bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovering novel subsystems using comparative genomics
Authors: Ferrer Luciana , Shearer Alexander G. , Karp Peter D. 
Published: July 2011

Abstract
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

Abstract
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

AbstractFaunce, 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.
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

Abstract
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

ABSTRACTAims  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

SummaryDespite 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 cytologiqueL'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 MaterialDie 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): 290–302AbstractBackground 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

AbstractFine 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.
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.AbstractAim  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.AbstractAim. 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

AbstractAim  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.