bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories
Authors: Massonnet Catherine , Vile Denis , Fabre Juliette , Hannah Matthew A. , Caldana Camila , Lisec Jan , Beemster Gerrit T.S. , Meyer Rhonda C. , Messerli Gaëlle , Gronlund Jesper T. , Perkovic Josip , Wigmore Emma , May Sean , Bevan Michael W. , Meyer Christian , Rubio-Díaz Silvia , Weigel Detlef , Micol José Luis , Buchanan-Wollaston Vicky , Fiorani Fabio , Walsh Sean , Rinn Bernd , Gruissem Wilhelm , Hilson Pierre , Hennig Lars , Willmitzer Lothar , Granier Christine 
Published: March 2010

AbstractA major goal of the life sciences is to understand how molecular processes control phenotypes. Because understanding biological systems relies on the work of multiple laboratories, biologists implicitly assume that organisms with the same genotype will display similar phenotypes when grown in comparable conditions. We investigated to what extent this holds true for leaf growth variables and metabolite and transcriptome profiles of three Arabidopsis (Arabidopsis thaliana) genotypes grown in 10 laboratories using a standardized and detailed protocol. A core group of four laboratories generated similar leaf growth phenotypes, demonstrating that standardization is possible. But some laboratories presented significant differences in some leaf growth variables, sometimes changing the genotype ranking. Metabolite profiles derived from the same leaf displayed a strong genotype × environment (laboratory) component. Genotypes could be separated on the basis of their metabolic signature, but only when the analysis was limited to samples derived from one laboratory. Transcriptome data revealed considerable plant-to-plant variation, but the standardization ensured that interlaboratory variation was not considerably larger than intralaboratory variation. The different impacts of the standardization on phenotypes and molecular profiles could result from differences of temporal scale between processes involved at these organizational levels. Our findings underscore the challenge of describing, monitoring, and precisely controlling environmental conditions but also demonstrate that dedicated efforts can result in reproducible data across multiple laboratories. Finally, our comparative analysis revealed that small variations in growing conditions (light quality principally) and handling of plants can account for significant differences in phenotypes and molecular profiles obtained in independent laboratories.
Concerted Modification of Flowering Time and Inflorescence Architecture by Ectopic Expression of TFL1-Like Genes in Maize
Authors: Danilevskaya Olga N. , Meng Xin , Ananiev Evgueni V. 
Published: March 2010

Abstract
TERMINAL FLOWER1 (TFL1)-like genes are highly conserved in plants and are thought to function in the maintenance of meristem indeterminacy. Recently, we described six maize (Zea mays) TFL1-related genes, named ZEA CENTRORADIALIS1 (ZCN1) to ZCN6. To gain insight into their functions, we generated transgenic maize plants overexpressing their respective cDNAs driven by a constitutive promoter. Overall, ectopic expression of the maize TFL1-like genes produced similar phenotypes, including delayed flowering and altered inflorescence architecture. We observed an apparent relationship between the magnitude of the transgenic phenotypes and the degree of homology between the ZCN proteins. ZCN2, -4, and -5 form a monophylogenetic clade, and their overexpression produced the strongest phenotypes. Along with very late flowering, these transgenic plants produced a “bushy” tassel with increased lateral branching and spikelet density compared with nontransgenic siblings. On the other hand, ZCN1, -3, and -6 produced milder effects. Among them, ZCN1 showed moderate effects on flowering time and tassel morphology, whereas ZCN3 and ZCN6 did not change flowering time but still showed effects on tassel morphology. In situ hybridizations of tissue from nontransgenic plants revealed that the expression of all ZCN genes was associated with vascular bundles, but each gene had a specific spatial and temporal pattern. Expression of four ZCN genes localized to the protoxylem, whereas ZCN5 was expressed in the protophloem. Collectively, our findings suggest that ectopic expression of the TFL1-like genes in maize modifies flowering time and inflorescence architecture through maintenance of the indeterminacy of the vegetative and inflorescence meristems.
Studies in Glycoproteins
Authors: BLIX GUNNAR 
Published: March 2010

Summary.A short review is given of the results of recent investigations on the chemistry of the glycoproteins and especially of the present state of the question concerning the relations between carbohydrate and protein in these substances.Hyalomucoid, synovial mucin and submaxillary mucin were investigated with the aid of electrophoresis. In approximately neutral solutions the hyalomucoid and the synovial mucin proved each to contain two electrophoretically well‐defined components. In both cases the faster migrating component was found to consist of a pure polysaccharide acid (hyaluronic acid). The slower components were simple proteins. In native synovial fluid and native vitreous body fluid the hyaluronic acid in all probability is in no way combined with protein but exists solely in the form of salts of the inorganic bases present. The glycoproteins precipitated from neutral synovial fluid or vitreous body fluid on addition of acetic acid are to be regarded as purely artificial products.Neutral solutions of submaxillary mucin were, on electrophoresis, found to contain two distinct components, both proteins. The main component, which was the faster migrating one, amounted to about 90 % of the whole and was a glycoprotein containing 27 % carbohydrate. The other component probably ought to be regarded as a contaminant.Pure water extracts from cartilage contain chondroitin sulphuric acid exclusively in the free form. This confirms the old opinion of Mörner that the chondroitin sulphuric acid in the cartilage is partly present as alkali salt.A chemical classification of the glycoproteins is suggested.
Saulfapyridine in Secretin Stimulated Pancreatic Juice and Bile of Cats
Authors: TAYLOR A. , ÅGREN G. 
Published: March 2010

Summary.The combined treatment of cats with sulfapyridine and secretin is described. In conformance with other investigations, in which secretin was not used, the concentration of sulfapyridine in pancreatic juice was found to be just lower than that of blood, but an extremely high concentration of the drug was found in the bile. The drug is not diluted by the increased flow of juice either from pancreas or liver and tends to be independent of rate of flow. Blood concentration of sulfapyridine is more important. While there was no change in the percentage of free drug excreted in the pancreatic juice, 30 % of the free drug had been bound when excreted in the bile, indicating acetylation by the liver.
Meta‐analysis: proton pump inhibitor use and the risk of community‐acquired pneumonia
Authors: JOHNSTONE J. , NERENBERG K. , LOEB M. 
Published: March 2010

Aliment Pharmacol Ther 31, 1165–1177SummaryBackground  Observational studies examining the association between proton pump inhibitor (PPI) use and risk of community‐acquired pneumonia are conflicting.Aim  To assess systematically the association between risk of community‐acquired pneumonia and PPI use in adults.Methods  We searched MEDLINE, EMBASE and CINAHL databases between 1988 and January 2010. Two reviewers independently selected studies based on eligibility criteria and extracted data. Included studies evaluated adults (≥18 years) who took PPIs as an out‐patient. The primary outcome was community‐acquired pneumonia. Only observational studies with a comparison arm were included.Results  Over 2600 citations were reviewed. Six studies were included. All were nested case‐control studies. Meta‐analysis found an increased risk of community‐acquired pneumonia associated with PPI use [OR 1.36 (95% CI 1.12–1.65)]; significant heterogeneity remained (I2 92%, P < 0.001). In exploratory subgroup analysis, short duration of use was associated with an increased odds of community‐acquired pneumonia [OR 1.92 (95% CI 1.40–2.63), I2 75%, P = 0.003], whereas chronic use was not [OR 1.11 (95% CI 0.90–1.38), I2 91%, P < 0.001], a significant interaction (P < 0.005).Conclusions  Heterogeneity precluded interpretation of the summary statistic. Exploratory analysis revealed that duration of PPI use may impact the risk of community‐acquired pneumonia, a finding that should be explored in future studies.
Single nucleotide polymorphism‐arrays provide new insights in the pathogenesis of post‐transplant diffuse large B‐cell lymphoma
Authors: Rinaldi Andrea , Capello Daniela , Scandurra Marta , Greiner Timothy C. , Chan Wing C. , Bhagat Govind , Rossi Davide , Morra Enrica , Paulli Marco , Rambaldi Alessandro , Rancoita Paola M. V. , Inghirami Giorgio , Ponzoni Maurilio , Moreno Santiago M. , Piris Miguel A. , Mian Michael , Chigrinova Ekaterina , Zucca Emanuele , Favera Riccardo D. , Gaidano Gianluca , Kwee Ivo , Bertoni Francesco 
Published: March 2010

SummaryPost‐transplant lymphoproliferative disorders (PTLD) are complications of solid organ transplantation associated with severe morbidity and mortality. Diffuse large B‐cell lymphoma (DLBCL) represents the most common form of monomorphic PTLD. We studied 44 cases of post‐transplant DLBCL (PT‐DLBCL) with high‐density genome wide single nucleotide polymorphism‐based arrays, and compared them with 105 cases of immunocompetent DLBCL (IC‐DLBCL) and 28 cases of Human Immunodeficiency Virus‐associated DLBCL (HIV‐DLBCL). PT‐DLBCL showed a genomic profile with specific features, although their genomic complexity was overall similar to that observed in IC‐ and HIV‐DLBCL. Among the loci more frequently deleted in PT‐DLBCL there were small interstitial deletions targeting known fragile sites, such as FRA1B, FRA2E and FRA3B. Deletions at 2p16.1 (FRA2E) were the most common lesions in PT‐DLBCL, occurring at a frequency that was significantly higher than in IC‐DLBCL. Genetic lesions that characterized post‐germinal center IC‐DLBCL were under‐represented in our series of PT‐DLBCL. Two other differences between IC‐DLBCL and PT‐DLBCL were the lack of del(13q14.3) (MIR15/MIR16) and of copy neutral LOH affecting 6p [major histocompatibility complex (MHC) locus] in the latter group. In conclusion, PT‐DLBCL presented unique features when compared with IC‐DLBCL. Changes in PT‐DLBCL were partially different to those in HIV‐DLBCL, suggesting different pathogenetic mechanisms in the two conditions linked to immunodeficiency.
Active survival in the lives of unaccompanied minors: coping strategies, resilience, and the relevance of religion
Authors: Ní Raghallaigh Muireann , Gilligan Robbie 
Published: March 2010

ABSTRACTAsylum‐seeking unaccompanied minors contend with numerous challenges as they adjust to living in a new country. Although increasing attention has been paid to their capacity for resilience, little research has been done on the exact manner in which they cope. This paper describes some of the insights gleaned from a qualitative study undertaken with unaccompanied minors living in Ireland. Six different coping strategies are identified, namely: (1) Maintaining continuity in a changed context, (2) Adjusting by learning and changing, (3) Adopting a positive outlook, (4) Suppressing emotions and seeking distraction, (5) Acting independently, and (6) Distrusting. These are described in turn. Particular attention is paid to the role of religion in relation to the participants' coping strategies.
Transforming growth factor‐β stimulates the expression of eotaxin/CC chemokine ligand 11 and its promoter activity through binding site for nuclear factor‐κB in airway smooth muscle cells
Authors: Matsukura S. , Odaka M. , Kurokawa M. , Kuga H. , Homma T. , Takeuchi H. , Notomi K. , Kokubu F. , Kawaguchi M. , Schleimer R. P. , Johnson M. W. , Adachi M. 
Published: March 2010

SummaryBackground
Chemokines ligands of CCR3 including eotaxin/CC chemokine ligand 11 (CCL11) may contribute to the pathogenesis of asthma. These chemokines and a growth factor (TGF‐β) may be involved in the process of airway remodelling.Objective
We analysed the effects of TGF‐β on the expression of CCR3 ligands in human airway smooth muscle (HASM) cells and investigated the mechanisms.Methods
HASM cells were cultured and treated with TGF‐β and Th2 cytokines IL‐4 or IL‐13. Expression of mRNA was analysed by real‐time PCR. Secretion of CCL11 into the culture medium was analysed by ELISA. Transcriptional regulation of CCL11 was analysed by luciferase assay using CCL11 promoter–luciferase reporter plasmids.Results
IL‐4 or IL‐13 significantly up‐regulated the expression of mRNAs for CCL11 and CCL26. TGF‐β alone did not increase the expression of chemokine mRNAs, but enhanced the induction of only CCL11 by IL‐4 or IL‐13 among CCR3 ligands. Activity of the CCL11 promoter was stimulated by IL‐4, and this activity was enhanced by TGF‐β. Activation by IL‐4 or IL‐4 plus TGF‐β was lost by mutation of the binding site for signal transducers and activators of transcription‐6 (STAT6) in the promoter. Cooperative activation by IL‐4 and TGF‐β was inhibited by mutation of the binding site for nuclear factor‐κB (NF‐κB) in the promoter. Pretreatment with an inhibitor of NF‐κB and glucocorticoid fluticasone propionate significantly inhibited the expression of CCL11 mRNA induced by IL‐4 plus TGF‐β, indicating the importance of NF‐κB in the cooperative activation of CCL11 transcription by TGF‐β and IL‐4.Conclusion
These results indicate that Th2 cytokines and TGF‐β may contribute to the pathogenesis of asthma by stimulating expression of CCL11. The transcription factors STAT6 and NF‐κB may play pivotal roles in this process. Cite this as: S. Matsukura, M. Odaka, M. Kurokawa, H. Kuga, T. Homma, H. Takeuchi, K. Notomi, F. Kokubu, M. Kawaguchi, R. P. Schleimer, M. W. Johnson and M. Adachi, Clinical & Experimental Allergy, 2010 (40) 763–771.
Hypertrophic cardiomyopathy: from genetics to treatment
Authors: Marian Ali J. 
Published: March 2010

Eur J Clin Invest 2010; 40 (4): 360–369AbstractBackground  Hypertrophic cardiomyopathy (HCM) is the prototypic form of pathological cardiac hypertrophy. HCM is an important cause of sudden cardiac death in the young and a major cause of morbidity in the elderly.Design  We discuss the clinical implications of recent advances in the molecular genetics of HCM.Results  The current diagnosis of HCM is neither adequately sensitive nor specific. Partial elucidation of the molecular genetic basis of HCM has raised interest in genetic‐based diagnosis and management. Over a dozen causal genes have been identified. MYH7 and MYBPC3 mutations account for about 50% of cases. The remaining known causal genes are uncommon and some are rare. Advances in DNA sequencing techniques have made genetic screening practical. The difficulty, particularly in the sporadic cases and in small families, is to discern the causal from the non‐causal variants. Overall, the causal mutations alone have limited implications in risk stratification and prognostication, as the clinical phenotype arises from complex and often non‐linear interactions between various determinants.Conclusions  The clinical phenotype of ‘HCM’ results from mutations in sarcomeric proteins and subsequent activation of multiple cellular constituents including signal transducers. We advocate that HCM, despite its current recognition and management as a single disease entity, involves multiple partially independent mechanisms, despite similarity in the ensuing phenotype. To treat HCM effectively, it is necessary to delineate the underlying fundamental mechanisms that govern the pathogenesis of the phenotype and apply these principles to the treatment of each subset of clinically recognized HCM.
Using Principal Components and Factor Analysis in Animal Behaviour Research: Caveats and Guidelines
Authors: Budaev Sergey V. 
Published: March 2010

AbstractPrincipal component (PCA) and factor analysis (FA) are widely used in animal behaviour research. However, many authors automatically follow questionable practices implemented by default in general‐purpose statistical software. Worse still, the results of such analyses in research reports typically omit many crucial details which may hamper their evaluation. This article provides simple non‐technical guidelines for PCA and FA. A standard for reporting the results of these analyses is suggested. Studies using PCA and FA must report: (1) whether the correlation or covariance matrix was used; (2) sample size, preferably as a footnote to the table of factor loadings; (3) indices of sampling adequacy; (4) how the number of factors was assessed; (5) communalities when sample size is small; (6) details of factor rotation; (7) if factor scores are computed, present determinacy indices; (8) preferably they should publish the original correlation matrix.
Interleukin‐1β and ‐10 polymorphisms influence erosive reflux esophagitis and gastritis in Taiwanese patients
Authors: Cheng Hsin‐Hung , Chang Chi‐Sen , Wang Hung‐Jung , Wang Wen‐Ching 
Published: March 2010

AbstractBackground and Aims:  Helicobacter pylori (H. pylori) infection induces cytokine production and is associated with gastrointestinal diseases. This study examined the relationship of gene polymorphisms, including interleukin (IL)‐1β, ‐10, ‐8, and tumor necrosis factor‐α (TNF‐α), H. pylori infection, and susceptibility to gastrointestinal disorders in Taiwanese patients.Methods:  IL‐1β−511/−31/+3953, ‐10−1082/−819/−592, ‐8−251, and TNF‐α−308 polymorphisms were assessed in 628 gastrointestinal disease patients, and 176 healthy controls were analyzed using the polymerase chain reaction−restriction fragment length polymorphism method.Results:  IL‐1β−511 T/T and −31 C/C genotypes, and IL‐1β−511 T and −31 C alleles were associated with an increased risk of reflux esophagitis (P = 0.034, odds ratio [OR] = 1.384, 95% confidence interval [CI]: 1.023–1.871; P = 0.031, OR = 1.388, 95% CI: 1.028–1.873; P = 0.044, OR = 1.342, 95% CI: 1.008–1.786; and P = 0.040, OR = 1.349, 95% CI: 1.014–1.796, respectively). No relationship was found between H. pylori infection and the risk of reflux esophagitis. IL‐10−819 C/T and ‐10−592 A/C genotypes and IL‐10−1082/−819/−592 ATA/ACC and ATA/GCC haplotypes were associated with an increased risk of gastritis (P = 0.021, OR = 1.721, 95% CI: 1.084–2.733; P = 0.016, OR = 1.766, 95% CI: 1.112–2.805; P = 0.039, OR = 1.662, 95% CI: 1.024–2.697; and P = 0.035, OR = 1.600, 95% CI: 1.024–2.499, respectively).Conclusion:  Among Taiwanese patients, IL‐1β and ‐10 polymorphisms were associated with an increased risk of erosive reflux esophagitis and gastritis, respectively.
Is irritable bowel syndrome associated with chronic hepatitis C?
Authors: Fouad Yasser M , Makhlouf Madeha M , Khalaf Hanna , Mostafa Zainab , Raheem Ehab Abdel , Meneasi Wesam 
Published: March 2010

AbstractBackground and Aim:  Hepatitis C virus (HCV) is a common chronic infection that is widely associated with symptoms of fatigue and abdominal pain. The aim of the present study was to determine the prevalence of irritable bowel syndrome (IBS) among patients with hepatitis C compared to controls.Methods:  This study included 258 patients with chronic hepatitis C, 36 patients with chronic hepatitis B, and 160 healthy volunteers. Clinical and laboratory data were recorded for every patient. All patients and controls were administered a questionnaire of IBS according to Rome III criteria.Results:  The percentage of patients with IBS was significantly higher in patients with chronic HCV (66%, 170/258) than chronic hepatitis B virus (HBV; 22%, 8/36) and normal controls (18%, 28/160 patients; P < 0.001 and P < 0.001, respectively). There was no significant difference between chronic HBV and normal controls. In chronic HCV patients, IBS with constipation was the predominant type (51%, 86/170) followed by mixed IBS (73/170, 43%). In patients with chronic HCV, the percentage of females with IBS (91%) was significantly higher than those without IBS (9%; P < 0.001), and the percentage of patients with a high fibrosis score (F2–3) was significantly higher in patients with IBS (45%) than in patients without IBS (6%; P < 0.001). There was no difference regarding age, alanine aminotransferase level, or HCV viremia. A multivariate regression analysis revealed a significant association between sex, fibrosis score, and IBS.Conclusion:  IBS is more prevalent in patients with chronic hepatitis C. Female patients with chronic HCV and those with higher fibrosis scores are more likely to have IBS.
Phenotypic and metabolic profiling of colony morphology variants evolved from Pseudomonas fluorescens biofilms
Authors: Workentine Matthew L. , Harrison Joe J. , Weljie Aalim M. , Tran Vy A. , Stenroos Pernilla U. , Tremaroli Valentina , Vogel Hans J. , Ceri Howard , Turner Raymond J. 
Published: March 2010

SummaryColony morphology variants isolated from natural and laboratory‐grown biofilms represent subpopulations of biofilm cells that may be important for multiple aspects of the sessile lifestyle, from surface colonization to stress resistance. There are many genetic and environmental factors that determine the frequency at which colony morphology variants are recovered from biofilms. One of these factors involves an increased selection for variants in biofilms of Pseudomonas species bearing inactivating mutations in the global activator of cyanide biosynthesis/regulator of secondary metabolism (gac/rsm) signal transduction pathway. Here we characterize two distinct colony morphology variants isolated from biofilms of Pseudomonas fluorescens missing the gacS sensor kinase. These variants produced more biofilm cell mass, and in one case, this was likely due to overproduction of the exopolysaccharide cellulose. Nuclear magnetic resonance (NMR) metabolomics revealed distinct metabolic changes for each of the two phenotypic variants, and these changes involved amino acids and metabolites produced through glutathione biochemistry. Some of these metabolites are hypothesized to play a role in redox and metal homeostasis, and corresponding to this, we show that biofilm populations grown from each of these variants had a different ability to survive when exposed to toxic doses of metal ions. These data suggest that colony morphology variants that evolve during growth of P. fluorescens as a biofilm may have distinct metabolic capacities that contribute to their individual abilities to withstand environmental stress.