bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the innate and adaptive immunity in type I and type II focal cortical dysplasias
Authors: Iyer Anand , Zurolo Emanuele , Spliet Wim G.M. , Van Rijen Peter C. , Baayen Johannes C. , Gorter Jan A. , Aronica Eleonora 
Published: March 2010

SummaryPurpose:  Induction of inflammatory pathways has been reported in epileptic patients with focal malformations of cortical development. In the present study we examined the innate and adaptive immune responses in focal cortical dysplasia (FCD) with different histopathologic and pathogenetic features.Methods:  The inflammatory cell components and the induction of major proinflammatory pathways and molecules [complement pathway, interleukin (IL)‐1β, and chemokine monocyte chemotactic protein‐1 (MCP1)] was investigated in surgical specimens of sporadic type IA and type IIB FCD using immunocytochemical methods.Results:  FCD II but not FCD I cases exhibit activation of the mammalian target of rapamycin (mTOR) cascade with strong neuronal expression of the phosphorylated isoform of S6 protein. Microglia reactivity was increased in all lesions (FCD I and II) compared to control tissue; however, the number of HLA‐DR–positive cells was significantly higher in FCD II than in FCD I. In FCD II specimens we also observed perivascular and parenchymal T lymphocytes (CD3+), with a predominance of CD8+ T‐cytotoxic/suppressor lymphocytes, as well as a few dendritic cells. Expression of components of the complement cascade, IL‐1β, and MCP1 was prominent in FCD II cases.Discussion:  Our findings indicate a prominent activation of both innate and adaptive immunity, with involvement of different inflammatory pathways in FCD II cases, supporting the possible involvement of inflammation in the epileptogenesis of these lesions, as well as the notion that FCD II is pathologically distinct from FCD I.
Increased expression of APAF‐1 in low‐risk myelodysplastic syndrome: a possible role in the pathophysiology of myelodysplasia
Authors: Benites Bruno Deltreggia , Traina Fabiola , Duarte Adriana da Silva Santos , Lorand‐Metze Irene Gyongyver H. , Costa Fernando Ferreira , Saad Sara Teresinha 
Published: March 2010

Abstract Objectives: APAF‐1 is a central component of the intrinsic pathway of apoptosis, where APAF‐1 dysregulation results in the development of diverse human neoplasms. The aim of this study was to characterize the mRNA expression levels of APAF‐1 transcripts in low‐risk and high‐risk MDS and to elucidate whether the expression levels of APAF‐1 transcripts are modulated with increased apoptosis in CD34+ MDS cells undergoing erythroid differentiation. Methods: APAF‐1 (NM_181861) expression was verified, by quantitative RT‐PCR, in bone marrow aspirates from 33 patients with myelodysplastic syndromes (MDS), at the time of diagnosis, and in erythroid differentiation cultures from CD34+ from normal donors and patients with MDS. Results: APAF‐1 expression was significantly higher in low‐risk, compared to high‐risk MDS, according to IPSS (P < 0.0001), FAB (P = 0.0265), and cytogenetic risk (P = 0.0134). Low‐risk MDS‐derived differentiated erythroid cells demonstrated an increased expression of APAF‐1, compared with normal cells, accompanied by an augmented rate of apoptosis. Conclusions: Increased expression of APAF‐1 in low‐risk disease and its positive correlation with the apoptotic rate observed during the erythroblast differentiation of low‐risk MDS cells may indicate that the modulation of APAF‐1, at the transcriptional level, participates in the pathophysiology of MDS.
APPLICATION OF ARTIFICIAL NEURAL NETWORKS TO PREDICT CLOSTRIDIUM BOTULINUM GROWTH AS A FUNCTION OF ZATARIA MULTIFLORA ESSENTIAL OIL, pH, NaCl AND TEMPERATURE
Authors: KHANZADI SAEID , GHARIBZADEH SHAHRIAR , RAOUFY MOHAMMAD REZA , RAZAVILAR VADUD , KHAKSAR RAMIN , RADMEHR BEHRAD 
Published: March 2010

ABSTRACT The present study is undertaken to predict the effects of Zataria multflora essential oil, NaCl, temperature and pH on the probability percentage of growth of Clostridium botulinum using artificial neural network (ANN). To assess the effects of essential oil, NaCl, pH and temperature on Log P% of C. botulinum type A spores, the experiment was arranged in a factorial design. This design (4 × 3 × 3 × 3) included four levels of EO (0.0, 0.015, 0.03 and 0.06%), three levels of NaCl (0.5, 4 and 6%), three levels of pH (6, 6.5 and 7.4), three storage temperatures (15, 25 and 35C) and repeated observations (12 times) for growth in BHI broth for up to 43 days (D). According to our results, the log P% of C. botulinum was affected significantly (P < 0.01) by Essential oil, pH, NaCl and temperature. The numbers of neurons in input hidden and output layers were 5, 11 and 1, respectively. The inputs to the ANN were temperature, pH, NaCl, essential oil and the number of days after inoculation. The output of the ANN was log P%. Our results show that the ANN is a suitable model for predicting the growth of C. botulinum when it is affected by different levels of pH, temperature, NaCl and essential oil.PRACTICAL APPLICATIONS Clostridium botulinum is an anaerobic bacterium that produces a powerful neurotoxin. Because there is concern over the safety of some chemical preservatives, an increased interest is started into more natural alternatives. Zataria multiflora has been used traditionally as flavor agent and its antimicrobial activities has been established in previous studies. In addition, predictive food microbiology involves the knowledge of microbial growth responses to environmental factors summarized as mathematical models. Over the last few years, artificial neural networks (ANNs), as nonlinear modeling techniques, have been proposed for use in predictive microbiology. Considering the importance of C. botulinum and using natural preservative in food safety and the power of ANN in predicting purposes, we suggest that ANN can be used as a prediction tool in food safety.
ISOLATION AND IDENTIFICATION OF SALMONELLA ENTERITIDIS AND SALMONELLA TYPHIMURIUM FROM THE EGGS OF RETAIL STORES IN MASHHAD, IRAN USING CONVENTIONAL CULTURE METHOD AND MULTIPLEX PCR ASSAY
Authors: JAMSHIDI A. , KALIDARI G.A. , HEDAYATI M. 
Published: March 2010

ABSTRACT In this study, a total of 250 eggs were collected randomly from 50 retail stores in Mashhad city over a period of 3 months in the summer of 2008. Five samples from each store were collected, and transferred to the laboratory. In order to isolate Salmonella spp., conventional culture method – including pre‐enrichment, enrichment, selective plating and differential plating – were performed. To confirm the identification of isolated colonies as Salmonella spp. and determining serovars as Typhimurium and Enteritidis serovars, a multiplex polymerase chain reaction assay using three pairs of primers were employed: S141 and S139 for the invA gene, specific for the genus of Salmonella; Fli15 and Tym for the fliC gene, specific for Typhimurium serovar; and Prot6e‐5 and Prot6e‐6 for Prot6E gene, specific for Enteritidis serovar. Four out of 250 samples (1.6%) from eggshells were determined as contaminated with Salmonella spp. Isolated colonies were confirmed as Salmonella, and their serovar was determined as Typhimurium. Salmonella spp. was not isolated from the eggs' contents.PRACTICAL APPLICATIONSIt seems that Salmonella Typhimurium is the most prevalent serotype of egg contaminant in the Mashhad area of Iran, and the multiplex polymerase chain reaction method based on amplification from conserved genes could be a reliable alternative for conventional culture methods.
STUDIES ON ENTEROTOXIGENIC BACILLUS CEREUS IN RAW MILK AND SOME DAIRY PRODUCTS
Authors: HASSAN G.M. , AL‐ASHMAWY M.A.M. , MESHREF A.M.S. , AFIFY S.I. 
Published: March 2010

ABSTRACT A total of 150 samples of raw milk, ice cream and yogurt (50 of each) were collected randomly in their packages from different localities in Beni‐Suef governorate, Egypt, to study the presence of Bacillus cereus in these products. B. cereus could be detected in 30, 48 and 2% of examined raw milk, ice cream and yogurt samples with a mean count of 9.11 × 102 ± 4.87 × 102, 6.37 × 103 ± 2.83 × 103 and 6 ± 5.9 cells/mL or g, respectively. All B. cereus isolates showed hemolytic activity; 95% of isolates showed vero cell toxicity and 27.5% of them killed adult mice. B. cereus could not be detected in artificially inoculated yogurt after 24 and 48 h. B. cereus was sensitive to pefloxacin, gentamycin, chloramphenicol and nalidixic acid, whereas all isolates were resistant to colistin sulfate. Public health significance and suggestive control measures are discussed.PRACTICAL APPLICATIONSThe incidence of contamination of raw milk and ice cream by Bacillus cereus is fairly high, and nearly all of the isolates showed hemolysin and cytotoxic toxin activities, so the risk of food poisoning caused by B. cereus in such products should not be neglected. B. cereus rapidly dies in yogurt, so acidification is a common method of preservation, and as the acidity of fermented milk increased, B. cereus fails to survive. Pefloxacin, gentamicin and chloramphenicol are effective antibiotics against B. cereus infection. B. cereus is highly resistant to colistin sulfate.
The analysis of JAK2 and MPL mutations and JAK2 single nucleotide polymorphisms in MPN patients by MassARRAY assay
Authors: ZHANG S.‐J. , QIU H.‐X. , LI J.‐Y. , SHI J.‐Y. , XU W. 
Published: March 2010

SummaryRecent studies have shown that JAK2 V617F, MPL W515L/K and JAK2 exon 12 mutations underlie the major molecular pathogenesis of myeloproliferative disorders (MPN). Allele‐Specific Polymerase Chain Reaction (AS‐PCR), direct sequencing and MassARRAY assay were used to ascertain the real prevalence of these mutations and the influence of genetic susceptibility in Chinese MPN patients. The positive rate of JAK2 V617F in polycythaemia vera (PV), essential thrombocythaemia (ET) and primary myelofibrosis (PMF) was 82.0%, 36.6% and 51.1% respectively. One ET patient and two PMF patients harboured the MPL W515L mutation and three PV patients harboured JAK2 exon 12 mutations. All of these patients were confirmed as JAK2 V617F negative. Clinical data demonstrated that PV patients with JAK2 exon 12 mutations were younger, had higher haemoglobin levels and white blood cell counts than PV patients with JAK2 V617F. In addition, through analysis of 4 polymorphic loci of JAK2 gene, no significant difference of distribution frequency was found among PV, ET and PMF patients. Distribution frequency of haplotype also was not significantly different among PV, ET and PMF patients. We conclude that JAK2 V617F is a major molecular pathogenesis in Chinese MPN patients. MPL W515L mutation and JAK2 exon 12 mutations can also be found in JAK2 V617F negative MPN patients.
Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009–31 January 2010
Authors:   Molecular Ecology Resources Primer Development Consortium, ANDERSON CYNTHIA M. , APARICIO GALLEGO J. , ATANGANA ALAIN R. , BEAULIEU JEAN , BRUFORD M.W. , CAIN FORREST , CAMPOS T. , CARIANI A. , CARVALHO M.A. , CHEN NAN , CHEN P.P. , CLAMENS A.‐L. , CLARK ANN M. , COEUR D’ACIER A. , CONNOLLY PAUL , CORDERO‐RIVERA ADOLFO , COUGHLAN JAMES P. , CROSS THOMAS S. , DAVID BRUNO , DE BRUYN COLIN , DE MEYER M. , DE RIDDER CHANTAL , DELATTE H. , DETTORI M.T. , DOWNER S.J. , DUBREUIL CHRISTINE , EVANS K.J. , FAN BIN , FERRARA G. , GAGNÉ ANDRÉ , GAILLARD MARIA , GIGLIARELLI L. , GIOVINAZZI J. , GOMEZ D.R. , GRÜNWALD N.J. , HANSSON BENGT , HUOTARI T. , JANK L. , JOUSSELIN E. , JUNGMANN L. , KACZMAREK M.E. , KHASA DAMASE P. , KNEEBONE JEFF , KORPELAINEN H. , KOSTAMO K. , LANFALONI L. , LIN HAORAN , LIU XIAOCHUN , LUCENTINI L. , MAES G.E. , MAHAFFEE W.F. , MENG ZINING , MICALI S. , MILANO I. , MOK H.F. , MORIN L. , NEILL T.M. , NEWTON CRAIG H. , GIGI OSTROW D. , PALOMBA A. , PANARA F. , PULETTI M.E. , QUARTA R. , QUILICI S. , RAMOS A.K.B. , RIGAUD THIERRY , RISTERUCCI A.M. , SALOMON MATTHEW P. , SÁNCHEZ‐GUILLÉN ROSA A. , SARVER SHANE K. , SEQUEIRA A.S. , SFORÇA D.A. , SIMIAND C. , SMITH BRIAN , SOUSA A.C.B. , SOUZA A.P. , STEPIEN C.C. , STUCKERT A.J. , SULIKOWSKI JAMES , TAYEH A. , TINTI F. , TSANG PAUL C.W. , VAN HOUDT J.K.J. , VENDRAMIN E. , VERDE I. , VIRGILIO M. , WANG HUAN L. , WANG LE , WATTIER RÉMI A. , WELLENREUTHER MAREN , XIE CONG X. , ZANE L. , ZHANG XIU J. , ZHANG YONG , ZHUANG ZHIMENG , ZUCCHI M.I. 
Published: March 2010

AbstractThis article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross‐tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.
A new environment for aerobic anoxygenic phototrophic bacteria: biological soil crusts
Authors: Csotonyi Julius T. , Swiderski Jolantha , Stackebrandt Erko , Yurkov Vladimir 
Published: March 2010

SummaryPhototrophic microorganisms are critical to the carbon cycling and productivity of biological soil crusts, which enhance water content, nutrient relations and mechanical stability of arid soils. Only oxygen‐producing phototrophs, including cyanobacteria and algae, are known from soil crusts, but Earth's second major branch of photosynthetic organisms, the evolutionarily earlier anoxygenic phototrophs, is unreported. We announce the discovery of aerobic anoxygenic phototrophs in three Canadian soil crust communities. We found in a culture‐based study that they comprised 0.1–5.9% of the cultivable bacterial community in moss‐, lichen‐ and cyanobacteria‐dominated crust from sand dunes and sandy soils. Comparable in density to aerobic phototrophs in other habitats, the bacteriochlorophyll a‐possessing pink and orange isolates were related to species of Methylobacterium (99.0–99.5%), Belnapia (97.4–98.8%), Muricoccus (94.4%) and Sphingomonas (96.6–98.5%), based on 16S rRNA gene sequences. Our results demonstrate that proteobacterial anoxygenic phototrophs may be found in dry soil environments, implying desiccation resistance as yet unreported for this group. By utilizing sunlight for part of their energy needs, aerobic phototrophs can accelerate organic carbon cycling in nutrient‐poor arid soils. Their effects will be especially important as global climate change enhances soil erosion and consequent nutrient loss.
Enhanced biodegradation of petroleum hydrocarbons in the mycorrhizosphere of sub‐boreal forest soils
Authors: Robertson Susan J. , Kennedy Nabla M. , Massicotte Hugues B. , Rutherford P. Michael 
Published: March 2010

SummaryPetroleum hydrocarbon (PHC) contamination is becoming more common in boreal forest soils. However, linkages between PHC biodegradation and microbial community dynamics in the mycorrhizosphere of boreal forest soils are poorly understood. Seedlings (lodgepole pine, paper birch, lingonberry) were established in reconstructed soil systems, consisting of an organic layer (mor humus, coarse woody debris, or previously oil‐contaminated mor humus) overlying mineral (Ae, Bf) horizons. Light crude oil was applied to the soil surface after 4 months; systems were destructively sampled at 1 and 16 weeks following treatment. Soil concentrations of four PHC fractions were determined using acetone–hexane extraction followed by gas chromatography – flame ionization detection analysis. Genotypic profiles of root‐associated bacterial communities were generated using length heterogeneity‐PCR of 16S rDNA. Most plant–soil treatments showed significant loss in the smaller fraction PHCs indicating an inherent capacity for biodegradation. Concentrations of total PHCs declined significantly only in planted (pine‐woody debris and birch‐humus) systems (averaging 59% and 82% loss between 1 and 16 weeks respectively), reinforcing the importance of the mycorrhizosphere for enhancing microbial catabolism. Bacterial community structure was correlated more with mycorrhizosphere type and complexity than with PHC contamination. However, results suggest that communities in PHC‐contaminated and pristine soils may become distinct over time.
Producing Spaces for Academic Discourse: The Impact of Research Assessment Exercises and Journal Quality Rankings
Authors: Northcott Deryl , Linacre Simon 
Published: March 2010

This study examines the impact of national research assessment exercises (NRAEs) and associated journal quality rankings on the development, scope and sustainability of the academic journals in which accounting research is disseminated. The reported exploratory study focused on the United Kingdom (UK), Australia and New Zealand as three countries in which NRAEs are well developed or imminent. Data were collected via a survey of authors, interviews with journal editors, and feedback from publishers responsible for producing academic accounting journals. The findings suggest that, despite cynicism around the reliability of published journal quality rankings, the entrenchment of NRAE ‘rules’ and journal quality perceptions has changed authors’ submission choices and left lower ranked journals struggling with a diminished quantity and quality of submissions. A clear perception is that NRAEs have done little to improve the overall quality of the accounting literature, but are impeding the diversity, originality and practical relevance of accounting research. Although strategies are suggested for meeting these challenges, they require strategic partnerships with publishers to enhance the profile and distribution of emerging journals, and depend on the willingness of accounting researchers to form supportive communities around journals that facilitate their research interests. The alternative may be a withering of the spaces for academic discourse, a stifling of innovation and a further entrenchment of current perceptions of what counts as ‘quality’ research.
Homozygous Triplicate Mutations in Three 16S rRNA Genes Responsible for High-Level Aminoglycoside Resistance inNocardia farcinicaClinical Isolates from a Canada-Wide Bovine Mastitis Epizootic
Authors: Kogure Takahisa , Shimada Reona , Ishikawa Jun , Yazawa Katsukiyo , Brown June M. , Mikami Yuzuru , Gonoi Tohru 
Published: March 2010

ABSTRACTNocardia farcinicastrains showing high-level resistance to amikacin were isolated from clinical cases in a Canada-wide bovine mastitis epizootic. Shotgun cloning of the resistance genes in the amikacin-resistant mastitis isolateN. farcinicaIFM 10580 (W6220 [Centers for Disease Control and Prevention]) using a multicopy vector system revealed that the 16S rRNA gene with an A-to-G single-point mutation at position 1408 (inEscherichia colinumbering) conferred “moderate” cross-resistance to amikacin and other aminoglycosides to an originally susceptibleN. farcinicastrain IFM 10152. Subsequent DNA sequence analyses revealed that, in contrast to the susceptible strain, all three chromosomal 16S rRNA genes of IFM 10580, the epizootic clinical strain, contained the same A1408G point mutations. Mutant colonies showing high-level aminoglycoside resistance were obtained when the susceptible strainN. farcinicaIFM 10152 was transformed with a multicopy plasmid carrying the A1408G mutant 16S rRNA gene and was cultured in the presence of aminoglycosides for 3 to 5 days. Of these transformants, at least two of the three chromosomal 16S rRNA genes contained A1408G mutations. A triple mutant was easily obtained from a strain carrying the two chromosomal A1408G mutant genes and one wild-type gene, even in the absence of the plasmid. The triple mutant showed the highest level of resistance to aminoglycosides, even in the absence of the plasmid carrying the mutant 16S rRNA gene. These results suggest that the homozygous mutations in the three 16S rRNA genes are responsible for the high-level aminoglycoside resistance found inN. farcinicaisolates of the bovine mastitis epizootic.
Novel Mechanism of Glycopeptide Resistance in the A40926 Producer
Nonomuraea
sp. ATCC 39727
Authors: Marcone Giorgia Letizia , Beltrametti Fabrizio , Binda Elisa , Carrano Lucia , Foulston Lucy , Hesketh Andrew , Bibb Mervyn , Marinelli Flavia 
Published: March 2010

ABSTRACT

In glycopeptide-resistant enterococci and staphylococci, high-level resistance is achieved by replacing the C-terminal
d
-alanyl-
d
-alanine of lipid II with
d
-alanyl-
d
-lactate, thus reducing glycopeptide affinity for cell wall targets. Reorganization of the cell wall in these organisms is directed by the
vanHAX
gene cluster. Similar self-resistance mechanisms have been reported for glycopeptide-producing actinomycetes. We investigated glycopeptide resistance in
Nonomuraea
sp. ATCC 39727, the producer of the glycopeptide A40926, which is the precursor of the semisynthetic antibiotic dalbavancin, which is currently in phase III clinical trials. The MIC of
Nonomuraea
sp. ATCC 39727 toward A40926 during vegetative growth was 4 μg/ml, but this increased to ca. 20 μg/ml during A40926 production.
vanHAX
gene clusters were not detected in
Nonomuraea
sp. ATCC 39727 by Southern hybridization or by PCR with degenerate primers. However, the
dbv
gene cluster for A40926 production contains a gene,
vanY
(ORF7), potentially encoding an enzyme capable of removing the terminal
d
-Ala residue of pentapeptide peptidoglycan precursors. Analysis of UDP-linked peptidoglycan precursors in
Nonomuraea
sp. ATCC 39727 revealed the predominant presence of the tetrapeptide UDP-MurNAc-
l
-Ala-
d
-Glu-
meso
-Dap-
d
-Ala and only traces of the pentapeptide UDP-MurNAc-
l
-Ala-
d
-Glu-
meso
-Dap-
d
-Ala-
d
-Ala. This suggested a novel mechanism of glycopeptide resistance in
Nonomuraea
sp. ATCC 39727 that was based on the
d
,
d
-carboxypeptidase activity of
vanY
. Consistent with this, a
vanY
-null mutant of
Nonomuraea
sp. ATCC 39727 demonstrated a reduced level of glycopeptide resistance, without affecting A40926 productivity. Heterologous expression of
vanY
in a sensitive
Streptomyces
species,
Streptomyces venezuelae
, resulted in higher levels of glycopeptide resistance.