bluuebunny/crossref_metadata_2025 huggingface dataset:
A Practical Guide for Gas Turbine Performance Field and Test Data Analysis
Authors: Krampf Francoise M.
Published: March 2015

This paper provides a simple method for correcting and analyzing the performance data from a simple cycle, two shaft gas turbine. This data may have been collected in a test cell, in the field or by a user who desires to closely monitor the performance of an engine.
Metatranscriptomic Analysis of Diminutive Thiomargarita-Like Bacteria (“Candidatus Thiopilula” spp.) from Abyssal Cold Seeps of the Barbados Accretionary Prism
Authors: Jones Daniel S. , Flood Beverly E. , Bailey Jake V.
Published: February 2015

Large sulfur-oxidizing bacteria in the family
Beggiatoaceae
are important players in the global sulfur cycle. This group contains members of the well-known genera
Beggiatoa
,
Thioploca
, and
Thiomargarita
but also recently identified and relatively unknown candidate taxa, including “
Candidatus
Thiopilula” spp. and “
Ca
. Thiophysa” spp. We discovered a population of “
Ca
. Thiopilula” spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to
Thiomargarita
spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 μm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados “
Ca
. Thiopilula” organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for “
Ca
. Thiopilula” and other sulfur-oxidizing microorganisms in the community. The novel observations of “
Ca
. Thiopilula” and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful
Beggiatoaceae
group and thus offer insight into the composition and ecology of deep cold seep microbial communities.
A Replicative Plasmid Vector Allows Efficient Complementation of Pathogenic Leptospira Strains
Authors: Pappas Christopher J. , Benaroudj Nadia , Picardeau Mathieu
Published: February 2015

Leptospirosis, an emerging zoonotic disease, remains poorly understood because of a lack of genetic manipulation tools available for pathogenic leptospires. Current genetic manipulation techniques include insertion of DNA by random transposon mutagenesis and homologous recombination via suicide vectors. This study describes the construction of a shuttle vector, pMaORI, that replicates within saprophytic, intermediate, and pathogenic leptospires. The shuttle vector was constructed by the insertion of a 2.9-kb DNA segment including the
parA
,
parB
, and
rep
genes into pMAT, a plasmid that cannot replicate in
Leptospira
spp. and contains a backbone consisting of an
aadA
cassette,
ori
R6K, and
oriT
RK2/RP4. The inserted DNA segment was isolated from a 52-kb region within
Leptospira
mayottensis
strain 200901116 that is not found in the closely related strain
L. mayottensis
200901122. Because of the size of this region and the presence of bacteriophage-like proteins, it is possible that this region is a result of a phage-related genomic island. The stability of the pMaORI plasmid within pathogenic strains was tested by passaging cultures 10 times without selection and confirming the presence of pMaORI. Concordantly, we report the use of
trans
complementation in the pathogen
Leptospira interrogans
. Transformation of a pMaORI vector carrying a functional copy of the
perR
gene in a null mutant background restores the expression of PerR and susceptibility to hydrogen peroxide comparable to that of wild-type cells. In conclusion, we demonstrate the replication of a stable plasmid vector in a large panel of
Leptospira
strains, including pathogens. The shuttle vector described will expand our ability to perform genetic manipulation of
Leptospira
spp.
Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation
Authors: Smith Steven D. , Bridou Romain , Johs Alexander , Parks Jerry M. , Elias Dwayne A. , Hurt Richard A. , Brown Steven D. , Podar Mircea , Wall Judy D.
Published: February 2015

Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of
hgcA
and
hgcB
, encodes two of the proteins essential for this activity.
hgcA
encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas
hgcB
encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator
Desulfovibrio desulfuricans
ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative “cap helix” region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. This study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.
Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae Isolated from Vegetables Imported from the Dominican Republic, India, Thailand, and Vietnam
Authors: Zurfluh Katrin , Nüesch-Inderbinen Magdalena , Morach Marina , Zihler Berner Annina , Hächler Herbert , Stephan Roger
Published: February 2015

To examine to what extent fresh vegetables imported into Switzerland represent carriers of extended-spectrum-β-lactamase (ESBL)-producing
Enterobacteriaceae
, 169 samples of different types of fresh vegetables imported into Switzerland from the Dominican Republic, India, Thailand, and Vietnam were analyzed. Overall, 25.4% of the vegetable samples yielded one or more ESBL-producing
Enterobacteriaceae
, 78.3% of which were multidrug resistant. Sixty isolates were obtained:
Escherichia coli
, 26;
Klebsiella pneumoniae
, 26;
Enterobacter cloacae
, 6;
Enterobacter aerogenes
, 1; and
Cronobacter sakazakii
, 1. We found 29 isolates producing CTX-M-15, 8 producing CTX-M-14, 7 producing CTX-M-55, 3 producing CTX-M-65, 1 each producing CTX-M-1, CTX-M-3, CTX-M-27, and CTX-M-63, 5 producing SHV-2, 3 producing SHV-12, and 1 producing SHV-2a. Four of the
E. coli
isolates belonged to epidemiologically important clones: CTX-M-15-producing B2:ST131 (1 isolate), D:ST405 (1 isolate), and D:ST38 (2 isolates). One of the D:ST38 isolates belonged to the extraintestinal enteroaggregative
E. coli
(EAEC) D:ST38 lineage. Two of the
K. pneumoniae
isolates belonged to the epidemic clones sequence type 15 (ST15) and ST147. The occurrence of antibiotic-resistant pathogenic and commensal
Enterobacteriaceae
in imported agricultural foodstuffs constitutes a source of ESBL genes and a concern for food safety.
Extensive Genetic Variability Linked to IS
26
Insertions in the
fljB
Promoter Region of Atypical Monophasic Variants of Salmonella enterica Serovar Typhimurium
Authors: Boland Cécile , Bertrand Sophie , Mattheus Wesley , Dierick Katelijne , Jasson Vicky , Rosseel Toon , Van Borm Steven , Mahillon Jacques , Wattiau Pierre
Published: February 2015

Fifty-nine monophasic
Salmonella enterica
serovar Typhimurium isolates, collected in Belgium during the period from 2008 to 2011, have been serotyped as 4,[5]:i:− and shown to harbor an
fljB
coding sequence. The genetic differences between these strains and phenotypically biphasic
Salmonella
Typhimurium were analyzed through PCR and DNA sequencing. Genetic alterations in the
fljB
promoter region affecting expression of the phase 2 flagellin were observed in 53 isolates. Other genetic events in the invertible region carrying the
fljB
promoter were observed in 2 isolates. For the remaining 4 isolates, no molecular differences with a reference biphasic
Salmonella
Typhimurium strain could be observed. Next-generation sequencing of one representative isolate affected in the
fljB
promoter region revealed a 26-kb IS
26
composite transposon insertion along with a local genomic rearrangement. Several other IS
26
element-mediated alterations of this genomic region were observed. This group of monophasic
Salmonella
Typhimurium isolates was genetically heterogeneous, as revealed by multilocus variable-number tandem-repeat analysis (MLVA), PCR, and sequencing. Pigs and pork represented a major source of such monophasic isolates in Belgium, as reported in other countries. Three out of 5 isolates of human origin presented genetic profiles identical to those of food isolates, demonstrating the pathogenic potential of the newly characterized variants and potential dissemination along the food chain. This study highlighted the key role played by IS
26
insertions in the loss of phase 2 flagellin expression and the subsequent generation of multiple monophasic variant lineages from biphasic
Salmonella
Typhimurium ancestors.
Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil
Authors: Zhao Jun , Wang Baozhan , Jia Zhongjun
Published: February 2015

Paddy fields represent a unique ecosystem in which regular flooding occurs, allowing for rice cultivation. However, the taxonomic identity of the microbial functional guilds that catalyze soil nitrification remains poorly understood. In this study, we provide molecular evidence for distinctly different phylotypes of nitrifying communities in a neutral paddy soil using high-throughput pyrosequencing and DNA-based stable isotope probing (SIP). Following urea addition, the levels of soil nitrate increased significantly, accompanied by an increase in the abundance of the bacterial and archaeal
amoA
gene in microcosms subjected to SIP (SIP microcosms) during a 56-day incubation period. High-throughput fingerprints of the total 16S rRNA genes in SIP microcosms indicated that nitrification activity positively correlated with the abundance of
Nitrosospira
-like ammonia-oxidizing bacteria (AOB), soil group 1.1b-like ammonia-oxidizing archaea (AOA), and
Nitrospira
-like nitrite-oxidizing bacteria (NOB). Pyrosequencing of
13
C-labeled DNA further revealed that
13
CO
2
was assimilated by these functional groups to a much greater extent than by marine group 1.1a-associated AOA and
Nitrobacter
-like NOB. Phylogenetic analysis demonstrated that active AOB communities were closely affiliated with
Nitrosospira
sp. strain L115 and the
Nitrosospira multiformis
lineage and that the
13
C-labeled AOA were related to phylogenetically distinct groups, including the moderately thermophilic “
Candidatus
Nitrososphaera gargensis,” uncultured fosmid 29i4, and acidophilic “
Candidatus
Nitrosotalea devanaterra” lineages. These results suggest that a wide variety of microorganisms were involved in soil nitrification, implying physiological diversification of soil nitrifying communities that are constantly exposed to environmental fluctuations in paddy fields.
Sialic Acid-Mediated Gene Expression in Streptococcus pneumoniae and Role of NanR as a Transcriptional Activator of the
nan
Gene Cluster
Authors: Afzal Muhammad , Shafeeq Sulman , Ahmed Hifza , Kuipers Oscar P.
Published: February 2015

In this study, we investigated the transcriptomic response of
Streptococcus pneumoniae
D39 to sialic acid (
N
-acetylneuraminic acid [Neu5Ac]). Transcriptome comparison of wild-type D39 grown in M17 medium with and without sialic acid revealed the elevated expression of various genes and operons, including the
nan
gene cluster (
nan
operon I and
nanA
gene). Our microarray analysis and promoter-
lacZ
fusion studies showed that the transcriptional regulator NanR acts as a transcriptional activator of
nan
operon I and the
nanA
gene in the presence of sialic acid. The putative regulatory site of NanR in the promoter region of
nan
operon I is predicted and confirmed by promoter truncation experiments. Furthermore, the role of CcpA in the regulation of the
nan
gene cluster is demonstrated through microarray analysis and promoter-
lacZ
fusion studies, suggesting that in the presence of sialic acid and glucose, CcpA represses the expression of
nan
operon I while the expression of the
nanA
gene is CcpA independent.
A Novel Triplex Quantitative PCR Strategy for Quantification of Toxigenic and Nontoxigenic Vibrio cholerae in Aquatic Environments
Authors: Bliem Rupert , Schauer Sonja , Plicka Helga , Obwaller Adelheid , Sommer Regina , Steinrigl Adolf , Alam Munirul , Reischer Georg H. , Farnleitner Andreas H. , Kirschner Alexander
Published: February 2015

Vibrio cholerae
is a severe human pathogen and a frequent member of aquatic ecosystems. Quantification of
V. cholerae
in environmental water samples is therefore fundamental for ecological studies and health risk assessment. Beside time-consuming cultivation techniques, quantitative PCR (qPCR) has the potential to provide reliable quantitative data and offers the opportunity to quantify multiple targets simultaneously. A novel triplex qPCR strategy was developed in order to simultaneously quantify toxigenic and nontoxigenic
V. cholerae
in environmental water samples. To obtain quality-controlled PCR results, an internal amplification control was included. The qPCR assay was specific, highly sensitive, and quantitative across the tested 5-log dynamic range down to a method detection limit of 5 copies per reaction. Repeatability and reproducibility were high for all three tested target genes. For environmental application, global DNA recovery (GR) rates were assessed for drinking water, river water, and water from different lakes. GR rates ranged from 1.6% to 76.4% and were dependent on the environmental background. Uncorrected and GR-corrected
V. cholerae
abundances were determined in two lakes with extremely high turbidity. Uncorrected abundances ranged from 4.6 × 10
2
to 2.3 × 10
4
cell equivalents liter
−1
, whereas GR-corrected abundances ranged from 4.7 × 10
3
to 1.6 × 10
6
cell equivalents liter
−1
. GR-corrected qPCR results were in good agreement with an independent cell-based direct detection method but were up to 1.6 log higher than cultivation-based abundances. We recommend the newly developed triplex qPCR strategy as a powerful tool to simultaneously quantify toxigenic and nontoxigenic
V. cholerae
in various aquatic environments for ecological studies as well as for risk assessment programs.
Constitutive Cylindrospermopsin Pool Size in Cylindrospermopsis raciborskii under Different Light and CO
2
Partial Pressure Conditions
Authors: Pierangelini Mattia , Sinha Rati , Willis Anusuya , Burford Michele A. , Orr Philip T. , Beardall John , Neilan Brett A.
Published: February 2015

Cylindrospermopsin (CYN) and 7-deoxy-cylindrospermopsin (dCYN) are potent hepatotoxic alkaloids produced by numerous species of cyanobacteria, including the freshwater
Cylindrospermopsis raciborskii
.
C. raciborskii
is an invasive cyanobacterium, and the study of how environmental parameters drive CYN production has received significant interest from water managers and health authorities. Light and CO
2
affect cell growth and physiology in photoautotrophs, and these are potential regulators of cyanotoxin biosynthesis. In this study, we investigated how light and CO
2
affect CYN and dCYN pool size as well as the expression of the key genes,
cyrA
and
cyrK
, involved in CYN biosynthesis in a toxic
C. raciborskii
strain. For cells growing at different light intensities (10 and 100 μmol photons m
−2
s
−1
), we observed that the rate of CYN pool size production (μ
CYN
) was coupled to the cell division rate (μ
c
) during batch culture. This indicated that CYN pool size under our experimental conditions is constant and cell quotas of CYN (Q
CYN
) and dCYN (Q
dCYN
) are fixed. Moreover, a lack of correlation between expression of
cyrA
and total CYN cell quotas (Q
CYNs
) suggests that the CYN biosynthesis is regulated posttranscriptionally. Under elevated CO
2
(1,300 ppm), we observed minor effects on Q
CYN
and no effects on expression of
cyrA
and
cyrK
. We conclude that the CYN pool size is constitutive and not affected by light and CO
2
conditions. Thus,
C. raciborskii
bloom toxicity is determined by the absolute abundance of
C. raciborskii
cells within the water column and the relative abundance of toxic and nontoxic strains.
Red Soils Harbor Diverse Culturable Actinomycetes That Are Promising Sources of Novel Secondary Metabolites
Authors: Guo Xiaoxuan , Liu Ning , Li Xiaomin , Ding Yun , Shang Fei , Gao Yongsheng , Ruan Jisheng , Huang Ying
Published: February 2015

Red soils, which are widely distributed in tropical and subtropical regions of southern China, are characterized by low organic carbon, high content of iron oxides, and acidity and, hence, are likely to be ideal habitats for acidophilic actinomycetes. However, the diversity and biosynthetic potential of actinomycetes in such habitats are underexplored. Here, a total of 600 actinomycete strains were isolated from red soils collected in Jiangxi Province in southeast China. 16S rRNA gene sequence analysis revealed a high diversity of the isolates, which were distributed into 26 genera, 10 families, and 7 orders within the class
Actinobacteria
; these taxa contained at least 49 phylotypes that are likely to represent new species within 15 genera. The isolates showed good physiological potentials for biosynthesis and biocontrol. Chemical screening of 107 semirandomly selected isolates spanning 20 genera revealed the presence of at least 193 secondary metabolites from 52 isolates, of which 125 compounds from 39 isolates of 12 genera were putatively novel. Macrolides, polyethers, diketopiperazines, and siderophores accounted for most of the known compounds. The structures of six novel compounds were elucidated, two of which had a unique skeleton and represented characteristic secondary metabolites of a putative novel
Streptomyces
phylotype. These results demonstrate that red soils are rich reservoirs for diverse culturable actinomycetes, notably members of the families
Streptomycetaceae
,
Pseudonocardiaceae
, and
Streptosporangiaceae
, with the capacity to synthesize novel bioactive compounds.
pH Influences the Importance of Niche-Related and Neutral Processes in Lacustrine Bacterioplankton Assembly
Authors: Ren Lijuan , Jeppesen Erik , He Dan , Wang Jianjun , Liboriussen Lone , Xing Peng , Wu Qinglong L.
Published: February 2015

pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity.
Organic Cultivation of Triticum turgidum subsp. durum Is Reflected in the Flour-Sourdough Fermentation-Bread Axis
Authors: Rizzello Carlo Giuseppe , Cavoski Ivana , Turk Jelena , Ercolini Danilo , Nionelli Luana , Pontonio Erica , De Angelis Maria , De Filippis Francesca , Gobbetti Marco , Di Cagno Raffaella
Published: February 2015

Triticum turgidumsubsp.durumwas grown according to four farming systems: conventional (CONV), organic with cow manure (OMAN) or green manure (OLEG), and without inputs (NOINPUT). Some chemical and technological characteristics differed between CONVand organic flours. As shown by two-dimensional electrophoresis (2-DE) analysis, OMANand OLEGflours showed the highest number of gliadins, and OMANflour also had the highest number of high-molecular-mass glutenins. Type I sourdoughs were prepared at the laboratory level through a back-slopping procedure, and the bacterial ecology during sourdough preparation was described by 16S rRNA gene pyrosequencing. Before fermentation, the dough made with CONVflour showed the highest bacterial diversity. Flours were variously contaminated by genera belonging to theProteobacteria,Firmicutes, andActinobacteria. Mature sourdoughs were completely and stably dominated by lactic acid bacteria. The diversity ofFirmicuteswas the highest for mature sourdoughs made with organic and, especially, NOINPUTflours. Beta diversity analysis based on the weighted UniFrac distance showed differences between doughs and sourdoughs. Those made with CONVflour were separated from the other with organic flours. Lactic acid bacterium microbiota structure was qualitatively confirmed through the culturing method. As shown by PCR-denaturing gradient gel electrophoresis (DGGE) analysis, yeasts belonging to the generaSaccharomyces,Candida,Kazachstania, andRhodotorulaoccurred in all sourdoughs. Levels of bound phenolic acids and phytase and antioxidant activities differed depending on the farming system. Mature sourdoughs were used for bread making. Technological characteristics were superior in the breads made with organic sourdoughs. The farming system is another determinant affecting the sourdough microbiota. The organic cultivation of durum wheat was reflected along the flour-sourdough fermentation-bread axis.
Defining the Morphology and Mechanism of the Hemoglobin Transport Pathway in Plasmodium falciparum-Infected Erythrocytes
Authors: Milani Katharine J. , Schneider Timothy G. , Taraschi Theodore F.
Published: February 2015

Hemoglobin degradation during the asexual cycle of
Plasmodium falciparum
is an obligate process for parasite development and survival. It is established that hemoglobin is transported from the host erythrocyte to the parasite digestive vacuole (DV), but this biological process is not well characterized. Three-dimensional reconstructions made from serial thin-section electron micrographs of untreated, trophozoite-stage
P. falciparum
-infected erythrocytes (IRBC) or IRBC treated with different pharmacological agents provide new insight into the organization and regulation of the hemoglobin transport pathway. Hemoglobin internalization commences with the formation of cytostomes from localized, electron-dense collars at the interface of the parasite plasma and parasitophorous vacuolar membranes. The cytostomal collar does not function as a site of vesicle fission but rather serves to stabilize the maturing cytostome. We provide the first evidence that hemoglobin transport to the DV uses an actin-myosin motor system. Short-lived, hemoglobin-filled vesicles form from the distal end of the cytostomes through actin and dynamin-mediated processes. Results obtained with IRBC treated with
N
-ethylmaleimide (NEM) suggest that fusion of hemoglobin-containing vesicles with the DV may involve a soluble NEM-sensitive factor attachment protein receptor-dependent mechanism. In this report, we identify new key components of the hemoglobin transport pathway and provide a detailed characterization of its morphological organization and regulation.
Positive Autoregulation ofmrkHIby the Cyclic Di-GMP-Dependent MrkH Protein in the Biofilm Regulatory Circuit of Klebsiella pneumoniae
Authors: Tan Jason W. H. , Wilksch Jonathan J. , Hocking Dianna M. , Wang Nancy , Srikhanta Yogitha N. , Tauschek Marija , Lithgow Trevor , Robins-Browne Roy M. , Yang Ji , Strugnell Richard A.
Published: March 2015

Klebsiella pneumoniaeis an important cause of nosocomial infections, primarily through the formation of surface-associated biofilms to promote microbial colonization on host tissues. Expression of type 3 fimbriae byK. pneumoniaefacilitates surface adherence, a process strongly activated by the cyclic di-GMP (c-di-GMP)-dependent transcriptional activator MrkH. In this study, we demonstrated the critical importance of MrkH in facilitatingK. pneumoniaeattachment on a variety of medically relevant materials and demonstrated the mechanism by which bacteria activate expression of type 3 fimbriae to colonize these materials. Sequence analysis revealed a putative MrkH recognition DNA sequence (“MrkH box”; TATCAA) located in the regulatory region of themrkHIoperon. Mutational analysis, electrophoretic mobility shift assay, and quantitative PCR experiments demonstrated that MrkH binds to the cognate DNA sequence to autoregulatemrkHIexpression in a c-di-GMP-dependent manner. A half-turn deletion, but not a full-turn deletion, between the MrkH box and the −35 promoter element rendered MrkH ineffective in activatingmrkHIexpression, implying that a direct interaction between MrkH and RNA polymerase exists.In vivoanalyses showed that residues L260, R265, N268, C269, E273, and I275 in the C-terminal domain of the RNA polymerase α subunit are involved in the positive control ofmrkHIexpression by MrkH and revealed the regions of MrkH required for DNA binding and transcriptional activation. Taken together, the data suggest a model whereby c-di-GMP-dependent MrkH recruits RNA polymerase to themrkHIpromoter to autoactivatemrkHexpression. Increased MrkH production subsequently drivesmrkABCDFexpression when activated by c-di-GMP, leading to biosynthesis of type 3 fimbriae and biofilm formation.

IMPORTANCEBacterial biofilms can cause persistent infections that are refractory to antimicrobial treatments. This study investigated how a commonly encountered hospital-acquired pathogen,Klebsiella pneumoniae, controls the expression of MrkH, the principal regulator of type 3 fimbriae and biofilm formation. We discovered a regulatory circuit whereby MrkH acts as a c-di-GMP-dependent transcriptional activator of both the gene cluster of type 3 fimbriae and themrkHIoperon. In this positive-feedback loop, whereby MrkH activates its own production,K. pneumoniaehas evolved a mechanism to ensure rapid MrkH production, expression of type 3 fimbriae, and subsequent biofilm formation under favorable conditions. Deciphering the molecular mechanisms of biofilm formation by bacterial pathogens is important for the development of innovative treatment strategies for biofilm infections.
Microcyclosporella mali: a novel fungal keratitis in a post-penetrating keratoplasty patient
Authors: Vyas Neil , Al-Hashimi Saba , Munir Wuqaas
Published: February 2015

An 86-year-old woman underwent penetrating keratoplasty for pseudophakic bullous keratopathy and presented with an acute corneal ulcer thereafter. Examination demonstrated a fluffy white infiltrate and epithelial defect with subsequent endothelial plaque formation and anterior chamber inflammation. The ulcer was cultured, and fortified topical vancomycin and tobramycin were initiated but failed to significantly improve the clinical course. Cultures were ultimately positive for fungusMicrocyclosporella malithat responded well to topical natamycin with stabilisation of the ulcer after 6 weeks of topical therapy. This is the first reported case of fungal keratitis due toM. mali.
Type I allergic hypersensitivity reactions due to ethylene oxide sterilised leucocyte filters in patients with thalassaemia: report of four cases
Authors: Belen Burcu , Polat Meltem
Published: February 2015

Ethylene oxide (EO) is a highly reactive gas used in sterilisation of heat sensitive medical devices, such as infusion sets, cannulae, intubation materials, ventriculoperitoneal shunts, dialysis catheters and stents. Allergic reactions due to EO have been reported in haemodialysis patients, patients undergoing extracorporeal photopheresis and donors of plasmapheresis. Clinical manifestations vary considerably and generally do not allow differentiation between IgE-mediated anaphylaxis and anaphylactoid reactions. We report four patients with thalassaemia who experienced anaphylaxis during transfusion due to ethylene oxide sterilised leucocyte filters. The aim of this report is to highlight the fact that frequently transfused patients can have allergic reactions due to EO particles left in leucocyte filters.
HIV-associated primary effusion lymphoma presenting as a paracardial mass
Authors: Katz Heather , Rose Cielo , Rivera Nina Thakker , Bray Natasha
Published: February 2015

Primary effusion lymphoma (PEL), a rare type of non-Hodgkin's lymphoma, is an AIDS-defining illness and always associated with human herpesvirus 8 (HHV-8). Classic presentations involve the pleural, pericardial or peritoneal cavities. Infrequently, extracavitary solid tumours develop. Treatment of PEL requires chemotherapy and highly active antiretroviral therapy (HAART).

We report a case of a 46-year-old man, who presented with right-sided chest pain, dyspnoea and night sweats. Evaluation revealed decreased breath sounds and dullness to percussion on the right side of the chest. Imaging demonstrated a 6.1 cm×6.3 cm right paracardial mass and right-sided pleural effusion. Pleural fluid was HHV-8 positive. The patient was diagnosed with PEL with extracavitary involvement and treated with chemotherapy and concurrent HAART.

This case is the first reported case of extracavitary paracardial involvement and adds new insight to the accepted treatment for PEL with extracavitary lesions.
An unexpected diagnosis of adenomyosis in the subfertile woman
Authors: Hunjan Tia , Davidson Andrew
Published: February 2015

A 38-year-old nulliparous female presented to an assisted conception clinic with subfertility and a long-standing history of dysmenorrhoea. Transvaginal ultrasound revealed two lesions in the body of the uterus, which were presumed to be fibroids. A decision was made to remove these lesions prior to attempting in vitro fertilisation (IVF). However, on laparotomy, deeply penetrating adenomyosis was discovered, resulting in an unexpected hysterectomy and significant blood loss. Based on our experience, we highlight the importance of suspecting a diagnosis of adenomyosis preoperatively and the methods by which this diagnosis can be made, in order to avoid potential unforeseen outcomes as described in this case. We discuss conservative management options for this condition, particularly in women wishing to preserve fertility.
Does long-distance air travel associated with the Sevens World Series increase players’ risk of injury?
Authors: Fuller Colin W , Taylor Aileen E , Raftery Martin
Published: February 2015

Objective

To assess whether players who cross ≥6 time zones and/or undertake ≥10 h air travel prior to competition experience a higher risk of injury during the Sevens World Series than players not required to undertake this level of travel.

Design

Five-year, prospective, cohort study.

Participants

All players from nine core teams competing in the Sevens World Series from 2008/2009 to 2013/2014.

Results

A total of 436 match injuries and 3363 player-match-hours of exposure were recorded in the study, which corresponds to an overall incidence of 129.6 injuries/1000 player-match-hours, irrespective of the nature of pretournament travel. The incidence of injury for those players crossing ≥6 time zones and undertaking ≥10 h air travel prior to competition (99.3 injuries/1000 player-match-hours) was significantly lower than that of players undertaking ≥10 h air travel but crossing ≤2 time zones prior to competition (148.8 injuries/1000 player-match-hours; p=0.003) and of those undertaking ≤3 h air travel and crossing ≤2 time zones prior to competition (146.4 injuries/1000 player-match-hours; p=0.004). There was no significant difference in the incidence of injury for players crossing ≤2 time zones in the week prior to competition, irrespective of whether the length of air travel was ≤3 h or ≥10 h (p=0.904). Precompetition air travel had no significant effect (p=0.879) on the performance of teams in terms of their final Tournament ranking positions.

Conclusions

There was no evidence to suggest that players were exposed to a greater risk of injury following extensive air travel and crossing multiple time zones prior to Tournaments in the Sevens World Series.
A review of the international Burn Injury Database (iBID) for England and Wales: descriptive analysis of burn injuries 2003–2011
Authors: Stylianou Neophytos , Buchan Iain , Dunn Ken W
Published: February 2015

Objective

To describe, for the first time, distribution (by geography, age, sex) and time trends in burn injury in England and Wales over the period that the international Burn Injury Database (iBID) has been in place.

Setting

Data from the iBID for the years 2003–2011 were used for a retrospective descriptive observational study of specialised services workload and admissions in England and Wales.

Participants

All patients who have been visited or admitted to the burn injury specialised health service of England and Wales during the time period 2003–2011. Data cleaning was performed omitting patients with incomplete records (missingness never exceeded 5%).

Outcome measures

Workload, admissions, mortality, length of stay (LOS), geographical distribution, sex differences, age differences, total burn surface area, mechanism of Injury.

Results

During 2003–2011, 81 181 patients attended the specialised burn service for assessment and admission in England and Wales. Of these, 57 801 were admitted to the services. Males accounted for 63% of the total workload in specialised burn injury services, and females for 37%. The median (IQR) burn surface area was 1.5% (3.5%). The most frequent reason for burn injury was scald (38%). The median (IQR) age for all the referred workload for both genders was 21 (40). The overall mortality of the admitted patients was 1.51% and the median (IQR) LOS was 1 (5) days.

Conclusions

Mortality from burn injuries in England and Wales is decreasing in line with western world trends. There is an observed increase in admissions to burn services but that could be explained in various ways. These results are vital for service development and planning, as well as the development and monitoring of prevention strategies and for healthcare commissioning.
An assessment of driving fitness in patients with visual impairment to understand the elevated risk of motor vehicle accidents
Authors: Kunimatsu-Sanuki Shiho , Iwase Aiko , Araie Makoto , Aoki Yuki , Hara Takeshi , Nakazawa Toru , Yamaguchi Takuhiro , Ono Hiroshi , Sanuki Tomoyuki , Itoh Makoto
Published: February 2015

Objective

To assess the driving fitness of patients with glaucoma by identifying specific areas and degrees of visual field impairment that threaten safe driving.

Design

Case–control study.

Setting, and participants

This prospective study included 36 patients with advanced glaucoma, defined as Humphrey field analyzer (HFA; 24-2 SITA standard program) measurements of mean deviation in both eyes of worse than −12 dB, and 36 age-matched and driving exposure time-matched normal subjects. All participants underwent testing in a novel driving simulator (DS) system. Participants were recruited between September 2010 and January 2012.

Main outcome measures

The number of collisions with simulated hazards and braking response time in 14 DS scenarios was recorded. Monocular HFA 24-2 test results from both eyes were merged to calculate the binocular integrated visual field (IVF). The position of the IVF subfields in which the collision-involved patients had lower sensitivity than the collision-uninvolved patients was compared with the track of the hazard. The cut-off value to predict an elevated risk of collisions was determined, as were its sensitivity and specificity, with the area under the receiver operating characteristic (AUROC) curve.

Results

Patients with advanced glaucoma were involved in a significantly higher number of collisions in the DS than the age-matched and driving exposure time-matched normal subjects (119 vs 40, respectively, p<0.0001), especially in four specific DS scenarios. In these four scenarios, IVF sensitivity was significantly lower in the collision-involved patients than in the collision-uninvolved patients in subfields on or near the track of the simulated hazard (p<0.05). The subfields with the largest AUROC curve had values ranging from 0.72 to 0.91 and were located in the paracentral visual field just below the horizontal.

Conclusions

Our novel DS system effectively assessed visual impairment, showing that simulators may have future potential in educating patients.
Perspectives on enhancing physical activity and diet for health promotion among at-risk urban UK South Asian communities: a qualitative study
Authors: Cross-Bardell Laura , George Tracey , Bhoday Mandeep , Tuomainen Helena , Qureshi Nadeem , Kai Joe
Published: February 2015

Objectives

To explore perspectives on enhancing physical activity and diet among South Asians in urban deprived communities at high risk of chronic disease and to inform development of culturally appropriate health promotion intervention.

Design

Qualitative study using semistructured one-to-one and family group interviews with thematic analysis of data.

Setting

Urban disadvantaged communities in the East Midlands of the UK.

Participants

45 respondents, including 34 people of South Asian origin (16 at-risk individuals, six family groups involving 18 relatives), of mainly Pakistani and Indian origin, including 16 non-English speakers; and 11 health professionals working locally with communities of concern.

Results

South Asian participants underlined the challenges of requiring family members across generations to engage in modifying dietary behaviours, and the central role of communal eating of traditional ‘Asian’ food in their cultural lives. Barriers to increasing physical activity included cost, personal safety and lack of time outside of long working hours and carer commitments. However, increasing walking activity was regarded as feasible by both community and health professional participants. Respondents emphasised using a social approach for potential interventions, undertaking activity with family or friends and with bilingual community peers to facilitate engagement, motivation and support. Spoken content and delivery of interventions was favoured, including personal stories and multilingual audio–visual information; within local informal rather than provider settings, including the home; and aided by pedometers for self-monitoring.

Conclusions

Focusing on physical activity by increasing walking may hold promise as health promotion in this deprived South Asian community context. Further intervention development, with exploration of feasibility and acceptability of the social approach and elements suggested, is merited.
Cost-effectiveness analyses of self-harm strategies aimed at reducing the mortality of pesticide self-poisonings in Sri Lanka: a study protocol
Authors: Madsen Lizell Bustamante , Eddleston Michael , Hansen Kristian Schultz , Pearson Melissa , Agampodi Suneth , Jayamanne Shaluka , Konradsen Flemming
Published: February 2015

Introduction

An estimated 803 900 people worldwide died as a result of self-harm in 2012. The deliberate ingestion of pesticides has been identified as the method most frequently used to commit fatal self-harm globally. In Sri Lanka, it is estimated that up to 60% of all suicides are committed using this method. The aim of the present study is to assess the cost-effectiveness of an ongoing safe storage intervention currently taking place in a rural Sri Lankan district and to model the cost-effectiveness of implementing the safe storage intervention as well as four potential interventions (legislative, medical management, follow-up contact and mobile phone contact) on a national level.

Methods and analysis

Study design for all the strategies is a cost-effectiveness analysis. A governmental perspective is adopted. The time horizon for tracking the associated costs and health outcomes of the safe storage intervention on district level runs over 3 years. The time horizon is extended to 5 years when modelling a full national roll-out of the respective interventions. The discounting of costs and health outcomes are undertaken at the recommended real rate of 3%. Threshold analyses of the modelled strategies are employed to assess the strategies potential for cost-effectiveness, running scenarios with health outcome improvements ranging from 1% to 100%. Sensitivity analyses are also performed. The main outcome measures of the safe storage intervention are incremental cost-effectiveness ratios.

Ethics and dissemination

Ethical approval was granted for the safe storage project from the University of Peradeniya, Sri Lanka, in March of 2008. An amendment for the present study was granted from Rajarata University of Sri Lanka in November of 2013. Findings will be disseminated to public and private stakeholders in local and national government in Sri Lanka as well as the wider academic audience through peer-reviewed publications and international conferences.

Trial registration number

The safe storage cluster trial is registered with the Clinical Trials, ref: NCT1146496 (http://clinicaltrialsfeeds.org/clinical-trials/show/NCT1146496).
Improving theatre efficiency and utilisation through early identification of trauma patients and enhanced communication between teams
Authors: Roberts Simon , Saithna Adnan , Bethune Rob
Published: February 2015

Surgical departments are increasingly put under pressure to improve services, cut waiting lists, increase efficiency and save money. At a district general hospital in the west-midlands we approached the challenge of improving efficiency and optimising the services available in our orthopaedic theatres.

Data was collected on: anaesthetic start times, operation start and finish times, and reasons for delay in our trauma theatre over a period from October 2014 to January 2015. During this period a change was implemented to improve the start time of the first operation of each day in the trauma theatre. Through adaptation of a method developed by Javed S et al, a patient was pre-selected by the on-call team and given the name the "golden patient" the day before they were due to be operated upon. This nominated patient would then be fixed at the start of the trauma theatre list the following day. The list would only then change if a "life or limb threatening" case was admitted overnight. The on-call team would prioritise that this patient was optimised for theatre and the theatre staff would ensure the surgical instruments were prepared.

A PDSA cycle method was used, collecting data on 80 orthopaedic trauma cases during the period, and demonstrated a 59 minute (95% CI 45-72) improvement in start times from 10:49 AM to 9:50 AM with a p-value of 0.00024 with the intervention of early allocation of the first patient on the trauma list.

A relatively simple intervention tool designed to improve communication within and between health-care teams can have a significant impact on the efficiency of a complex environment such as a trauma theatre.
Field study of pneumonia in vaccinated cattle associated with incorrect vaccination and Pasteurella multocida infection
Authors: Crawshaw W. M. , Caldow G. L.
Published: February 2015

This field study used data on the vaccine courses against bovine respiratory disease sold by one pharmaceutical company in conjunction with pharmacovigilance data to explore reported suspected lack of expected efficacy and the reasons for this. The study ran from May 1, 2007, to April 30, 2010, and covered vaccines sold in Scotland and part of Northumberland. In total, 83 groups of cattle reported suspected lack of expected efficacy, representing 1.6 per cent of the 804,618 vaccine courses sold. It was possible to investigate 45 of these outbreaks in depth using a standard questionnaire and diagnostic protocol. Vaccine usage outwith the specific product characteristics (SPC) occurred in 47 per cent of cases (21/45). The proportion of vaccination courses used where a pathogen contained in the vaccine was detected in the diseased cattle and vaccine use was consistent with the SPC was estimated at 0.12 per cent of the courses sold. Pasteurella multocida was the most common pathogen detected and was found in 21 of the outbreaks. For outbreaks where a pathogen contained in the vaccine was detected, P. multocida was found at a significantly greater frequency (P=0.03) where vaccine use was compliant with the SPC (five of six outbreaks) compared with outbreaks where vaccine use had not been compliant with the SPC (one of seven outbreaks). The limitations of the study, including the diagnostic tests employed and definition of vaccination outwith the SPC, are discussed.
Context-dependent foraging by seed-eating birds does not necessarily mean low ecological predictability
Authors: Marone L. , Camín S.R. , Cueto V.R.
Published: March 2015

Flexibility of foraging behaviour affects our capacity to predict ecological outputs such as population responses to habitat change. Some birds forage following rules of absolute value of the food item (i.e., absolute valuation). Their realized diet is strongly correlated with the profitability of the food item and it is predictable. Consumers, however, do not always follow absolute rules. Opportunistic foragers adjust food consumption based on the availability of the food item. Their diet is still predictable but more elusive. Relativistic or context-dependent foragers change the ranks of food preferences depending on the presence of alternative food options in the choice set. Predicting their contingent diet is particularly difficult. We tested if the context of seed availability affects foraging decisions of three seed-eating bird species (the Rufous-collared Sparrow (Zonotrichia capensis (Statius Muller, 1776)), the Many-colored Chaco Finch (Saltatricula multicolor (Burmeister, 1860)), and the Common Diuca Finch (Diuca diuca (Molina, 1782))) using choice experiments aimed at detecting if seed preferences for two types of target seeds changed according to context. Birds showed very similar rankings of preferences for target seeds; however, preferences for attractive food items were not fixed but often increased in less valuable contexts. Although results imply some degree of context-dependent behaviour, predictability of bird diet was preserved because the ranking of preferences remained mostly unchanged between contexts (and among bird species), and the higher consumption of target grass seeds in a less attractive context was widely expected from the intrinsic properties of the seeds.