bluuebunny/crossref_metadata_2025 huggingface dataset:
Some comments and corrections regarding the calculation of electrostatic potential derivatives using the Ewald summation technique
Authors: Stenhammar Joakim , Trulsson Martin , Linse Per
Published: June 2011

A review of the literature on the calculation of electrostatic potentials, fields, and field gradients in systems consisting of charges and dipoles using the Ewald summation technique is presented. Discrepancies between the previous formulas are highlighted, and an error in the derivation of the reciprocal contributions to the electrostatic field and field gradient is corrected. The new formulas for the field and field gradient are shown to exhibit a termwise identity with the ones for the electrostatic energy.
Effect of air exposure on metal/organic interface in organic field-effect transistors
Authors: Lu Xubing , Minari Takeo , Kumatani Akichika , Liu Chuan , Tsukagoshi Kazuhito
Published: June 2011

We report the effect of air exposure on charge injection process through the metal/organic interface in organic field-effect transistors. Pentacene-based field-effect transistors and metal-insulator-semiconductor capacitors having gold or copper contact were fabricated without exposing to air. An air exposure caused remarkable improvement on the electrical characteristics of the devices, particularly on the contact resistance and frequency response characteristics. Measurements of photoelectron yield spectroscopy revealed that natural oxidation significantly shifted the work function of contact metal and thus charge injection efficiency was improved. This result provides critical insights on control of desirable metal/organic interface in organic electronics devices.
Simulations of slow positron production using a low-energy electron accelerator
Authors: O’Rourke B. E. , Hayashizaki N. , Kinomura A. , Kuroda R. , Minehara E. J. , Ohdaira T. , Oshima N. , Suzuki R.
Published: June 2011

Monte Carlo simulations of slow positron production via energetic electron interaction with a solid target have been performed. The aim of the simulations was to determine the expected slow positron beam intensity from a low-energy, high-current electron accelerator. By simulating (a) the fast positron production from a tantalum electron-positron converter and (b) the positron depth deposition profile in a tungsten moderator, the slow positron production probability per incident electron was estimated. Normalizing the calculated result to the measured slow positron yield at the present AIST linear accelerator, the expected slow positron yield as a function of energy was determined. For an electron beam energy of 5 MeV (10 MeV) and current 240 μA (30 μA), production of a slow positron beam of intensity 5 × 106 s−1 is predicted. The simulation also calculates the average energy deposited in the converter per electron, allowing an estimate of the beam heating at a given electron energy and current. For low-energy, high-current operation the maximum obtainable positron beam intensity will be limited by this beam heating.
Conductance and shot noise in graphene superlattice
Authors: Guo Xiao-Xiao , Liu De , Li Yu-Xian
Published: June 2011

The conductance and the shot noise were investigated in graphene superlattice. A new Dirac point appears in the graphene superlattice and the position of the new Dirac point depends on the ratio of the width of the barriers to that of the wells. At the new Dirac point the conductance is minimum and the Fano factor reaches its max value 1/3. This Dirac point is robust against the magnetic field. In the energy window below the Dirac point, the magnetic field weakens the conductance but enhances the Fano factor.
Graphene oxide as a photocatalytic material
Authors: Krishnamoorthy Karthikeyan , Mohan Rajneesh , Kim S.-J.
Published: June 2011

The photocatalytic characteristics of graphene oxide (GO) nanostructures synthesized by modified Hummer’s method were investigated by measuring reduction rate of resazurin (RZ) into resorufin (RF) as a function of UV irradiation time. The progress of the photocatalytic reaction was monitored by change in color from blue (RZ) into pink (RF) followed by absorption spectra. It exhibited excellent photocatalytic activity, leading to the reduction of RZ in UV irradiation. The fitting of absorbance maximum versus time suggests that the reduction of RZ follow the pseudo first-order reaction kinetics. These results indicate that GO have great potential for use as a photocatalyst.
Role of electronic correlations in Ga
Authors: Zhu Zhiyong , Wang Xuhui , Schwingenschlögl Udo
Published: June 2011

An extended around mean field (AMF) functional for less localized p electrons is developed to quantify the influence of electronic correlations in α-Ga. Both the local density approximation (LDA) and generalized gradient approximation are known to mispredict the Ga positional parameters. The extended AMF functional together with an onsite Coulomb interaction of Ueff=1.1 eV, as obtained from constraint LDA calculations, reduces the deviations by about 20%. The symmetry lowering coming along with the electronic correlations turns out to be in line with the Ga phase diagram.
Positive and negative components of magnetoconductance in hole transport limited organic light-emitting diodes
Authors: Zhang Q. M. , Lei Y. L. , Song Q. L. , Chen P. , Zhang Y. , Xiong Z. H.
Published: June 2011

Two kinds of devices using N,N′-Di(naphthalen-1-yl)-N,N′-diphenyl-benzidine (NPB) and dye-doped NPB as emitting layer were fabricated to study their magnetoconductance (MC) response. The MC of the NPB devices contains a positive low-field (0<|B|<40 mT) component but a negative high-field (|B|>40 mT) component at low temperatures. Similar MC is presented in the dye-doped NPB devices even at room temperature. Magnetoelectroluminescence results and energy-level diagram indicate that long lifetime triplet excitons and excessive holes are in these devices. All these observations suggest that triplet exciton-hole reaction is responsible for the negative MC while positive MC is assigned to hyperfine mixing of electron-hole pairs.
Physical origin of the resistance drift exponent in amorphous phase change materials
Authors: Boniardi Mattia , Ielmini Daniele
Published: June 2011

The resistance of amorphous chalcogenides used in phase change memory devices increases over time due to structural relaxation (SR). The resistance drift usually follows a power law with time described by an exponent ν. Understanding the origin of may lead to engineering methods to improve the stability in memory devices. This work presents an analytical model to describe the activation energies for conduction and SR based on the Meyer–Neldel rule. The model accounts for the observed temperature and time dependence of resistance, and highlights that νis related to the ratio between conduction and SR activation energies at any given time during drift.
Narrowband fluorescent nanodiamonds produced from chemical vapor deposition films
Authors: Neu E. , Arend C. , Gross E. , Guldner F. , Hepp C. , Steinmetz D. , Zscherpel E. , Ghodbane S. , Sternschulte H. , Steinmüller-Nethl D. , Liang Y. , Krueger A. , Becher C.
Published: June 2011

We report on the production of nanodiamonds (NDs) with 70–80 nm size via bead assisted sonic disintegration (BASD) of a polycrystalline chemical vapor deposition film. The high crystalline quality NDs display intense narrowband (7 nm) room temperature luminescence at 738 nm from in situ incorporated silicon vacancy centers. We demonstrate bright, narrowband single photon emission with >100 000 cps. Due to the narrow fluorescence bandwidth as well as the near-infrared emission these NDs are also suitable as fluorescence labels with significantly enhanced performance for in vivo imaging.
A piezoelectric multilayer-stacked hybrid actuation/transduction system
Authors: Xu Tian-Bing , Jiang Xiaoning , Su Ji
Published: June 2011

A piezoelectric multilayer-stacked hybrid actuation/transduction system (stacked-HYBATS) is reported in this letter. It uses synergetic contributions from positive-strain and negative-strain piezoelectric multilayer-stacks to give displacements of about 3.5 times those of the same-sized piezoelectric flextensional actuator/transducer. The resonance of a stacked-HYBATS is enhanced comparing with that of actuators with either stack alone. The effective piezoelectric coefficient of the stacked-HYBATS is 2.5×106 pm/V at the resonance frequency and 1.5×105 pm/V at off-resonance frequencies. The stacked-HYBATS provides an approach for high performance electromechanical devices.
Far-field subwavelength imaging for ultrasonic elastic waves in a plate using an elastic hyperlens
Authors: Lee Hyung Jin , Kim Hoe Woong , Kim Yoon Young
Published: June 2011

Subwavelength imaging was experimentally performed for ultrasonic elastic waves by using an angularly stratified plat, an elastic plate hyperlens. It consists of alternating layers of aluminum and air, exhibiting a large contrast in elastic stiffness. A specially configured experimental setup is used to locate two sources within half the wavelength at 100 kHz. To explain the observed phenomenon, the homogenization of the elasticity coefficients of the stratified structure is employed. Because of the strong cylindrical anisotropy, an equifrequency contour becomes nearly flat along the angular wave vector so that evanescent waves involved with high angular resolution are converted to propagating waves.
HOW CREDIT INSTITUTIONS LOOK AT SOCIETY
Authors: Lopes Daniel Seabra , Marques Rafael
Published: June 2011

Twenty years ago, Anthony Giddens proclaimed that modernity was, inherently, deeply and intrinsically sociological in the sense that sociological knowledge tended to be rapidly assimilated by individuals and institutions and therefore incorporated into subsequent processes of change. Thus, it may seem relevant to question just how much sociology is actually being put into practice in economic institutions in general and in credit institutions in particular. Drawing on fieldwork conducted in the marketing, risk, and financial departments of two Portuguese retail banks, this article describes how these institutions use specific views of society which are predominantly statistical and bear little resemblance to more qualitative sociological or anthropological accounts. Hence, there is a clear need to reconsider the problem of social reflexivity and to grasp to what extent the social sciences are still important in providing a framework for perceiving the economy and society.
Dangerous Severe Personality Disordered (DSPD) Patients: Characteristics and Comparison with Other High-Risk Offenders
Authors: Burns Tom , Fazel Seena , Fahy Tom , Fitzpatrick Ray , Rogers Robert , Sinclair Julia , Linsell Louise , Doll Helen , Yiend Jenny , group IDEA
Published: June 2011

England and Wales introduced the administrative category of Dangerous Severe Personality Disorder (DSPD) and established special units in prisons and high-secure psychiatric hospitals for their treatment. To examine their characteristics, we approached 202 patients admitted to DSPD units; 174 consented to participate in research. All were male, and the median age was 38 years. Most were white and born in the UK. Most patients (75%) met full DSPD criteria as suffering from severe personality disorder that caused them to be dangerous.  With  respect to personality disorder, most had elevated psychopathic traits and 40% met criteria for psychopathy on the Psychopathy Checklist-Revised (Hare, 2003). With respect to dangerousness, 25% of patients had a history of homicide; 28%, sexual offenses; and 41%, other violent offenses. Median time spent in prison was more than 12 years. According to standardized measures of violence risk, those admitted to DSPD units resembled other groups of high risk offenders described in the international literature. There were some significant differences between those admitted to prison- versus hospital-based units. The findings confirmed that DSPD units contain dangerous offenders with no evidence of preemptive incarceration.
David Bilder: Getting to know epithelia inside and out
Authors: Sedwick Caitlin
Published: June 2011

Bilder explores epithelial form and function in Drosophila using forward genetic screens.
Septin filaments exhibit a dynamic, paired organization that is conserved from yeast to mammals
Authors: DeMay Bradley S. , Bai Xiaobo , Howard Louisa , Occhipinti Patricia , Meseroll Rebecca A. , Spiliotis Elias T. , Oldenbourg Rudolf , Gladfelter Amy S.
Published: June 2011

The septins are conserved, GTP-binding proteins important for cytokinesis, membrane compartmentalization, and exocytosis. However, it is unknown how septins are arranged within higher-order structures in cells. To determine the organization of septins in live cells, we developed a polarized fluorescence microscopy system to monitor the orientation of GFP dipole moments with high spatial and temporal resolution. When GFP was fused to septins, the arrangement of GFP dipoles reflected the underlying septin organization. We demonstrated in a filamentous fungus, a budding yeast, and a mammalian epithelial cell line that septin proteins were organized in an identical highly ordered fashion. Fluorescence anisotropy measurements indicated that septin filaments organized into pairs within live cells, just as has been observed in vitro. Additional support for the formation of pairs came from the observation of paired filaments at the cortex of cells using electron microscopy. Furthermore, we found that highly ordered septin structures exchanged subunits and rapidly rearranged. We conclude that septins assemble into dynamic, paired filaments in vivo and that this organization is conserved from yeast to mammals.
PDZ-RhoGEF ubiquitination by Cullin3–KLHL20 controls neurotrophin-induced neurite outgrowth
Authors: Lin Mei-Yao , Lin Yu-Min , Kao Te-chan , Chuang Hsiang-Hao , Chen Ruey-Hwa
Published: June 2011

The induction of neurite outgrowth and arborization is critical for developmental and regenerative processes. In this paper, we report that the BTB-kelch protein KLHL20 promoted neurite outgrowth and arborization in hippocampal and cortical neurons through its interaction with Cullin3 to form a ubiquitin ligase complex. This complex targeted PDZ–Rho guanine nucleotide exchange factor (RhoGEF), a protein abundantly expressed in the brain, for ubiquitin-dependent proteolysis, thereby restricting RhoA activity and facilitating growth cone spreading and neurite outgrowth. Importantly, targeting PDZ-RhoGEF to KLHL20 required PDZ-RhoGEF phosphorylation by p38 mitogen-activated protein kinase. In response to p38-activating neurotrophins, such as brain-derived neurotrophic factor and neurotrophin-3, KLHL20-mediated PDZ-RhoGEF destruction was potentiated, leading to neurotrophin-induced neurite outgrowth. Our study identified a ubiquitin-dependent pathway that targets PDZ-RhoGEF destruction to facilitate neurite outgrowth and indicates a key role of this pathway in neurotrophin-induced neuronal morphogenesis.
Focused Correlation, Confirmation, and the Jigsaw Puzzle of Variable Evidence
Authors: Schlosshauer Maximilian , Wheeler Gregory
Published: June 2011

Focused correlation compares the degree of association within an evidence set to the degree of association in that evidence set given that some hypothesis is true. Wheeler and Scheines have shown that a difference in incremental confirmation of two evidence sets is robustly tracked by a difference in their focus correlation. In this essay, we generalize that tracking result by allowing for evidence having unequal relevance to the hypothesis. Our result is robust as well, and we retain conditions for bidirectional tracking between incremental confirmation measures and focused correlation.
Conservation Laws in Scientific Explanations: Constraints or Coincidences?
Authors: Lange Marc
Published: June 2011

A conservation law in physics can be either a constraint on the kinds of interaction there could be or a coincidence of the kinds of interactions there actually are. This is an important, unjustly neglected distinction. Only if a conservation law constrains the possible kinds of interaction can a derivation from it constitute a scientific explanation despite failing to describe the causal/mechanical details behind the result derived. This conception of the relation between “bottom-up” scientific explanations and one kind of “top-down” scientific explanation is motivated by several examples from classical and modern physics.
Nagelian Reduction beyond the Nagel Model
Authors: van Riel Raphael
Published: June 2011

Nagel's official model of theory reduction and the way it is represented in the literature are shown to be incompatible with the careful remarks on the notion of reduction Nagel gave while developing his model. Based on these remarks, an alternative model is outlined, which does not face some of the problems the official model faces. Taking the context in which Nagel developed his model into account, it is shown that the way Nagel shaped his model and, thus, its well-known deficiencies are best conceived of as a mere by-product of his philosophical background.
Epistemic Groundings of Abstraction and Their Cognitive Dimension
Authors: Martínez Sergio F. , Huang Xiang
Published: June 2011

In the philosophy of science, abstraction has usually been analyzed in terms of the interface between our experience and the design of our concepts. The often implicit assumption here is that such interface has a definite identifiable and universalizable structure, determining the epistemic correctness of any abstraction. Our claim is that, on the contrary, the epistemic grounding of abstraction should not be reduced to the structural norms of such interface but is also related to the constraints on the cognitive processes of specific abstractions. This suggests that we should understand abstraction as embodied in different kinds of abstraction practices.
Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
Authors: Munchel Sarah E. , Shultzaberger Ryan K. , Takizawa Naoki , Weis Karsten
Published: June 2011

RNA levels are determined by the rates of both transcription and decay, and a mechanistic understanding of the complex networks regulating gene expression requires methods that allow dynamic measurements of transcription and decay in living cells with minimal perturbation. Here, we describe a metabolic pulse-chase labeling protocol using 4-thiouracil combined with large-scale RNA sequencing to determine decay rates of all mRNAs in Saccharomyces cerevisiae. Profiling in various growth and stress conditions reveals that mRNA turnover is highly regulated both for specific groups of transcripts and at the system-wide level. For example, acute glucose starvation induces global mRNA stabilization but increases the degradation of all 132 detected ribosomal protein mRNAs. This effect is transient and can be mimicked by inhibiting the target-of-rapamycin kinase. Half-lives of mRNAs critical for galactose (GAL) metabolism are also highly sensitive to changes in carbon source. The fast reduction of GAL transcripts in glucose requires their dramatically enhanced turnover, highlighting the importance of mRNA decay in the control of gene expression. The approach described here provides a general platform for the global analysis of mRNA turnover and transcription and can be applied to dissect gene expression programs in a wide range of organisms and conditions.
Confinement of β1- and β2-adrenergic receptors in the plasma membrane of cardiomyocyte-like H9c2 cells is mediated by selective interactions with PDZ domain and A-kinase anchoring proteins but not caveolae
Authors: Valentine Cathleen D. , Haggie Peter M.
Published: June 2011

The sympathetic nervous system regulates cardiac output by activating adrenergic receptors (ARs) in cardiac myocytes. The predominant cardiac ARs, β1- and β2AR, are structurally similar but mediate distinct signaling responses. Scaffold protein–mediated compartmentalization of ARs into discrete, multiprotein complexes has been proposed to dictate differential signaling responses. To test the hypothesis that βARs integrate into complexes in live cells, we measured receptor diffusion and interactions by single-particle tracking. Unstimulated β1- and β2AR were highly confined in the membrane of H9c2 cardiomyocyte-like cells, indicating that receptors are tethered and presumably integrated into protein complexes. Selective disruption of interactions with postsynaptic density protein 95/disks large/zonula occludens-1 (PDZ)–domain proteins and A-kinase anchoring proteins (AKAPs) increased receptor diffusion, indicating that these scaffold proteins participate in receptor confinement. In contrast, modulation of interactions between the putative scaffold caveolae and β2AR did not alter receptor dynamics, suggesting that these membrane domains are not involved in β2AR confinement. For both β1- and β2AR, the receptor carboxy-terminus was uniquely responsible for scaffold interactions. Our data formally demonstrate that distinct and stable protein complexes containing β1- or β2AR are formed in the plasma membrane of cardiomyocyte-like cells and that selective PDZ and AKAP interactions are responsible for the integration of receptors into complexes.
c-Met recruits ICAM-1 as a coreceptor to compensate for the loss of CD44 inCd44null mice
Authors: Olaku Vivienne , Matzke Alexandra , Mitchell Claudia , Hasenauer Susanne , Sakkaravarthi Arul , Pace Giuseppina , Ponta Helmut , Orian-Rousseau Véronique
Published: June 2011

CD44 isoforms act as coreceptors for the receptor tyrosine kinases c-Met and VEGFR-2. However, Cd44 knockout mice do not show overt phenotypes, in contrast to Met and Vegfr-2 knockout mice. We hypothesized that CD44 is being compensated for by another factor in Cd44 null mice. Using RNAi technology and blocking experiments with antibodies, peptides, and purified ectodomains, as well as overexpression studies, we identified intercellular adhesion molecule-1 (ICAM-1) as a new coreceptor for c-Met in CD44-negative tumor cells and in primary hepatocytes obtained from Cd44 null mice. Most strikingly, after partial hepatectomy, CD44v6-specific antibodies inhibited liver cell proliferation and c-Met activation in wild-type mice, whereas ICAM-1–specific antibodies interfered with liver cell proliferation and c-Met activation in Cd44 knockout mice. These data show that ICAM-1 compensates for CD44v6 as a coreceptor for c-Met in Cd44 null mice. Compensation of proteins by members of the same family has been widely proposed to explain the lack of phenotype of several knockout mice. Our experiments demonstrate the functional substitution of a protein by a heterologous one in a knockout mouse.
vipR: variant identification in pooled DNA using R
Authors: Altmann Andre , Weber Peter , Quast Carina , Rex-Haffner Monika , Binder Elisabeth B. , Müller-Myhsok Bertram
Published: June 2011

Motivation: High-throughput-sequencing (HTS) technologies are the method of choice for screening the human genome for rare sequence variants causing susceptibility to complex diseases. Unfortunately, preparation of samples for a large number of individuals is still very cost- and labor intensive. Thus, recently, screens for rare sequence variants were carried out in samples of pooled DNA, in which equimolar amounts of DNA from multiple individuals are mixed prior to sequencing with HTS. The resulting sequence data, however, poses a bioinformatics challenge: the discrimination of sequencing errors from real sequence variants present at a low frequency in the DNA pool.

Results: Our method vipR uses data from multiple DNA pools in order to compensate for differences in sequencing error rates along the sequenced region. More precisely, instead of aiming at discriminating sequence variants from sequencing errors, vipR identifies sequence positions that exhibit significantly different minor allele frequencies in at least two DNA pools using the Skellam distribution. The performance of vipR was compared with three other models on data from a targeted resequencing study of the TMEM132D locus in 600 individuals distributed over four DNA pools. Performance of the methods was computed on SNPs that were also genotyped individually using a MALDI-TOF technique. On a set of 82 sequence variants, vipR achieved an average sensitivity of 0.80 at an average specificity of 0.92, thus outperforming the reference methods by at least 0.17 in specificity at comparable sensitivity.

Availability: The code of vipR is freely available via: http://sourceforge.net/projects/htsvipr/

Contact:  altmann@mpipsykl.mpg.de
Sorting the nuclear proteome
Authors: Bauer Denis C. , Willadsen Kai , Buske Fabian A. , Lê Cao Kim-Anh , Bailey Timothy L. , Dellaire Graham , Bodén Mikael
Published: June 2011

Motivation: Quantitative experimental analyses of the nuclear interior reveal a morphologically structured yet dynamic mix of membraneless compartments. Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed.

Results: This study investigates determinants of associations between eight intra-nuclear compartments and their proteins in heterogeneous genome-wide data. We develop a model based on a range of candidate determinants, capable of mapping the intra-nuclear organization of proteins. The model integrates protein interactions, protein domains, post-translational modification sites and protein sequence data. The predictions of our model are accurate with a mean AUC (over all compartments) of 0.71.

We present a complete map of the association of 3567 mouse nuclear proteins with intra-nuclear compartments. Each decision is explained in terms of essential interactions and domains, and qualified with a false discovery assessment. Using this resource, we uncover the collective role of transcription factors in each of the compartments. We create diagrams illustrating the outcomes of a Gene Ontology enrichment analysis. Associated with an extensive range of transcription factors, the analysis suggests that PML bodies coordinate regulatory immune responses.

Contact:  m.boden@uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Possible effects of global warming on fish recruitment: shifts in spawning season and latitudinal distribution can alter growth of fish early life stages through changes in daylength
Authors: Shoji Jun , Toshito Shun-ichi , Mizuno Ken-ichiro , Kamimura Yasuhiro , Hori Masakazu , Hirakawa Koji
Published: June 2011

Shoji, J., Toshito, S., Mizuno, K., and Kamimura, Y., Hori, M., Hirakawa, K. 2011. Possible effects of global warming on fish recruitment: shifts in spawning season and latitudinal distribution can alter growth of fish early life stages through changes in daylength. – ICES Journal of Marine Science, 68: 1165–1169. Changes in growth rates, shifts in the spawning season, and shifts in the spawning area (latitude) are expected after an increase in sea temperature resulting from global warming. Fish can avoid higher temperatures by a poleward shift in the spawning area and a temporal shift in spawning timing. However, these shifts will include changes in daylength experienced during their early life stages. To understand comprehensively the possible effects of global warming on fish recruitment, effects of temperature and daylength on growth, daily ration, and growth efficiency of black rockfish, Sebastes cheni, a dominant species in coastal waters of the western North Pacific, were examined under wild and laboratory conditions. The growth rate was elevated at higher temperatures between 11.1 and 21.3°C. Growth efficiency was highest at 16°C. The effect of photoperiod on growth was also significant, with enhanced growth resulting from the longer daylength. The effect of shifts in spawning season and spawning area would differ among fish species and spawning season. Comparison of early growth under different daylength conditions between S. cheni and ayu, Plecoglossus altivelis altivelis, indicated that the shifts in spawning season and spawning area would have different effects on fish early life stages (FELSs) related to changes in daylength. Changes in daylength resulting from a poleward shift in the spawning area will have opposite effects for summer- and winter-growing FELSs, and the effects are more prominent at higher latitudes.
What ocean biogeochemical models can tell us about bottom-up control of ecosystem variability
Authors: Gnanadesikan A. , Dunne J. P. , John J.
Published: June 2011

Gnanadesikan, A., Dunne, J. P., and John, J. 2011. What ocean biogeochemical models can tell us about bottom-up control of ecosystem variability. – ICES Journal of Marine Science, 68: 1030–1044. Processes included in earth system models amplify the impact of climate variability on phytoplankton biomass and, therefore, on upper trophic levels. Models predict much larger relative interannual variability in large phytoplankton biomass than in total phytoplankton biomass, supporting the goal of better constraining size-structured primary production and biomass from remote sensing. The largest modelled variability in annually averaged large phytoplankton biomass is associated with changes in the areal extent of relatively productive regions. Near the equator, changes in the areal extent of the high-productivity zone are driven by large-scale shifts in nutrient fields, as well as by changes in currents. Along the poleward edge of the Subtropical Gyres, changes in physical mixing dominate. Finally, models indicate that high-latitude interannual variability in large phytoplankton biomass is greatest during spring. Mechanisms for producing such variability differ across biomes with internal ocean processes, such as convection complicating efforts to link ecosystem variability to climate modes defined using sea surface temperature alone. In salinity-stratified subpolar regions, changes in bloom timing driven by salinity can produce correlations between low surface temperatures and high productivity, supporting the potential importance of using coupled atmosphere–ocean reanalyses, rather than simple forced ocean reanalyses, for attributing past ecosystem shifts.
Physiological individual-based modelling of larval Atlantic herring (Clupea harengus) foraging and growth: insights on climate-driven life-history scheduling
Authors: Hufnagl Marc , Peck Myron A.
Published: June 2011

Hufnagl, M., and Peck, M. A. 2011. Physiological individual-based modelling of larval Atlantic herring (Clupea harengus) foraging and growth: insights on climate-driven life-history scheduling. – ICES Journal of Marine Science, 68: 1170–1188. A physiological individual-based model for the foraging and growth of Atlantic herring (Clupea harengus) larvae was constructed, validated using laboratory and field data, tested for parameter sensitivity, and used to examine climate-driven constraints on life-history scheduling. Model scenarios examined how natural (phenological and magnitude) changes in key environmental factors (temperature, prey, and photoperiod/daylength) affected the estimates of survival and growth of spring- and autumn-spawned larvae. The most suitable hatching seasons agreed well with the periods of larval abundance in Northeast Atlantic waters. Modelled survival is unlikely in June, July, and November. Mean annual temperature, prey concentration, and composition significantly influenced larval growth of both autumn and spring spawners. The model suggested that climate-driven changes in bottom-up factors will affect spring- and autumn-spawned larvae in different ways. It is unlikely that autumn-spawning herring will be able to avoid unfavourable conditions by delaying their spawning time or by utilizing more northern spawning grounds because of limitations in daylength to larval growth and survival. Conversely, earlier spawning in spring, or later, midsummer spawning will be tightly constrained by match–mismatch dynamics between larvae and zooplankton production.
Effects of climate change on fish and fisheries: forecasting impacts, assessing ecosystem responses, and evaluating management strategies
Authors: Hollowed Anne Babcock , Barange Manuel , Ito Shin-ichi , Kim Suam , Loeng Harald , Peck Myron A.
Published: June 2011

Hollowed, A. B., Barange, M., Ito, S-I., Kim, S., Loeng, H., and Peck, M. 2011. Effects of climate change on fish and fisheries: forecasting impacts, assessing ecosystem responses, and evaluating management strategies. – ICES Journal of Marine Science, 68: 984–985.
The potential use of a Gadget model to predict stock responses to climate change in combination with Bayesian networks: the case of Bay of Biscay anchovy
Authors: Andonegi Eider , Fernandes Jose Antonio , Quincoces Iñaki , Irigoien Xabier , Uriarte Andrés , Pérez Aritz , Howell Daniel , Stefánsson Gunnar
Published: June 2011

Andonegi, E., Fernandes, J. A., Quincoces, I., Irigoien, X., Uriarte, A., Pérez, A., Howell, D., and Stefánsson, G. 2011. The potential use of a Gadget model to predict stock responses to climate change in combination with Bayesian networks: the case of Bay of Biscay anchovy. – ICES Journal of Marine Science, 68: 1257–1269. The European anchovy (Engraulis encrasicolus) is a short-lived pelagic species distributed in Atlantic European waters, with the Bay of Biscay being one of the main centres of abundance. Because it is a short-lived species, the state of the stock is determined largely by incoming recruitment. Recruitment is highly variable and depends on a variety of factors, such as the size of the spawning stock and environmental conditions in the area. The use of a coupled model that could serve to predict the evolution of the anchovy stock in the short, medium, and long term under several fishing-pressure scenarios and given climate scenarios is demonstrated. This coupled model consists of a Gadget (Globally Applicable Disaggregated General Ecosystem Toolbox) model that was used to analyse the status of the Bay of Biscay anchovy population and to simulate future scenarios based on the estimated recruitment levels, combined with a probabilistic Bayesian network model for recruitment estimation based on machine-learning methods and using climatic indices as potential forecasting factors. The results indicate that certain combinations of medium to high fishing pressure and adverse environmental conditions could force the stock outside its biological reference boundaries.
Support for Older People and Their Carers
Authors: Simon Chantal
Published: June 2011

The UK population is ageing. As a GP, it is important to attend to the full range of physical, psychological and social needs of elderly patients and their carers. To do this, it is important to have a well-coordinated multidisciplinary team and know, at least in outline, about social benefits and services available to patients and carers. This article is intended as a broad guide to the types of support available for elderly patients in the UK.
Colonization of Rice Leaf Blades by an African Strain of Xanthomonas oryzae pv. oryzae Depends on a New TAL Effector That Induces the Rice Nodulin-3 Os11N3 Gene
Authors: Yu Yanhua , Streubel Jana , Balzergue Sandrine , Champion Antony , Boch Jens , Koebnik Ralf , Feng Jiaxun , Verdier Valérie , Szurek Boris
Published: June 2011

African strains of Xanthomonas oryzae pv. oryzae contain fewer TAL effectors than Asian strains, and their contribution to pathogenicity is unknown. Systematic mutagenesis of tal genes was used to decipher the contribution of each of the eight TAL effector paralogs to pathogenicity of African X. oryzae pv. oryzae BAI3. A strain mutated in talC was severely affected in the production of disease symptoms. Analysis of growth in planta upon leaf-clip inoculation showed that mutant bacteria multiplied only at the site of inoculation at the apex of the leaf, suggesting a requirement for talC during colonization of vascular tissues. Such tissue-specific effect of a tal mutant is a novel phenotype, which has not yet been characterized in other xanthomonads. Microarray experiments comparing the host response of rice leaves challenged with BAI3R vs. BAI3RΔtalC were performed to identify genes targeted by TalC. A total of 120 upregulated and 21 downregulated genes were identified, among them Os11N3, which is a member of the MtN3/saliva family. Based on semiquantitative reverse transcription-polymerase chain reaction and β-glucuronidase reporter assays, we show that Os11N3 is directly upregulated by TalC and identify a TalC DNA target box within the Os11N3 upstream sequence.
Conservation and management of seahorses and other Syngnathidae
Authors: Vincent A. C. J. , Foster S. J. , Koldewey H. J.
Published: June 2011

This article analyses the pressures on seahorses and explores conservation responses. It focuses on seahorses (Hippocampus spp.) but also considers pipefishes and seadragons, especially where they can fill gaps in seahorse knowledge. The charisma of many syngnathids can make them good flagship species for threats and solutions in marine conservation. The article combines a synthesis of published literature with new data on the trade in seahorses for traditional medicine, aquarium display and curiosities. Most traded seahorses come from trawl by‐catch, although seahorses are also targeted. The total extraction is large, tens of millions of animals annually, and unsustainable. A first review of the effect of habitat change on syngnathids raises many questions, while suggesting that some species may cope better than others. The combination of pressures means that many species of syngnathid are now included in the IUCN Red List of Threatened Species or national equivalents. In addition, seahorse exports from 175 countries are limited to sustainable levels under the Convention on International Trade in Endangered Species (CITES) of Wild Fauna and Flora. Possible conservation measures include marine protected areas, fisheries management, select aquaculture ventures, trade regulation, improved governance (particularly) and consumer engagement.
Review article: cyclic vomiting syndrome in adults – rediscovering and redefining an old entity
Authors: Hejazi R. A. , McCallum R. W.
Published: June 2011

Aliment Pharmacol Ther 2011; 34: 263–273

Background  Cyclic vomiting syndrome is a disorder characterised by recurrent episodes of severe nausea and vomiting separated by symptom‐free periods.

Aims  To review the history, epidemiology, clinical aspects, pathophysiology, diagnosis and treatments of adult cyclic vomiting syndrome as well as to identify areas for further clinical research and the unanswered questions in this field.

Methods  We conducted a PubMed search using such keywords as cyclic vomiting syndrome; nausea; vomiting; pathophysiology; diagnosis; treatment; trigger factors; gastric emptying test; autonomic nerve function test; gastrointestinal hormones; outcome and natural history and combined this information with the knowledge and extensive clinical research and publications from the authors.

Results  Available data show that in adult cyclic vomiting syndrome, severe epigastric and sometimes diffuse abdominal pain accompanies most cycles of nausea and vomiting interspersed with periods of symptomatic remission. Psychological disorders, specifically anxiety and depression are common, and gastric emptying is actually rapid in approximately 60% of patients and normal in the remainder. There is an impressive and sustained response to high‐dose tricyclic antidepressants. In up to 15% who are regarded as poor responders to tricyclic antidepressants, a predictable profile can be identified related to co‐existing psychological disorders, marijuana use, poorly controlled migraine headache or chronic narcotic use.

Conclusions  Cyclic vomiting syndrome in adults is an entity that is being increasingly recognised, but the need to educate Internists, Gastroenterologists and Emergency Department staff remains an ongoing challenge.
What is the optimal type of fluid to be used for peri‐operative fluid optimisation directed by oesophageal Doppler monitoring?
Authors: Morris C. , Rogerson D.
Published: June 2011

The objective of this review was to determine the optimal type or class of intravenous fluid to be used during peri‐operative patient optimisation guided by oesophageal Doppler monitoring and to identify future directions for research. We undertook a literature review of patients undergoing major (general, colorectal, orthopaedic and urological) surgery, whose fluid therapy was managed using peri‐operative oesophageal Doppler monitoring. We identified 10 studies that included 891 randomised patients. A variety of regimens and types of fluid were used in association with oesophageal Doppler monitoring, including crystalloid, gelatin and hydroxyethyl starch. A wide variety of hydroxyethyl starch preparations were used, including high molecular weight and highly substituted hetastarches, and lower molecular weight tetrastarches. Most studies were of high quality, associated with reduced hospital stay, but underpowered to evaluate other outcomes. In units with established enhanced recovery facilities, the benefits of colloid based on oesophageal Doppler monitoring were not reproduced. There is little evidence to support preferential use of any particular type of fluid during oesophageal Doppler guided optimisation; however, routine use of colloids is associated with significantly higher costs and may increase hospital stay. Furthermore, many of these fluids have not been evaluated in patient populations in whom optimisation is being applied or proposed, and the potential for harm cannot be excluded. Recommendations for future studies are provided, including adequate power for primary end points beyond hospital stay and adequate follow‐up, and inclusion of a crystalloid comparison group.
‘Now I understand’: consulting parents on chart design and parental information for the UK‐WHO child growth charts
Authors: Sachs M. , Sharp L. , Bedford H. , Wright C. M.
Published: June 2011

Background  Regular assessment of growth is an important part of child health surveillance in the UK and most parents are very interested in their child's growth. UK parents are given a personal child health record (PCHR), including growth charts, which are plotted during baby clinic visits. Parents were consulted as part of the process of designing new UK charts to incorporate the World Health Organization growth standard. This paper describes the main themes that emerged and how they influenced the final design.

Method  Three sets of consultations with 47 parents were conducted to collect preliminary information, and to evaluate proposed chart designs, instructions and written information for parents.

Results  At every consultation, the impact of the depiction of the 50th centile line in bold was mentioned spontaneously by parents. They also found aspects of the charts unclear, including the implications of a recorded weight on any particular centile, the difficulty of understanding existing text about charts in the PCHR, their preference for using pounds and ounces rather than metric weights and confusion about how frequently babies should be weighed. This led to the production of parental information including explanation of these issues which were then tested in two further sets of focus groups.

Conclusion  Involving parents in the process of designing growth charts and information influenced the finished design and the text in the PCHR. Ensuring information meets parents' needs is important to ensure successful growth monitoring.
Gastrointestinal stromal tumours – an update for histopathologists
Authors: Wong Newton A C S
Published: June 2011

Wong N A C S (2011) Histopathology59, 807–821 Gastrointestinal stromal tumours – an update for histopathologists

This review aims to summarize recent knowledge gained about gastrointestinal stromal tumour (GIST) of particular relevance to histopathologists. KIT and PDGFRA mutation analyses can be useful for confirming a diagnosis of GIST, but there are some diagnostic limitations to these analyses, and so immunohistochemical markers currently remain crucial to the diagnostic process. Of these markers, CD117 and Discovered on GIST 1 (DOG1) are currently the most sensitive and specific markers of GIST, and recent data appear to disprove the fear that antigen retrieval causes false‐positive CD117 immunostaining. The accurate prognostication of GIST has been greatly helped by the National Institutes of Health (NIH) and Armed Forces Institute of Pathology (AFIP) classification systems, although both systems still have limitations, and the behaviours of certain GIST subgroups are less well predicted by both systems. KIT and PDGFRA mutation analyses can help to predict the response of GISTs to receptor tyrosine kinase inhibitors, and both GISTs that respond and those that show resistance to these inhibitors may show characteristic pathological changes. Some GIST subgroups (e.g. Carney syndrome and paediatric GISTs) have had recently described clinicopathological and/or molecular characteristics which may help with the diagnosis and/or treatment of these specific neoplasms.
The fittest person in the morgue?
Authors: Sheppard Mary N
Published: June 2011

Sheppard M N (2012) Histopathology 60, 381–396 The fittest person in the morgue?

The cardiovascular benefits of regular physical activity are well established (J. Sci. Med. Sport,7, 2004, 6). James Fixx wrote the best‐selling book on running entitled The Complete Book of Running (1977), which led to an increase in popularity. However, when Fixx collapsed and died suddenly while running in 1984, people began to consider the adverse effects of sport on cardiac conditions. Going back in time, in 490 bc Phidippides, a young Greek messenger, ran 26.2 miles from Marathon to Athens delivering the news of the Greek victory over the Persians, and immediately collapsed and died. This is probably the first recorded incident of sudden death of an athlete running a marathon. According to Noakes (Med. Sci. Sports Exerc.,19, 1987, 187), one of the earliest reports on the association between running and cardiac risk was published in 1909, which claimed that school cross‐country races over one mile for boys below the age of 19 years were totally inappropriate, and that the associated stress will cause damage in the heart and other organs. Death in athletes is highly publicized and has a substantial emotional impact on the community at large, given that athletes are perceived as the healthiest segment of society.
Power relations in patient′s experiences of suffering during treatment for cancer
Authors: Saarnio Lotta , Arman Maria , Ekstrand Per
Published: June 2011

saarnio l., arman m. & ekstrand p. (2012) Power relations in patient′s experiences of suffering during treatment for cancer. Journal of Advanced Nursing 68(2), 271–279.

Aim.  This paper is a report of how patients who have cancer experience suffering in the context of power relations.

Background.  Many studies in Sweden and in other countries have detected inequality in healthcare use and resources, including unseen influences that can be connected to gender and distribution of resources. Few studies have examined how multiple relations of power – such as gender, ethnicity, age and education – influence how people with cancer experience suffering during treatment.

Method.  A hermeneutic design was used. Qualitative interviews were conducted with 12 women and 14 men receiving treatment for a variety of cancer diagnoses. The data collection was done at two hospitals in Sweden during 2008–2009. The interpretation of data was based on two theoretical perspectives – suffering and intersectionality.

Results.  The results highlight patients suffering where two or more positions of power relations interacted with each other. Three main themes were identified: the complexity of control, the vulnerable effects of body changes, and the internal battle of survival.

Conclusion.  A vulnerable social situation for people with cancer concretely increased their suffering. Social inequalities, seemingly linked to social hierarchy, increased the suffering of people with cancer. For example, women with cancer with a low education belonging to an ethnic minority suffered more than highly educated patients belonging to the ethnic majority.