bluuebunny/crossref_metadata_2025 huggingface dataset:
Cassis: detection of genomic rearrangement breakpoints
Authors: Baudet Christian , Lemaitre Claire , Dias Zanoni , Gautier Christian , Tannier Eric , Sagot Marie-France
Published: June 2010

Summary: Genomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints.

Availability: Perl and R scripts are freely available for download at http://pbil.univ-lyon1.fr/software/Cassis/. Documentation with methodological background, technical aspects, download and setup instructions, as well as examples of applications are available together with the package. The package was tested on Linux and Mac OS environments and is distributed under the GNU GPL License.

Contact:  Marie-France.Sagot@inria.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
EpiTOP—a proteochemometric tool for MHC class II binding prediction
Authors: Dimitrov Ivan , Garnev Panayot , Flower Darren R. , Doytchinova Irini
Published: June 2010

Motivation: T-cell epitope identification is a critical immunoinformatic problem within vaccine design. To be an epitope, a peptide must bind an MHC protein.

Results: Here, we present EpiTOP, the first server predicting MHC class II binding based on proteochemometrics, a QSAR approach for ligands binding to several related proteins. EpiTOP uses a quantitative matrix to predict binding to 12 HLA-DRB1 alleles. It identifies 89% of known epitopes within the top 20% of predicted binders, reducing laboratory labour, materials and time by 80%. EpiTOP is easy to use, gives comprehensive quantitative predictions and will be expanded and updated with new quantitative matrices over time.

Availability: EpiTOP is freely accessible at http://www.pharmfac.net/EpiTOP

Contact:  idoytchinova@pharmfac.net

Supplementary information:  Supplementary data are available at Bioinformatics online.
A probabilistic framework for aligning paired-end RNA-seq data
Authors: Hu Yin , Wang Kai , He Xiaping , Chiang Derek Y. , Prins Jan F. , Liu Jinze
Published: June 2010

Motivation: The RNA-seq paired-end read (PER) protocol samples transcript fragments longer than the sequencing capability of today's technology by sequencing just the two ends of each fragment. Deep sampling of the transcriptome using the PER protocol presents the opportunity to reconstruct the unsequenced portion of each transcript fragment using end reads from overlapping PERs, guided by the expected length of the fragment.

Methods: A probabilistic framework is described to predict the alignment to the genome of all PER transcript fragments in a PER dataset. Starting from possible exonic and spliced alignments of all end reads, our method constructs potential splicing paths connecting paired ends. An expectation maximization method assigns likelihood values to all splice junctions and assigns the most probable alignment for each transcript fragment.

Results: The method was applied to 2 × 35 bp PER datasets from cancer cell lines MCF-7 and SUM-102. PER fragment alignment increased the coverage 3-fold compared to the alignment of the end reads alone, and increased the accuracy of splice detection. The accuracy of the expectation maximization (EM) algorithm in the presence of alternative paths in the splice graph was validated by qRT–PCR experiments on eight exon skipping alternative splicing events. PER fragment alignment with long-range splicing confirmed 8 out of 10 fusion events identified in the MCF-7 cell line in an earlier study by (Maher et al., 2009).

Availability: Software available at http://www.netlab.uky.edu/p/bioinfo/MapSplice/PER

Contact:  liuj@cs.uky.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Chromaligner: a web server for chromatogram alignment
Authors: Wang San-Yuan , Ho Tsung-Jung , Kuo Ching-Hua , Tseng Yufeng J.
Published: June 2010

Summary: Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis for metabolomics works. Chromaligner resolves peak shifts by a constrained chromatogram alignment. For a collection of chromatograms and a set of defined peaks, Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW). Chromaligner is faster than the original COW algorithm by k2 times, where k is the number of defined peaks in a chromatogram. It also provides alignments based on known component peaks to reach the best results for further chemometric analysis.

Availability: Chromaligner is freely accessible at http://cmdd.csie.ntu.edu.tw/∼chromaligner

Contact:  kuoch@ntu.edu.tw; yjtseng@csie.ntu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Foot ulcer caused by multidrug-resistant Mycobacterium tuberculosis in a diabetic patient
Authors: Baveja C. P. , Gumma Vidya Nidhi , Jain Manisha , Jha Himanshu
Published: June 2010

Osteoarticular tuberculosis is the fourth leading type of extrapulmonary tuberculosis. The disease has a progressive course and the diagnosis is often made in the later stages of bone destruction. We describe a case of a foot ulcer caused by drug-resistant Mycobacterium tuberculosis in a patient with known diabetes where the diagnosis was not suspected initially. Although tuberculous foot ulcers are rare, they should be included in the differential diagnosis of unknown foot ulcers. A greater awareness of this rare clinical entity may help in commencing specific evidence-based therapy quickly and preventing undue morbidity and mortality.
Clonal spread of CTX-M-15-producing Klebsiella pneumoniae in a Croatian hospital
Authors: Vranic-Ladavac Mirna , Bosnjak Zrinka , Beader Natasa , Barisic Nada , Kalenic Smilja , Bedenic Branka
Published: June 2010

This study was conducted to detect and analyse the presence of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae associated with a nosocomial outbreak at a Croatian hospital. During 2007, 162 K. pneumoniae isolates with reduced susceptibility to third-generation cephalosporins were collected from various hospital units and patient specimens. Most of the strains were isolated from urine (61 %), followed by blood cultures (13 %), wound swabs (13 %), tracheal aspirates (5 %), intra-abdominal abscess aspirates (4 %), intravascular catheters (3 %) and cerebrospinal fluid (1 %). Medical wards were the most important source of the isolates (46 %); 21 % of the isolates originated from surgical intensive-care units. All patients had infections acquired during their stay in hospital. No community-acquired infections were reported. Sixty of these isolates were chosen for further analysis. A double-disc synergy test (DDST) was used to detect ESBLs. MICs were determined by the broth microdilution method according to CLSI guidelines. The transferability of ceftazidime resistance was tested by conjugation (broth mating method). PCR was used to detect alleles encoding ESBL enzymes. Plasmids encoding ESBLs were extracted with the Macherey Nagel Mini kit according to the manufacturer's recommendations. The genotypes of the strains were compared by analysis of banding patterns generated by PFGE of XbaI-digested genomic DNA. ESBLs were found by DDST in all isolates. All strains were resistant to cefuroxime, ceftazidime, cefotaxime, ceftriaxone, aztreonam, piperacillin/tazobactam and ciprofloxacin. There was variable susceptibility/resistance to cefepime and gentamicin. No resistance to ceftazidime/clavulanate and carbapenems was observed. Only six strains transferred resistance to an Escherichia coli recipient strain, with low frequency. All isolates yielded an amplicon of 545 bp with consensus MA primers. Multiplex PCR was positive for group 1 CTX-M β-lactamases. Sequencing of selected amplicons revealed the presence of bla
CTX-M-15, with coding regions containing identical nucleotide sequences. Similarly to isolates from India, our isolates contained the ISEcpI insertion sequence located upstream of the bla
CTX-M-15 gene, which has recently been demonstrated to mobilize 3′-adjacent genes to transfer between DNA replicons. The isolates contained a large plasmid of approximately 150 kb. The isolates were assigned to five clusters (>85 % similarity), which contained subclusters. The results of this work provided insights into the molecular epidemiology of the spread of ESBLs in K. pneumoniae involved in an outbreak at a Croatian hospital. The hospital antibiotic policy resulted in ceftriaxone being the most heavily prescribed third-generation cephalosporin, which might be expected to select for cefotaximases such as CTX-M-15.
Bacterial lipopolysaccharides variably modulate in vitro biofilm formation of Candida species
Authors: Bandara H. M. H. N. , Lam O. L. T. , Watt R. M. , Jin L. J. , Samaranayake L. P.
Published: June 2010

The objective of this study was to evaluate the effect of the bacterial endotoxin LPS onCandidabiofilm formationin vitro. The effect of the LPS ofPseudomonas aeruginosa,Klebsiella pneumoniae,Serratia marcescensandSalmonella typhimuriumon six different species ofCandida, comprisingCandida albicansATCC 90028,Candida glabrataATCC 90030,Candida kruseiATCC 6258,Candida tropicalisATCC 13803,Candida parapsilosisATCC 22019 andCandida dubliniensisMYA 646, was studied using a standard biofilm assay. The metabolic activity ofin vitro Candidabiofilms treated with LPS at 90 min, 24 h and 48 h was quantified by XTT reduction assay. Viable biofilm-forming cells were qualitatively analysed using confocal laser scanning microscopy (CLSM), while scanning electron microscopy (SEM) was employed to visualize the biofilm structure. Initially, adhesion ofC. albicanswas significantly stimulated byPseudomonasandKlebsiellaLPS. A significant inhibition ofCandidaadhesion was noted for the following combinations:C. glabratawithPseudomonasLPS,C. tropicaliswithSerratiaLPS, andC. glabrata,C. parapsilosisorC. dubliniensiswithSalmonellaLPS (P<0.05). After 24 h of incubation, a significant stimulation of initial colonization was noted for the following combinations:C. albicans/C. glabratawithKlebsiellaLPS,C. glabrata/C. tropicalis/C. kruseiwithSalmonellaLPS. In contrast, a significant inhibition of biofilm formation was observed inC. glabrata/C. dubliniensis/C. kruseiwithPseudomonasLPS,C. kruseiwithSerratiaLPS,C. dubliniensiswithKlebsiellaLPS andC. parapsilosis/C. dubliniensis/C. kruseiwithSalmonellaLPS (P<0.05). On further incubation for 48 h, a significant enhancement of biofilm maturation was noted for the following combinations:C. glabrata/C. tropicaliswithSerratiaLPS,C. dubliniensiswithKlebsiellaLPS andC. glabratawithSalmonellaLPS, and a significant retardation was noted forC. parapsilosis/C. dubliniensis/C. kruseiwithPseudomonasLPS,C. tropicaliswithSerratiaLPS,C. glabrata/C. parapsilosis/C. dubliniensiswithKlebsiellaLPS andC. dubliniensiswithSalmonellaLPS (P<0.05). These findings were confirmed by SEM and CLSM analyses. In general, the inhibition of the biofilm development of LPS-treatedCandidaspp.was accompanied by a scanty architecture with a reduced numbers of cells compared with the profuse and densely colonized control biofilms. These data are indicative that bacterial LPSs modulatein vitro Candidabiofilm formation in a species-specific and time-dependent manner. The clinical and the biological relevance of these findings have yet to be explored.
Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism
Authors: Plugge Caroline M. , Scholten Johannes C. M. , Culley David E. , Nie Lei , Brockman Fred J. , Zhang Weiwen
Published: June 2010

Desulfovibrio vulgarisis a metabolically flexible micro-organism. It can use sulfate as an electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with a hydrogen-scavenging partner to relieve inhibition by hydrogen. These alternative metabolic types increase the chance of survival forD. vulgarisin environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genomeD. vulgarismicroarrays were used to determine relative transcript levels asD. vulgarisshifted its metabolism from syntrophic in a lactate-oxidizing dual-culture withMethanosarcina barkerito a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed inD. vulgaris2 h after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Upregulation was observed for genes encoding ATPase and the membrane-integrated energy-conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipoproteins and membrane-bound proteins was downregulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologues found only in another syntrophic bacterium,Syntrophobacter fumaroxidans, and four recently sequencedDesulfovibriostrains. This study also identified several novelc-type cytochrome-encoding genes, which may be involved in the sulfidogenic metabolism.
Agrobacterium tumefaciens ExoR represses succinoglycan biosynthesis and is required for biofilm formation and motility
Authors: Tomlinson Amelia D. , Ramey-Hartung Bronwyn , Day Travis W. , Merritt Peter M. , Fuqua Clay
Published: June 2010

The ubiquitous plant pathogenAgrobacterium tumefaciensattaches efficiently to plant tissues and abiotic surfaces and can form complex biofilms. A genetic screen for mutants unable to form biofilms on PVC identified disruptions in a homologue of theexoRgene. ExoR is a predicted periplasmic protein, originally identified inSinorhizobium meliloti, but widely conserved among alphaproteobacteria. Disruptions in theA. tumefaciens exoRgene result in severely compromised attachment to abiotic surfaces under static and flow conditions, and to plant tissues. These mutants are hypermucoid due to elevated production of the exopolysaccharide succinoglycan, via derepression of theexogenes that direct succinoglycan synthesis. In addition,exoRmutants have lost flagellar motility, do not synthesize detectable flagellin and are diminished in flagellar gene expression. The attachment deficiency is, however, complex and not solely attributable to succinoglycan overproduction or motility disruption.A. tumefaciensExoR can function independently of the ChvG–ChvI two component system, implicated in ExoR-dependent regulation inS. meliloti. Mutations that suppress theexoRmotility defect suggest a branched regulatory pathway controlling succinoglycan synthesis, motility and biofilm formation.
The Candida albicans homologue of PIG-P, CaGpi19p: gene dosage and role in growth and filamentation
Authors: Victoria Guiliana Soraya , Kumar Pravin , Komath Sneha Sudha
Published: June 2010

Glycosylphosphatidyl inositol (GPI)-anchored proteins inCandida albicansare responsible for a vast range of functions, and deletions in certain GPI-anchored proteins severely reduce adhesion and virulence of this organism. In addition, completely modified GPIs are necessary for virulence. GPI anchor biosynthesis is essential for viability and starts with the transfer ofN-acetylglucosamine to phosphatidylinositol. This step is catalysed by a multi-subunit complex, GPI–N-acetylglucosaminyltransferase (GPI–GnT). In this, the first report to our knowledge on a subunit of theCandidaGPI–GnT complex, we show thatCaGpi19p is the functional equivalent of theSaccharomyces cerevisiaeGpi19p. An N-terminal truncation mutant ofCaGpi19p functionally complements a conditionally lethalS. cerevisiae gpi19mutant. Further, we constructed a conditional null mutant ofCaGPI19by disrupting one allele and placing the remaining copy under the control of the MET3 promoter. Repression leads to growth defects, cell wall biogenesis aberrations, azole sensitivity and hyperfilamention. In addition, there is a noticeable gene dosage effect, with the heterozygote also displaying intermediate degrees of most phenotypes. The mutants also displayed a reduced susceptibility to the antifungal agent amphotericin B. Collectively, the results suggest thatCaGPI19is required for normal morphology and cell wall architecture.
The type III secretion system of Vibrio alginolyticus induces rapid apoptosis, cell rounding and osmotic lysis of fish cells
Authors: Zhao Zhe , Chen Chang , Hu Chao-Qun , Ren Chun-Hua , Zhao Jing-Jing , Zhang Lv-Ping , Jiang Xiao , Luo Peng , Wang Qing-Bai
Published: June 2010

Vibrio alginolyticus is a Gram-negative bacterium and has been recognized as an opportunistic pathogen in humans as well as marine animals. However, the virulence mechanisms for this species of Vibrio have not been elucidated. This study characterized multiple mechanisms that induce cell death in fish cells upon infection with a V. alginolyticus strain, ZJO. The bacterium required its type III secretion system (T3SS) to cause rapid death of infected fish cells. Dying cells exhibited some features of apoptotic cells, such as membrane blebbing, nuclear condensation and DNA fragmentation. Further studies showed that caspase-3 was activated by the T3SS of the ZJO strain, confirming that infection with V. alginolyticus rapidly induces T3SS-dependent apoptosis in fish cells. Infection with the ZJO strain also led to membrane pore formation and release of cellular contents from infected fish cells, as evidenced by lactate dehydrogenase release and the uptake of a membrane-impermeable dye. Importantly, inhibition of apoptosis did not prevent ZJO-infected cells from releasing cellular contents and did not block cell rounding. Taken together, these data demonstrate that infection with V. alginolyticus may promote at least three different T3SS-dependent events, which lead to the death of fish cells. This study provides an important insight into the mechanism used by Vibrio species to cause host-cell death.
Nitric Oxide Functions as a Signal and Acts Upstream of AtCaM3 in Thermotolerance in Arabidopsis Seedlings
Authors: Xuan Yi , Zhou Shuo , Wang Lei , Cheng Yudou , Zhao Liqun
Published: June 2010

To characterize the role of nitric oxide (NO) in the tolerance of Arabidopsis (Arabidopsis thaliana) to heat shock (HS), we investigated the effects of heat on three types of Arabidopsis seedlings: wild type, noa1(rif1) (for nitric oxide associated1/resistant to inhibition by fosmidomycin1) and nia1nia2 (for nitrate reductase [NR]-defective double mutant), which both exhibit reduced endogenous NO levels, and a rescued line of noa1(rif1). After HS treatment, the survival ratios of the mutant seedlings were lower than those of wild type; however, they were partially restored in the rescued line. Treatment of the seedlings with sodium nitroprusside or S-nitroso-N-acetylpenicillamine revealed that internal NO affects heat sensitivity in a concentration-dependent manner. Calmodulin 3 (CaM3) is a key component of HS signaling in Arabidopsis. Real-time reverse transcription-polymerase chain reaction analysis after HS treatment revealed that the AtCaM3 mRNA level was regulated by the internal NO level. Sodium nitroprusside enhanced the survival of the wild-type and noa1(rif1) seedlings; however, no obvious effects were observed for cam3 single or cam3noa1(rif1) double mutant seedlings, suggesting that AtCaM3 is involved in NO signal transduction as a downstream factor. This point was verified by phenotypic analysis and thermotolerance testing using seedlings of three AtCaM3-overexpressing transgenic lines in an noa1(rif1) background. Electrophoretic mobility-shift and western-blot analyses demonstrated that after HS treatment, NO stimulated the DNA-binding activity of HS transcription factors and the accumulation of heat shock protein 18.2 (HSP18.2) through AtCaM3. These data indicate that NO functions in signaling and acts upstream of AtCaM3 in thermotolerance, which is dependent on increased HS transcription factor DNA-binding activity and HSP accumulation.
A peri‐operative statin update for non‐cardiac surgery. Part II: Statin therapy for vascular surgery and peri‐operative statin trial design
Authors: Biccard B. M.
Published: June 2010

This is the second of two review articles evaluating peri‐operative statin therapy. In surgical patients, the utility of peri‐operative statin therapy is strongly suggested by retrospective studies, although it is probably overestimated, as important confounding factors have not been controlled for and hence the literature is considered to be currently inconclusive.

This review examines the potential mechanisms and indications for peri‐operative statin protection, the efficacy of acute peri‐operative beta‐blockade in addition to statin therapy, the effect of peri‐operative statin therapy withdrawal and the implications of comorbidities associated with peri‐operative cardiovascular risk on statin therapy. Recommendations concerning appropriate dosing, duration, therapeutic targets and necessary investigations when prescribing peri‐operative statins are made. Peri‐operative study design recommendations are suggested, so that future meta‐analyses may be more informative. Recommendations are made regarding retrospective reporting of statin studies to minimise the bias inherent in a number of the current retrospective studies on this subject.
Manikin study of fibreoptic‐guided intubation through the classic laryngeal mask airway with the Aintree intubating catheter vs the intubating laryngeal mask airway in the simulated difficult airway*
Authors: Heard A. M. B. , Lacquiere D. A. , Riley R. H.
Published: June 2010

In this randomised crossover manikin study of simulated difficult intubation, 26 anaesthetists attempted to intubate the trachea using two fibreoptic‐guided techniques: via a classic laryngeal mask airway using an Aintree intubating catheter and via an intubating laryngeal mask airway using its tracheal tube. Successful intubation was the primary endpoint, which was completed successfully in all 26 cases using the former technique, and in 5 of 26 cases using the latter (p < 0.0001). The former technique also proved quicker to reach the vocal cords with the fibrescope (median (IQR [range])) time 18 (14–20 [8–44]) s vs 110 (70–114 [30–118]) s, respectively; p = 0.008); and to first ventilation (93 (74–109 [52–135]) s vs 135 (79–158 [70–160]) s, respectively; p = 0.0038)]. We conclude that in simulated difficult intubation, fibreoptic intubation appears easier to achieve using a classic laryngeal mask airway and an Aintree intubating catheter than through an intubating laryngeal mask airway.
The impact of menstrual disorders on quality of life in women with inherited bleeding disorders
Authors: KADIR R. A. , EDLUND M. , VON MACKENSEN S.
Published: June 2010

Summary.  Menorrhagia, heavy menstrual bleeding, is a common condition that has a substantial impact on the lives of many women. The objective measurement of menorrhagia is often impractical; therefore diagnosis and treatment are usually based on the direct perception of the woman. Menstrual problems are likely to be worse in women with bleeding disorders, as they are more likely to have heavy and painful menstrual periods and ovulation bleeding and pain. These can have a major impact on the quality of women's lives, especially those who suffer heavy menstruation. These problems can also lead to limitations at work and school and hinder educational and academic achievements. Only few studies describe how quality of life (QOL) changes in women with an underlying haemostatic defect; poorer QOL being associated with more frequent bleeding symptoms. Early recognition, accurate diagnosis and appropriate management of bleeding disorders should improve not only the quality of care for affected women but also their QOL. Increased awareness of the high prevalence of menstrual problems especially menorrhagia is essential for early diagnosis and provision of appropriate treatments without any delay. Accurate knowledge of the impact of menorrhagia on health‐related quality of life (HRQOL) and its adequate assessment help individualize treatment and assess the magnitude of changes in HRQOL. An ideal situation would be to use a generic and a disease‐specific measure together so that comparisons can be made on a general and disease‐specific level.
Thyrocyte interleukin‐18 expression is up‐regulated by interferon‐γ and may contribute to thyroid destruction in Hashimoto’s thyroiditis
Authors: Liu Zhe , Wang Haining , Xiao Wenhua , Wang Chen , Liu Guoqiang , Hong Tianpei
Published: June 2010

Interferon‐γ (IFN‐γ) has a direct role in thyroid destruction in autoimmune thyroiditis. Interleukin‐18 (IL‐18), a pro‐inflammatory cytokine with potent IFN‐γ inducing activities, may play an important role in Th1‐mediated autoimmune diseases. The purpose of this study was to characterize the expression and localization of IL‐18 in the thyroid tissues of Hashimoto’s thyroiditis (HT) and to investigate the effect of IFN‐γ on IL‐18 expression in isolated human thyroid follicular cells (TFCs). Thyroid tissues obtained from six euthyroid patients with HT and six control subjects were used to detect IL‐18 expression by reverse transcription‐polymerase chain reaction (RT‐PCR) and immunohistochemical staining. Human TFCs were isolated and incubated for 48 h with or without IFN‐γ, tumour necrosis factor‐α (TNF‐α) or IL‐1β. IL‐18 expression was analysed by RT‐PCR, immunofluorescent double staining and western blot. We found that IL‐18 expression was increased in the thyroid tissues of HT compared with control thyroid tissues. TFCs were major cell types expressing IL‐18 in the thyroid tissues of HT. IL‐18 was constitutively expressed in isolated human TFCs, and the expression was significantly up‐regulated by IFN‐γ rather than TNF‐α or IL‐1β. Western bolt revealed that a 24‐kDa band corresponding to pro‐IL‐18 was broadened in the lysates of IFN‐γ‐treated TFCs. Our results demonstrated that IL‐18 expression is up‐regulated in the TFCs of HT patients and in primary human TFCs exposed to IFN‐γ. Therefore, intrathyroidal interaction between IL‐18 and IFN‐γ may have a role in promoting the local immune response, which contributes to the thyroid destruction seen in HT.
Effects of long‐term diabetes on the structure and cell proliferation of the myometrium in the early pregnancy of mice
Authors: Favaro Rodolfo R. , Salgado Renato M. , Raspantini Priscila R. , Fortes Zuleica B. , Zorn Telma M. T.
Published: June 2010

It is known that the development of diabetic complications in human pregnancy is directly related to the severity and the duration of this pathology. In this study, we developed a model of long‐term type 1 diabetes to investigate its effects on the cytoarchitecture, extracellular matrix and cell proliferation during the first adaptation phase of the myometrium for pregnancy. A single dose of alloxan was used to induce diabetes in mice prior to pregnancy. To identify the temporal effects of diabetes the mice were divided into two groups: Group D1 (females that became pregnant 90–100 days after alloxan); Group D2 (females that became pregnant 100–110 days after alloxan). Uterine samples were collected after 168 h of pregnancy and processed for light and electron microscopy. In both groups the histomorphometric evaluation showed that diabetes promoted narrowing of the myometrial muscle layers which was correlated with decreased cell proliferation demonstrated by PCNA immunodetection. In D1, diabetes increased the distance between muscle layers and promoted oedema. Contrarily, in D2 the distance between muscle layers decreased and, instead of oedema, there was a markedly deposition of collagen in the myometrium. Ultrastructural analysis showed that diabetes affects the organization of the smooth muscle cells and their myofilaments. Consistently, the immunoreaction for smooth muscle α‐actin revealed clear disorganization of the contractile apparatus in both diabetic groups. In conclusion, the present model demonstrated that long‐term diabetes promotes significant alterations in the myometrium in a time‐sensitive manner. Together, these alterations indicate that diabetes impairs the first phenotypic adaptation phase of the pregnant myometrium.
On the use of ultrafiltration for the concentration and desalting of phosvitin from egg yolk protein concentrate
Authors: Chay Pak Ting Bertrand P. , Pouliot Yves , Juneja Lekh R. , Okubo Tutomu , Gauthier Sylvie F. , Mine Yoshinori
Published: June 2010

An ultrafiltration‐based approach was integrated in the preparation of phosvitin (PVs) from delipidated egg yolk proteins. An attempt was made to concentrate PVs as well as to desalt by means of the diafiltration technique. Primary experiments were devoted to optimise the ultrafiltration performance as function of parameters such as the effects of pH, feed concentration and transmembrane pressure on permeate flux with the 10‐kDa molecular weight cut‐off (MWCO) polyethersulfone membrane at laboratory scale. Higher permeate flux values were observed at low concentration and at alkaline pH, whatever transmembrane pressure studied. Then, desalting of PVs was carried out at 50 °C with 10‐ and 30‐kDa MWCO membranes. The results showed that desalting of PVs was obtained with both the 10‐ and 30‐kDa MWCO membranes and with a few loss of protein in the permeate side.
Visualising knowledge from chat debates in argument diagrams
Authors: Salminen T. , Marttunen M. , Laurinen L.
Published: June 2010

This study investigates whether combining chat discussion and construction of an argument diagram stimulates students to formulate new ideas in practising argumentation. In this study, 16 secondary school students discussed vivisection and gender equality in pairs using both free and structured chat tools. In structured chat, the students selected and completed partial sentences provided by the computer. After the discussion, they jointly constructed either argument diagrams freely based on the previous discussions with an Internet tool or modified a diagram the computer had constructed automatically during the structured chat. The freely constructed diagrams contained more of the students' prior knowledge than the modified diagrams. However, the different types of diagrams did not differ significantly in breadth, depth, or balance of argumentation. Thus, free construction of argument diagrams seems to activate students to incorporate their prior knowledge into those diagrams.
Dental and gastrointestinal changes as indicators of nutritional depletion in elderly inpatients
Authors: Leandro‐Merhi Vânia Aparecida , Portero‐McLellan Kátia Cristina , Delbue Bernardi Júlia Laura , Frenhani Patrícia Baston , De Camargo José Gonzaga Teixeira , De Aquino José Luiz Braga
Published: June 2010

Objective  The objective of this study was to identify the associations between the nutritional status of elderly patients and length of hospital stay and presence of dental and gastrointestinal changes.

Casuistic and method  This cross‐sectional study analyzed anthropometric and food intake indicators, dental and gastrointestinal changes and length of hospital stay of 441 elderly patients of both genders. The Pearson's correlation coefficient was used to verify the correlation between the nutritional status of the elderly patients and length of hospital stay and presence of dental and gastrointestinal changes. The significance level was set at P < 0.05.

Results  Dietary and anthropometric variables as well as length of hospital stay were similar for patients with and without dental changes. Patients with gastrointestinal changes consumed less energy (P < 0.05) than patients without gastrointestinal changes. Length of hospital stay was inversely correlated with body mass index (r = −0.15; P < 0.05); arm circumference was inversely correlated with presence of dental changes (r = −0.12; P < 0.05) and mid‐arm muscle circumference was inversely correlated with gastrointestinal changes (r = −0.12; P < 0.05).

Conclusion  Dental and gastrointestinal changes are important indicators of nutritional depletion and dietary intake of inpatients.
An assessment of drug administration compliance in a university hospital centre
Authors: Alemanni Jordane , Touzin Karine , Bussières Jean‐François , Descoteaux Renée , Lemay Michel
Published: June 2010

Rationale, aims and objectives  Ensuring the safety of the medication process is a major world health concern. Within this framework, a field study of compliance at various stages of the medication process in health care units was conducted. The objective of our study was to compare compliance at the moment of drug administration at the patient's bedside before and after implementing certain measures (self‐study activities for the nursing staff, publication of the findings of the preliminary study and identification of priorities for action, among others).

Methods  This is an observational study aimed at comparing compliance at various stages of the medication process in terms of dose verification, preparation and administration, on ward, before and after the implementation of corrective measures. Compliance was evaluated using an observational checklist that included 36 criteria. The evaluation was conducted on inpatients in nine health care units and the Emergency Care Unit of a university hospital centre. Compliance rates were calculated for each evaluated criterion separately and by category. The degree of significance and corresponding changes between 2007 and 2008 were also measured.

Results  The compliance rate for all the applicable criteria used on the checklist showed a significant increase from 16% in 2007 to 28% in 2008. A significant increase was also observed in the compliance rates for drug verification (91% vs. 76%) and drug preparation on wards (50% vs. 23%), particularly with regard to entering drug names and a second identifier on the label.

Conclusions  Compliance rates at various separately evaluated stages in 2008 were relatively satisfactory. There is, however, room for improvement in total compliance. The introduction of simple tools and adapted communication strategies led to a sizeable improvement in the medication process at our facility.
Comparing simulation and threshold approaches when analysing data with probabilities of categories
Authors: Zhang Fang , Wharam J. Frank , Ross‐Degnan Dennis
Published: June 2010

Objective Constructing categories based on probabilities is not unusual in defining the outcome or the exposure. We compare the threshold approach and the simulation approach in making inferences.

Method We used a simple structured example as well as published data to illustrate the difference between the simulation and the threshold approaches.

Results We demonstrated that simulation results were different from the threshold approach in estimating the effect of a high‐deductible health plan. For repeat visits, we estimated a statistically significant ratio of incident rate ratio (IRR) 0.78 (95% CI: 0.64, 0.93) for non‐preventable emergency department visits using the simulation approach while the high‐severity category showed no statistical significance with the ratio of IRR 0.98 (95% CI: 0.64, 1.49) using a threshold of 75%. We also demonstrated that none of the threshold values could achieve the results of the simulation approach.

Conclusions The simulation approach is preferred over the threshold one when analysing data with probability‐based outcome, exposure and/or other covariates if the size of the data permits.
Rice leaf growth and water potential are resilient to evaporative demand and soil water deficit once the effects of root system are neutralized
Authors: PARENT BORIS , SUARD BENOÎT , SERRAJ RACHID , TARDIEU FRANÇOIS
Published: June 2010

Rice is known to be sensitive to soil water deficit and evaporative demand, with a greatest sensitivity of lowland‐adapted genotypes. We have analysed the responses of plant water relations and of leaf elongation rate (LER) to soil water status and evaporative demand in seven rice genotypes belonging to different species, subspecies, either upland‐ or lowland‐adapted. In the considered range of soil water potential (0 to −0.6 MPa), stomatal conductance was controlled in such a way that the daytime leaf water potential was similar in well‐watered, droughted or flooded conditions (isohydric behaviour). A low sensitivity of LER to evaporative demand was observed in the same three conditions, with small differences between genotypes and lower sensitivity than in maize. The sensitivity of LER to soil water deficit was similar to that of maize. A tendency towards lower sensitivities was observed in upland than lowland genotypes but with smaller differences than expected. We conclude that leaf water status and leaf elongation of rice are not particularly sensitive to water deficit. The main origin of drought sensitivity in rice may be its poor root system, whose effect was alleviated in the study presented here by growing plants in pots whose soil was entirely colonized by roots of all genotypes.
Bacteria and viruses that cause respiratory tract infections during the pilgrimage (Haj) season in Makkah, Saudi Arabia
Authors: El‐Sheikh Soliman M. , El‐Assouli Sufian M. , Mohammed Khalid A. , Albar Mohammed
Published: June 2010

objective To determine the incidence and type of RTI‐causing bacteria and viruses during a period of epidemic infections.

method A total of 395 sputum specimens and 761 throat swabs were collected during the 1991 and 1992 pilgrimage seasons (Haj to Makkah Al‐Mukarama, Saudi Arabia) from patients referred to one hospital and three dispensaries with symptoms of respiratory tract infections. All 761 throat swabs of both Haj seasons were also screened for the presence of viral pathogens with monoclonal antibodies specific for 7 viruses known to cause respiratory infections.

results Bacterial pathogens were detected in 118 (29.9%) specimens. During the 1991 Haj season Haemophilus influenzae was the most frequent bacterial pathogen detected (10%), followed by Klebsiella pneumoniae (5.2%), Streptococcus pneumoniae (4.8%), Staphylococcus aureus (3.8%) and Streptococcus pyogenes (2.4%). In the 1992 Haj season Klebsiella pneumoniae was predominant (15.1%), followed by Haemophilus influenzae and Streptococcus pneumoniae (12.3%). Screening of all sputum specimens for acid‐fast bacteria showed that the overall incidence rate of tuberculosis was 1%. Cultures from the 761 throat swabs were largely negative for bacteria except for Streptococcus pyogenes isolated from 7 patients. Viruses were detected in 148 (19.5%) specimens with influenza A and adenovirus being the most common viruses.

conclusion The pattern of virus prevalence in the 1991 and 1992 pilgrimage seasons was identical: influenza A and adenovirus predominated. Thus these two viruses should be targeted in future prophylactic measures.
Schistosomiasis haematobia in Mali: prevalence rate in school‐age children as index of endemicity in the community.
Authors: Traoré Mamadou , Maude Gillian H. , Bradley David J.
Published: June 2010

In a nationwide survey of schistosomiasis conducted in Mali from 1984 to 1989, 56265 individuals from 323 villages had their urine examined parasitologically using a filtration technique. From a sample of 242 children in 3 villages, aged 7 to 14 years, urine samples were collected and tested for haematuria using reagent strips. Analysis of the age‐specific prevalence rates of Schistosoma haematobium infection showed a strong positive correlation between the prevalence rate in the 7–14 year‐old age group, and both the overall prevalence (r = 0.90; P < 0.001) and the prevalences at other ages. An index was derived from this relationship using the equation: overall prevalence =–1.14 + 0.74 (prevalence in 7–14 year‐olds). The sensitivity and specificity of reagent strip testing for microhaematuria as compared to urine filtration were 73.3% and 83.2% respectively. We conclude that reagent strip testing of urine samples collected from a sample of individuals aged 7–14 years would be sufficient to estimate the overall prevalence of Schistosoma haematobium infection in a Malian community and suggest that this assessment procedure be used at the peripheral level of primary health care to decide on treatment regimes.
Zinc–carnosine and vitamin E supplementation does not ameliorate gastrointestinal side effects associated with ciclosporin therapy of canine atopic dermatitis
Authors: Wilson Laura S. , Rosenkrantz Wayne S. , Roycroft Linda M.
Published: June 2010

Chelated zinc–carnosine and vitamin E [GastriCalm® (GCM); Teva Animal Health] is marketed as an anti‐emetic supplement for dogs to assist the repair of damaged stomach and intestinal mucosa. The purpose of this prospective, double‐blinded, placebo‐controlled trial was to determine whether GCM reduced the frequency of vomiting, diarrhoea and appetite changes during initiation of ciclosporin (Atopica®; Novartis Animal Health) therapy for the treatment of canine atopic dermatitis. Sixty privately owned dogs diagnosed with atopic dermatitis were randomly assigned to GCM (n = 30) or placebo (n = 30) groups. All dogs received ∼5 mg/kg ciclosporin (range, 3.5–5.8 mg/kg) once daily. Dogs <13.6 kg received half a tablet of GCM or placebo; dogs ≥13.6 kg received one tablet once daily. GastriCalm® or placebo was administered 30 min prior to eating, and the ciclosporin was administered 2 h after feeding. Owners recorded episodes of vomiting, diarrhoea and appetite changes. Dogs were examined on days 0 and 14. Forty‐one of 60 dogs (68.3%) had at least one episode of vomiting, diarrhoea or appetite change, leaving nine placebo dogs (30%) and ten GCM dogs (33.3%) free of adverse events (AE). Twenty‐seven of 60 dogs (45%) vomited, and 15 of 60 (25%) had diarrhoea. There was no significant difference in episodes of individual AEs, but the placebo group had a significantly lower total AE score (summation of episodes of appetite change, vomiting and diarrhoea; P = 0.022). Small dogs (<6.82 kg) had significantly fewer total AEs in both treatment groups and tolerated ciclosporin better than larger dogs (P < 0.05).
Depth of anesthesia with desflurane does not influence the endocrine‐metabolic response to pelvic surgery
Authors: BALDINI G. , BAGRY H. , CARLI F.
Published: June 2010

Background: It has been reported that, with deep levels of anesthesia achieved with general anesthetic agents and opioids, post‐operative consumption of morphine and pain intensity can be reduced. It is not clear whether the depth of anesthesia modifies pain intensity by influencing the endocrine‐metabolic stress response. The purpose of this study was to assess the influence of a high concentration of desflurane on peri‐operative plasma cortisol.

Methods: The study was prospective and observer blinded, and included 20 women scheduled for elective total abdominal hysterectomy. They were randomly divided in to two groups: a deep group (D) (n=10) and a light group (L) (n=10). Anesthesia was induced with propofol, fentanyl and rocuronium: desflurane was administered at two different concentrations according to Bispectral Index monitoring (deep, 25 and light, 50). Post‐operative pain relief was achieved with patient‐controlled analgesia (PCA) with intravenous morphine. Blood samples were taken before, during and after surgery for the measurement of plasma cortisol, glucose and lactate. Post‐operative pain visual analog scale (VAS) and morphine consumption were recorded at regular intervals for the first 24 h.

Results: The Concentrations of plasma cortisol, glucose and lactate increased with surgery in both groups, and remained elevated, with no difference between the two groups. VAS and morphine consumptions were similar in both groups.

Conclusion: The results show that there is no relationship between the intra‐operative level of anesthesia depth achieved with desflurane and the extent of endocrine‐metabolic stress response.
Standard basic life support vs. continuous chest compressions only in out‐of‐hospital cardiac arrest
Authors: OLASVEENGEN T. M. , WIK L. , STEEN P. A.
Published: June 2010

Background: The importance of ventilations after cardiac arrest has been much debated recently and eliminating mouth‐to‐mouth ventilations for bystanders has been suggested as a means to increase bystander cardiopulmonary resuscitation (CPR). Standard basic life support (S‐BLS) is not documented to be superior to continuous chest compressions (CCC).

Methods: Retrospective, observational study of all non‐traumatic cardiac arrest patients older than 18 years between May 2003 and December 2006 treated by the community‐run emergency medical service (EMS) in Oslo. Outcome for patients receiving S‐BLS was compared with patients receiving CCC. All Utstein characteristics were registered for both patient groups as well as for patients not receiving any bystander CPR by reviewing Ambulance run sheets, Utstein forms and hospital records. Method of bystander CPR as well as dispatcher instruction was registered by first‐arriving ambulance personnel.

Results: Six‐hundred ninety‐five out of 809 cardiac arrests in our EMS were included in this study. Two‐hundred eighty‐one (40%) received S‐CPR and 145 (21%) received CCC. There were no differences in outcome between the two patient groups, with 35 (13%) discharged with a favourable outcome for the S‐BLS group and 15 (10%) in the CCC group (P=0.859). Similarly, there was no difference in survival subgroup analysis of patients presenting with initial ventricular fibrillation/ventricular tachycardia after witnessed arrest, with 32 (29%) and 10 (28%) patients discharged from hospital in the S‐BLS and CCC groups, respectively (P=0.972).

Conclusions: Patients receiving CCC from bystanders did not have a worse outcome than patients receiving standard CPR, even with a tendency towards a higher distribution of known negative predictive features.