bluuebunny/crossref_metadata_2025 huggingface dataset:
Solar neutrinos, helioseismology and the solar internal dynamics
Authors: Turck-Chièze Sylvaine , Couvidat Sébastien
Published: July 2011

Neutrinos are fundamental particles ubiquitous in the Universe and whose properties remain elusive despite more than 50 years of intense research activity. This review illustrates the importance of solar neutrinos in astrophysics, nuclear physics and particle physics. After a description of the historical context, we remind the reader of the noticeable properties of these particles and of the stakes of the solar neutrino puzzle. The standard solar model triggered persistent efforts in fundamental physics to predict the solar neutrino fluxes, and its constantly evolving predictions have been regularly compared with the detected neutrino signals. Anticipating that this standard model could not reproduce the internal solar dynamics, a seismic solar model was developed which enriched theoretical neutrino flux predictions within situobservation of acoustic and gravity waves propagating in the Sun. This seismic model contributed to the stabilization of the neutrino flux predictions. This review recalls the main historical steps, from the pioneering Homestake mine experiment and the GALLEX-SAGE experiments capturing the first proton–proton neutrinos. It emphasizes the importance of the SuperKamiokande and SNO detectors. Both experiments demonstrated that the solar-emitted electron neutrinos are partially transformed into other neutrino flavors before reaching the Earth. This sustained experimental effort opens the door to neutrino astronomy, with long-base lines and underground detectors. The success of BOREXINO in detecting the7Be neutrino signal alone instills confidence in physicists' ability to detect each neutrino source separately. It justifies the building of a new generation of detectors to measure the entire solar neutrino spectrum in greater detail, as well as supernova neutrinos. A coherent picture has emerged from neutrino physics and helioseismology. Today, new paradigms take shape in these two fields: neutrinos are massive particles, but their masses are still unknown, and the research on the solar interior focuses on the dynamical aspects and on the signature of dark matter. The magnetic moment of the neutrino begins to be an actor in stellar evolution. The third part of the review is dedicated to this prospect. The understanding of the crucial role of both rotation and magnetism in solar physics benefits from SoHO, SDO and PICARD space observations, and from a new prototype, GOLF-NG. The magnetohydrodynamical view of the solar interior is a new way of understanding the impact of the Sun on the Earth's environment and climate. For now, the particle and stellar challenges seem decoupled, but this is only a superficial appearance. The development of asteroseismology—with the COROT and KEPLER spacecraft—and of neutrino physics will both contribute to improvements in our understanding of, for instance, supernova explosions. This shows the far-reaching impact of neutrino and stellar astronomy.
A conserved signal and GTPase complex are required for the ciliary transport of polycystin-1
Authors: Ward Heather H. , Brown-Glaberman Ursa , Wang Jing , Morita Yoshiko , Alper Seth L. , Bedrick Edward J. , Gattone Vincent H. , Deretic Dusanka , Wandinger-Ness Angela
Published: July 2011

Primary cilia regulate epithelial differentiation and organ function. Failure of mutant polycystins to localize to cilia abolishes flow-stimulated calcium signaling and causes autosomal dominant polycystic kidney disease. We identify a conserved amino acid sequence, KVHPSST, in the C-terminus of polycystin-1 (PC1) that serves as a ciliary-targeting signal. PC1 binds a multimeric protein complex consisting of several GTPases (Arf4, Rab6, Rab11) and the GTPase-activating protein (GAP), ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1) in the Golgi, which facilitates vesicle budding and Golgi exocytosis. A related N-terminal ciliary-targeting sequence in polycystin-2 similarly binds Arf4. Deletion of the extreme C-terminus of PC1 ablates Arf4 and ASAP1 binding and prevents ciliary localization of an integral membrane CD16.7-PC1 chimera. Interactions are confirmed for chimeric and endogenous proteins through quantitated in vitro and cell-based approaches. PC1 also complexes with Rab8; knockdown of trafficking regulators Arf4 or Rab8 functionally blocks CD16.7-PC1 trafficking to cilia. Mutations in rhodopsin disrupt a similar signal and cause retinitis pigmentosa, while Bardet-Biedl syndrome, primary open-angle glaucoma, and tumor cell invasiveness are linked to dysregulation of ASAP1 or Rab8 or its effectors. In this paper, we provide evidence for a conserved GTPase-dependent ciliary-trafficking mechanism that is shared between epithelia and neurons, and is essential in ciliary-trafficking and cell homeostasis.
Geography Matters: International Trade Patterns and the Indirect Land Use Effects of Biofuels
Authors: Villoria Nelson B. , Hertel Thomas W.
Published: July 2011

This article investigates the relationship between international trade patterns and the global distribution of coarse grain production responses to market developments in the United States. Our null hypothesis is that world markets are fully integrated, rendering the geographic persistence of bilateral trade flows irrelevant in the global production response to a change in U.S. prices. The alternative hypothesis allows price transmission to vary along with the intensity of competition among countries in specific markets. Using data from 1975 to 2002, we reject the null hypothesis. Our work has direct implications for the analysis of the global land use impacts of biofuel mandates.
Agricultural Water Security and Instream Flows for Endangered Species
Authors: Newburn David A. , Brozovic Nicholas , Mezzatesta Mariano
Published: July 2011

We analyze the potential effects of listing threatened salmonid species on landowner behavior using parcel‐level data from Sonoma County, California. We estimate a bivariate probit model, representing the landowner's joint decision on land use and water management during the period 1973–2006, both before and after listing. Our results indicate that after listing, vineyard development with on‐site reservoirs became significantly less likely, particularly in upland watersheds with seasonal streams. This interseasonal shift from stored surface water in winter toward groundwater or direct diversion in summer may lead to negative unintended consequences on summer flows needed for juvenile fish survivorship.
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
Authors: Xu Mengyuan , Weinberg Clarice R. , Umbach David M. , Li Leping
Published: July 2011

Motivation: ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a coregulator. Biologists are interested in knowing which coregulatory factor motifs may be present in the sequences bound by the protein ChIP'ed.

Results: We present a finite mixture framework with an expectation–maximization algorithm that considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. Tested on 10 simulated ChIP-seq datasets, our method performed better than repeated application of MEME in predicting sequences containing both motifs. When applied to a mouse liver Foxa2 ChIP-seq dataset involving ~ 12 000 400-bp sequences, coMOTIF identified co-occurrence of Foxa2 with Hnf4a, Cebpa, E-box, Ap1/Maf or Sp1 motifs in ~6–33% of these sequences. These motifs are either known as liver-specific transcription factors or have an important role in liver function.

Availability: Freely available at http://www.niehs.nih.gov/research/resources/software/comotif/.

Contact:  li3@niehs.nih.gov

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Making whole genome multiple alignments usable for biologists
Authors: Blankenberg Daniel , Taylor James , Nekrutenko Anton ,   The Galaxy Team
Published: July 2011

Summary: Here we describe a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface.

Availability and Implementation: This open-source toolset was implemented in Python and has been integrated into the online data analysis platform Galaxy (public web access: http://usegalaxy.org; download: http://getgalaxy.org). Additional help is available as a live supplement from http://usegalaxy.org/u/dan/p/maf.

Contact:  james.taylor@emory.edu; anton@bx.psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Discovering novel subsystems using comparative genomics
Authors: Ferrer Luciana , Shearer Alexander G. , Karp Peter D.
Published: July 2011

Motivation: Key problems for computational genomics include discovering novel pathways in genome data, and discovering functional interaction partners for genes to define new members of partially elucidated pathways.

Results: We propose a novel method for the discovery of subsystems from annotated genomes. For each gene pair, a score measuring the likelihood that the two genes belong to a same subsystem is computed using genome context methods. Genes are then grouped based on these scores, and the resulting groups are filtered to keep only high-confidence groups. Since the method is based on genome context analysis, it relies solely on structural annotation of the genomes. The method can be used to discover new pathways, find missing genes from a known pathway, find new protein complexes or other kinds of functional groups and assign function to genes. We tested the accuracy of our method in Escherichia coli K-12. In one configuration of the system, we find that 31.6% of the candidate groups generated by our method match a known pathway or protein complex closely, and that we rediscover 31.2% of all known pathways and protein complexes of at least 4 genes. We believe that a significant proportion of the candidates that do not match any known group in E.coli K-12 corresponds to novel subsystems that may represent promising leads for future laboratory research. We discuss in-depth examples of these findings.

Availability: Predicted subsystems are available at http://brg.ai.sri.com/pwy-discovery/journal.html.

Contact:  lferrer@ai.sri.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
GaggleBridge: collaborative data analysis
Authors: Battke Florian , Symons Stephan , Herbig Alexander , Nieselt Kay
Published: July 2011

Motivation: Tools aiding in collaborative data analysis are becoming ever more important as researchers work together over long distances. We present an extension to the Gaggle framework, which has been widely adopted as a tool to enable data exchange between different analysis programs on one computer.

Results: Our program, GaggleBridge, transparently extends this functionality to allow data exchange between Gaggle users at different geographic locations using network communication. GaggleBridge can automatically set up SSH tunnels to traverse firewalls while adding some security features to the Gaggle communication.

Availability:  GaggleBridge is available as open-source software implemented in the Java language at http://it.inf.uni-tuebingen.de/gb.

Contact:  florian.battke@uni-tuebingen.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A comparison between industry and observer catch compositions within the Gulf of Alaska rockfish fishery
Authors: Faunce Craig H.
Published: July 2011

Faunce, C. H. A 2011. comparison between industry and observer catch compositions within the Gulf of Alaska rockfish fishery. – ICES Journal of Marine Science, 68: 1769–1777. Stock assessment scientists and fishery managers operate under the necessary assumption that the identities of species in official catch reports are known without error. To test this assumption, the incidence, magnitude, and possible causes of species misidentification between industry and fishery-observer data sources were investigated for 29 rockfish landings made in Kodiak, AK. Rockfish species were misidentified in nearly all these landings, and the incidence of misidentification between data sources differed among species rather than the processing plant examined. Although observers failed to identify species recorded by processing plant staff as a result of small sampling fractions, the industry missed species that were identified by observers in more than half the offloads examined. The presence of management species complexes did not reduce the likelihood of erroneous quota debiting as a result of species misidentification. In one landing, the misidentification of the main rockfish species corresponded to the release of a weekly report on total allowable catch and resulted in a delayed fishery closure. Efforts to improve the accuracy of species identifications reported by industry in landing reports are warranted in Alaska, and methods to accomplish this through efficient deployment of observers are discussed.
Motivational Interviewing: A Positive Approach
Authors: Storr Emma
Published: July 2011

How do we encourage our patients to give up smoking, drink less alcohol and engage in healthy activities that would enhance and possibly lengthen their lives? Health promotion and explaining risk are part of the GP's everyday job but it is a skill that could be improved. One suggestion for improving health promotion by GPs is that a motivational interviewing (MI) approach could be used. This article aims to describe the MI method and its practical relevance to primary care practitioners in dealing with common patient concerns.
John Evan Baldwin. 6 December 1931 — 7 December 2010
Authors: Longair Malcolm S.
Published: July 2011

Professor John Baldwin was an experimental astrophysicist of the highest distinction who made many innovative contributions to radio and optical astronomy. He pursued his entire research career as a member, and then head, of the Radio Astronomy Group of the Cavendish Laboratory at Cambridge University. His deep understanding and physical intuition for all aspects of interferometry, first at radio and then at optical wavelengths, resulted in a series of ground-breaking telescope systems for astronomy. These led to new approaches to the construction and operation of telescopes in these astronomical disciplines. For a considerable part of his career he was a fellow of Queens' College Cambridge.
North American West Nile virus genotype isolates demonstrate differential replicative capacities in response to temperature
Authors: Andrade Christy C. , Maharaj Payal D. , Reisen William K. , Brault Aaron C.
Published: July 2011

The presence of West Nile virus (WNV) was first documented in California, USA, during the summer of 2003, and subsequently the virus has become endemic throughout the state. Sequence analysis has demonstrated that the circulating strains are representative of the North American (WN02) genotype that has displaced the East Coast genotype (NY99). A recent study has indicated that enhanced vector competence at elevated temperatures may have played a role in the displacement of the East Coast genotype by WN02. In the current study, four WN02 strains from California, including an initial 2003 isolate (COAV997), were compared to strain NY99 in growth curve assays in mosquito and duck embryonic fibroblast (DEF) cell lines at differing, biologically relevant temperatures to assess the relative temperature sensitivities of these natural isolates. COAV997 was significantly debilitated in viral replication in DEF cells at 44 °C. Full-length sequence comparison of COAV997 against the NY99 reference strain revealed non-synonymous mutations in the envelope glycoprotein (V159A), non-structural protein 1 (NS1) (K110N) and non-structural protein 4A (NS4A) (F92L), as well as two mutations in the 3′ UTR: C→T at nt 10 772 and A→G at nt 10 851. These non-synonymous mutations were introduced into the NY99 viral backbone by site-directed mutagenesis. A mutant containing the NS1-K110N and NS4A-F92L mutations exhibited a debilitated growth phenotype in DEF cells at 44 °C, similar to that of COAV997. One explanation for the subsistence of this genotype is that COAV997 was obtained from an area of California where avian host species might not present elevated temperatures. These data indicate that the NS1 and NS4A mutations identified in some WN02 isolates could reduce thermal stability and impede replication of virus at temperatures observed in febrile avian hosts.
Upregulation of equine matrix metalloproteinase 1 by bovine papillomavirus type 1 is through the transcription factor activator protein-1
Authors: Yuan ZhengQiang , Gault Elizabeth A. , Campo M. Saveria , Nasir Lubna
Published: July 2011

Equine sarcoids represent the most common skin tumours in equids worldwide, characterized by extensive invasion and infiltration of lymphatics, rare regression and high recurrence after surgical intervention. Bovine papillomavirus type 1 (BPV-1) activity is necessary for the transformation phenotype of equine fibroblasts. Among the many changes induced by BPV-1, matrix metalloproteinase 1 (MMP-1) upregulation contributes to the invasiveness of equine fibroblasts. However, it is not yet known how BPV-1 proteins regulate equine MMP-1 expression. To elucidate this mechanism, the equine MMP-1 promoter was cloned and analysed. A putative activator protein-1 (AP-1)-binding site was demonstrated to be crucial for upregulated MMP-1 promoter activity by BPV-1. BPV-1 E6 and E7 proteins increased MMP-1 promoter activity, and inhibition of BPV-1 gene expression by small interfering RNA significantly reduced the promoter activity. c-Jun and Fra-1, two components of the AP-1 transcription factor complex, were overexpressed and activated by BPV-1 in equine fibroblasts. Finally, BPV-1 E5, E6 and E7 proteins increased MMP-1 mRNA and protein expression. In conclusion, the expression of MMP-1 can be enhanced by BPV-1 oncoproteins E6 and E7 through the AP-1 transcription factor and by E5 via an indirect mechanism. These findings shed light on the mechanism of BPV-1-mediated equine fibroblast infiltration and indicate that both BPV-1 oncoproteins and AP-1 could be potential targets for equine sarcoid therapy.
Phylogenetic relationships of Western Mediterranean West Nile virus strains (1996–2010) using full-length genome sequences: single or multiple introductions?
Authors: Sotelo Elena , Fernández-Pinero Jovita , Llorente Francisco , Vázquez Ana , Moreno Ana , Agüero Montserrat , Cordioli Paolo , Tenorio Antonio , Jiménez-Clavero Miguel Ángel
Published: July 2011

In recent years, West Nile virus (WNV) has re-emerged in the Western Mediterranean region. As a result, the number of complete WNV genome sequences available from this region has increased, allowing more detailed phylogenetic analyses, which may help to understand the evolutionary history of WNV circulating in the Western Mediterranean. To this aim, the present work describes six new complete WNV sequences from recent outbreaks and surveillance in Italy in 2008–2009 and in Spain in 2008 and 2010. Comparison with other sequences from different WNV clusters within lineage 1 (clade 1a) confirmed that all Western Mediterranean WNV isolates obtained since 1996 (except one from Tunisia, collected in 1997) cluster in a single monophyletic group (here called ‘WMed’ subtype). The analysis differentiated two subgroups within this subtype, which appear to have evolved from earlier WMed strains, suggesting a single introduction in the area, and further dissemination and evolution. Close similarities between WNV variants circulating in consecutive years, one in Spain, between 2007 and 2008, and another in Italy between 2008 and 2009, suggest that the virus possibly overwinters in Western Mediterranean sites. The NS3249-proline genotype, recently proposed as a virulence determinant for WNV, has arisen independently at least twice in the area. Overall, these results indicate that the frequent recurrence of outbreaks caused by phylogenetically homogeneous WNV in the Western Mediterranean since 1996 is consistent with a single introduction followed by viral persistence in endemic foci in the area, rather than resulting from independent introductions from exogenous endemic foci.
Experimental infection with chamois border disease virus causes long-lasting viraemia and disease in Pyrenean chamois (Rupicapra pyrenaica)
Authors: Cabezón Oscar , Velarde Roser , Mentaberre Gregorio , Fernández-Sirera Laura , Casas-Díaz Encarna , López-Olvera Jorge , Serrano Emmanuel , Rosell Rosa , Riquelme Cristina , Lavín Santiago , Segalés Joaquim , Marco Ignasi
Published: July 2011

Since 2001, severe outbreaks of disease associated with border disease virus (BDV) infection have been reported in Pyrenean chamois. The disease is characterized by variable degrees of cachexia, alopecia and neurological manifestations prior to death. The aim of this study was to investigate this disease under experimental conditions. To assess viral virulence, humoral immune response, dissemination and probable routes of transmission, seven chamois (five seronegative and two seropositive for BDV) were inoculated with a BDV isolated from a naturally infected chamois. A group of three chamois were maintained as uninfected controls. The five seronegative chamois became viraemic from day 2 post-inoculation (p.i.) until their death (three animals) or the end of the experiment (on day 34 p.i.) and developed neutralizing antibodies from day 18 p.i. until the end of the study. Continuous shedding of the virus was detected by RT-PCR in oral, nasal and rectal swabs in viraemic chamois from day 5 p.i. Despite none of the viraemic chamois showing obvious neurological signs, all of them had a non-suppurative meningoencephalitis as seen in naturally infected chamois. The two inoculated BDV-seropositive chamois did not become viraemic. This study confirms that BDV is the primary agent of the disease that has been affecting chamois populations in recent years in the Pyrenees and that previously acquired humoral immunity is protective.
Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses
Authors: Li Linlin , Pesavento Patricia A. , Shan Tongling , Leutenegger Christian M. , Wang Chunlin , Delwart Eric
Published: July 2011

The close interactions of dogs with humans and surrounding wildlife provide frequent opportunities for cross-species virus transmissions. In order to initiate an unbiased characterization of the eukaryotic viruses in the gut of dogs, this study used deep sequencing of partially purified viral capsid-protected nucleic acids from the faeces of 18 diarrhoeic dogs. Known canine parvoviruses, coronaviruses and rotaviruses were identified, and the genomes of the first reported canine kobuvirus and sapovirus were characterized. Canine kobuvirus, the first sequenced canine picornavirus and the closest genetic relative of the diarrhoea-causing human Aichi virus, was detected at high frequency in the faeces of both healthy and diarrhoeic dogs. Canine sapovirus constituted a novel genogroup within the genusSapovirus, a group of viruses also associated with human and animal diarrhoea. These results highlight the high frequency of new virus detection possible even in extensively studied animal species using metagenomics approaches, and provide viral genomes for further disease-association studies.
Intracompartmental and Intercompartmental Transcriptional Networks Coordinate the Expression of Genes for Organellar Functions
Authors: Leister Dario , Wang Xi , Haberer Georg , Mayer Klaus F.X. , Kleine Tatjana
Published: July 2011

Genes for mitochondrial and chloroplast proteins are distributed between the nuclear and organellar genomes. Organelle biogenesis and metabolism, therefore, require appropriate coordination of gene expression in the different compartments to ensure efficient synthesis of essential multiprotein complexes of mixed genetic origin. Whereas organelle-to-nucleus signaling influences nuclear gene expression at the transcriptional level, organellar gene expression (OGE) is thought to be primarily regulated posttranscriptionally. Here, we show that intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. Nearly 1,300 ATH1 microarray-based transcriptional profiles of nuclear and organellar genes for mitochondrial and chloroplast proteins in the model plant Arabidopsis (Arabidopsis thaliana) were analyzed. The activity of genes involved in organellar energy production (OEP) or OGE in each of the organelles and in the nucleus is highly coordinated. Intracompartmental networks that link the OEP and OGE gene sets serve to synchronize the expression of nucleus- and organelle-encoded proteins. At a higher regulatory level, coexpression of organellar and nuclear OEP/OGE genes typically modulates chloroplast functions but affects mitochondria only when chloroplast functions are perturbed. Under conditions that induce energy shortage, the intercompartmental coregulation of photosynthesis genes can even override intracompartmental networks. We conclude that dynamic intracompartmental and intercompartmental transcriptional networks for OEP and OGE genes adjust the activity of organelles in response to the cellular energy state and environmental stresses, and we identify candidate cis-elements involved in the transcriptional coregulation of nuclear genes. Regarding the transcriptional regulation of chloroplast genes, novel tentative target genes of σ factors are identified.
Cigarette price, affordability and smoking prevalence in the European Union
Authors: Bogdanovica Ilze , Murray Rachael , McNeill Ann , Britton John
Published: July 2011

Aims  To describe current and recent changes in cigarette affordability across the current 27 European Union (EU) Member States, and to assess the impact of these changes on smoking prevalence in countries that were EU members in 2004 (old Member States) compared to countries that have joined since 2004 (new Member States).

Design  Investigation of cigarette affordability using the minutes of labour measure, and comparisons of changes in affordability, tax and smoking prevalence in old and new EU Member States.

Participants  Current 27 EU Member States.

Settings  European Union.

Measurements  Cigarette prices, overall tax yield and incidence, hourly wages and smoking prevalence in the EU were obtained from published sources, and the affordability of the EU Most Popular Price Category (MPPC) cigarettes estimated as the number of minutes of labour required to earn the price of 20 cigarettes in the years 2003, 2006 and 2009.

Findings  The mean [standard deviation (SD)] number of minutes of labour required to purchase 20 MPPC cigarettes in EU Member States in 2009 was 31.3 (SD 10.7), but ranged fourfold across the EU, and was significantly higher in new than old Member States. The number of minutes of labour measure increased more, although not significantly so, between 2003 and 2009 in new [mean (SD) 12.1 (10.9)] than in old [6.7 (4.0)] Member States, largely because of proportionately higher increases in taxation. However, there was no correlation between change in affordability and change in smoking prevalence in recent years.

Conclusions  Cigarette affordability varies substantially and cigarettes are generally becoming less affordable in European Union Member States. However, these reductions in affordability do not appear to have impacted substantially on smoking prevalence in recent years.
Monoclonal antibodies in the treatment of multiple myeloma
Authors: Richardson Paul G. , Lonial Sagar , Jakubowiak Andrzej J. , Harousseau Jean‐Luc , Anderson Kenneth C.
Published: July 2011

Despite recent advances in treatment that have significantly improved overall survival, multiple myeloma (MM) remains incurable. Although rituximab, the first monoclonal antibody (MAb) evaluated in MM treatment, provided only very limited benefit, research is ongoing into a number of other MAbs directed against a variety of MM‐related target antigens. Given the inherent immune dysfunction associated with MM, newer strategies that may enhance immune function in conjunction with antibodies may also provide a more fruitful clinical approach. Potential MAb targets in MM include growth factors and their receptors, other signalling molecules, and antigens expressed exclusively or predominantly on MM cells. MAb therapy involves a range of mechanisms, including antibody‐dependent cellular cytotoxicity, complement‐dependent cytotoxicity, interference with receptor‐ligand interactions, and MAb conjugation to radioisotopes or toxins. The antigens currently targeted in MM therapy are discussed, along with the development status of the corresponding MAb therapeutics. Elotuzumab, an anti‐CS1 MAb, has recently achieved clinically meaningful responses when combined with lenalidomide or bortezomib in patients with relapsed and relapsed/refractory MM. Other MAbs are also showing early promise. More ongoing clinical research is required to identify optimal combination regimens and biomarkers that may help predict response to specific MAb‐based combinations.
Analysis of clonality in cytologic material using the polymerase chain reaction (PCR)
Authors: JEFFERS M. D. , McCORRISTON J. , FARQUHARSON M. A. , STEWART C. J. R. , MUTCH A. F.
Published: July 2011

Analysis of clonality in cytologic material using the polymerase chain reaction (PCR)

Immunoglobulin heavy chain (IgH) gene rearrangement analysis was performed on 27 fine needle aspiration (FNA) specimens (13 reactive hyperplasia, 11 B cell non‐Hodgkin's lymphoma (B‐NHL), one Hodgkin's disease and two suspicious of non‐Hodgkin's lymphoma). Satisfactory amplification was achieved in 23/27 cases. A polyclonal pattern was seen in 14 cases (11 reactive hyperplasia, one B‐NHL, one suspicious of lymphoma, one Hodgkin's disease). A monoclonal band was seen in nine cases (eight B‐NHL, one reactive hyperplasia). Amplification was unsuccessful in four cases. Clonal analysis by PCR‐based IgH gene rearrangement analysis can be successfully applied to FNA material and can be useful in diagnosis, but the results must be interpreted in conjunction with morphology and other ancillary information.

Analyse de la clonalité en utilisant la PCR sur matériel cytologique

L'analyse des réarrangements géniques des chaînes lourdes des immunoglobulines (IgH) a été réalisée sur 27 produits de ponction à l'aiguille fine (13 cas d'hyperplasie réactionnelle, 11 cas de lymphome non hodgkinien de type B (LNH‐B), un cas de maladie de Hodgkin et deux cas suspects de lymphome malin non hodgkinien. Une amplification satisfaisante a été obtenue dans 23 cas sur 27. Un aspect polychonal a été observé dans 14 cas (11 hyperplasies réactionnelles, 1 lymphome malin non hodgkinien de type B, 1 cas suspect de lymphome, 1 cas de maladie de Hodgkin). Une bande monoclonale a été observée dans 9 cas (8 LNH‐B, 1 hyperplasie réactionnelle). L'amplification n'a pas réussi dans quatre cas. L'analyse de la clonalité par analyse des réarrangements géniques par PCR peut être appliquée avec succès au matériel cytologique qui est obtenu par ponction à l'aiguille fine et elle peut être utile au plan diagnostique, mais les résultats doivent étre interprétés en intégrant les informations morphologiques et les autres données complémentaires.

Polymerase Chain Reaction an zytologischem Material

Die Analyse schwerer Immunglobulinketten (IgH) wurde an 27 FNP (13 reaktive Hyperplasien, 11 B‐NHL, 1 Hodgkin und und zwie verdächtige Fälle) analysiert. Eine ausreichende Amplifikation wurde in 23/27 Fällen erzielt. Ein polyklonales Muster wurde in 14 Fällen beobachtet (11 reaktive Hyperplasien, 1 B‐NHL, 1 Hodgkin sowie 1 verdächtiger Fall). Ein monoklonales Band wurde 9 mal gefunden (8 B‐NHL, 1 reaktive Hyperplasie). Die Amplifikation war ungenügend in 4 Fällen. Die PCR‐Analyse kann für die Diagnostik von Nutzen sein muss jedoch zusammen mit der Morphologie und anderen Informationen interpretiert werden.
Short‐term infusion of a fish oil‐based lipid emulsion modulates fatty acid status, but not immune function or (anti)oxidant balance: a randomized cross‐over study
Authors: Versleijen Michelle W. , Roelofs Hennie M. , Rombouts Charlotte , Hermans Peter W. , Noakes Paul S. , Calder Philip C. , Wanten Geert J.
Published: July 2011

Eur J Clin Invest 2012; 42 (3): 290–302

Background and aims  Studies suggest clinical benefits of parenteral fish oil (FO), rich in n‐3 polyunsaturated fatty acids (PUFAs), over soyabean oil (SO), rich in n‐6 PUFAs, in patients with pro‐inflammatory conditions such as sepsis and trauma. Because the mechanisms behind these observations remain unclear, the present study explored the effects of intravenous infusion of FO and SO on fatty acid incorporation, immune functions and (anti)oxidant balance in healthy human volunteers.

Methods  Saline, a SO emulsion and a FO emulsion were administered for one hour on three consecutive days at a rate of 0·2 g/kg BW/h to eight subjects in a randomized cross‐over design with a 3‐week interval between treatments. Plasma phospholipid and peripheral blood mononuclear cell (PBMC) fatty acid compositions, and leucocyte counts and functions were assessed prior to the first infusion (T = 0, baseline) and 1 day (T = 4, early effects) and 8 days (T = 11, late effects) after the third infusion.

Results  Fish oil infusion significantly increased n‐3 PUFA proportions and decreased n‐6 PUFA proportions in plasma phospholipids and PBMCs. There were no differences in immune functions or (anti)oxidant balance between treatments at any time.

Conclusions  The present lipid infusion protocol appears to be safe and well tolerated and provides significant incorporation of n‐3 PUFAs into plasma phospholipids and PBMCs. In the absence of overt inflammation, no direct effects of FO were observed on immune function or (anti)oxidant balance. This model may be useful to evaluate effects of parenteral lipids in other settings, for example in individuals displaying an inflammatory state.
Fine root foraging strategies in Norway spruce forests across a European climate gradient
Authors: Ostonen Ivika , Helmisaari Heljä‐Sisko , Borken Werner , Tedersoo Leho , Kukumägi Mai , Bahram Mohammad , Lindroos Antti‐Jussi , Nöjd Pekka , Uri Veiko , Merilä Päivi , Asi Endla , Lõhmus Krista
Published: July 2011

Fine root acclimation to different environmental conditions is crucial for growth and sustainability of forest trees. Relatively small changes in fine root standing biomass (FRB), morphology or mycorrhizal symbiosis may result in a large change in forest carbon, nutrient and water cycles. We elucidated the changes in fine root traits and associated ectomycorrhizal (EcM) fungi in 12 Norway spruce stands across a climatic and N deposition gradient from subarctic‐boreal to temperate regions in Europe (68°N–48°N). We analysed the standing FRB and the ectomycorrhizal root tip biomass (EcMB, g m−2) simultaneously with measurements of the EcM root morphological traits (e.g. mean root length, root tissue density (RTD), N% in EcM roots) and frequency of dominating EcM fungi in different stands in relation to climate, soil and site characteristics. Latitude and N deposition explained the greatest proportion of variation in fine root traits. EcMB per stand basal area (BA) increased exponentially with latitude: by about 12.7 kg m−2 with an increase of 10° latitude from southern Germany to Estonia and southern Finland and by about 44.7 kg m−2 with next latitudinal 10° from southern to northern Finland. Boreal Norway spruce forests had 4.5 to 11 times more EcM root tips per stand BA, and the tips were 2.1 times longer, with 1.5 times higher RTD and about 1/3 lower N concentration. There was 19% higher proportion of root tips colonized by long‐distance exploration type forming EcM fungi in the southern forests indicating importance of EcM symbiont foraging strategy in fine root nutrient acquisition. In the boreal zone, we predict ca. 50% decrease in EcMB per stand BA with an increase of 2 °C annual mean temperature. Different fine root foraging strategies in boreal and temperate forests highlight the importance of complex studies on respective regulatory mechanisms in changing climate.
Functional characterization of a novel missense mutation identified in a Turkish patient affected by severe coagulation factor V deficiency
Authors: PARABOSCHI E. M. , KAYIRAN S. M. , ÖZBEK N. , GÜRAKAN B. , PEYVANDI F. , GUELLA I. , DUGA S. , ASSELTA R.
Published: July 2011

Summary.  Factor V (FV) deficiency is a rare coagulation disorder, characterized by a bleeding phenotype varying from mild to severe. To date, 115 mutations have been described along the gene encoding for FV (F5) but only few of them have been functionally characterized. Aim of this study was the identification and the molecular characterization of genetic defects underlying severe FV deficiency in a 7‐month‐old Turkish patient. Mutation detection was performed by sequencing the whole F5 coding region, exon–intron boundaries and about 300 bp of the promoter region. Functional analysis of the identified missense mutation was conducted by transient expression of wild‐type and mutant FV recombinant molecules in COS‐1 cells. Two novel mutations: a missense (Pro132Arg) and a 1‐bp deletion (Ile1890TyrfsX19) were identified in the F5 gene. While the frameshift mutation is responsible for the introduction of a premature stop codon, likely triggering F5 mRNA to nonsense‐mediated mRNA degradation, the demonstration of the pathogenic role of the Pro132Arg mutation required an experimental validation. Expression experiments showed that the missense mutation causes a significant reduction in FV secretion and in the specific activity of the residual secreted molecule (77% and 78% decrease, respectively). This paper reports the identification of two novel mutations responsible for FV deficiency, thus widening the mutational spectrum of the F5 gene. The Pro132Arg mutation adds to the only other two functionally characterized missense defects in the FV A1 domain.
Uptake of calcium and silicon released from calcium silicate–based endodontic materials into root canal dentine
Authors: Han L. , Okiji T.
Published: July 2011

Han L, Okiji T. Uptake of calcium and silicon released from calcium silicate–based endodontic materials into root canal dentine. International Endodontic Journal, 44, 1081–1087, 2011.

Aim  To compare Biodentine and White ProRoot mineral trioxide aggregate (MTA) with regard to Ca and Si uptake by adjacent root canal dentine in the presence of phosphate‐buffered saline (PBS).

Methodology  Root canals of bovine incisor root segments were instrumented, filled with either Biodentine or MTA (n = 20 each) and then immersed in Ca‐and Mg‐free PBS for 1, 7, 30 or 90 days (n = 5 each). Unfilled, unimmersed dentine specimens (n = 5) served as controls. The specimens were sectioned longitudinally, and the ultrastructure of the dentine–material interface and the elemental composition/distribution in the material–adjacent dentine were analysed using a wavelength‐dispersive X‐ray spectroscopy electron probe microanalyser with image observation function. Data were statistically analyzed using one‐way anova and Tukey’s honestly significant difference test or the Mann–Whitney U‐test.

Results  Along the material–dentine interface, both materials formed a tag‐like structure that was composed of either Ca‐ and P‐rich crystalline deposits or the material itself. The width of a Ca‐ and Si‐rich layer detected along the dentine layer of the material–dentine interface showed increases over time. The Ca‐ and Si‐rich layer width was significantly larger (P < 0.05) in Biodentine than MTA at 30 and 90 days.

Conclusions  Both Biodentine and MTA caused the uptake of Ca and Si in the adjacent root canal dentine in the presence of PBS. The dentine element uptake was more prominent for Biodentine than MTA.
Social structures in the operating theatre: how contradicting rationalities and trust affect work
Authors: Rydenfält Christofer , Johansson Gerd , Larsson Per Anders , Åkerman Kristina , Odenrick Per
Published: July 2011

rydenfält c., johansson g., larsson p.a., åkerman k. & odenrick p.(2011) Social structures in the operating theatre: how contradicting rationalities and trust affect work.Journal of Advanced Nursing68(4), 783–795.

Aim. This article is a report of a study of how healthcare professionals involved in surgery orientate themselves to their common task, and how this orientation can be affected by the social and organizational context.

Background. Previous research indicates that surgical teams are not as cohesive as could be expected and that communication failures frequently occur. However, little is known about how these problems are related to their social, cultural and organizational context.

Methods. Semi‐structured interviews were conducted with 15 healthcare professionals, representing all personnel categories of the surgical team. During the interview, a virtual model, visualizing a real operating theatre, was used to facilitate reflection. The interviews were conducted in 2009. Themes were created from the interviews, with a focus on similarities and differences. An activity analysis was conducted based on the themes.

Findings. Poor team functionality and communication failures in the operating theatre can to some degree be explained by differences in activity orientation between professions and by insufficient support from social and organizational structures. Differences in activity orientation resulted in different views between professional groups in their perceptions of work activities, resulting in tension. Insufficient support resulted in communication thresholds that inhibited the sharing of information.

Conclusion. Organizing work to promote cross‐professional interaction can help the creation of social relations and norms, providing support for a common view. It can also help to decrease communication thresholds and establish stronger relations of trust. How this organization structure should be developed needs to be further investigated.
Biogeographical patterns of algal communities in the Mediterranean Sea: Cystoseira crinita‐dominated assemblages as a case study
Authors: Sales Marta , Ballesteros Enric , Anderson Marti J. , Iveša Ljiljana , Cardona Eva
Published: July 2011

Aim  The aim of this study was to describe the composition, community structure and biogeographical variation of subtidal algal assemblages dominated by the brown alga Cystoseira crinita across the Mediterranean Sea.

Location  The Mediterranean coast, from Spain (1°25′ E) to Turkey (30°26′ E).

Methods  Data on the species composition and structure of assemblages dominated by the species C. crinita were collected from 101 sites in nine regions across the Mediterranean Sea. Multivariate and univariate statistical tools were used to investigate patterns of variation in the composition of the assemblages among sites and regions, and to compare these with previously defined biogeographical regions. Linear regressions of species richness versus longitude and versus latitude were also carried out to test previously formulated hypotheses of biodiversity gradients in the Mediterranean Sea.

Results  The main features characterizing C. crinita‐dominated assemblages across the Mediterranean included a similar total cover of species, a similar cover of C. crinita, and consistency in the presence of the epiphyte Haliptilon virgatum. Biogeographical variation was detected as shifts in relative abundances of species among regions, partly coinciding with previously described biogeographical sectors. A significant positive correlation was found between species richness and latitude, while no significant correlation was detected between species richness and longitude.

Main conclusions  The patterns of variation in community structure detected among the studied regions reflected their geographical positions quite well. However, latitude seemed to contribute more to the explanation of biological patterns of diversity than did geographical distances or boundaries, which classically have been used to delimit biogeographical sectors. Moreover, the positive correlation between species richness and latitude reinforced the idea that latitude, and possibly temperature as a related environmental factor, plays a primary role in structuring biogeographical patterns in the Mediterranean Sea. The lack of correlation between species richness and longitude contradicts the notion that there is a decrease in species richness from west to east in the Mediterranean, following the direction of species colonization from the Atlantic.
Phylogeography of related diadromous species in continental and island settings, and a comparison of their potential and realized dispersal patterns
Authors: Cook Benjamin D. , Page Timothy J. , Hughes Jane M.
Published: July 2011

Aim  To compare patterns of potential and realized dispersal in ecologically similar and phylogenetically related amphidromous shrimps (Atyidae) in continental and island‐dominated landscapes.

Location  Eastern Australia and the Caribbean region.

Methods  Population genetic and phylogeographic analyses of mitochondrial DNA data for Australatya striolata from eastern Australia (a continental landscape) and Atya scabra from the Caribbean (an island‐dominated landscape).

Results  Australatya striolata contained two highly divergent genetic lineages in eastern Australia, corresponding to the disjunct northern and southern populations, respectively. These lineages probably represent allopatric cryptic species, both of which were found to have genetically homogeneous population structures within their regions of occurrence. Atya scabra was genetically homogeneous throughout the Caribbean. Recent population expansions were detected for Atya scabra in the Caribbean, but not for northern or southern Australatya striolata.

Main conclusions  The findings of this study are consistent with previously reported patterns of genetic population structure in amphidromous species in both continental and island‐dominated landscapes, suggesting that potential for widespread dispersal is typically matched by realized patterns of panmixia. We therefore raise the hypothesis that landscape setting (i.e. continent or island‐dominated) does not influence dispersal patterns in amphidromous species. Further studies, especially of population genetic patterns of amphidromous species on continents, are needed to test this idea. Interestingly, results of the genetic neutrality tests led us to hypothesize that demographic and drift‐mutation equilibrium is attainable although not always evident for amphidromous species on continents, but is not attainable for those species distributed across island settings.