bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of housekeeping genes for real-time PCR in atopic human bronchial epithelial cells
Authors: He J-Q. , Sandford A. J. , Wang I-M. , Stepaniants S. , Knight D. A. , Kicic A. , Stick S. M. , Paré P. D. 
Published: April 2008

The stability of housekeeping genes (HKGs) is critical when performing real-time quantitative PCR. To date, the stability of common HKGs has not been systematically compared in human airway epithelial cells (AEC) in normal and atopic subjects.Expression levels of 12 HKGs were measured in AECs from a cohort of 30 healthy atopic nonasthmatic or atopic asthmatic children. Gene expression stability was determined using three different Visual Basic for Applications applets (geNorm, NormFinder and BestKeeper).All 12 HKGs were expressed in AECs. However, the hypoxanthine ribosyltransferase and TATA-binding protein genes were excluded from further analysis due to low expression levels. The cyclophilin A gene was ranked the most stable by all three methods. The expression levels of the β-actin and glyceraldehyde-3-phosphate dehydrogenase genes were significantly different between the three groups of patients, with atopic asthmatics showing the highest expression levels for both genes.The results suggest that the cyclophilin A gene is the most suitable housekeeping gene analysed for expression studies utilising uncultured bronchial airway epithelial cells from healthy and asthmatic children, and highlight the importance of validating housekeeping genes for each experimental model.
Smoke exposure, airway symptoms and exhaled nitric oxide in infants: the Generation R study
Authors: Gabriele C. , Asgarali R. , Jaddoe V. W. , Hofman A. , Moll H. A. , de Jongste J. C. 
Published: April 2008

The effect of pre- and post-natal smoke exposure on exhaled nitric oxide fraction (FeNO) in infants was evaluated and the association between respiratory symptoms andFeNOin the first 2 months of life was investigated. The Generation R study is a population-based, prenatally recruited birth cohort.Exposures were assessed by means of questionnaires prospectively administered during pregnancy and after birth. Successful off-lineFeNOmeasurements during tidal breathing were obtained in 187 infants (median age 6.9 weeks). The association between possible determinants and logFeNOwas investigated with multiple linear regression analysis.Infants exposed pre- and post-natally to smoke showed lowerFeNOthan infants exposed only after birth (geometric mean difference (95% confidence interval) 1.5 (1.0–2.1) ppb) and never-exposed infants (1.4 (1.0–1.8) ppb).FeNOwas reduced in infants with severe upper respiratory symptoms compared with infants with nonsevere symptoms (1.6 (1.0–2.4) ppb). Infants with symptoms of the lower respiratory tract had lowerFeNOthan asymptomatic infants (1.2 (1.0–1.50) ppb).In conclusion, the nature of the association between smoke exposure and exhaled nitric oxide fraction is dependent on timing and intensity of exposure. The occurrence and the severity of respiratory symptoms in the first 2 months of life are associated with lower exhaled nitric oxide fraction.
Interleukin 13,CD14, pet and tobacco smoke influence atopy in three Dutch cohorts: the allergenic study
Authors: Bottema R. W. B. , Reijmerink N. E. , Kerkhof M. , Koppelman G. H. , Stelma F. F. , Gerritsen J. , Thijs C. , Brunekreef B. , van Schayck C. P. , Postma D. S. 
Published: April 2008

Studying gene–environment interactions may elucidate the complex origins of atopic diseases but requires large study populations. Pooling data from several cohort studies may help but may also obscure findings. Gene–environment interactions in atopy development were studied and the benefits of pooling data were evaluated.Haplotype-tagging polymorphisms in the genesinterleukin (IL)13andCD14were genotyped in 3,062 children from the following birth cohorts: the Prevention and Incidence of Asthma and Mite Allergy (PIAMA) study; the Prevention of Asthma in Children (PREVASC) study; and the Child, Parent, Health, Focus on Lifestyle and Predisposition (KOALA) study, and tested for association with total and specific immunoglobulin (Ig)E and interaction with tobacco smoke and pet exposure at ages 1, 2, 4 and 8 yrs by analysis of variance, Chi-squared tests and regression analyses.At all ages, inIL13, minor alleles of rs1295685 and rs20541 were significantly associated with elevated IgE levels in pooled analyses. InCD14, the rs2569190-TT and rs2569191-CC genotypes associated with lower IgE and decreased risk of sensitisation at 4 and 8 yrs in children exposed to pets, with an opposite effect in nonexposed children. Findings forIL13andCD14were comparable in separate cohorts.The present study indicates that atopy is importantly influenced byinterleukin 13at age 1–8 yrs and byCD14in interaction with pet exposure at ages 4 and 8 yrs. Additionally, pooled data improved effect estimates and genetic effects could be detected in interaction with important environmental factors.
Non-invasive monitoring of tissue oxygenation during laparoscopic donor nephrectomy
Authors: Crane Nicole J , Pinto Peter A , Hale Douglas , Gage Frederick A , Tadaki Doug , Kirk Allan D , Levin Ira W , Elster Eric A 
Published: April 2008

Abstract

Background
Standard methods for assessment of organ viability during surgery are typically limited to visual cues and tactile feedback in open surgery. However, during laparoscopic surgery, these processes are impaired. This is of particular relevance during laparoscopic renal donation, where the condition of the kidney must be optimized despite considerable manipulation. However, there is no in vivo methodology to monitor renal parenchymal oxygenation during laparoscopic surgery.

Methods
We have developed a method for the real time, in vivo, whole organ assessment of tissue oxygenation during laparoscopic nephrectomy to convey meaningful biological data to the surgeon during laparoscopic surgery. We apply the 3-CCD (charge coupled device) camera to monitor qualitatively renal parenchymal oxygenation with potential real-time video capability.

Results
We have validated this methodology in a porcine model across a range of hypoxic conditions, and have then applied the method during clinical laparoscopic donor nephrectomies during clinically relevant pneumoperitoneum. 3-CCD image enhancement produces mean region of interest (ROI) intensity values that can be directly correlated with blood oxygen saturation measurements (R2 > 0.96). The calculated mean ROI intensity values obtained at the beginning of the laparoscopic nephrectomy do not differ significantly from mean ROI intensity values calculated immediately before kidney removal (p > 0.05).

Conclusion
Here, using the 3-CCD camera, we qualitatively monitor tissue oxygenation. This means of assessing intraoperative tissue oxygenation may be a useful method to avoid unintended ischemic injury during laparoscopic surgery. Preliminary results indicate that no significant changes in renal oxygenation occur as a result of pneumoperitoneum.
Axonin-1/TAG-1 is required for pathfinding of granule cell axons in the developing cerebellum
Authors: Baeriswyl Thomas , Stoeckli Esther T 
Published: April 2008

Abstract
Background
Neural development consists of a series of steps, including neurogenesis, patterning, cell migration, axon guidance, and finally, synaptogenesis. Because all these steps proceed in a constantly changing environment, functional gene analyses during development have to take time into account. This is quite challenging, however, as loss-of-function approaches based on classic genetic tools do not allow for the precise temporal control that is required for developmental studies. Gene silencing by RNA interference (RNAi) in combination with the chicken embryo or with cultured embryos opens new possibilities for functional gene analysis in vivo. Axonin-1/TAG-1 is a cell adhesion molecule of the immunoglobulin superfamily with a well defined temporal and spatial expression pattern in the developing vertebrate nervous system. Axonin-1/TAG-1 was shown to promote neurite outgrowth in vitro and to be required for commissural and sensory axon pathfinding in vivo.

Results
To knock down axonin-1 in a temporally and spatially controlled manner during development of the nervous system, we have combined RNAi with the accessibility of the chicken embryo even at late stages of development. Using ex ovo RNAi, we analyzed the function of axonin-1/TAG-1 in cerebellar development. Axonin-1 is expressed in postmitotic granule cells while they extend their processes, the parallel fibers. In the absence of axonin-1 these processes still extend but no longer in a parallel manner to each other or to the pial surface of the cerebellum.

Conclusion
Axonin-1/TAG-1 is required for the navigation, but not for the elongation, of granule cell processes in the developing cerebellum in vivo.
The complete genome, comparative and functional analysis of Stenotrophomonas maltophiliareveals an organism heavily shielded by drug resistance determinants
Authors: Crossman Lisa C , Gould Virginia C , Dow J Maxwell , Vernikos Georgios S , Okazaki Aki , Sebaihia Mohammed , Saunders David , Arrowsmith Claire , Carver Tim , Peters Nicholas , Adlem Ellen , Kerhornou Arnaud , Lord Angela , Murphy Lee , Seeger Katharine , Squares Robert , Rutter Simon , Quail Michael A , Rajandream Mari-Adele , Harris David , Churcher Carol , Bentley Stephen D , Parkhill Julian , Thomson Nicholas R , Avison Matthew B 
Published: April 2008

Abstract
Background
Stenotrophomonas maltophilia is a nosocomial opportunistic pathogen of the Xanthomonadaceae. The organism has been isolated from both clinical and soil environments in addition to the sputum of cystic fibrosis patients and the immunocompromised. Whilst relatively distant phylogenetically, the closest sequenced relatives of S. maltophilia are the plant pathogenic xanthomonads.

Results
The genome of the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and of high G+C content. The sequence reveals an organism with a remarkable capacity for drug and heavy metal resistance. In addition to a number of genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, nine resistance-nodulation-division (RND)-type putative antimicrobial efflux systems are present. Functional genomic analysis confirms a role in drug resistance for several of the novel RND efflux pumps. S. maltophilia possesses potentially mobile regions of DNA and encodes a number of pili and fimbriae likely to be involved in adhesion and biofilm formation that may also contribute to increased antimicrobial drug resistance.

Conclusion
The panoply of antimicrobial drug resistance genes and mobile genetic elements found suggests that the organism can act as a reservoir of antimicrobial drug resistance determinants in a clinical environment, which is an issue of considerable concern.
Evaluation of Tumor Response, Disease Control, Progression-Free Survival, and Time to Progression As Potential Surrogate End Points in Metastatic Breast Cancer
Authors: Burzykowski Tomasz , Buyse Marc , Piccart-Gebhart Martine J. , Sledge George , Carmichael James , Lück Hans-Joachim , Mackey John R. , Nabholtz Jean-Marc , Paridaens Robert , Biganzoli Laura , Jassem Jacek , Bontenbal Marijke , Bonneterre Jacques , Chan Stephen , Basaran Gul Atalay , Therasse Patrick 
Published: April 2008

Purpose Overall survival (OS) can be observed only after prolonged follow-up, and any potential effect of first-line therapies on OS may be confounded by the effects of subsequent therapy. We investigated whether tumor response, disease control, progression-free survival (PFS), or time to progression (TTP) could be considered a valid surrogate for OS to assess the benefits of first-line therapies for patients with metastatic breast cancer. Patients and Methods Individual patient data were collected on 3,953 patients in 11 randomized trials that compared an anthracycline (alone or in combination) with a taxane (alone or in combination with an anthracycline). Surrogacy was assessed through the correlation between the end points as well as through the correlation between the treatment effects on the end points. Results Tumor response (survival odds ratio [OR], 6.2; 95% CI, 5.3 to 7.0) and disease control (survival OR, 5.5; 95% CI, 4.8 to 6.3) were strongly associated with OS. PFS (rank correlation coefficient, 0.688; 95% CI, 0.686 to 0.690) and TTP (rank correlation coefficient, 0.682; 95% CI, 0.680 to 0.684) were moderately associated with OS. Response log ORs were strongly correlated with PFS log hazard ratios (linear coefficient [ρ], 0.96; 95% CI, 0.73 to 1.19). Response and disease control log ORs and PFS and TTP log hazard ratios were poorly correlated with log hazard ratios for OS, but the confidence limits of ρ were too wide to be informative. Conclusion No end point could be demonstrated as a good surrogate for OS in these trials. Tumor response may be an acceptable surrogate for PFS.
Validation of Patient's Self-Reported Social Functioning As an Independent Prognostic Factor for Survival in Metastatic Colorectal Cancer Patients: Results of an International Study by the Chronotherapy Group of the European Organisation for Research and Treatment of Cancer
Authors: Efficace Fabio , Innominato Pasquale F. , Bjarnason Georg , Coens Corneel , Humblet Yves , Tumolo Salvatore , Genet Dominique , Tampellini Marco , Bottomley Andrew , Garufi Carlo , Focan Christian , Giacchetti Sylvie , Lévi Francis 
Published: April 2008

Purpose A recent study identified a prognostic model for survival in metastatic colorectal cancer patients which included WBC count, alkaline phosphatase (AP), number of metastatic sites, and patients’ self-reported social functioning. The aim of this research is to validate this model on data from an independent sample. Patients and Methods This validation study is based on a prospective randomized controlled trial in patients with metastatic colorectal cancer conducted by the European Organisation for Research and Treatment of Cancer (EORTC) Chronotherapy Group. Overall, 564 patients in 10 countries were enrolled. For the purpose of this independent validation, patients with health-related quality of life (HRQOL) baseline data were analyzed. HRQOL was assessed using the EORTC Quality of Life Questionnaire C30 (QLQ-C30). The Cox proportional hazards regression model was used for both univariate and multivariate analyses of survival. Results The previous model with an additional adjustment, by stratification for sex, was replicated and its parameters were confirmed to independently predict survival: WBC count with an hazard ratio (HR) of 1.31 (95% CI, 1.021 to 1.698; P = .034); AP with an HR of 1.53 (95% CI, 1.188 to 1.979; P = .001); number of sites involved with an HR of 1.90 (95% CI, 1.531 to 2.364; P < .0001); and patients’ self-reported social functioning with an HR of 0.94 (95% CI, 0.905 to 0.976; P = .001). The latter translates into a 6% increase in the likelihood of an earlier death for every 10-point decrease in the social functioning scale of the EORTC QLQ-C30. Conclusion This study provides confirmatory evidence of the independent prognostic value of patients’ self-reported social functioning in patients with advanced colorectal cancer.
Bevacizumab in Combination With Oxaliplatin-Based Chemotherapy As First-Line Therapy in Metastatic Colorectal Cancer: A Randomized Phase III Study
Authors: Saltz Leonard B. , Clarke Stephen , Díaz-Rubio Eduardo , Scheithauer Werner , Figer Arie , Wong Ralph , Koski Sheryl , Lichinitser Mikhail , Yang Tsai-Shen , Rivera Fernando , Couture Felix , Sirzén Florin , Cassidy Jim 
Published: April 2008

Purpose To evaluate the efficacy and safety of bevacizumab when added to first-line oxaliplatin-based chemotherapy (either capecitabine plus oxaliplatin [XELOX] or fluorouracil/folinic acid plus oxaliplatin [FOLFOX-4]) in patients with metastatic colorectal cancer (MCRC). Patients and Methods Patients with MCRC were randomly assigned, in a 2 × 2 factorial design, to XELOX versus FOLFOX-4, and then to bevacizumab versus placebo. The primary end point was progression-free survival (PFS). Results A total of 1,401 patients were randomly assigned in this 2 × 2 analysis. Median progression-free survival (PFS) was 9.4 months in the bevacizumab group and 8.0 months in the placebo group (hazard ratio [HR], 0.83; 97.5% CI, 0.72 to 0.95; P = .0023). Median overall survival was 21.3 months in the bevacizumab group and 19.9 months in the placebo group (HR, 0.89; 97.5% CI, 0.76 to 1.03; P = .077). Response rates were similar in both arms. Analysis of treatment withdrawals showed that, despite protocol allowance of treatment continuation until disease progression, only 29% and 47% of bevacizumab and placebo recipients, respectively, were treated until progression. The toxicity profile of bevacizumab was consistent with that documented in previous trials. Conclusion The addition of bevacizumab to oxaliplatin-based chemotherapy significantly improved PFS in this first-line trial in patients with MCRC. Overall survival differences did not reach statistical significance, and response rate was not improved by the addition of bevacizumab. Treatment continuation until disease progression may be necessary in order to optimize the contribution of bevacizumab to therapy.
Number of Alleles as a Predictor of the Relative Assignment Accuracy of Short Tandem Repeat (STR) and Single‐Nucleotide‐Polymorphism (SNP) Baselines for Chum Salmon
Authors: Smith Christian T. , Seeb Lisa W. 
Published: April 2008

AbstractShort tandem repeat (STR) markers, which exhibit many alleles per locus, are commonly used to assign fish to their populations of origin. Single‐nucleotide polymorphisms (SNPs), which have many technical advantages over STRs, typically exhibit only two alleles per locus. Simulation studies have indicated that the number of independent alleles is a good predictor of the accuracy of genetic markers for fishery applications. Extant STR baselines for salmon Oncorhynchus spp. contain hundreds of alleles, and it has been estimated that hundreds of SNP markers will need to be developed before the SNP baselines will be comparable to the STR baselines. We compared 15 STRs exhibiting 349 independent alleles with 61 SNPs exhibiting 66 independent alleles for accuracy in assigning individuals to closely related populations of chum salmon O. keta. The SNP baseline yielded slightly higher mean accuracies for proportional assignment and comparable accuracies for individual assignment. Based on the number of independent alleles in each baseline, the SNP baseline performed considerably better than the STR baseline. We suggest that this discrepancy is due to the fact that the simulation studies do not capture the impacts of the different strategies commonly employed for discovering and selecting STR and SNP markers.
Influence of Skipped Spawning and Misspecified Reproductive Schedules on Biological Reference Points in Sustainable Fisheries
Authors: Secor David H. 
Published: April 2008

AbstractDuring the spawning season, adult striped bass Morone saxatilis can occur outside known spawning tributaries. This phenomenon has been observed in other fishes, suggesting that investigators have misspecified reproductive schedules by assuming annual spawning. Across a range of species, skipped (i.e., nonannual) spawning is positively correlated with longevity. Therefore, reproductive schedules that are misspecified due to skipped spawning or poorly known age at maturation are likely for many moderately to extremely long‐lived species. To explore the relevance of misspecified reproductive schedules on sustainable fisheries, a range of types of skipped spawning was modeled for the Chesapeake Bay striped bass population to test for effects on the biological reference point of egg production per recruit. The influence of misspecified reproductive rates was minor, particularly in relation to the effects of the two alternative size limits (46 and 71 cm) that are most commonly used in fisheries management. Among misspecification scenarios, reduced frequency of spawning later in life had the largest effect on reproductive rate. As fisheries management increasingly focuses on thresholds that promote resiliency, increased recognition of variation in reproductive schedules will probably place greater emphasis on conservation of age structure.
Enhanced reactivity of hydroxylated polycyclic aromatic hydrocarbons to birnessite in soil: Reaction kinetics and nonextractable residue formation
Authors: Jung Jae-Woong , Lee Seunghwan , Ryu Hyerim , Nam Kyoungphile , Kang Ki-Hoon 
Published: April 2008

Abstract
Phenanthrene and pyrene were not transformed by birnessite (δ-MnO2) in the presence of phenol. The phenoxy radicals generated from phenol by birnessite did not act as a mediator for polycyclic aromatic hydrocarbon radical reaction under the studied conditions. In contrast, 9-hydroxyphenanthrene and 1-hydroxypyrene were remarkably sensitive to birnessite. The disappearance patterns of the test compounds both in the aqueous phase and soil followed first-order kinetics, with a linear relationship found between the rate constants and the surface area of birnessite. Moreover, the data indicated that the reaction was faster in the presence of soil than in the aqueous phase probably because of the presence of hydroxyl groups in soil organic matter. Sequential solvent extraction was not successful in the recovery of 9-hydroxyphenanthrene from the birnessite-treated soil samples, and capillary electrophoresis data suggest the formation of nonextractable residues of the compound in soil. In addition, the acute toxicity determined by Microtox® declined approximately 8.3 times in the soil samples treated with birnessite compared to untreated samples, demonstrating that the toxic compound was no longer present as its parent form.
A fugacity approach for assessing the bioaccumulation of hydrophobic organic compounds from estuarine sediment
Authors: Golding Christopher J , Gobas Frank A.P.C , Birch Gavin F 
Published: April 2008

AbstractThe bioavailability of four sediment-spiked hydrophobic organic contaminants (HOCs; chrysene, benzo[a]pyrene, chlordane, and Aroclor 1254) was investigated by comparing bioaccumulation by the amphipod Corophium colo with uptake into a thin film of ethylene/vinyl acetate (EVA) copolymer. The EVA thin film is a solid-phase extraction medium previously identified as effective at measuring the bioavailable contaminant fraction in sediment. The present study presents the results of 11 separate treatments in which chemical uptake into EVA closely matched uptake into lipid over 10 d. For all compounds, the concentration in EVA was a good approximation for the concentration in lipid, suggesting that this medium would be an appropriate biomimetic medium for assessing the bioaccumulation of HOCs during risk assessment of contaminated sediment. For chrysene and benzo[a]pyrene, limitations on bioaccumulation and toxicity because of low aqueous solubility were observed. The fugacity of the compounds in lipid (flip) and in the EVA thin film (fEVA) also was determined. The ratio of flip to fEVA was greater than one for all chemicals, indicating that all chemicals biomagnified over the duration of the exposure and demonstrating the potential for EVA thin-film extraction to assess trophic transfer of HOCs.