bluuebunny/crossref_metadata_2025 huggingface dataset:
Landscape of protein–protein interactions in
Drosophila
immune deficiency signaling during bacterial challenge
Authors: Fukuyama Hidehiro , Verdier Yann , Guan Yongsheng , Makino-Okamura Chieko , Shilova Victoria , Liu Xi , Maksoud Elie , Matsubayashi Jun , Haddad Iman , Spirohn Kerstin , Ono Kenichiro , Hetru Charles , Rossier Jean , Ideker Trey , Boutros Michael , Vinh Joëlle , Hoffmann Jules A.
Published: June 2013

The
Drosophila
defense against pathogens largely relies on the activation of two signaling pathways: immune deficiency (IMD) and Toll. The IMD pathway is triggered mainly by Gram-negative bacteria, whereas the Toll pathway responds predominantly to Gram-positive bacteria and fungi. The activation of these pathways leads to the rapid induction of numerous NF-κB–induced immune response genes, including antimicrobial peptide genes. The IMD pathway shows significant similarities with the TNF receptor pathway. Recent evidence indicates that the IMD pathway is also activated in response to various noninfectious stimuli (i.e., inflammatory-like reactions). To gain a better understanding of the molecular machinery underlying the pleiotropic functions of this pathway, we first performed a comprehensive proteomics analysis to identify the proteins interacting with the 11 canonical members of the pathway initially identified by genetic studies. We identified 369 interacting proteins (corresponding to 291 genes) in heat-killed
Escherichia coli-
stimulated
Drosophila
S2 cells, 92% of which have human orthologs. A comparative analysis of gene ontology from fly or human gene annotation databases points to four significant common categories: (
i
) the NuA4, nucleosome acetyltransferase of H4, histone acetyltransferase complex, (
ii
) the switching defective/sucrose nonfermenting-type chromatin remodeling complex, (
iii
) transcription coactivator activity, and (
iv
) translation factor activity. Here we demonstrate that sumoylation of the IκB kinase homolog immune response-deficient 5 plays an important role in the induction of antimicrobial peptide genes through a highly conserved sumoylation consensus site during bacterial challenge. Taken together, the proteomics data presented here provide a unique avenue for a comparative functional analysis of proteins involved in innate immune reactions in flies and mammals.
Bad news from an aberrant city: a critical analysis of the British press's portrayal of organised crime and the refuse crisis in Naples
Authors: Dines Nick
Published: June 2013

This article examines the coverage of Naples since 2000 in the Guardian and the Independent, paying particular attention to their portrayal of the Camorra and the refuse crisis. It argues that this coverage was not simply riddled with stereotypes but was also characterised by significant inaccuracies and omissions. Analysts in Italy have detailed how the trash emergency in 2008 was the outcome of corporate malpractice and institutional complicity and that organised crime, although intent on exploiting the situation, was not a determining factor. The British press, instead, tended to conflate the breakdown of the urban waste cycle with the dumping of toxic waste and, by inverting cause and effect, to point the blame at the Camorra. These accounts, it is argued, are partially explained by the very nature of foreign news that seeks out dramatic and clearcut stories for an otherwise disinterested audience. They also reflect the heightened interest in the Camorra following the Secondigliano War and the English translation of Roberto Saviano's Gomorrah. However, the article suggests that it is the press's assumption that Naples is already an ‘out of the ordinary’ urban setting that ultimately precludes the possibility of an informed coverage of the city and its predicaments.
The perspectives of 'disengaged' students in the 14–19 phase on motivations and barriers to learning within the contexts of institutions and classrooms
Authors: Duffy Gavin , Elwood Jannette
Published: June 2013

In addressing educational disengagement, government policy in England focuses primarily on raising the age of educational participation, promoting vocationalism and directing resources at the population of young people not engaged in any education, employment or training (NEETs). However,
'disengagement' is a more fluid and dynamic concept than policy allows for and is visible within a wide range of students, even those deemed to be engaged by their presence in education and educational settings. This paper presents students' accounts of their educational experiences which
suggest that the context of the classroom, student–teacher relationships, peer relationships and pedagogical methods used in classrooms are salient factors in understanding engagement.
Differential network analysis for the identification of condition-specific pathway activity and regulation
Authors: Gambardella Gennaro , Moretti Maria Nicoletta , de Cegli Rossella , Cardone Luca , Peron Adriano , di Bernardo Diego
Published: June 2013

Motivation: Identification of differential expressed genes has led to countless new discoveries. However, differentially expressed genes are only a proxy for finding dysregulated pathways. The problem is to identify how the network of regulatory and physical interactions rewires in different conditions or in disease.

Results: We developed a procedure named DINA (DIfferential Network Analysis), which is able to identify set of genes, whose co-regulation is condition-specific, starting from a collection of condition-specific gene expression profiles. DINA is also able to predict which transcription factors (TFs) may be responsible for the pathway condition-specific co-regulation. We derived 30 tissue-specific gene networks in human and identified several metabolic pathways as the most differentially regulated across the tissues. We correctly identified TFs such as Nuclear Receptors as their main regulators and demonstrated that a gene with unknown function (YEATS2) acts as a negative regulator of hepatocyte metabolism. Finally, we showed that DINA can be used to make hypotheses on dysregulated pathways during disease progression. By analyzing gene expression profiles across primary and transformed hepatocytes, DINA identified hepatocarcinoma-specific metabolic and transcriptional pathway dysregulation.

Availability: We implemented an on-line web-tool http://dina.tigem.it enabling the user to apply DINA to identify tissue-specific pathways or gene signatures.

Contact:  dibernardo@tigem.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Tasuke: a web-based visualization program for large-scale resequencing data
Authors: Kumagai Masahiko , Kim Jungsok , Itoh Ryutaro , Itoh Takeshi
Published: June 2013

Summary: Because an enormous amount of sequence data is being collected, a method to effectively display sequence variation information is urgently needed. tasuke is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and read depths of multiple genomes, as well as annotations, can be shown simultaneously at various scales. We demonstrate the use of TASUKE by applying it to 50 rice and 100 human genome resequencing datasets.

Availability and implementation: The tasuke program package and user manual are available from http://tasuke.dna.affrc.go.jp/.

Contact:  taitoh@affrc.go.jp
Inferring disease association using clinical factors in a combinatorial manner and their use in drug repositioning
Authors: Jung Jinmyung , Lee Doheon
Published: June 2013

Motivation: Complex physiological relationships exist among human diseases. Thus, the identification of disease associations could provide new methods of disease care and diagnosis. To this end, numerous studies have investigated disease associations. However, combinatorial effect of physiological factors, which is the main characteristic of biological systems, has not been considered in most previous studies.

Results: In this study, we inferred disease associations with a novel approach that considered disease-related clinical factors in combinatorial ways by using the National Health and Nutrition Examination Survey data, and the results have been shown as disease networks. Here, the FP-growth algorithm, an association rule mining algorithm, was used to generate a clinical attribute combination profile of each disease. In addition, we characterized the 22 clinical risk attribute combinations frequently discovered from the 26 diseases in this study. Furthermore, we validated that the results of this study have great potential for drug repositioning and outperform other existing disease networks in this regard. Finally, we suggest a few disease pairs as new candidates for drug repositioning and provide the evidence of their associations from the literature.

Contact:  dhlee@kaist.ac.kr or jmjung.kr@gmail.com

Supplementary information:  Supplementary data are available at the Bioinformatics online.
A simulation framework for evaluating fisheries management decisions using environmental information
Authors: Skagen Dankert W. , Skern-Mauritzen Mette , Dankel Dorothy , Enberg Katja , Kjesbu Olav S. , Nash Richard D. M.
Published: June 2013

Skagen, D. W., Skern-Mauritzen, M., Dankel, D., Enberg, K., Kjesbu, O. S., and Nash, R. D. M. 2013. A simulation framework for evaluating fisheries management decisions using environmental information. – ICES Journal of Marine Science, 70: 743–754. The population dynamics of marine fish stocks are influenced by both physical and biological conditions. Yet, such environmental impacts on stock dynamics, and hence stock production, are rarely included in applied fisheries management. To test the utility of taking ecosystem information into account in management decisions requires efficient tools. We propose a simulation framework for evaluating fisheries management schemes that use environmental information as part of the decision basis. A key feature is to link environmental signals to parameters in functions that define the population dynamics. This allows a direct incorporation of environmental drivers into models of population dynamic processes and emphasizes the need for a quantitative understanding of the influence of environmental drivers on such processes. The utility of the simulation framework is demonstrated through a worked example with different management scenarios, where decisions to increase or decrease the exploitation rely on environmental indicators only, or also on information on stock abundance. In this example, a management that was based on indicators only, without updated measures of the state of the stock itself, failed to respond adequately to changes in stock productivity.
A link between measured neutron star masses and lattice QCD data
Authors: Bombaci Ignazio , Logoteta Domenico
Published: June 2013

We study the hadron–quark phase transition in neutron star matter and the structural properties of hybrid stars using an equation of state (EOS) for the quark phase derived with the field correlator method (FCM). We make use of the measured neutron star masses, and particularly the mass of PSR J1614−2230, to constrain the values of the gluon condensate G2 which is one of the EOS parameter within the FCM. We find that the values of G2 extracted from the mass measurement of PSR J1614−2230 are fully consistent with the values of the same quantity derived, within the FCM, from recent lattice quantum chromodynamics (QCD) calculations of the deconfinement transition temperature at zero baryon chemical potential. The FCM thus provides a powerful tool to link numerical calculations of QCD on a space–time lattice with neutron stars physics.
Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify
Herbaspirillum soli

,

Herbaspirillum aurantiacum

,

Herbaspirillum canariense
and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis
Authors: Lin Shih-Yao , Hameed Asif , Arun A. B. , Liu You-Cheng , Hsu Yi-Han , Lai Wei-An , Rekha P. D. , Young Chiu-Chung
Published: June 2013

An aerobic, Gram-negative, rod-shaped bacterium with polar flagella, strain CC-AFH3T, was isolated from an oil-contaminated site located in Kaohsiung county, Taiwan. Strain CC-AFH3T grew at 20–40 °C, pH 5.0–10.0 and <2 % (w/v) NaCl. 16S rRNA gene sequence analysis indicated that strain CC-AFH3T showed the greatest degree of similarity to

Herbaspirillum soli

SUEMI10T (96.5 %),

H. aurantiacum

SUEMI08T (96.3 %),

H. canariense

SUEMI03T (96.0 %), H. psychrotolerans PB1T (95.4 %) and members of other

Herbaspirillum

species (94.1–95.2 %), and lower similarity to members of other genera (<94 %). Phylogenetic analyses also positioned the novel strain in the genus

Herbaspirillum

as an independent lineage. The major fatty acids in strain CC-AFH3T were C10 : 0 3-OH, C12 : 0, C14 : 0 2-OH, C16 : 0, iso-C15 : 0 3-OH, C17 : 0 cyclo, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids of strain CC-AFH3T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The predominant quinone was ubiquinone 8 (Q-8) and the DNA G+C content was 63.4 mol%. On the basis of 16S rRNA gene sequence analysis in combination with physiological and chemotaxonomic data, strain CC-AFH3T represents a novel species in a new genus, for which we propose the name Noviherbaspirillum malthae gen. nov., sp. nov.; the type strain of Noviherbaspirillum malthae is CC-AFH3T ( = BCRC 80516T = JCM 18414T). We also propose the reclassification of

Herbaspirillum soli

,

Herbaspirillum aurantiacum

,

Herbaspirillum canariense

and ‘Herbaspirillum psychrotolerans’ as Noviherbaspirillum soli comb. nov. (type strain SUEMI10T = LMG 26149T = CECT 7840T), Noviherbaspirillum aurantiacum comb. nov. (type strain SUEMI08T = LMG 26150T = CECT 7839T), Noviherbaspirillum canariense comb. nov. (type strain SUEMI03T = LMG 26151T = CECT 7838T) and Noviherbaspirillum psychrotolerans comb. nov. (type strain PB1T = DSM 26001T = LMG 27282T), respectively. An emended description of

Herbaspirillum seropedicae

is also presented.
Streptococcus rubneri sp. nov., isolated from the human throat
Authors: Huch Melanie , De Bruyne Katrien , Cleenwerck Ilse , Bub Achim , Cho Gyu-Sung , Watzl Bernhard , Snauwaert Isabel , Franz Charles M. A. P. , Vandamme Peter
Published: June 2013

The novel, Gram-stain-positive, ovoid, lactic acid bacterial isolates LMG 27205, LMG 27206, LMG 27207T and MRI-F 18 were obtained from throat samples of healthy humans. 16S rRNA gene sequence analyses indicated that these isolates belong to the genus

Streptococcus

, specifically the

Streptococcus mitis

group, with

Streptococcus australis

and

Streptococcus mitis

as the nearest neighbours (99.45 and 98.56 % 16S rRNA gene sequence similarity to the respective type strains). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism (FAFLP) and pulsed-field gel electrophoresis (PFGE), DNA–DNA hybridizations, comparative sequence analysis of pheS, rpoA and atpA and physiological and biochemical tests revealed that these bacteria formed a taxon well separated from its nearest neighbours and other species of the genus

Streptococcus

with validly published names and, therefore, represent a novel species, for which the name Streptococcus rubneri sp. nov. is proposed, with LMG 27207T ( = DSM 26920T) as the type strain.
Paraperlucidibaca wandonensis sp. nov., isolated from seawater, and emended description of the genus

Paraperlucidibaca

Oh et al. 2011
Authors: Yoon Jung-Hoon , Park Sooyeon , Jung Yong-Taek , Lee Jung-Sook , Lee Keun-Chul
Published: June 2013

A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated WT-RY4T, was isolated from wood falls in the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain WT-RY4T grew optimally at 25 °C, at pH 7.0–7.5 and in the absence of NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WT-RY4T clustered with the type strain of

Paraperlucidibaca baekdonensis

with a bootstrap resampling value of 100 %. Strain WT-RY4T exhibited 16S rRNA gene sequence similarity values of 98.8 % and 96.3 % to

Paraperlucidibaca baekdonensis

RL-2T and

Perlucidibaca piscinae

IMCC 1704T, respectively and less than 91.5 % to the type strains of other species used in the phylogenetic analysis. The DNA G+C content of strain WT-RY4T was 52.4 mol% and the mean DNA–DNA relatedness value with

Paraperlucidibaca baekdonensis

RL-2T was 25 %. Strain WT-RY4T contained Q-11 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 3-OH as the major fatty acids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain WT-RY4T was distinguishable from

Paraperlucidibaca baekdonensis

RL-2T. On the basis of the data presented, strain WT-RY4T is considered to represent a novel species of the genus

Paraperlucidibaca

, for which the name Paraperlucidibaca wandonensis sp. nov. is proposed. The type strain is WT-RY4T ( = KCTC 32216T = CCUG 63419T). An emended description of the genus

Paraperlucidibaca

is also provided.
Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment
Authors: Park Sooyeon , Jung Yong-Taek , Yoon Jung-Hoon
Published: June 2013

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated D1-W3T, was isolated from tidal flat sediment of the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain D1-W3T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic analyses based on 16S rRNA gene sequences revealed that strain D1-W3T fell within the clade comprising species of the genus

Loktanella

, clustering with the type strains of

Loktanella tamlensis

,

Loktanella rosea

and

Loktanella maricola

, with which it exhibited the highest 16S rRNA gene sequence similarity values (98.1–98.2 %). The 16S rRNA gene sequence similarity values between strain D1-W3T and the type strains of other species of the genus

Loktanella

were in the range 93.5–96.5 %. The DNA G+C content of strain D1-W3T was 58.1 mol% and the mean DNA–DNA hybridization values with

L. tamlensis

KCTC 12722T,

L. rosea

LMG 22534T and

L. maricola

DSW-18T were 13–25 %. Strain D1-W3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, showed that strain D1-W3T could be differentiated from other species of the genus

Loktanella

. On the basis of the data presented, strain D1-W3T represents a novel species of the genus

Loktanella

, for which the name Loktanella sediminilitoris sp. nov. is proposed. The type strain is D1-W3T ( = KCTC 32383T = CECT 8284T).
Ogataea kolombanensis sp. nov., Ogataea histrianica sp. nov. and Ogataea deakii sp. nov., three novel yeast species from plant sources
Authors: Čadež Neža , Dlauchy Dénes , Raspor Peter , Péter Gábor
Published: June 2013

Nine methanol-assimilating yeast strains isolated from olive oil sediments in Slovenia, extra virgin olive oil from Italy and rotten wood collected in Hungary were found to form three genetically separated groups, distinct from the currently recognized yeast species. Sequence analysis from genes of the small subunit (SSU) rRNA, internal transcribed spacer region/5.8S rRNA, large subunit (LSU) rRNA D1/D2 domains and translational elongation factor-1α (EF-1α) revealed that the three closely related groups represent three different undescribed yeast species. Sequence analysis of the LSU rRNA gene D1/D2 domains placed the novel species in the Ogataea clade. The three novel species are designated as Ogataea kolombanensis sp. nov. (type strain: ZIM 2322T = CBS 12778T = NRRL Y-63657T), Ogataea histrianica sp. nov. (type strain: ZIM 2463T = CBS 12779T = NRRL Y-63658T) and Ogataea deakii sp. nov. (type strain: NCAIM Y.01896T = CBS 12735T = NRRL Y-63656T).
Performance of the Vitek MS matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for identification of Gram-positive cocci routinely isolated in clinical microbiology laboratories
Authors: Moon Hee-Won , Lee Sun Hwa , Chung Hae-Sun , Lee Miae , Lee Kyungwon
Published: June 2013

We evaluated the performance of the Vitek MS for identification of Gram-positive cocci routinely isolated in clinical microbiology laboratories. With a total of 424 well-characterized isolates, the results of the Vitek MS were compared to those of conventional methods and 16S rRNA gene sequencing. The Vitek MS correctly identified 97.9 % of the isolates tested to species level. The Vitek MS correctly identified the species of 97.2 % of the staphylococci (95.9 % of coagulase-negative staphylococci), 97.8 % of the streptococci, and 100 % of the enterococci. For the identification of Gram-positive cocci isolates, the overall concordance rate between conventional identification and the Vitek MS was 94.5 %. The Vitek MS matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system can be a reliable and rapid method for the identification of most relevant Gram-positive cocci. In addition, expanding the database of the Vitek MS, especially for coagulase-negative staphylococci, is needed to enhance the performance of the Vitek MS.
There's More to the Picture Than Meets the Eye: Nitric Oxide Cross Talk with Ca2+ Signaling
Authors: Jeandroz Sylvain , Lamotte Olivier , Astier Jérémy , Rasul Sumaira , Trapet Pauline , Besson-Bard Angélique , Bourque Stéphane , Nicolas-Francès Valérie , Ma Wei , Berkowitz Gerald A. , Wendehenne David
Published: June 2013

Calcium and nitric oxide (NO) are two important biological messengers. Increasing evidence indicates that Ca2+ and NO work together in mediating responses to pathogenic microorganisms and microbe-associated molecular patterns. Ca2+ fluxes were recognized to account for NO production, whereas evidence gathered from a number of studies highlights that NO is one of the key messengers mediating Ca2+ signaling. Here, we present a concise description of the current understanding of the molecular mechanisms underlying the cross talk between Ca2+ and NO in plant cells exposed to biotic stress. Particular attention will be given to the involvement of cyclic nucleotide-gated ion channels and Ca2+ sensors. Notably, we provide new evidence that calmodulin might be regulated at the posttranslational level by NO through S-nitrosylation. Furthermore, we report original transcriptomic data showing that NO produced in response to oligogalacturonide regulates the expression of genes related to Ca2+ signaling. Deeper insight into the molecules involved in the interplay between Ca2+ and NO not only permits a better characterization of the Ca2+ signaling system but also allows us to further understand how plants respond to pathogen attack.
Hierarchical Nuclear and Cytoplasmic Genetic Architectures for Plant Growth and Defense withinArabidopsis
Authors: Joseph Bindu , Corwin Jason A. , Züst Tobias , Li Baohua , Iravani Majid , Schaepman-Strub Gabriela , Turnbull Lindsay A. , Kliebenstein Daniel J.
Published: June 2013

To understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth rates. This population contains genetic variation in both the nuclear and cytoplasmic genomes, allowing us to separate their contributions. The cytoplasmic genome regulated a significant variance in growth but not defense, which was due to cytonuclear epistasis. Furthermore, growth adhered to an infinitesimal model of genetic architecture, while defense metabolism was more of a moderate-effect model. We found a lack of concordance between quantitative trait loci (QTL) regulating defense and those regulating growth. Given the published evidence proving the link between glucosinolates and growth, this is likely a false negative result caused by the limited population size. This size limitation creates an inability to test the entire potential genetic landscape possible between these two parents. We uncovered a significant effect of glucosinolates on growth once we accounted for allelic differences in growth QTLs. Therefore, other growth QTLs can mask the effects of defense upon growth. Investigating direct links across phenotypic hierarchies is fraught with difficulty; we identify issues complicating this analysis.
Endothelial caveolar subcellular domain regulation of endothelial nitric oxide synthase
Authors: Ramadoss Jayanth , Pastore Mayra B , Magness Ronald R
Published: June 2013

Complex regulatory processes alter the activity of endothelial nitric oxide synthase (eNOS) leading to nitric oxide (NO) production by endothelial cells under various physiological states. These complex processes require specific subcellulareNOSpartitioning between plasma membrane caveolar domains and non‐caveolar compartments.

Translocation ofeNOSfrom the plasma membrane to intracellular compartments is important foreNOSactivation and subsequent NO biosynthesis. We present data reviewing and interpreting information regarding: (i) the coupling of endothelial plasma membrane receptor systems in the caveolar structure relative toeNOStrafficking; (ii) howeNOStrafficking relates to specific protein–protein interactions for inactivation and activation ofeNOS; and (iii) how these complex mechanisms confer specific subcellular location relative toeNOSmultisite phosphorylation and signalling.

Dysfunction in the regulation ofeNOSactivation may contribute to several disease states, in particular gestational endothelial abnormalities (pre‐eclampsia, gestational diabetes etc.), that have life‐long deleterious health consequences that predispose the offspring to develop hypertensive disease, Type 2 diabetes and adiposity.
Effect of the Addition of Basil Essential Oil on the Degradation of Palm Olein during Repeated Deep Frying of French Fries
Authors: Cardoso‐Ugarte Gabriel Abraham , Morlán‐Palmas C. Christian , Sosa‐Morales María Elena
Published: June 2013

The potential antioxidant power of basil essential oil under frying conditions was explored. Two concentrations (200 or 500 ppm) were added to palm olein (PO) to evaluate their effect on fat oxidation/degradation during repeated frying of French fries at 180 °C. A higher oxidative stability index was detected for PO with basil essential oil at 200 ppm. Both concentrations showed lower p‐anisidine values than PO without basil essential oil after 5 d of frying. Addition at 500 ppm resulted in the lowest total polar compounds and free fatty acids contents. Thus, the addition of basil essential oil improved the performance of PO during repeated frying of French fries.
Inhibitory Activity of Paenibacillus polymyxa on the Biofilm Formation of Cronobacter spp. on Stainless Steel Surfaces
Authors: Yang Soonwook , Kim Seonhwa , Ryu Jee‐Hoon , Kim Hoikyung
Published: June 2013

The objective of this study was to control the survival or biofilm formation of Cronobacter spp. on stainless steel surfaces using Paenibacillus polymyxa. The antibacterial activity of a cell‐free culture supernatant (CFCS) of P. polymyxa against Cronobacter spp. was found to vary with P. polymyxa incubation time. Maximum activity occurred when P. polymyxa was incubated at 25 or 30 °C for 96 h. When the CFCS was introduced to Cronobacter spp. adhered to stainless steel strips at 25 °C for up to 72 h, the CFCS successfully inhibited Cronobacter biofilm formation. Additionally, stainless steel surfaces with a preformed P. polymyxa biofilm were exposed to Cronobacter spp. suspensions in PBS or 0.1% peptone water at 3, 5, or 7 log CFU/mL to facilitate its attachment. The Cronobacter population significantly decreased on this surface, regardless of inoculum level or carrier, when the P. polymyxa biofilm was present. However, the microbial population decreased within 6 h and remained unchanged thereafter when the surface was immersed in an inoculum suspended in 0.1% peptone water at 5 or 7 log CFU/mL. These results indicate that P. polymyxa is able to use a promising candidate competitive‐exclusion microorganism to control Cronobacter spp.
Tropomyosin Contains IgE‐Binding Epitopes Sensitive to Periodate but Not to Enzymatic Deglycosylation
Authors: Ruan Wei‐Wei , Cao Min‐Jie , Chen Feng , Cai Qiu‐Feng , Su Wen‐Jin , Wang You‐Zhao , Liu Guang‐Ming
Published: June 2013

Glycosylation has been reported to affect the epitopes of food allergens, however, there are few reports on its role in crab allergen. In the present study, the effect of glycosylation on the IgE‐binding activity of tropomyosin (TM), a major allergen in Scylla paramamosain, was investigated. The results showed that TM was a glycoprotein with a 0.2% carbohydrate moiety and contained O‐glycan. Moreover, enzymatic deglycosylation of TM by glycosidase had no effect on the IgE‐binding activity of TM. In contrast, treatment with periodate resulted in a significant reduction in its IgE‐binding activity.
Predictive Factors of Vascular Complications after Transcatheter Aortic Valve Implantation in Patients Treated with a Default Percutaneous Strategy
Authors: Vavuranakis Manolis , Kariori Maria , Voudris Vassilis , Kalogeras Konstantinos , Vrachatis Dimitrios , Aznaouridis Constantinos , Moldovan Carmen , Masoura Constantina , Thomopoulou Sophia , Lazaros Georgios , Stefanadis Christodoulos
Published: June 2013

Background

Percutaneous approach techniques with closure device after transcatheter aortic valve implantation (TAVI) have diminished vascular complications (VC). In this retrospective study, we will report incidence and angiographic factors predisposing to major VC in patients undergoing TAVI using Prostar® XL closure device as a default strategy.

Methods

Consecutive patients, who underwent TAVI transfemorally using Prostar® XL, were evaluated for the incidence of VC according to VARC criteria. Using arterial angiography, the femoral‐iliac arterial tortuosity was adjusted for large arterial diameters and expressed as the ratio total tortuosity/arterial diameter (TT/AD). Arterial calcification, the combination of angulation and atheromatosis at the puncture site and ideal puncture were evaluated too. In all patients, 30 days of follow‐up was available.

Results

Eighty‐four patients (80.2 ± 5.86 years, 39 males [46.4%]), who were consecutively treated with the transfemoral approach, were evaluated. In patients with major VC (17/84 [20.23%]) comparing to those without, arterial calcification (11 [64.7%] vs. 8 [11.9%], P < 0.01) and the TT/AD (30.2 ± 11.25 vs. 22.06 ± 8.64, P < 0.01) were independent predictors. Ideal puncture was achieved more frequently among patients without VC comparing to those with major (94.1% vs. 70.6%, P = 0.01). Blood transfusions (1.48 ± 0.37 vs. 2.45 ± 0.59, P = 0.023) were more frequent among patients with major VC. Finally, minimum creatinin clearance after TAVI predicted all‐cause 30‐day mortality (P = 0.021).

Conclusions

Major VC after TAVI with the use of Prostar closure device can be predicted by arterial calcification at the puncture site and TT/AD ratio. Minimum creatinin clearance after TAVI predicted 30‐day mortality.
Remission in rheumatoid arthritis by different criteria does not converge over the inflammatory markers
Authors: Chandrashekara S. , Priyanka B. U.
Published: June 2013

Objective

Remission is an ideal target in the management of rheumatoid arthritis (RA). We compared American College of Rheumatology (ACR) 1981 preliminary definition of remission, European League Against Rheumatism (EULAR) disease activity score of 28 joints – C‐reactive protein (DAS28 (3)‐CRP) and DAS28 (3)‐ESR (erythrocyte sedimentation rate) and newer ACR/EULAR remission criteria from 2011. We assessed the agreement between these definitions using kappa statistics in a real‐time clinical scenario.

Materials and methods

This is a cross sectional study in which 460 patients' charts were reviewed. Their data on tender and swollen joint counts, visual analogue scale of patient global assessment (Pt GA), ESR and CRP were retrieved. One hundred patients who fulfilled one of the remission criteria and had all the required five variables were selected and they were categorized into remission using all the four definitions.

Results

Only one case out of 100 fulfilled all four remission criteria. Among 100 cases: ACR 1981 classified six in remission; ACR/EULAR 2011, eight; DAS28 (3)‐ESR, 24; and DAS28 (3)‐CRP classified 100 patients in remission. A substantial number of patients continued to have features suggesting persisting active inflammation, despite being categorized into remission. A major portion of disagreement was in ESR and CRP. The value spread of all clinical parameters such as swollen joint count, tender joint count and Pt GA had no significant difference in the patients classified as being in remission.

Conclusion

The DAS28 (3)‐CRP overestimated remission compared to all other criteria. Disagreement was more in laboratory inflammatory parameters. A uniform definition of remission is needed.
The use of temporal artery ultrasound in the diagnosis of giant cell arteritis in routine practice
Authors: Black Rachel , Roach Denise , Rischmueller Maureen , Lester Susan L. , Hill Catherine L.
Published: June 2013

Aim

The exact diagnostic role of temporal artery ultrasound (TAU) remains unclear. The aim of this study was to determine the sensitivity and specificity of a positive halo sign in patients undergoing TAU in a clinical setting, and to perform a review of existing evidence.

Method

Patients who had undergone TAU at a single centre in Australia were included in the study. The presence or absence of a halo sign and whether it was unilateral or bilateral was determined retrospectively from radiology reports. Pathology results were used to determine which patients underwent a temporal artery biopsy and if the biopsy was positive or negative. A case note review was performed to determine presenting clinical features and if a clinical diagnosis of giant cell arteritis was made. The sensitivity, specificity and likelihood ratios of TAU compared to both biopsy and clinical diagnosis were calculated.

Results

Fifty patients were identified as having had a TAU (28% male, mean age 69). When compared to biopsy‐proven cases, the sensitivity of a halo sign was 40%, specificity 81%, positive likelihood ratio 2.1 and negative likelihood ratio 0.7. When compared to clinical diagnosis, the sensitivity was 42%, specificity 94%, positive likelihood ratio 7.1 and negative likelihood 0.6.

Conclusions

Sensitivity and specificity results were comparable to the literature. A halo sign may preclude the need for biopsy in cases of high clinical suspicion and contraindications to surgery. Biopsy remains necessary in most cases, irrespective of whether a halo sign is present.
Hippocampal volume in relation to clinical and cognitive outcome after electroconvulsive therapy in depression
Authors: Nordanskog P. , Larsson M. R. , Larsson E.‐M. , Johanson A.
Published: June 2013

Objective

In a previous magnetic resonance imaging (MRI) study, we found a significant increase in hippocampal volume immediately after electroconvulsive therapy (ECT) in patients with depression. The aim of this study was to evaluate hippocampal volume up to 1 year after ECT and investigate its possible relation to clinical and cognitive outcome.

Method

Clinical and cognitive outcome in 12 in‐patients with depression receiving antidepressive pharmacological treatment referred for ECT were investigated with the Montgomery–Asberg Depression Rating Scale (MADRS) and a broad neuropsychological test battery within 1 week before and after ECT. The assessments were repeated 6 and 12 months after baseline in 10 and seven of these patients, respectively. Hippocampal volumes were measured on all four occasions with 3 Tesla MRI.

Results

Hippocampal volume returned to baseline during the follow‐up period of 6 months. Neither the significant antidepressant effect nor the significant transient decrease in executive and verbal episodic memory tests after ECT could be related to changes in hippocampal volume. No persistent cognitive side effects were observed 1 year after ECT.

Conclusion

The immediate increase in hippocampal volume after ECT is reversible and is not related to clinical or cognitive outcome.
Land use and economic effects of alternative biofuel policies in Brazil and the United States
Authors: Nuñez Hector M. , Önal Hayri , Khanna Madhu
Published: June 2013

Being the two largest ethanol producers in the world, biofuel policies in Brazil and the United States affect both their domestic markets and the global food and biofuel economy. In this article we develop a price endogenous mathematical programming model to simulate and analyze the impacts of biofuel mandates and trade distortions on land use, agricultural commodity and transportation fuel markets, and global environment. We find that an 80% increase in total biofuel production from its 103 billion liter baseline level to the mandated 183 billion liter level in 2022 can be achieved with less than 2% increase in total cropland use in both countries. In the United States, this would occur with cellulosic biofuels meeting nearly half of the biofuels consumed and produced largely on cropland pasture and corn ethanol meeting the rest of the mandate and resulting in a 2% increase in corn price. In Brazil, the expansion in sugarcane production would be achieved by reducing land under pasture and a marginal increase in intensification of livestock production. In the aggregate, biofuel policies increase economic surplus in both countries by 1% and redistribute the benefits from agricultural consumers to agricultural producers and the fuel sector. Finally, we also find that full implementation of the mandates in North America, China, and the European Union would reduce the global life‐cycle global greenhouse gas emissions by about 5%.
Biofuels and developing economies: is the timing right?
Authors: Msangi Siwa , Evans Martin
Published: June 2013

In this article, we discuss some key aspects of biofuel production in developing countries, and where constraints and tradeoffs are likely to occur. We use the example of two countries, Senegal and India, to highlight some of the issues of cost competitiveness, problems with ensuring stable supply of feedstock as well as critical missing links in the biofuels value chain that pose problems to scaling up national programs in these countries. We discuss the particularly problematic nature of jatropha, as a biodiesel feedstock, and underline some helpful guiding principles that can help country‐level policy. We point to an underlying “duality” between a well‐functioning food system and favorable conditions for agribusiness enterprises, such as biofuels, and the relevance it has to achieving food security goals.
Fetal growth in relation to maternal and fetal IGF‐axes: a systematic review and meta‐analysis
Authors: Elhddad Agzail S.A. , Lashen Hany
Published: June 2013

Insulin‐like growth factors (IGFs) and their binding proteins (IGFBPs) are key regulators of fetal growth. However, the literature is inconsistent. Our objective was to systematically and objectively evaluate the available literature and to develop a balanced opinion on the relation between maternal and fetal IGF‐axes and birthweight. A systematic review and a meta‐analysis were conducted according to the published Moose (Meta‐analysis of Observational Studies in Epidemiology) guidelines. A robust recognized systematic methodology was used in the literature search and analysis to avoid bias. Weighted mean difference and 95% confidence intervals of cord/maternal IGFs and IGFBP‐1 and ‐3 were calculated. Eleven observational studies were included. Cord IGF‐I (p < 0.0001) and IGFBP‐3 (p = 0.003) were significantly higher in large‐for‐gestational age (LGA) than appropriate‐for‐gestational age (AGA) babies. Cord IGFBP‐1 was significantly higher in small‐for‐gestational age (SGA) than AGA babies (p < 0.0001). LGA and AGA babies had similar IGF‐II levels, whereas SGA and AGA babies had comparable IGF‐I levels. IGF‐I was significantly higher in mothers of AGA than SGA babies (p < 0.0001). The assay methods and background population marginally affect the overall homogeneity and the direction of the primary analysis. Fetal IGFs and their binding proteins play different roles in fetal growth at either end of the growth spectrum. Fetal IGF‐I and IGFBP‐3 may be influential in LGA. However, fetal IGFBP‐1 has a more prominent role in SGA.
Consuming a low‐fat diet from weaning to adulthood reverses the programming of food preferences in male, but not in female, offspring of ‘junk food’‐fed rat dams
Authors: Ong Z. Y. , Muhlhausler B. S.
Published: June 2013

Aim

This study aimed to determine whether the negative effects of maternal ‘junk food’ feeding on food preferences and gene expression in the mesolimbic reward system could be reversed by weaning the offspring onto a low‐fat diet.

Methods

Offspring of control (n = 11) and junk food‐fed (JF, n = 12) dams were weaned onto a standard rodent chow until 6 weeks (juvenile) or 3 months (adult). They were then given free access to both chow and junk food for 3 weeks and food preferences determined. mRNA expression of key components of the mesolimbic reward system was determined by qRT‐PCR at 6 weeks, 3 and 6 months of age.

Results

In the juvenile group, both male and female JF offspring consumed more energy and carbohydrate during the junk food exposure at 6 weeks of age and had a higher body fat mass at 3 months (P < 0.05). Female juvenile JF offspring had higher tyrosine hydroxylase, dopamine receptors and dopamine active transporter expression in the ventral tegmental area (P < 0.05). In the adult group, there was no difference between control and JF offspring in energy and macronutrient intakes during exposure to junk food; however, female JF offspring had a higher body fat mass at 6 months (P < 0.05).

Conclusion

These results suggest that the effects of perinatal junk food exposure on food preferences and fat mass can be reversed by consuming a low‐fat diet from weaning to adulthood in males. Females, however, retain a higher propensity for diet‐induced obesity even after consuming a low‐fat diet for an extended period after weaning.
A Rare Case of a Mosaic Unbalanced Translocation After Chorionic Villous Sampling
Authors: Jeelani Roohi , Chelliah Anushka , Rauch Kristen , Soto Eleazar , Ebrahim Saleh , Bahado‐Singh Ray , Jones Theodore
Published: June 2013

Background

Most of the literature suggests that unbalanced chromosomal translocations may lead to poor obstetrical outcomes. We present a case of an unbalanced translocation resulting in trisomy 1q and partial monosomy 20p identified on chorionic villous sampling (CVS).

Method

Case report with expert‐derived clinical management and guidance.

Results

After the abnormal CVS result, a subsequent amniocentesis revealed a normal 46,XX fetal karyotype. Detailed second trimester ultrasound of the fetus revealed no gross structural abnormalities. The CVS karyotype results were attributed to confined placental mosaicism (CPM) of the unbalanced translocation. The infant is 18 months old and has normal phenotype and karyotype.

Conclusion

We recommend that if CPM with an unbalanced translocation is diagnosed on CVS, parental karyotype and an amniocentesis should be offered in conjunction with genetic counseling. In rare instances, such as this one, an unbalanced translocation may have a favorable outcome. (BIRTH 40:2 June 2013)
Understanding Women's Interpretations of Infant Formula Advertising
Authors: Parry Kathleen , Taylor Emily , Hall‐Dardess Pam , Walker Marsha , Labbok Miriam
Published: June 2013

Background

Exclusive breastfeeding for 6 months and continued breastfeeding for at least 1 year is recommended by all major health organizations. Whereas 74.6 percent of mothers initiate breastfeeding at birth, exclusivity and duration remain significantly lower than national goals. Empirical evidence suggests that exposure to infant formula marketing contributes to supplementation and premature cessation. The objective of this study was to explore how women interpret infant formula advertising to aid in an understanding of this association.

Methods

Four focus groups were structured to include women with similar childbearing experience divided according to reproductive status: preconceptional, pregnant, exclusive breastfeeders, and formula feeders. Facilitators used a prepared protocol to guide discussion of infant formula advertisements. Authors conducted a thematic content analysis with special attention to women's statements about what they believed the advertisements said about how the products related to human milk (superior, inferior, similar) and how they reported reacting to these interpretations.

Results

Participants reported that the advertisements conveyed an expectation of failure with breastfeeding, and that formula is a solution to fussiness, spitting up, and other normal infant behaviors. Participants reported that the advertisements were confusing in terms of how formula‐feeding is superior, inferior or the same as breastfeeding. This confusion was exacerbated by an awareness of distribution by health care practitioners and institutions, suggesting provider endorsement of infant formula.

Conclusions

Formula marketing appears to decrease mothers' confidence in their ability to breastfeed, especially when provided by health care practitioners and institutions. Therefore, to be supportive of breastfeeding, perinatal educators and practitioners could be more effective if they did not offer infant formula advertising to mothers. (BIRTH 40:2 June 2013)
No small slam: increasing incidents of genitourinary injury from toilets and toilet seats
Authors: Glass Allison S. , Bagga Herman S. , Tasian Gregory E. , McGeady James B. , McCulloch Charles E. , Blaschko Sarah D. , McAninch Jack W. , Breyer Benjamin N.
Published: June 2013

Objective

To describe the epidemiology of genitourinary (GU) injury from toilets that present to USA Emergency rooms (ERs).

Materials and Methods

The National Electronic Injury Surveillance System (NEISS) is a stratified probability sample of hospital ER visits for USA consumer product‐related injuries.

NEISS was used to estimate total toilet‐ and toilet seat‐related GU injury for the years 2002–2010, as well as to describe demographics and injury characteristics.

Analyses were performed using strata, primary sampling units and sample weights to accommodate the complex sample survey design.

Data are reported as national estimates with 95% confidence intervals (CIs) provided.

Results

In all, 13 175 (95% CI 10 185–16 165) GU injuries related to toilets presented to ERs during 2002–2010.

The most common mechanism involved crush from accidental fall of toilet seat, described in 9011 (68.4%, 95% CI 6907–11 115) cases.

Most crush injuries were isolated to the penis (98.1%). Of crush injuries, 81.7% occurred in children aged 2–3 years and 99.3% occurred in the home. Crush injuries increased over the period 2002–2010 (P = 0.017) by ≈100 per year, ending with an estimated 1707 (95% CI 1011–2402) by 2010.

Most patients who sustained toilet‐ and toilet seat‐related GU injuries were treated in the ER and then discharged.

Conclusion

While penile crush injury related to a toilet seat is an uncommon mechanism of urological injury in children, the number of incidents appears to be rising.

These findings support educational efforts and interventions, such as exchange of heavy toilet seats with slow‐close toilet seat technology.