bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of culture and real‐time PCR for detection and quantification of five putative periodontopathogenic bacteria in subgingival plaque samples
Authors: Jervøe‐Storm P.‐M. , Koltzscher M. , Falk W. , Dörfler A. , Jepsen S. 
Published: June 2005

AbstractObjectives: Bacterial cultivation is a well‐established method for analyzing plaque samples. Real‐time polymerase chain reaction (PCR) is a novel rapid method for the identification and quantification of periodontopathogenic bacteria that has been recently introduced. In this study, we compared real‐time PCR with conventional anaerobic cultivation.Method: A total of 78 subgingival plaque samples were harvested from pockets 5 mm in 22 patients with advanced chronic periodontitis and immediately transferred into transport medium. Aliquots were evaluated with species‐specific probes by real‐time PCR (meridol® Perio Diagnostics, GABA) and anaerobic bacteria culture on selective media for the detection of Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia and Tannerella forsythensis. The analysis was performed by two separate, blinded examiners.Results: When real‐time PCR was compared with the culture method (golden standard) for the detection of putative periodontopathogenic bacteria, the sensitivity and specificity for A. actinomycetemcomitans were 67% and 100%, respectively (κ: 0.79); for F. nucleatum 73% and 53%, respectively (κ: 0.21); for P. gingivalis 94% and 84%, respectively (κ: 0.77); for P. intermedia 33% and 94%, respectively (κ: 0.26) and for T. forsythensis 92% and 56%, respectively (κ: 0.51). Spearman's correlation coefficients for the quantitative results of both methods were 0.82 for A. actinomycetemcomitans, 0.33 for F. nucleatum, 0.83 for P. gingivalis, 0.38 for P. intermedia and 0.67 for T. forsythensis.Conclusion: Overall, the agreement between both test methods was excellent for A. actinomycetemcomitans and P. gingivalis, fair for T. forsythensis and poor for F. nucleatum and P. intermedia. The discrepancies in the results may be explained by the inability of cultivation methods to distinguish between close related taxa, and the problems of keeping periopathogenic bacteria viable, which is required for standard cultivation.
QUANTUM DIAGONALIZATION METHOD IN THE TAVIS–CUMMINGS MODEL
Authors: FUJII KAZUYUKI , HIGASHIDA KYOKO , KATO RYOSUKE , SUZUKI TATSUO , WADA YUKAKO 
Published: June 2005

To obtain the explicit form of evolution operator in the Tavis–Cummings model we must calculate the term e -itg(S+⊗a+S-⊗ a† explicitly which is very hard. In this paper we try to make the quantum matrix A ≡ S+ ⊗ a +S- ⊗ a† diagonal to calculate e -itgA and, moreover, to know a deep structure of the model. For the case of one, two and three atoms we give such a diagonalization which is the first nontrivial examples as far as we know, and reproduce the calculations of e -itgA given in quant-ph/0404034. We also give a hint to an application to non-commutative differential geometry. However, a quantum diagonalization is not unique and is affected by some ambiguity arising from the non-commutativity of operators in quantum physics. Our method may open a new point of view in mathematical or quantum physics.
Influence of photoperiod and running wheel access on the entrainment of split circadian rhythms in hamsters
Authors: Rosenthal Sheila L , Vakili Martin M , Evans Jennifer A , Elliott Jeffrey A , Gorman Michael R 
Published: June 2005

Abstract

Background
In the laboratory, behavioral and physiological states of nocturnal rodents alternate, with a period near 24 h, between those appropriate for the night (e.g., elevated wheel-running activity and high melatonin secretion) and for the day (e.g., rest and low melatonin secretion). Under appropriate 24 h light:dark:light:dark conditions, however, rodents may be readily induced to express bimodal rest/activity cycles that reflect a global temporal reorganization of the central neural pacemaker in the hypothalamus. We examine here how the relative length of the light and dark phases of the environmental cycle influences this rhythm splitting and the necessity of a running wheel for expression of this entrainment condition.

Results
Rhythm splitting was observed in wheel-running and general locomotion of Siberian and Syrian hamsters. The latter also manifest split rhythms in body temperature. Access to a running wheel was necessary neither for the induction nor maintenance of this entrainment pattern. While rhythms were only transiently split in many animals with two 5 h nights, the incidence of splitting was greater with twice daily nights of shorter duration. Removal of running wheels altered the body temperature rhythm but did not eliminate its clear bimodality.

Conclusion
The expression of entrained, split circadian rhythms exhibits no strict dependence on access to a running wheel, but can be facilitated by manipulation of ambient lighting conditions. These circadian entrainment patterns may be of therapeutic value to human shift-workers and others facing chronobiological challenges.
Prognostic impact of epidermal growth factor receptor (EGFR) expression on loco-regional recurrence after preoperative radiotherapy in rectal cancer
Authors: Azria David , Bibeau Frederic , Barbier Nicolas , Zouhair Abderrahim , Lemanski Claire , Rouanet Philippe , Ychou Marc , Senesse Pierre , Ozsahin Mahmut , Pèlegrin André , Dubois Jean-Bernard , Thèzenas Simon 
Published: June 2005

Abstract
Background
Epidermal growth factor receptor (EGFR) represents a major target for current radiosensitizing strategies. We wished to ascertain whether a correlation exists between the expression of EGFR and treatment outcome in a group of patients with rectal adenocarcinoma who had undergone preoperative radiotherapy (RT).

Methods
Within a six-year period, 138 patients underwent preoperative radiotherapy and curative surgery for rectal cancer (UICC stages II-III) at our institute. Among them, 77 pretherapeutic tumor biopsies were available for semi-quantitative immunohistochemical investigation evaluating the intensity and the number (extent) of tumor stained cells. Statistical analyses included Cox regression for calculating risk ratios of survival endpoints and logistic regression for determining odds ratios for the development of loco-regional recurrences.

Results
Median age was 64 years (range: 30–88). Initial staging showed 75% and 25% stage II and III tumors, respectively. RT consisted of 44-Gy pelvic irradiation in 2-Gy fractions using 18-MV photons. In 25 very low-rectal-cancer patients the primary tumor received a boost dose of up to 16 Gy for a sphincter-preservation approach. Concomitant chemotherapy was used in 17% of the cases. All patients underwent complete total mesorectal resection. Positive staining (EGFR+) was observed in 43 patients (56%). Median follow-up was 36 months (range: 6–86). Locoregional recurrence rates were 7 and 20% for EGFR extent inferior and superior to 25%, respectively. The corresponding locoregional recurrence-free survival rate at two years was 94% (95% confidence interval, CI, 92–98%) and 84% (CI 95%, 58–95%), respectively (P = 0.06). Multivariate analyses showed a significant correlation between the rate of loco-regional recurrence and three parameters: EGFR extent superior to 25% (hazard ratio = 7.18, CI 95%, 1.17–46, P = 0.037), rectal resection with microscopic residue (hazard ratio = 6.92, CI 95%, 1.18–40.41, P = 0.032), and a total dose of 44 Gy (hazard ratio = 5.78, CI 95%, 1.04–32.05, P = 0.045).

Conclusion
EGFR expression impacts on loco-regional recurrence. Knowledge of expression of EGFR in rectal cancer could contribute to the identification of patients with an increased risk of recurrences, and to the prediction of prognosis.
Palm is expressed in both developing and adult mouse lens and retina
Authors: Castellini Meryl , Wolf Louise V , Chauhan Bharesh K , Galileo Deni S , Kilimann Manfred W , Cvekl Ales , Duncan Melinda K 
Published: June 2005

Abstract

Background
Paralemmin (Palm) is a prenyl-palmitoyl anchored membrane protein that can drive membrane and process formation in neurons. Earlier studies have shown brain preferred Palm expression, although this protein is a major water insoluble protein in chicken lens fiber cells and the Palm gene may be regulated by Pax6.

Methods
The expression profile of Palm protein in the embryonic, newborn and adult mouse eye as well as dissociated retinal neurons was determined by confocal immunofluorescence. The relative mRNA levels of Palm, Palmdelphin (PalmD) and paralemmin2 (Palm2) in the lens and retina were determined by real time rt-PCR.

Results
In the lens, Palm is already expressed at 9.5 dpc in the lens placode, and this expression is maintained in the lens vesicle throughout the formation of the adult lens. Palm is largely absent from the optic vesicle but is detectable at 10.5 dpc in the optic cup. In the developing retina, Palm expression transiently upregulates during the formation of optic nerve as well as in the formation of both the inner and outer plexiform layers. In short term dissociated chick retinal cultures, Palm protein is easily detectable, but the levels appear to reduce sharply as the cultures age. Palm mRNA was found at much higher levels relative to Palm2 or PalmD in both the retina and lens.

Conclusion

Palm is the major paralemmin family member expressed in the retina and lens and its expression in the retina transiently upregulates during active neurite outgrowth. The expression pattern of Palm in the eye is consistent with it being a Pax6 responsive gene. Since Palm is known to be able to drive membrane formation in brain neurons, it is possible that this molecule is crucial for the increase in membrane formation during lens fiber cell differentiation.
Online clinical reasoning assessment with the Script Concordance test: a feasibility study
Authors: Sibert Louis , Darmoni Stefan J , Dahamna Badisse , Weber Jacques , Charlin Bernard 
Published: June 2005

Abstract

Background
The script concordance (SC) test is an assessment tool that measures capacity to solve ill-defined problems, that is, reasoning in context of uncertainty. This tool has been used up to now mainly in medicine. The purpose of this pilot study is to assess the feasibility of the test delivered on the Web to French urologists.

Methods
The principle of SC test construction and the development of the Web site are described. A secure Web site was created with two sequential modules: (a) The first one for the reference panel (n = 26) with two sub-tasks: to validate the content of the test and to elaborate the scoring system; (b) The second for candidates with different levels of experience in Urology: Board certified urologists, residents, medical students (5 or 6th year). Minimum expected number of participants is 150 for urologists, 100 for residents and 50 for medical students. Each candidate is provided with an individual access code to this Web site. He/she may complete the Script Concordance test several times during his/her curriculum.

Results
The Web site has been operational since April 2004. The reference panel validated the test in June of the same year during the annual seminar of the French Society of Urology. The Web site is available for the candidates since September 2004. In six months, 80% of the target figure for the urologists, 68% of the target figure for the residents and 20% of the target figure for the student passed the test online. During these six months, no technical problem was encountered.

Conclusion
The feasibility of the web-based SC test is successful as two-thirds of the expected number of participants was included within six months. Psychometric properties (validity, reliability) of the test will be evaluated on a large scale (N = 300). If positive, educational impact of this assessment tool will be useful to help urologists during their curriculum for the acquisition of clinical reasoning skills, which is crucial for professional competence.
An overview of the design and methods for retrieving high-quality studies for clinical care
Authors: Wilczynski Nancy L , Morgan Douglas , Haynes R Brian ,   the Hedges Team
Published: June 2005

Abstract
Background
With the information explosion, the retrieval of the best clinical evidence from large, general purpose, bibliographic databases such as MEDLINE can be difficult. Both researchers conducting systematic reviews and clinicians faced with a patient care question are confronted with the daunting task of searching for the best medical literature in electronic databases. Many have advocated the use of search filters or "hedges" to assist with the searching process. The purpose of this report is to describe the design and methods of a study that set out to develop optimal search strategies for retrieving sound clinical studies of health disorders in large electronics databases.

Objective
To describe the design and methods of a study that set out to develop optimal search strategies for retrieving sound clinical studies of health disorders in large electronic databases.

Design
An analytic survey comparing hand searches of 170 journals in the year 2000 with retrievals from MEDLINE, EMBASE, CINAHL, and PsycINFO for candidate search terms and combinations. The sensitivity, specificity, precision, and accuracy of unique search terms and combinations of search terms were calculated.

Conclusion
A study design modeled after a diagnostic testing procedure with a gold standard (the hand search of the literature) and a test (the search terms) is an effective way of developing, testing, and validating search strategies for use in large electronic databases.
Molecular analysis of two local falciparum malaria outbreaks on the French Guiana coast confirms the msp1 B-K1/varD genotype association with severe malaria
Authors: Legrand Eric , Volney Beatrice , Lavergne Anne , Tournegros Caroline , Florent Loïc , Accrombessi Doris , Guillotte Micheline , Mercereau-Puijalon Odile , Esterre Philippe 
Published: June 2005

Abstract

Background

Plasmodium falciparum outbreaks can occur in the coastal area of French Guiana, where the population is essentially non-immune. Two sporadic outbreaks were observed, including one with severe malaria cases. To characterize these outbreaks and verify previous observations of specific genotype characteristics in severe malaria in this area, all cases from each outbreak were studied.

Methods

P. falciparum genotypes for six genetic loci were determined by PCR amplification from peripheral blood parasites. The msp1/ block2 and msp2 genotypes were determined by DNA sequencing. Microsatellite and varD genotyping was based on size polymorphism and locus-specific amplification.

Results
The outbreak including severe malaria cases was associated with a single genotype. The other mild malaria outbreak was due to at least five distinct genotypes.

Conclusion
Two distinct types of outbreak occured despite systematic and sustained deployement of malaria control measures, indicating a need for reinforced vigilance. The varD/B-K1 msp1 linkage and its association with severe malaria in this area was confirmed.
Morbidity and mortality after esophagectomy for esophageal carcinoma: A risk analysis
Authors: Gockel Ines , Exner Christoph , Junginger Theodor 
Published: June 2005

Abstract

Background
The study was aimed to identify pre- and intraoperative risk factors that potentially influence morbidity and mortality after esophagectomy for esophageal carcinoma with particular emphasis on the predominant tumor types.

Patients and methods
Between September 1985 and March 2004, 424 patients underwent esophagectomy for esophageal carcinoma. Of these, 186 (43.9%) patients had a transhiatal, and 231 (54.5%) patients underwent a transthoracic procedure with two-field lymphadenectomy. Pre-, intraoperative risk factors and tumor characteristics were included in the risk analysis to assess their influence on postoperative morbidity and mortality.

Results
Multivariate analysis (logistic regression model) identified the surgical procedure as the most important risk factor for postoperative morbidity and mortality with the transthoracic technique associated with a significant higher risk. The comparison of the risk profile between the different histological tumor types, a significantly higher nutritional risk, poorer preoperative lung function and a higher prevalence of hepatopathy was observed in patients with squamous cell carcinoma (n = 229) compared to adenocarcinoma (n = 150) (p < 0.05). Although there was no significant difference in surgical complications between the two groups, the rate of general complications, length of postoperative intensive care unit-stay and mortality rate was significantly higher in patients with squamous cell carcinoma (p < 0.05).

Conclusion
The present risk analysis shows that the selection and the type of the surgical procedure are crucial factors for both the incidence of postoperative complications and the mortality rate. The higher risk of the transthoracic procedure is justified with a view to a better long term prognosis.
Multilocus Analysis of Introgression Between Two Sympatric Sister Species of Drosophila:Drosophila yakubaandD. santomea
Authors: Llopart Ana , Lachaise Daniel , Coyne Jerry A 
Published: June 2005

AbstractDrosophila yakuba is widely distributed in sub-Saharan Africa, while D. santomea is endemic to the volcanic island of São Tomé in the Atlantic Ocean, 280 km west of Gabon. On São Tomé, D. yakuba is found mainly in open lowland forests, and D. santomea is restricted to the wet misty forests at higher elevations. At intermediate elevations, the species form a hybrid zone where hybrids occur at a frequency of ∼1%. To determine the extent of gene flow between these species we studied polymorphism and divergence patterns in 29 regions distributed throughout the genome, including mtDNA and three genes on the Y chromosome. This multilocus approach, together with the comparison to the two allopatric species D. mauritiana and D. sechellia, allowed us to distinguish between forces that should affect all genes and forces that should act on some genes (e.g., introgression). Our results show that D. yakuba mtDNA has replaced that of D. santomea and that there is also significant introgression for two nuclear genes, yellow and salr. The majority of genes, however, has remained distinct. These two species therefore do not form a “hybrid swarm” in which much of the genome shows substantial introgression while disruptive selection maintains distinctness for only a few traits (e.g., pigmentation and male genitalia).
Combining the Meiosis Gibbs Sampler With the Random Walk Approach for Linkage and Association Studies With a General Complex Pedigree and Multimarker Loci
Authors: Lee S H , Van der Werf J H J , Tier B 
Published: June 2005

Abstract
A linkage analysis for finding inheritance states and haplotype configurations is an essential process for linkage and association mapping. The linkage analysis is routinely based upon observed pedigree information and marker genotypes for individuals in the pedigree. It is not feasible for exact methods to use all such information for a large complex pedigree especially when there are many missing genotypic data. Proposed Markov chain Monte Carlo approaches such as a single-site Gibbs sampler or the meiosis Gibbs sampler are able to handle a complex pedigree with sparse genotypic data; however, they often have reducibility problems, causing biased estimates. We present a combined method, applying the random walk approach to the reducible sites in the meiosis sampler. Therefore, one can efficiently obtain reliable estimates such as identity-by-descent coefficients between individuals based on inheritance states or haplotype configurations, and a wider range of data can be used for mapping of quantitative trait loci within a reasonable time.
A Drosophila Model of Multiple Endocrine Neoplasia Type 2
Authors: Read Renee D , Goodfellow Paul J , Mardis Elaine R , Novak Nancy , Armstrong Jon R , Cagan Ross L 
Published: June 2005

Abstract
Dominant mutations in the Ret receptor tyrosine kinase lead to the familial cancer syndrome multiple endocrine neoplasia type 2 (MEN2). Mammalian tissue culture studies suggest that RetMEN2 mutations significantly alter Ret-signaling properties, but the precise mechanisms by which RetMEN2 promotes tumorigenesis remain poorly understood. To determine the signal transduction pathways required for RetMEN2 activity, we analyzed analogous mutations in the Drosophila Ret ortholog dRet. Overexpressed dRetMEN2 isoforms targeted to the developing retina led to aberrant cell proliferation, inappropriate cell fate specification, and excessive Ras pathway activation. Genetic analysis indicated that dRetMEN2 acts through the Ras-ERK, Src, and Jun kinase pathways. A genetic screen for mutations that dominantly suppress or enhance dRetMEN2 phenotypes identified new genes that are required for the phenotypic outcomes of dRetMEN2 activity. Finally, we identified human orthologs for many of these genes and examined their status in human tumors. Two of these loci showed loss of heterozygosity (LOH) within both sporadic and MEN2-associated pheochromocytomas, suggesting that they may contribute to Ret-dependent oncogenesis.
Kin Selection Is Implicated in Partial Sib-Mating Populations With Constant Viability Differences Before Mating
Authors: Lessard Sabin 
Published: June 2005

Abstract
The change in the frequency of a rare mutant allele under constant sex-differentiated viability selection in an infinite, partial full-sib mating population is studied. The diplo-diploid and haplo-diploid polygynous models are considered with a Poisson distribution for the number of offspring produced by every mated female. Reproduction is followed by weak selection among the offspring and then mating to form the next generation. It is shown that the rate of change with respect to the frequency of the mutant allele and the intensity of selection can be expressed in terms of costs or benefits of substituting the mutant type for the wild type, which correspond to average excesses in viability in females and males, multiplied by coefficients of relatedness to the individuals affected by such a substitution and reproductive values associated to the sexes of these individuals. This reveals hidden interactions between mated individuals and between males for mating, the former having positive effects on the reproductive success of related individuals and the latter having negative effects. Such interactions are the result of reproductive constraints when a fixed proportion of females must mate with a male sib and all females are fertilized as long as one mate is available. However, they affect the change in allele frequency because there is inbreeding or relatedness between mates and more generally relatedness between interacting individuals. Surprisingly, the effects of these interactions cancel out in a diploid population when the number of offspring is large enough so that the possibility for a female to have no male sib to mate with can be neglected and the viability differences are the same in both sexes.