiments, can provide preliminary insight into the elements and factors that regulate a gene of interest. When pursuing a more complete understanding of a control region of interest, a comprehensive mutant analysis should generally be performed as a critical step toward more advanced functional studies. This article describes strategies for such a comprehensive analysis. It also summarizes the insights provided by a comprehensive mutant analysis versus a phylogenetic analysis.
Assessment of generalizability, applicability and predictability (GAP) for evaluating external validity in studies of universal family‐based prevention of alcohol misuse in young people: systematic methodological review of randomized controlled trials
Authors: Fernandez‐Hermida Jose Ramon , Calafat Amador , Becoña Elisardo , Tsertsvadze Alexander , Foxcroft David R.
Published: February 2012

Aims  To assess external validity characteristics of studies from two Cochrane Systematic Reviews of the effectiveness of universal family‐based prevention of alcohol misuse in young people.

Methods  Two reviewers used an a priori developed external validity rating form and independently assessed three external validity dimensions of generalizability, applicability and predictability (GAP) in randomized controlled trials.

Results  The majority (69%) of the included 29 studies were rated ‘unclear’ on the reporting of sufficient information for judging generalizability from sample to study population. Ten studies (35%) were rated ‘unclear’ on the reporting of sufficient information for judging applicability to other populations and settings. No study provided an assessment of the validity of the trial end‐point measures for subsequent mortality, morbidity, quality of life or other economic or social outcomes. Similarly, no study reported on the validity of surrogate measures using established criteria for assessing surrogate end‐points.

Conclusions  Studies evaluating the benefits of family‐based prevention of alcohol misuse in young people are generally inadequate at reporting information relevant to generalizability of the findings or implications for health or social outcomes. Researchers, study authors, peer reviewers, journal editors and scientific societies should take steps to improve the reporting of information relevant to external validity in prevention trials.
Quality of life in newly diagnosed children with specific learning disabilities (SpLD) and differences from typically developing children: a study of child and parent reports
Authors: Ginieri‐Coccossis M. , Rotsika V. , Skevington S. , Papaevangelou S. , Malliori M. , Tomaras V. , Kokkevi A.
Published: February 2012

Introduction  Research on quality of life (QoL) of school children with specific learning disabilities (SpLD) and their parents is scarce. The present study explores QoL deficits in newly diagnosed children with SpLD and their parents, in comparison to a similar age group of typically developing children. Possible associations between parental and child QoL were statistically explored in both groups of children.

Methods  70 newly diagnosed children with SpLD [International Classification of Diseases‐10 (ICD‐10) criteria] (38 boys, 32 girls, mean age 10.1 years) and a control group of 69 typically developing children of the same age (40 boys, 29 girls, mean age 10.6 years) were recruited. Children were of normal intelligence quotient, attending mainstream schools. Their parents were also recruited so a child's scores could be associated with corresponding parental scores (mother or father). Children's QoL was assessed by the German questionnaire for measuring quality of life in children and adolescents (KINDLR) questionnaire and parental QoL by World Health Organization Quality of Life brief questionnaire (WHOQOL‐BREF) of the World Health Organization.

Results  Children with SpLD in comparison to typically developing children reported according to the KINDLR measurement poorer emotional well‐being, lower self‐esteem and satisfaction in their relationships with family and friends. Surprisingly, school functioning was not reported by these children as an area of concern. Parents of children with SpLD indicated experiencing lower satisfaction in the WHOQOL‐BREF domains of social relationships and environment. Correlational and regression analysis with parental–child QoL scores provided evidence that in the SpLD group, parental scores on WHOQOL‐BREF social relationships and psychological health domains could be predictors of the child's emotional well‐being, satisfaction with family, friends and school functioning. Stepwise regression analysis verified the effect of parents' WHOQOL‐BREF social relationships domain on several dimensions of children's KINDLR QoL.

Conclusions  The results may suggest certain significant effects of the SpLD condition on newly diagnosed children's QoL. Emotional and social deficits seem to be experienced by this cohort of children and their parents. Investigation into the possible interrelationships between parental and child QoL seems to indicate that parental social wellbeing may to a certain extend influence some dimensions of the child's QoL. The findings are useful for policy making and specialized interventions for children with SpLD and their families.
Cortisol response to synacthen stimulation is attenuated following abusive head trauma
Authors: Heather Natasha L. , Derraik José G. B. , Brennan Christine , Jefferies Craig , Hofman Paul L. , Kelly Patrick , Jones Rhys G. , Rowe Deborah L. , Cutfield Wayne S.
Published: February 2012

Background

Child abuse and other early‐life environmental stressors are known to affect the hypothalamic–pituitary–adrenal axis. We sought to compare synacthen‐stimulated cortisol responses in children who suffered inflicted or accidental traumatic brain injury (TBI).

Methods

Children with a history of early‐childhood TBI were recruited from the Starship Children's Hospital database (Auckland, New Zealand, 1992–2010). All underwent a low‐dose ACTH1–24 (synacthen 1 μg IV) test, and serum cortisol response was compared between inflicted (TBII) and accidental (TBIA) groups.

Results

We assessed 64 children with TBII and 134 with TBIA. Boys were more likely than girls to suffer accidental (P < 0·001), but not inflicted TBI. TBII children displayed a 14% reduction in peak stimulated cortisol in comparison with the TBIA group (P < 0·001), as well as reduced cortisol responses at + 30 (P < 0·01) and + 60 min (P < 0·001). Importantly, these differences were not associated with severity of injury. The odds ratio of TBII children having a mother who suffered domestic violence during pregnancy was 6·2 times that of the TBIA group (P < 0·001). However, reported domestic violence during pregnancy or placement of child in foster care did not appear to affect cortisol responses.

Conclusion

Synacthen‐stimulated cortisol response is attenuated following inflicted TBI in early childhood. This may reflect chronic exposure to environmental stress as opposed to pituitary injury or early‐life programming.
Sediments, not plants, offer the preferred refuge for Daphnia against fish predation in Mediterranean shallow lakes: an experimental demonstration
Authors: NIHAN TAVŞANOĞLU ÜLKÜ , IDIL ÇAKIROĞLU AYŞE , ERDOĞAN ŞEYDA , MEERHOFF MARIANA , JEPPESEN ERIK , BEKLIOGLU MERYEM
Published: March 2012

1. Different behavioural responses of planktonic animals to their main predators, fish, have been reported from shallow lakes. In north temperate lakes, large‐bodied zooplankton may seek refuge from predation among macrophytes, whereas in subtropical lakes, avoidance of macrophytes has been observed. The prevalent behaviour probably depends on the characteristics of the fish community, which in Mediterranean lakes is typically dispersed in both the open water zone and in the littoral, as in temperate lakes, and is dominated by small size classes, as in subtropical lakes.

2. We performed ‘habitat choice’ experiments to test the response of Daphnia magna to predation cues at both the horizontal and vertical level by mimicking a ‘shallow littoral’ zone with plants and a ‘deeper pelagic’ zone with sediments.

3. Initial separate response experiments showed that natural plants, artificial plants and predation cues all repelled D. magna in the absence of other stimuli, while sediments alone did not trigger any significant response by D. magna.

4. The habitat choice experiments showed that, in the presence of predation cues and absence of plants, Daphnia moved towards areas with sediment. In the presence of both plants and sediments, Daphnia moved away from the plants towards the sediments under both shallow and deep water treatment conditions.

5. Based on these results, we suggest that Daphnia in Mediterranean shallow lakes avoid submerged macrophytes and instead prefer to hide near the sediment when exposed to predation risk, as also observed in subtropical shallow lakes. This pattern is not likely to change with water level alterations, a common feature of lakes in the region, even if the effectiveness of the refuge may be reduced.
Ecosystem transformation by emerging infectious disease: loss of large tanoak from California forests
Authors: Cobb Richard C. , Filipe João A. N. , Meentemeyer Ross K. , Gilligan Christopher A. , Rizzo David M.
Published: February 2012

1. Few pathogens are the sole or primary cause of species extinctions, but forest disease has caused spectacular declines in North American overstorey trees and restructured forest ecosystems at large spatial scales over the past 100 years. These events threaten biodiversity associated with impacted host trees and other resources valued by human societies even when they do not directly cause host extinction.

2. Invasion of Phytophthora ramorum and emergence of the forest disease sudden oak death has caused a large‐scale decline of tanoak (Notholithocarpus densiflorus) in Californian coastal forests. Here, we describe structural changes to tanoak forests and develop predictive models of infection rates, mortality rates and changes in tanoak biomass and abundance by combining regionally extensive longitudinal field studies and mathematical modelling.

3. Pathogen‐invaded stands had smaller average tanoak tree size and higher proportions of large dead tanoak trees compared with uninvaded stands. This pattern is caused in part by a positive relationship between tanoak size and mortality rate, as well as prolific basal sprouting from trees killed by the disease. Tanoak infection, mortality and biomass decline rates were positively related to the prevalence of infection in sporulation‐supporting species, especially California bay laurel (Umbellularia californica).

4. We developed a stage‐structured and spatially explicit mathematical model including species dynamics and P. ramorum transmission, where the long‐term outcome of disease ranges from host extinction when densities of bay laurel are high to limited or no disease outbreak. Low densities of tanoak in a matrix of non‐susceptible neighbouring species resulted in slow‐enough transmission to retain overstorey tanoak, suggesting host‐density thresholds may exist in real forests.

5.
Synthesis. Tanoak is likely to persist in many disease‐impacted forests via vegetative reproduction, but overstorey trees may be eliminated or greatly reduced in abundance, a pattern similar to other forest diseases that have emerged in the last century including chestnut blight and beech bark disease. Our results support a general model of disease‐caused changes to forest trees useful for the analysis of emerging forest pathogens where vegetative reproduction, community‐level epidemiology and stage‐specific mortality rate interact to determine local disease intensity and host decline.
Lymphoid organ cell culture system from Penaeus monodon (Fabricius) as a platform for white spot syndrome virus and shrimp immune‐related gene expression
Authors: Jose S , Jayesh P , Sudheer N S , Poulose G , Mohandas A , Philip R , Bright Singh I S
Published: February 2012

Shrimp cell lines are yet to be reported and this restricts the prospects of investigating the associated viral pathogens, especially white spot syndrome virus (WSSV). In this context, development of primary cell cultures from lymphoid organs was standardized. Poly‐l‐lysine‐coated culture vessels enhanced growth of lymphoid cells, while the application of vertebrate growth factors did not, except insulin‐like growth factor‐1 (IGF‐1). Susceptibility of the lymphoid cells to WSSV was confirmed by immunofluoresence assay using monoclonal antibody against the 28 kDa envelope protein of WSSV. Expression of viral and immune‐related genes in WSSV‐infected lymphoid cultures could be demonstrated by RT‐PCR. This emphasizes the utility of lymphoid primary cell culture as a platform for research in virus–cell interaction, virus morphogenesis, up and downregulation of shrimp immune‐related genes, and also for the discovery of novel drugs to combat WSSV in shrimp culture.