bluuebunny/crossref_metadata_2025_split huggingface dataset:
The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae
Authors: Pieretti Isabelle , Royer Monique , Barbe Valérie , Carrere Sébastien , Koebnik Ralf , Cociancich Stéphane , Couloux Arnaud , Darrasse Armelle , Gouzy Jérôme , Jacques Marie-Agnès , Lauber Emmanuelle , Manceau Charles , Mangenot Sophie , Poussier Stéphane , Segurens Béatrice , Szurek Boris , Verdier Valérie , Arlat Matthieu , Rott Philippe 
Published: December 2009

AbstractBackgroundTheXanthomonadaceaefamily contains two xylem-limited plant pathogenic bacterial species,Xanthomonas albilineansandXylella fastidiosa.X. fastidiosawas the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possesshrpgenes which encode a Type III secretion system found in most plant pathogenic bacteria.X. fastidiosawas excluded from theXanthomonasgroup based on phylogenetic analyses with rRNA sequences.ResultsThe complete genome ofX. albilineanswas sequenced and annotated.X. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possesshrpgenes. Phylogenetic analysis usingX. albilineansgenomic sequences showed thatX. fastidiosabelongs to theXanthomonasgroup. Order of divergence of theXanthomonadaceaerevealed thatX. albilineansandX. fastidiosaexperienced a convergent reductive genome evolution during their descent from the progenitor of theXanthomonasgenus. Reductive genome evolutions of the two xylem-limitedXanthomonadaceaewere compared in light of their genome characteristics and those of obligate animal symbionts and pathogens.ConclusionThe two xylem-limitedXanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics ofX. albilineansdiffer from those ofX. fastidiosaand obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced byX. albilineans, is discussed.
Identification and characterization of intervening sequences within 23S rRNA genes from more than 200 Campylobacterisolates from seven species including atypical campylobacters
Authors: Tazumi Akihiro , Kakinuma Yuki , Misawa Naoaki , Moore John E , Millar Beverley C , Matsuda Motoo 
Published: December 2009

Abstract

Background
Identification and characterization of intervening sequences (IVSs) within 23S rRNA genes from Campylobacter organisms including atypical campylobacters were carried out using two PCR primer pairs, designed to generate helix 25 and 45 regions.

Results
Only C. sputorum biovar sputorum LMG7975 and fecalis LMG8531, LMG8534 and LMG6728 of a total of 204 Campylobacter isolates (n = 56 C. jejuni; n = 11 C. coli; n = 33 C. fetus; n = 43 C. upsaliensis; n = 30 C. hyointestinalis; n = 4 C. sputorum biovar sputorum; n = 5 C. sputorum biovar fecalis; n = 5 C. sputorum biovar paraureolyticus; n = 10 C. concisus; n = 7 C. curvus) were shown to carry IVSs in helix 25 region. C. sputorum biovar fecalis LMG8531 and LMG8534, interestingly, carried two different kinds of the 23S rRNA genes with and without the IVS, respectively. Consequently, in a total of 265 isolates of 269, including 65 C. lari isolates examined previously, the absence of IVSs was identified in the helix 25 region. In the helix 45 region, all the C. hyointestinalis, C. sputorum and C. concisus isolates were shown not to carry any IVSs. However, the 30 of 56 C. jejuni isolates (54%), 5 of 11 C. coli (45%), 25 of 33 C. fetus (76%), 30 of 43 C. upsaliensis (70%) and 6 of 7 C. curvus (90%) were shown to carry IVSs. In C. jejuni and C. upsaliensis isolates, two different kinds of the 23S rRNA genes were also identified to occur with and without IVSs in the helix 45 region, respectively.

Conclusions
Secondary structure models were also constructed with all the IVSs identified in the present study. In the purified RNA fractions from the isolates which carried the 16S or 23S rRNA genes with the IVSs, no 16S or 23S rRNA was evident, respectively.
Mutations in the coding regions of the hepatocyte nuclear factor 4 alpha in Iranian families with maturity onset diabetes of the young
Authors: Taghavi Seyed Morteza , Fatemi Seyedeh Seddigheh , Rafatpanah Houshang , Ganjali Rashin , Tavakolafshari Jalil , Valizadeh Narges 
Published: December 2009

Abstract
Hepatocyte nuclear factor 4α (HNF4α) is a nuclear receptor involved in glucose homeostasis and is required for normal β cell function. Mutations in the HNF4α gene are associated with maturity onset diabetes of the young type 1 (MODY1). The aim of the present study was to determine the prevalence and nature of mutations in HNF4α gene in Iranian patients with a clinical diagnosis of MODY and their family members. Twelve families including 30 patients with clinically MODY diagnosis and 21 members of their family were examined using PCR-RFLP method and in case of mutation confirmed by sequencing techniques. Fifty age and sex matched subjects with normal fasting blood sugar (FBS) and Glucose tolerance test (GTT) were constituted the control group and investigated in the similar pattern. Single mutation of V255M in the HNF4α gene was detected. This known mutation was found in 8 of 30 patients and 3 of 21 individuals in relatives. Fifty healthy control subjects did not show any mutation. Here, it is indicated that the prevalence of HNF4α mutation among Iranian patients with clinical MODY is considerable. This mutation was present in 26.6% of our patients, but nothing was found in control group. In the family members, 3 subjects with the age of ≤25 years old carried this mutation. Therefore, holding this mutation in this range of age could be a predisposing factor for developing diabetes in future.
A comparative study of a flow-cytometry-based assessment of in vitro Plasmodium falciparum drug sensitivity
Authors: Karl Stephan , Wong Rina PM , St Pierre Tim G , Davis Timothy ME 
Published: December 2009

Abstract

Background
Recently developed Sybr Green-based in vitro Plasmodium falciparum drug sensitivity assays provide an attractive alternative to current manual and automated methods. The present study evaluated flow cytometry measurement of DNA staining with Sybr Green in comparison with the P. falciparum lactate dehydrogenase assay, the tritiated hypoxanthine incorporation assay, a previously described Sybr Green based plate reader assay and light microscopy.

Methods
All assays were set up in standardized format in 96-well plates. The 50% inhibitory concentrations (IC50) of chloroquine, mefloquine and dihydroartemisinin against the laboratory adapted P. falciparum strains 3D7, E8B, W2mef and Dd2 were determined using each method.

Results
The resolution achieved by flow cytometry allowed quantification of the increase in individual cell DNA content after an incubation period of only 24 h. Regression, and Bland and Altman analyses showed that the IC50 values determined using the flow cytometry assay after 24 h agreed well with those obtained using the hypoxanthine incorporation assay, the P. falciparum lactate dehydrogenase assay, the Sybr Green plate reader assay and light microscopy. However the values obtained with the flow cytometry assay after 48 h of incubation differed significantly from those obtained with the hypoxanthine incorporation assay, and the P. falciparum lactate dehydrogenase assay at low IC50 values, but agreed well with the Sybr Green plate reader assay and light microscopy.

Conclusions
Although flow cytometric equipment is expensive, the necessary reagents are inexpensive, the procedure is simple and rapid, and the cell volume required is minimal. This should allow field studies using fingerprick sample volumes.
Cultured skin microbiota attracts malaria mosquitoes
Authors: Verhulst Niels O , Beijleveld Hans , Knols Bart GJ , Takken Willem , Schraa Gosse , Bouwmeester Harro J , Smallegange Renate C 
Published: December 2009

Abstract

Background
Host-seeking of the African malaria mosquito, Anopheles gambiae sensu stricto, is guided by human odours. The precise nature of the odours, and the composition of attractive blends of volatiles, remains largely unknown. Skin microbiota plays an important role in the production of human body odours. It is hypothesized that host attractiveness and selection of An. gambiae is affected by the species composition, density, and metabolic activity of the skin microbiota. A study is presented in which the production and constituency of volatile organic compounds (VOCs) by human skin microbiota is examined and the behavioural responses of An. gambiae to VOCs from skin microbiota are investigated.

Methods
Blood agar plates incubated with skin microbiota from human feet or with a reference strain of Staphylococcus epidermidis were tested for their attractiveness to An. gambiae in olfactometer bioassays and indoor trapping experiments. Entrained air collected from blood agar plates incubated with natural skin microbiota or with S. epidermidis were analysed using GC-MS. A synthetic blend of the compounds identified was tested for its attractiveness to An. gambiae. Behavioural data were analysed by a χ2-test and GLM. GC-MS results were analysed by fitting an exponential regression line to test the effect of the concentration of bacteria.

Results
More An. gambiae were caught with blood agar plates incubated with skin bacteria than with sterile blood agar plates, with a significant effect of incubation time and dilution of the skin microbiota. When bacteria from the feet of four other volunteers were tested, similar effects were found. Fourteen putative attractants were found in the headspace of the skin bacteria. A synthetic blend of 10 of these was attractive to An. gambiae.

Conclusions
The discovery that volatiles produced by human skin microorganisms in vitro mediate An. gambiae host-seeking behaviour creates new opportunities for the development of odour-baited trapping systems. Additionally, identification of bacterial volatiles provides a new method to develop synthetic blends, attractive to An. gambiae and possibly other anthropophilic disease vectors.
Thermogenic effect of meltdown RTD™ energy drink in young healthy women: a double blind, cross-over design study
Authors: Rashti Stefanie L , Ratamess Nicholas A , Kang Jie , Faigenbaum Avery D , Chilakos Aristomen , Hoffman Jay R 
Published: December 2009

Abstract

Background
The purpose of this study was to examine the acute metabolic effects of a high-energy drink in healthy, physically-active women.

Methods
Ten women (20.4 ± 0.70 y; 166.9 ± 7.2 cm; 67.0 ± 7.0 kg; 29.6 ± 6.5% body fat) underwent two testing sessions administered in a randomized and double-blind fashion. Subjects reported to the laboratory in a 3-hr post-absorptive state and were provided either 140 ml of the high-energy drink (SUP; commercially marketed as Meltdown RTD™) or placebo (P). Subjects consumed two 70 ml doses of SUP or P, separated by 30 min and rested in a semi-recumbent position for 3 hours. Resting oxygen consumption (VO2) and heart rate (HR) were determined every 5 min during the first 30 min and every 10 min during the next 150 min. Blood pressure (BP) was determined every 15 min during the first 30 min and every 30 min thereafter. Area under the curve (AUC) analysis was computed for VO2, whereas a 3-hour average and hourly averages were calculated for respiratory quotient (RQ), total kcal, HR, BP, and profile of mood states (POMS).

Results
AUC analysis revealed a 10.8% difference (p = 0.03) in VO2 between SUP and P. No difference in VO2 was seen between the groups in the first hour, but VO2 in SUP was significantly greater than P in the second (13.9%, p = 0.01) and third hours (11.9%, p = 0.03). A difference (p = 0.03) in energy expenditure was seen between SUP (1.09 ± 0.10 kcal·min-1) and P (0.99 ± 0.09 kcal·min-1) for the 3-hour period. Although no difference in energy expenditure was seen in the first hour, significant differences between SUP and P were observed in the second (1.10 ± 0.11 kcal·min-1 and 0.99 ± 0.09 kcal·min-1, respectively; p = 0.02) and third hour (1.08 ± 0.11 kcal·min-1 and 0.99 ± 0.09 kcal·min-1, respectively; p = 0.05). Average systolic BP was significantly higher (p = 0.007) for SUP (110.0 ± 3.9 mmHg) compared to P (107.3 ± 4.4 mmHg). No differences were seen in HR, diastolic BP, or POMS at any time point.

Conclusions
Results showed a significant increase in energy expenditure in young, healthy women following an acute ingestion of a high-energy drink.
Copy number variation in the Framingham Heart Study
Authors: Shtir Corina , Pique-Regi Roger , Siegmund Kim , Morrison John , Schumacher Fredrick , Marjoram Paul 
Published: December 2009

Abstract
In this paper we test for association between copy number variation and diabetes in a subset of individuals from the Framingham Heart Study. We used the 500 k SNP data and called copy number variation using two algorithms: the genome alteration detection algorithm of Pique-Regi et al. and the software Golden Helix. We then tested for association between copy number and diabetes using a gene-based analysis. Our results show little evidence of association between copy number and diabetes status. Furthermore, our results indicate a relatively poor level of agreement between copy number calls resulting from the two programs. We then examined potential causes for this difference in results and the implications for future studies.
Application of imputation methods to the analysis of rheumatoid arthritis data in genome-wide association studies
Authors: Childers Douglas K , Kang Guolian , Liu Nianjun , Gao Guimin , Zhang Kui 
Published: December 2009

Abstract
Most genetic association studies only genotype a small proportion of cataloged single-nucleotide polymorphisms (SNPs) in regions of interest. With the catalogs of high-density SNP data available (e.g., HapMap) to researchers today, it has become possible to impute genotypes at untyped SNPs. This in turn allows us to test those untyped SNPs, the motivation being to increase power in association studies. Several imputation methods and corresponding software packages have been developed for this purpose. The objective of our study is to apply three widely used imputation methods and corresponding software packages to a data from a genome-wide association study of rheumatoid arthritis from the North American Rheumatoid Arthritis Consortium in Genetic Analysis Workshop 16, to compare the performances of the three methods, to evaluate their strengths and weaknesses, and to identify additional susceptibility loci underlying rheumatoid arthritis. The software packages used in this paper included a program for Bayesian imputation-based association mapping (BIMBAM), a program for imputing unobserved genotypes in case-control association studies (IMPUTE), and a program for testing untyped alleles (TUNA). We found some untyped SNP that showed significant association with rheumatoid arthritis. Among them, a few of these were not located near any typed SNP that was found to be significant and thus may be worth further investigation.
Genome-wide association studies of rheumatoid arthritis data via multiple hypothesis testing methods for correlated tests
Authors: Kang Guolian , Childers Douglas K , Liu Nianjun , Zhang Kui , Gao Guimin 
Published: December 2009

Abstract
Genome-wide association studies often involve testing hundreds of thousands of single-nucleotide polymorphisms (SNPs). These tests may be highly correlated because of linkage disequilibrium among SNPs. Multiple testing correction ignoring the correlation among markers, as is done in the Bonferroni procedure, can cause loss of power. Several multiple testing adjustment methods accounting for correlations among tests have been developed and have shown improved power compared to the Bonferroni procedure. These methods include a Monte Carlo (MC) method and a method of computing p-values adjusted for correlated tests. The objective of this study is to apply these two multiple testing methods to genome-wide association study of the Genetic Analysis Workshop 16 rheumatoid arthritis data from the North American Rheumatoid Arthritis Consortium, to compare the performance of these two methods to the Bonferroni procedure in identifying susceptibility loci underlying rheumatoid arthritis, and to discuss the strengths and weaknesses of these methods. The results show that both the MC method and p-values adjusted for correlated tests method identified more significant SNPs, thus potentially have higher power than the corresponding Bonferroni methods using the same test statistics as in the MC method and p-values adjusted for correlated tests, respectively. Simulation studies demonstrate that the MC method may have slightly higher power than the p-values adjusted for correlated tests method.
Detecting gene-by-smoking interactions in a genome-wide association study of early-onset coronary heart disease using random forests
Authors: Maenner Matthew J , Denlinger Loren C , Langton Asher , Meyers Kristin J , Engelman Corinne D , Skinner Halcyon G 
Published: December 2009

Abstract

Background
Genome-wide association studies are often limited in their ability to attain their full potential due to the sheer volume of information created. We sought to use the random forest algorithm to identify single-nucleotide polymorphisms (SNPs) that may be involved in gene-by-smoking interactions related to the early-onset of coronary heart disease.

Methods
Using data from the Framingham Heart Study, our analysis used a case-only design in which the outcome of interest was age of onset of early coronary heart disease.

Results
Smoking status was dichotomized as ever versus never. The single SNP with the highest importance score assigned by random forests was rs2011345. This SNP was not associated with age alone in the control subjects. Using generalized estimating equations to adjust for sex and account for familial correlation, there was evidence of an interaction between rs2011345 and smoking status.

Conclusion
The results of this analysis suggest that random forests may be a useful tool for identifying SNPs taking part in gene-by-environment interactions in genome-wide association studies.
Integration of a priori gene set information into genome-wide association studies
Authors: Sohns Melanie , Rosenberger Albert , Bickeböller Heike 
Published: December 2009

Abstract
In genome-wide association studies (GWAS) genetic markers are often ranked to select genes for further pursuit. Especially for moderately associated and interrelated genes, information on genes and pathways may improve the selection. We applied and combined two main approaches for data integration to a GWAS for rheumatoid arthritis, gene set enrichment analysis (GSEA) and hierarchical Bayes prioritization (HBP). Many associated genes are located in the HLA region on 6p21. However, the ranking lists of genes and gene sets differ considerably depending on the chosen approach: HBP changes the ranking only slightly and primarily contains HLA genes in the top 100 gene lists. GSEA includes also many non-HLA genes.
Bilateral choanal atresia in an adult - management with mitomycin C and without stents: a case report
Authors: Aksoy Fadlullah , Demirhan Hasan , Yildirim Yavuz Selim , Ozturan Orhan 
Published: December 2009

Abstract

Background
A 23-year-old female patient presented to the outpatient clinic with bilateral nasal obstruction and discharge since birth. Endoscopic examination and paranasal sinus tomography revealed bilateral choanal atresia. She did not have any other congenital abnormalities. Her parents reported cyanosis in childhood that worsened during feeding and improved during crying; however, they had not visited a physician. She did not have remarkable complaints during early childhood or adolescence.

Methods
The patient was operated under general anesthesia, using a 0° 4 mm rigid endoscope. The orifice was widened with a curette and, to prevent stenosis, mitomycin-C (1 mg/ml) was applied topically to the nasopharyngeal orifice for 5 minutes. No stents were placed.

Results
Follow-up evaluation at postoperative 12th month showed that her symptoms improved significantly and, on endoscopic examination, both choanae remained patent.
Separating therapeutic efficacy from glucocorticoid side-effects in rodent arthritis using novel, liposomal delivery of dexamethasone phosphate: long-term suppression of arthritis facilitates interval treatment
Authors: Rauchhaus Una , Schwaiger Franz Werner , Panzner Steffen 
Published: December 2009

Abstract
Introduction
Glucocorticoids have extensively been used in the treatment of rheumatoid arthritis and other inflammatory diseases. However, their side-effects remain the major limitation in clinical use and an improved therapeutic index is needed.

Methods
Therapeutic efficacy and persistence of free and liposomal dexamethasone phosphate (DXM-P) were determined in mouse collagen-induced arthritis. For regimens with equal therapeutic benefit, the side-effect profiles were analysed over time with respect to collagen breakdown, suppression of the hypothalamus-pituitary-adrenal (HPA) axis, changes in blood glucose levels and the haematological profile. In addition, the presence of drug was monitored in plasma.

Results
Liposomal DXM-P, but not free drug, resulted in a persistent anti-inflammatory effect. Comparable clinical benefit was achieved with a single administration of 4 mg/kg liposomal DXM-P or daily administrations of 1.6 mg/kg free drug for at least 7 days. For the liposomal form, but not for the free form, we observed a limitation of the suppression of the HPA axis in time and an absence of the drug-induced gluconeogenesis.

Conclusions
Liposomal DXM-P, but not free DXM-P, achieves therapeutic persistence in mouse collagen-induced arthritis, which results in drug-free periods of therapeutic benefit. The physical absence of drug after day 2 is associated with a reduction of the typical glucocorticoid side-effects profile. Liposomal DXM-P thereby has an improved therapeutic window.