bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization ofMelioribacter roseusgen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the classIgnavibacteria, and a proposal of a novel bacterial phylumIgnavibacteriae
Authors: Podosokorskaya Olga A. , Kadnikov Vitaly V. , Gavrilov Sergey N. , Mardanov Andrey V. , Merkel Alexander Y. , Karnachuk Olga V. , Ravin Nikolay V. , Bonch‐Osmolovskaya Elizaveta A. , Kublanov Ilya V. 
Published: December 2012

SummaryA novel moderately thermophilic, facultatively anaerobic chemoorganotrophic bacterium strainP3M‐2Twas isolated from a microbial mat developing on the wooden surface of a chute under the flow of hot water (46°C) coming out of a 2775‐m‐deep oil exploration well (Tomsk region,Russia). StrainP3M‐2Tis a moderate thermophile and facultative anaerobe growing on mono‐, di‐ or polysaccharides by aerobic respiration, fermentation or by reducing diverse electron acceptors [nitrite,Fe(III),As(V)]. Its closest cultivated relative (90.8%rRNAgene sequence identity) isIgnavibacterium album, the only chemoorganotrophic member of the phylumChlorobi. New genus and speciesMelioribacter roseusare proposed for isolateP3M‐2T. Together withI. album, the new organism represents the classIgnavibacteriaassigned to the phylumChlorobi. The revealed group includes a variety of uncultured environmental clones, the16S rRNAgene sequences of some of which have been previously attributed to the candidate divisionZB1. Phylogenetic analysis ofM. roseusandI. albumbased on their23S rRNAandRecAsequences confirmed that these two organisms could represent an even deeper, phylum‐level lineage. Hence, we propose a new phylumIgnavibacteriaewithin theBacteroidetes–Chlorobigroup with a sole classIgnavibacteria, two familiesIgnavibacteriaceaeandMelioribacteraceaeand two speciesI. albumandM. roseus. This proposal correlates with chemotaxonomic data and phenotypic differences of both organisms from other cultured representatives ofChlorobi. The most essential differences, supported by the analyses of complete genomes of both organisms, are motility, facultatively anaerobic and obligately organotrophic mode of life, the absence of chlorosomes and the apparent inability to grow phototrophically.
Direct sequencing of haplotypes from diploid individuals through a modified emulsion PCR‐based single‐molecule sequencing approach
Authors: Metzger Brian Patrick Hansen , Gelembiuk Gregory William , Lee Carol Eunmi 
Published: December 2012

AbstractWhile standard DNA‐sequencing approaches readily yield genotypic sequence data, haplotype information is often of greater utility for population genetic analyses. However, obtaining individual haplotype sequences can be costly and time‐consuming and sometimes requires statistical reconstruction approaches that are subject to bias and error. Advancements have recently been made in determining individual chromosomal sequences in large‐scale genomic studies, yet few options exist for obtaining this information from large numbers of highly polymorphic individuals in a cost‐effective manner. As a solution, we developed a simple PCR‐based method for obtaining sequence information from individual DNA strands using standard laboratory equipment. The method employs a water‐in‐oil emulsion to separate the PCR mixture into thousands of individual microreactors. PCR within these small vesicles results in amplification from only a single starting DNA template molecule and thus a single haplotype. We improved upon previous approaches by including SYBR Green I and a melted agarose solution in the PCR, allowing easy identification and separation of individually amplified DNA molecules. We demonstrate the use of this method on a highly polymorphic estuarine population of the copepod Eurytemora affinis for which current molecular and computational methods for haplotype determination have been inadequate.
SNP discovery using Paired‐End RAD‐tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae)
Authors: Vandepitte K. , Honnay O. , Mergeay J. , Breyne P. , Roldán‐Ruiz I. , De Meyer T. 
Published: December 2012

AbstractSingle nucleotide polymorphisms SNPs are rapidly replacing anonymous markers in population genomic studies, but their use in non model organisms is hampered by the scarcity of cost‐effective approaches to uncover genome‐wide variation in a comprehensive subset of individuals. The screening of one or only a few individuals induces ascertainment bias. To discover SNPs for a population genomic study of the Pyrenean rocket (Sisymbrium austriacum subsp. chrysanthum), we undertook a pooled RAD‐PE (Restriction site Associated DNA Paired‐End sequencing) approach. RAD tags were generated from the PstI‐digested pooled genomic DNA of 12 individuals sampled across the species distribution range and paired‐end sequenced using Illumina technology to produce ~24.5 Mb of sequences, covering ~7% of the specie's genome. Sequences were assembled into ~76 000 contigs with a mean length of 323 bp (N50 = 357 bp, sequencing depth = 24x). In all, >15 000 SNPs were called, of which 47% were annotated in putative genic regions based on homology with the Arabidopsis thaliana genome. Gene ontology (GO) slim categorization demonstrated that the identified SNPs covered extant genic variation well. The validation of 300 SNPs on a larger set of individuals using a KASPar assay underpinned the utility of pooled RAD‐PE as an inexpensive genome‐wide SNP discovery technique (success rate: 87%). In addition to SNPs, we discovered >600 putative SSR markers.
Executive Summary: Education Research in Emergency Medicine—Opportunities, Challenges, and Strategies for Success
Authors: LaMantia Joseph , Deiorio Nicole M. , Yarris Lalena M. 
Published: December 2012

AbstractThe 2012 Academic Emergency Medicine (AEM) consensus conference “Education Research In Emergency Medicine: Opportunities, Challenges, and Strategies for Success” convened a diverse group of stakeholders in medical education to target gaps in emergency medicine (EM) education research and identify priorities for future study. A total of 175 registrants collaborated in preparatory and conference‐day activities to explore subtopics in educational interventions, learner assessment, faculty development, and research funding and infrastructure. The conference was punctuated by didactic sessions led by key international medical education experts and ended with consensus formation in many domains. This issue of AEM presents the exciting results of this process.
Avoidable mortality in people with schizophrenia or bipolar disorder in England
Authors: Hoang U. , Goldacre M. J. , Stewart R. 
Published: December 2012

ObjectiveTo quantify the extent of ‘avoidable mortality’ in those with schizophrenia or bipolar disorder and to quantify the effect a reduction in these might have on the mortality gap associated with severe mental illness.MethodA cohort was studied of people aged <75 years, discharged from inpatient care with schizophrenia or bipolar disorder in 2006–2007, and followed up for 365 days. Standardised mortality ratios (SMRs) were calculated followed by hypothetical SMRs, estimating the residual mortality gap if ‘avoidable’ causes and suicide in the cohorts had occurred at the same level as those in the general population.ResultsAvoidable deaths comprised 60.2% and 59.2% of all deaths in the schizophrenia and bipolar disorder cohorts respectively. All‐cause SMRs were 4.23 (95% CI 3.85–4.60) and 2.60 (2.21–3.00) respectively. After discounting the excess attributable to avoidable causes and suicide, the SMRs fell to 2.38 (2.09–2.66) and 1.66 (1.35–1.98) respectively.ConclusionBringing mortality from avoidable causes and suicide down to general population levels would reduce the overall mortality excess in severe mental illness substantially, by about 50%, but would not eliminate it. Other underlying factors beyond those conventionally considered as ‘avoidable’ need further research.
An incidence study of diagnosed autism‐spectrum disorders among immigrants to the Netherlands
Authors: van der Ven E. , Termorshuizen F. , Laan W. , Breetvelt E. J. , van Os J. , Selten J. P. 
Published: December 2012

ObjectiveTo estimate the risk of developing autism‐spectrum disorder (ASD) in children born to immigrants as compared with children of Dutch‐born parents.MethodRetrospective, population‐based cohort study of all live births (n = 106 953) between 1998 and 2007 in a circumscribed geographical region in the Netherlands. Cohort members were linked to the Psychiatric Case Register to identify diagnosed cases.ResultsA total of 518 cases of ASD were identified, including 150 children with autism and 368 children with Asperger syndrome or Pervasive Developmental Disorder Not Otherwise Specified (PDD‐NOS). Children born to migrants from developing countries were at significantly lower risk of ASD [rate ratio (RR) = 0.6, 95% confidence interval (CI) 0.5–0.9] than children of Dutch‐born parents. Within the ASD group, the risk for the subgroup with Asperger syndrome and PDD‐NOS was reduced (RR = 0.4, 95% CI 0.3–0.6), whereas that for narrowly defined autism was non‐significantly increased (RR = 1.4, 95% CI 0.9–2.4). Migrant groups did not differ in age at diagnosis.ConclusionThe results echo Swedish findings indicating a reversal of risk gradient in children of parents from developing countries, specifically a decreased risk for high‐functioning and increased risk for low‐functioning autism.
No reduction of manual removal after misoprostol for retained placenta: a double‐blind, randomized trial
Authors: van Stralen Giel , Veenhof Marieke , Holleboom Cas , van Roosmalen Jos 
Published: December 2012

AbstractObjectiveTo test the effect of 800 μg of misoprostol orally on the prevention of manual removal of retained placenta.DesignMulticenter, double‐blinded, placebo‐controlled, randomized trial.SettingOne university and one non‐university teaching hospital in the Netherlands.Sample99 women with retained placenta (longer than 60 min after childbirth) in the absence of postpartum hemorrhage.MethodsEligible women were administered either 800 μg of misoprostol or placebo orally.Main outcome measuresNumber of manual removals of retained placenta and amount of blood loss.ResultsManual removal of retained placenta was performed in 50% of the women who received misoprostol and in 55% who received placebo (relative risk 0.91, 95% confidence interval 0.62–1.34). No difference in the amount of blood loss (970 vs. 1120 mL; p = 0.34) was observed between the two groups.ConclusionsAdministration of 800 μg of oral misoprostol, one hour after childbirth, does not seem to reduce the number of manual removals of retained placentas. The time elapsing results in the delivery of 50% of the retained placentas at the expense of an increased risk of postpartum hemorrhage.
Development and validation of 26‐item dysfunctional attitude scale
Authors: Ebrahimi Amrollah , Samouei Rahele , Mousavii Sayyed Ghafour , Bornamanesh Ali Reza 
Published: December 2012

AbstractIntroductionDysfunctionalAttitudeScale is one of the most common instruments used to assess cognitive vulnerability. This study aimed to develop and validate a short form ofDysfunctionalAttitudeScale appropriate for an Iranian clinical population.MethodsParticipants were 160 psychiatric patients from medical centers affiliated withIsfahanMedicalUniversity, as well as 160 non‐patients. Research instruments were clinical interviews based on theDiagnostic andStatisticalManual‐IV‐TR,DysfunctionalAttitudeScale andGeneralHeathQuestionnaire (GHQ‐28). Data was analyzed using multicorrelation calculations and factor analysis.ResultsBased on the results of factor analysis and item‐total correlation, 14 items were judged candidates for omission. Analysis of the 26‐itemDysfunctionalAttitudeScale (DAS‐26) revealed aCronbach's alpha of 0.92. Evidence for the concurrent criterion validity was obtained through calculating the correlation between theDysfunctional Attitude Scale and psychiatric diagnosis (r = 0.55),GHQ−28 (r = 0.56) and somatization, anxiety, social dysfunction, and depression subscales (0.45,0.53,0.48, and 0.57, respectively). Factor analysis deemed a four‐factor structure the best. The factors were labeled as success‐perfectionism, need for approval, need for satisfying others, and vulnerability‐performance evaluation.DiscussionThe results showed that the Iranian version of the Dysfunctional Attitude Scale (DAS‐26) bears satisfactory psychometric properties suggesting that this cognitive instrument is appropriate for use in an Iranian cultural context.
Correlation of domestic violence during pregnancy with plasma amino‐acid neurotransmitter, cortisol levels and catechol‐o‐methyltransferase Val(158)Met polymorphism in neonates
Authors: Zhang Yong , Zou Shaohong , Zhang Xianghui , Zhang Yalin 
Published: December 2012

AbstractIntroductionTo explore the correlation between domestic violence during pregnancy and glutamate (Glu), r‐aminobutyric acid (GABA), plasma cortisol levels and catechol‐o‐methyltransferase (COMT) gene polymorphism (rs4818) in neonates.MethodsUsing the Abuse Assessment Survey, 64 abused pregnant women (DV) and 117 non‐abused pregnant women (non‐DV) were screened for two study groups. Blood in neonatal umbilical vein was collected immediately after delivery. Plasma Glu, GABA, cortisol levels and rs4818 polymorphism in the genotypes and alleles of the two neonatal groups were compared.ResultsIn the DV group, 49 women (76.6%) experienced emotional abuse, 29 women (45.3%) experienced sexual abuse, 28 (43.8%) women experienced emotional abuse plus sexual abuse, and two women (3.1%) experienced emotional abuse plus physical abuse. We found that plasma Glu, GABA and cortisol levels were higher in DV neonates than in non‐DV neonates. Furthermore, we observed a significantly positive correlation between maternal emotional abuse, sexual abuse and plasma levels of Glu, GABA and cortisol in neonates. By genetic analysis we found a significant difference in rs4818SNP genotype and allele between the two neonatal groups. The ratios of CC genotype and C allele were higher in DV neonates than in non‐DV neonates, and the ratios of GG genotype and G allele were lower in DV neonates than in non‐DV neonates. One‐way ANOVA test showed that GABA level was lower in CC carriers than CG carriers.DiscussionDomestic violence during pregnancy might be associated with increased plasma levels of glutamate, GABA, cortisol and COMT gene polymorphism in neonates.
Identification and antibiotic susceptibility of bacterial isolates from dogs with otitis externa in Australia
Authors: Bugden DL 
Published: December 2012

ObjectiveTo identify and quantify the five most frequently isolated significant bacterial microorganisms, and their antibiotic susceptibility, from bacterial cultures of samples taken from the ears of dogs with otitis externa.MethodsBacterial culture and susceptibility testing data for ear swabs from dogs with presumed otitis externa were collated and evaluated.ResultsThe five most frequently isolated microorganisms were: Pseudomonas aeruginosa, Staphylococcus pseudintermedius, Proteus sp., beta‐haemolytic streptococci and Escherichia coli. Susceptibility to gentamicin was very high for most isolates, whereas for polymyxin B, high levels of resistance were seen. Beta‐haemolytic streptococci had high levels of resistance to all of the antibiotics tested.ConclusionsThis study provides veterinarians with Australian data to assist in cytological interpretation and initial empirical therapy of canine otitis externa.
Fragment size, vegetation structure and physical environment control grassland functioning: a test based on artificial neural networks
Authors: Herrera Lorena P. , Texeira M. , Paruelo J.M. 
Published: December 2012

AbstractQuestionsHow do fragment‐level characteristics affect remnant grassland functioning in a highly transformed landscape? Are artificial neural networks (ANNs) a better statistical tool to model variations in grassland functioning compared to linear regression models (LRMs)?LocationTandilia Range, Southern Pampa, Buenos Aires Province, Argentina.MethodsWe characterized the dynamics of the vegetation functioning in 60 remnant grasslands using enhanced vegetation index (EVI) data provided by MODIS/Terra images from July 2000 to June 2005. First, we performed a principal components analysis (PCA) on the fragment mean monthly values of EVI in order to obtain synthetic measures (i.e. the PCA axes) of grassland functioning. Grassland fragments were also characterized by size, vegetation structure (abundance of the tall‐tussock grass Paspalum quadrifarium) and physical environment (soil type – abundance of litholitic soils – elevation, aspect and slope). The relationship between grassland functioning and these explanatory variables was explored using linear regression models (LRMs) and artificial neural networks (ANNs).ResultsThe first and second PCA axes were related to the annual integral of EVI (EVI‐I) and EVI seasonality (EVI‐S), respectively; these explained jointly ca. 80% of total variability in mean EVI values. ANNs captured better than regression models the relationships among the proposed controls and the spatial variability of grassland functioning in Southern Pampa. Results showed that EVI‐I variability was related to all independent variables except aspect. While fragment size, litholitic soils and slope were negatively related to EVI‐I, the abundance of P. quadrifarium had a positive effect on the spectral index. Grasslands with high seasonality were large and had high slope and aspect, low abundance of P. quadrifarium and increased abundance of litholitic soils.ConclusionsOur results showed that grassland functioning in Southern Pampa, as estimated by EVI, depends on fragment size, vegetation structure and physical factors (soil type, aspect and slope). Paspalum quadrifarium may have an important functional role in this grassland system.
MiR‐383 is Downregulated in Medulloblastoma and Targets Peroxiredoxin 3 (PRDX3)
Authors: Li Kay Ka‐Wai , Pang Jesse Chung‐Sean , Lau Kin‐Mang , Zhou Liangfu , Mao Ying , Wang Yin , Poon Wai‐Sang , Ng Ho‐Keung 
Published: December 2012

AbstractAccumulating evidence suggests that microRNAs (miRNAs) are over‐ or under‐expressed in tumors, and abnormalities in miRNA expression may contribute to carcinogenesis. MiR‐383 was previously identified as one of the under‐expresssed miRNAs in medulloblastoma (MB) by miRNA expression profiling. Quantitative reverse transcription polymerase chain reaction (RT‐PCR)‐based miRNA assays showed an enrichment of miR‐383 in normal brain. Based on these data, we speculated that miR‐383 is important in MB pathogenesis. In this study, we demonstrated significant downregulation of miR‐383 in 23/29 (79%) MB samples and 7/7 (100%) MB cells lines. Ectopic expression of miR‐383 in MB cells led to suppression of cell growth, cell accumulation at sub‐G1 phase and alteration of apoptosis‐related proteins. By transcriptomic analysis and computational algorithms, we identified peroxiredoxin 3 (PRDX3) as a target gene of miR‐383. Luciferase reporter assay confirmed that miR‐383 negatively regulated PRDX3 by interaction between miR‐383 and complementary sequences in the 3′ UTR of PRDX3. MiR‐383 repressed PRDX3 at transcriptional and translational levels as revealed by quantitative RT‐PCR and Western blot analysis. Furthermore, depletion of PRDX3 by siRNAs resulted in similar effects as observed in miR‐383‐transfected cells. In conclusion, miR‐383 acts as a regulator controlling cell growth of MB, at least in part, through targeting PRDX3.
Does hypopituitarism recover when macroprolactinomas are treated with cabergoline?
Authors: Karavitaki Niki , Dobrescu Ruxandra , Byrne James V. , Grossman Ashley B. , Wass John A. H. 
Published: December 2012

SummaryObjectiveThe frequency and the degree of recovery of anterior pituitary hormone deficits in patients with macroprolactinoma responsive to cabergoline are not clear. Our aim was to evaluate pituitary function in these patients with particular reference to an assessment of the possible restoration of pituitary deficits.Subjects and MethodsThe records of all subjects prospectively presenting to our Department with macroprolactinomas treated with cabergoline over a 2‐year period were reviewed. Pituitary function was assessed at diagnosis and, if abnormal, for three consecutive years for the GH, FSH/LH and ACTH axes, and at 3 years for the TSH axis.ResultsTwelve patients were included. Severe GH deficiency was found in 83% at diagnosis and did not resolve in any patient at last assessment. Gonadotrophin deficiency was found in 90% at diagnosis and in 50% at last evaluation (showing reversal in 44% of deficient patients, all achieved within 1 year). ACTH deficiency was found in 17% at diagnosis and it did not reverse in any patient at last assessment. TSH deficiency was found in 36% at diagnosis and in 27% at last assessment (reversal in 25% of deficient patients).ConclusionsIn our study, in a group of patients with macroprolactinoma systematically assessed at intervals, pituitary dysfunction in response to cabergoline was found to be mostly irreversible, except for the gonadotroph axis which showed restoration in a subset of subjects following achievement of normoprolactinaemia. It would appear that the reversibility of pituitary axes may be less common than previously thought.
Functional characterization of nonmetastatic paraganglioma and pheochromocytoma by 18F‐FDOPA PET: focus on missed lesions
Authors: Gabriel Sophie , Blanchet Elise M. , Sebag Frédéric , Chen Clara C. , Fakhry Nicolas , Deveze Arnaud , Barlier Anne , Morange Isabelle , Pacak Karel , Taïeb David 
Published: December 2012

SummaryAims and methodsTo evaluate the clinical value of 18F‐fluorodihydroxyphenylalanine (18F‐FDOPA) PET in relation to tumour localization and the patient's genetic status in a large series of pheochromocytoma/paraganglioma (PHEO/PGL) patients and to discuss in detail false‐negative results.A retrospective study of PGL patients who were investigated with 18F‐FDOPA PET or PET/CT imaging in two academic endocrine tumour centres was conducted (La Timone University Hospital, Marseilles, France and National Institutes of Health (NIH), Bethesda, MD, USA).ResultsOne hundred sixteen patients (39·7% harbouring germline mutations in known disease susceptibility genes) were evaluated for a total of 195 PHEO/PGL foci. 18F‐FDOPA PET correctly detected 179 lesions (91·8%) in 107 patients (92·2%).Lesion‐based sensitivities for parasympathetic PGLs (head, neck, or anterior/middle thoracic ones), PHEOs, and extra‐adrenal sympathetic (abdominal or posterior thoracic) PGLs were 98·2% [96·5% for Timone and 100% for NIH], 93·9% [93·8 and 93·9%] and 70·3% [47·1 and 90%] respectively (P < 0·001).Sympathetic (adrenal and extra‐adrenal) SDHx‐related PGLs were at a higher risk for negative 18F‐FDOPA PET than non‐SDHx‐related PGLs (14/24 vs 0/62, respectively, P < 0·001). In contrast, the risk of negative 18F‐FDOPA PET was lower for parasympathetic PGLs regardless of the genetic background (1/90 in SDHx vs 1/19 in non‐SDHx tumours, P = 0·32).18F‐FDOPA PET failed to detect two head and neck PGLs (HNPGL), likely due to their small size, whereas most missed sympathetic PGL were larger and may have exhibited a specific 18F‐FDOPA‐negative imaging phenotype. 18F‐FDG PET detected all the missed sympathetic lesions.Conclusions18F‐FDOPA PET appears to be a very sensitive functional imaging tool for HNPGL regardless of the genetic status of the tumours. Patients with false‐negative tumours on 18F‐FDOPA PET should be tested for SDHx mutations.