bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip datasets
Authors: Pyne Saumyadipta , Futcher Bruce , Skiena Steve 
Published: August 2006

AbstractMotivation: High-throughput microarray technology can be used to examine thousands of features, such as all the genes of an organism, and measure their expression. Two important issues of microarray bioinformatics are first, how to combine the significance values for each feature across experiments with high statistical power, and second, how to control the proportion of false positives. Existing methods address these issues separately, in spite of their linked usage.Results: We present a novel method (ESP) to address the two requirements in an interdependent way. It generalizes the truncated product method of Zaykin et al. to combine only those significance values which clear their respective experiment-specific false discovery restrictive thresholds, thus allowing us to control the false discovery rate (FDR) for the final combined result. Further, we introduce several concepts that together offer FDR control, high power, quality control and speed-up in meta-analysis as done by our algorithm. Computational and statistical methods of research synthesis like the one described here will be increasingly important as additional genome-wide datasets accumulate in databases.We apply our method to combine three well-known ChIP-chip transcription factor binding datasets for budding yeast to identify significant intergenic regulatory sequences for nine cell cycle regulating transcription factors, both with high power and controlled FDR.Contact: spyne@cs.sunysb.eduSupplementary Materials and Appendices:
Review article: thiopurines in inflammatory bowel disease
Authors: DERIJKS L. J. J. , GILISSEN L. P. L. , HOOYMANS P. M. , HOMMES D. W. 
Published: August 2006

SummaryBackgroundIn the past 10–20 years, knowledge of both thiopurine pharmacology and ‐pharmacogenetics has been extended dramatically and used to develop new strategies to improve efficacy and reduce toxicity.AimTo review thiopurine efficacy, toxicity, pharmacology, pharmacogenetics, interactions in patients with inflammatory bowel disease. Special attention was paid to new strategies for optimization of pharmacotherapy.MethodsTo collect relevant scientific articles, a Pubmed search was performed from 1966 through January 2006 with the following key words (MeSH terms preferentially) in multiple combinations: ‘azathioprine’, ‘6‐mercaptopurine’, ‘6‐MP’, ‘6‐thioguanine’, ‘6‐TG’, ‘thiopurine(s)’, ‘metabolites’, ‘level(s)’, ‘TDM’, ‘TMPT’, ‘ITPA’, ‘genotype(s)’, ‘phenotype(s)’, ‘inflammatory bowel disease’, ‘Crohn(’s) disease’, ‘ulcerative colitis’.ResultsStrategies for optimization of pharmacotherapy include therapeutic drug monitoring of thiopurine metabolites, geno‐ or phenotyping crucial enzymes in thiopurine metabolism like thiopurine S‐methyltransferase and inosine triphosphate pyrophosphatase, and the use of thioguanine as such.ConclusionsThiopurine S‐methyltransferase genotyping and therapeutic drug monitoring are useful instruments for individualizing thiopurine pharmacotherapy of inflammatory bowel disease. Inosine triphosphate pyrophosphatase genotyping may be helpful in case of unexplainable myelotoxicity. In case of azathioprine‐ or mercaptopurine‐intolerance, thioguanine seems a promising alternative. However, more knowledge needs to be gathered about its potential hepatotoxicity.
R5 An audit of local compliance with general anaesthetic guidelines outlined for paediatric dentistry
Authors: MODARAI F. , DARWISH* C. 
Published: August 2006

Objectives:  To assess current practice in terms of diagnosis, treatment planning and consent in the use of dental general anaesthetic (GA). To compare current practice to national guidelines and implement any changes required to improve clinical practice.Methods:  A retrospective study was carried out over 1 year (2004–2005). 100 paediatric patients undergoing long (comprehensive care) and short (extractions only) dental GA were randomly selected. A proforma was designed to collect data, from patient records, regarding presenting complaint, medical history, treatment carried out during and before GA and consent. Patients who attended oral and maxillofacial clinics were not included.Results:  In most cases, GA was justified inline with guidelines but consent and treatment planning could be improved.Conclusion:  The department is adhering to guidelines in prescribing GA for patients. It is hoped that by producing a departmental policy, this could improve.
C1 Retarded eruption of all permanent teeth. An extreme case report
Authors: ARHAKIS* A , DALAMPIRAS S 
Published: August 2006

Presenting problem:  A 14 year old male patient with delayed eruption of all permanent teeth with the exception of maxillary first permanent molars was referred to our clinic. The clinical examination of the patient showed no signs of abnormality. Mental and physical development was normal for his age and there were no signs or symptoms supporting the presence of syndromes related to eruption problems. Blood tests were within normal limits and there was no history of such a problem in the family. Radiological examination showed that all permanent first molars were present but only the maxillary first molars had erupted. In order to achieve spontaneous eruption of their permanent successors a general practitioner extracted the central primary mandibular incisors. However no eruption of the permanent successors was observed over a period of two years.Clinical management:  A decision was made to surgically expose the crowns of the permanent central incisors in the lower jaw in order to promote spontaneous eruption. A year after the operation these teeth together with the mandibular third molars were partially erupted. No other teeth had erupted at this stage.Discussion:  A case of delayed eruption of all permanent teeth is very rare, especially when it is not related to any known syndrome. The pathogenesis is a diagnostic riddle and the treatment demands a very careful approach.
Remote control of photosynthetic genes by the mitochondrial respiratory chain
Authors: Matsuo Mitsuhiro , Obokata Junichi 
Published: August 2006

SummaryIn this paper, we study whether mitochondrial respiration has an impact on the biogenesis of photosynthetic apparatus in the unicellular alga, Chlamydomonas reinhardtii. When respiration was activated by acetate in the dark, mRNAs of nuclear‐encoded photosynthetic genes were induced. This induction did not occur in the cells treated with respiration inhibitors or in respiration mutants. An uncoupler of oxidative phosphorylation did not inhibit this mRNA induction; rather, it enhanced it in response to the increase in respiratory electron transport (RET). Plant and algal mitochondria have two RET pathways: the cytochrome pathway and the alternative pathway. Inhibitors of the former pathway inhibited mRNA induction, but inhibitors of the latter enhanced it. Taken together, these indicate that photosynthetic gene mRNAs are induced in response to activation of the cytochrome pathway. This RET‐responsive induction is analogous to the photosynthetic electron transport (PET)‐responsive induction of photosynthetic gene mRNAs (Matsuo and Obokata, Plant Cell Physiol. 43, 1189). PET‐responsive induction occurred in photo‐autotrophic and mixotrophic conditions, while RET‐responsive induction occurred in mixotrophic and dark heterotrophic conditions. These results indicate that the regulatory system of photosynthetic genes changes between chloroplastic PET‐dependent type and mitochondrial RET‐dependent type in response to shifts in the dominant energy source between photosynthesis and respiration.
Determinants of native and alien species richness in the urban flora of Rome
Authors: Celesti‐Grapow Laura , Pyšek Petr , Jarošík Vojtěch , Blasi Carlo 
Published: August 2006

ABSTRACTUntil now, analytical studies on European urban floras have mostly concentrated on the central and north‐western parts of the continent. In this paper, factors determining species richness of urban flora were studied for the city of Rome, Italy, based on a comprehensive floristic survey carried out between 1985 and 1994, and updated in 2005. All species were recorded in grid cells of 1.6 km2 and classified into native and alien (the latter divided into archaeophytes and neophytes). The grids were classified with respect to the prevailing habitat type, area available to vegetation, level of disturbance and geographical position within the city. Data were analysed using minimal adequate models. Total species number was determined by habitat and its interaction with position on the north‐west gradient; other variables explained much less variance. Holding other variables constant, the average species number per grid cell was highest in archaeological sites and parks, followed by woodlands and rivers, and grasslands and recent developments. Residential areas and the historical centre were poorest in species number. Towards the north of the city, species richness in corresponding habitats increases because of higher landscape heterogeneity and closer association with diaspore pools in the surroundings. Native species make up on average 84% of the total species numbers, and trends opposite to those for the total number of species were found for the proportional representation of aliens. The occurrence of alien and native species in the flora of Rome is driven by similar factors, but factors that increase representation of aliens decrease that of natives and vice versa. The representation of neophytes and native species in grid cells was easier to explain (74% of variation accounted for) than that of archaeophytes (27%); this result reflects that in terms of ecology and response to factors, archaeophytes take an intermediate position between native plants and neophytes. Proportional representation of neophytes decreased with increasing area available to vegetation, reflecting that semi‐natural vegetation is better developed where less fragmented.
Does seasonal fine‐tuning of climatic variables improve the performance of bioclimatic envelope models for migratory birds?
Authors: Heikkinen R. K. , Luoto M. , Virkkala R. 
Published: August 2006

ABSTRACTWe examined the influence of ‘seasonal fine‐tuning’ of climatic variables on the performance of bioclimatic envelope models of migrating birds. Using climate data and national bird atlas data from a 10 × 10 km uniform grid system in Finland, we tested whether the replacement of one ‘baseline’ set of variables including summer (June–August) temperature and precipitation variables with climate variables tailored (‘fine‐tuned’) for each species individually improved the bird‐climate models. The fine‐tuning was conducted on the basis of time of arrival and early breeding of the species. Two generalized additive models (GAMs) were constructed for each of the 63 bird species studied, employing (1) the baseline climate variables and (2) the fine‐tuned climate variables. Model performance was measured as explanatory power (deviance change) and predictive power (area under the curve; AUC) statistics derived from cross‐validation. Fine‐tuned climate variables provided, in many cases, statistically significantly improved model performance compared to using the same baseline set of variables for all the species. Model improvements mainly concerned bird species arriving and starting their breeding in May–June. We conclude that the use of the fine‐tuned climate variables tailored for each species individually on the basis of their arrival and critical breeding periods can provide important benefits for bioclimatic modelling.
Challenging Wallacean and Linnean shortfalls: knowledge gradients and conservation planning in a biodiversity hotspot
Authors: Bini Luis Mauricio , Diniz‐Filho José Alexandre F. , Rangel Thiago F. L. V. B. , Bastos Rogério Pereira , Pinto Miriam Plaza 
Published: August 2006

ABSTRACTKnowledge about biodiversity remains inadequate because most species living on Earth were still not formally described (the Linnean shortfall) and because geographical distributions of most species are poorly understood and usually contain many gaps (the Wallacean shortfall). In this paper, we developed models to infer the size and placement of geographical ranges of hypothetical non‐described species, based on the range size frequency distribution of anurans recently described in the Cerrado Biome, on the level of knowledge (number of inventories) and on surrogates for habitat suitability. The rationale for these models is as follow: (1) the range size frequency distribution of these species should be similar to the range‐restricted species, which have been most recently described in the Cerrado Biome; (2) the probability of new discoveries will increase in areas with low biodiversity knowledge, mainly in suitable areas, and (3) assuming range continuity, new species should occupy adjacent cells only if the level of knowledge is low enough to allow the existence of undiscovered species. We ran a model based on the number of inventories only, and two models combining effects of number of inventories and two different estimates of habitat suitability, for a total of 100 replicates each. Finally, we performed a complementary analysis using simulated annealing to solve the set‐covering problem for each simulation (i.e. finding the smallest number of cells so that all species are represented at least once), using extents of occurrence of 160 species (131 real anuran species plus 29 new simulated species). The revised reserve system that included information about unknown or poorly sampled taxa significantly shifted northwards, when compared to a system based on currently known species. This main result can be explained by the paucity of biodiversity data in this part of the biome, associated with its relatively high habitat suitability. As a precautionary measure, weighted by the inferred distribution data, the prioritization of a system of reserves in the north part of the biome appears to be defensible.
MULTIPARAMETER QUANTITATIVE COMPUTER‐ASSISTED TOMOGRAPHY ASSESSMENT OF UNICOMPARTMENTAL KNEE ARTHROPLASTIES
Authors: Campbell DAVID G. , Johnson LUKE J. , West SIMON C. 
Published: August 2006

Background:  Unicompartmental knee arthroplasty is a popular alternative to total knee replacement in selected patients. Component alignment has not yet been described by computer‐assisted tomography (CAT) imaging techniques; these have been developed for total knee arthroplasty analysis. The aims of this study were to report two new technologies; a new unicompartmental knee arthroplasty system was radiographically assessed with a new CAT scan protocol.Methods:  In a consecutive cohort study, 60 knees were analysed by the ‘UniCAT Protocol’. Patients were implanted with a unicompartmental knee arthroplasty system that uses a unique ligament tensor for femoral component alignment. The uniCAT protocol requires a long anteroposterior and lateral scout scan to measure limb alignment and component orientation. A spiral computer‐assisted tomography at the knee is used to measure component rotation. The total scan time was 20 s with a calculated unshielded radiation dose of 1 mSv or less.Results:  The mechanical axis had a mean of 2.7° varus. Femoral components were implanted with a mean of 0.37° valgus and 1.3° flexion. Tibial components were implanted with a mean 3.47° varus and 5.1° posterior slope. Femoral components were externally rotated a mean of 3.36°, tibial components were externally rotated 6.59° from the posterior tibia and 5.68° from the transepicondylar axis.Conclusion:  The UniCAT protocol uses less radiation than whole‐limb spiral scans and is a method that can be used with all modern computer‐assisted tomography machines. The coronal and sagital alignment results compare favourably with previous published reports without computer‐assisted tomography. Component rotation has not previously been reported and its implications are yet to be defined.
DEVELOPMENT OF PATIENT PATHWAYS FOR THE SURGICAL MANAGEMENT OF BURN INJURY
Authors: Greenwood John E. 
Published: August 2006

Background:  There are many reasons for the development of patient pathways in burn surgery introduced at the Royal Adelaide Hospital in South Australia at the beginning of January 2005. These include education, standardization of technique, scheduling of surgical episodes and rationalization of the use of expensive therapies.Methods:  A critical appraisal of both evidence based on published work and personal/peer experience has been used to generate the current pathways.Results:  The year 2005 was the busiest in the history of the hospital, both in numerical terms and in the proportion of major burn injuries. These protocols were effective in enabling us to cope with negligible mortality.Conclusion:  Although the first draft pathways work in our unit, they will undergo regular audit. It is hoped that they will form a template that can assist other services to create their own pathways.
NON‐ENTRY OF ELIGIBLE PATIENTS INTO THE AUSTRALASIAN LAPAROSCOPIC COLON CANCER STUDY
Authors: Abraham Ned S. , Hewett Peter , Young Jane M. , Solomon Michael J. 
Published: August 2006

Background:  There is currently a need to assess the reasons for non‐entry of eligible patients into surgical randomized controlled trials to determine measures to improve the low recruitment rates in such trials.Methods:  Reasons for non‐entry of all eligible patients not recruited into the Australasian Laparoscopic Colon Cancer Study were prospectively recorded using a survey completed by the participating surgeons for a period of 6 months.Results:  In the 6‐month period of the study, 51 (45%) out of 113 eligible patients examined by the 18 actively participating surgeons were recruited into the trial. Eighty‐nine reasons were recorded for the non‐entry of the 62 eligible patients. The most commonly recorded reason was preference for one form of surgery (42%) or the surgeon (31%) by the patient (45 patients (73%) in total). This was followed by lack of time (10 patients (16%)), hospital accreditation (7 patients (11%)) or staffing/equipment (6 patients (10%)). Concern about the doctor–patient relationship or causing the patient anxiety was recorded for three (5%) and two (3%) patients, respectively. Recruitment was positively associated with the availability of a data manager (χ2 = 19.91; P < 0.001, odds ratio (95% confidence interval) = 9.50 (3.53–25.53)) and negatively associated with an increased caseload (more than five eligible patients seen by the surgeon in the study period) (continuity adjusted χ2 = 16.052; P < 0.001, odds ratio (95% confidence interval) = 0.11(0.04–0.30)).Conclusion:  Having a preference for one form of surgery by the patient or the surgeon was the most common reason for non‐entry of eligible patients in the Australasian Laparoscopic Colon Cancer Study. Concern about the doctor–patient relationship played a minimal role in determining the outcome of recruitment. Patient and surgeon preferences, caseload and the distribution of supportive staff such as data managers according to patient population density should be considered in the planning of future trials.
Nuclear magnetic resonance‐determined lipoprotein subclass profile in the DCCT/EDIC cohort: associations with carotid intima‐media thickness
Authors: Lyons T. J. , Jenkins A. J. , Zheng D. , Klein R. L. , Otvos J. D. , Yu Y. , Lackland D. T. , McGee D. , McHenry M. B. , Lopes‐Virella M. , Garvey W. T. ,   The DCCT/EDIC Research Group
Published: August 2006

AbstractAims  To relate nuclear magnetic resonance lipoprotein subclass profiles (NMR‐LSP) and other lipoprotein‐related factors with carotid intima‐media thickness (IMT) in Type 1 diabetes.Methods  Lipoprotein‐related factors were determined in sera (obtained in 1997–1999) from 428 female [age 39 ± 7 years (mean ± sd)] and 540 male (age 40 ± 7 years) Diabetes Control and Complications Trial (DCCT)/Epidemiology of Diabetes Interventions and Complications (EDIC) participants. NMR quanti‐fies chylomicrons, three very low‐density lipoprotein (VLDL) subclasses, intermediate density lipoprotein (IDL), three low‐density lipoprotein (LDL) subclasses, two high‐density lipoprotein (HDL) subclasses, mean VLDL, LDL and HDL size, and LDL particle concentration. Conventional lipids, ApoA1, ApoB and Lp(a) and in vitro LDL oxidizibility were also measured. IMT was determined (in 1994–1995) using high‐resolution B‐mode ultrasound. Relationships between IMT and lipoproteins were analysed by multiple linear regression, controlling for age, diabetes‐related factors, and cardiovascular disease (CVD) risk factors.Results  IMT associations with lipoproteins were stronger for the internal than the common carotid artery, predominantly involving LDL. Internal carotid IMT was positively (P < 0.05) associated with NMR‐based LDL subclasses and particle concentration, and with conventional LDL‐cholesterol and ApoB in both genders. Common carotid IMT was associated, in men only, with large VLDL, IDL, conventional LDL cholesterol and ApoB.Conclusions  NMR‐LSP reveals significant associations with carotid IMT in Type 1 diabetic patients, even 4 years after IMT measurement. NMR‐LSP may aid early identification of high‐risk diabetic patients and facilitate monitoring of interventions. Longer DCCT/EDIC cohort follow‐up will yield CVD events and IMT progression, permitting more accurate assessment of pre‐morbid lipoprotein profiles as determinants of cardiovascular risk in Type 1 diabetes.
Routinely collected general practice data aids identification of people with hyperglycaemia and metabolic syndrome
Authors: Heldgaard P. E. , Griffin S. J. 
Published: August 2006

AbstractAims  To assess the performance of a risk score comprising data routinely available in general practice records (age, gender, body mass index, family history of diabetes, smoking habits and prescribed anti‐hypertensive drugs or steroids) in detecting diabetes, impaired glucose tolerance and metabolic syndrome.Methods  In a population‐based, cross‐sectional study in a semi‐rural general practice in Jutland, Denmark, Cambridge Risk Scores were calculated for 1355 patients without known diabetes (69% response rate) who completed questionnaires and underwent anthropometric measurement and an oral glucose tolerance test.Results  Prevalences of diabetes, impaired glucose tolerance and metabolic syndrome were 2.29% (95% CI: 1.56–3.23), 6.64% (95% CI: 5.38–8.10) and 13.4% (95% CI: 11.5–15.2), respectively. Area under the ROC curve for the risk score and diabetes was 83.8% (75.9–91.7) and for metabolic syndrome [European Group for the Study of Insulin Resistance (EGIR)] was 78.1% (74.6–81.6). Twenty per cent of the population had a risk score above 0.246; at this threshold the sensitivity to detect diabetes was 71.0% (53.4–83.9), the specificity 81.2% (79.0–83.2), positive predictive value 8.1% (6.6–10.0) and likelihood ratio 3.77 (2.94–4.85). For metabolic syndrome (EGIR) corresponding values for sensitivity were 50.3% (43.1–57.5), specificity 84.7% (82.5–85.6), positive predictive value 33.6% (28.2–39.4), and likelihood ratio 3.28 (2.69–4.00).Conclusions  Undiagnosed hyperglycaemia and metabolic syndrome are common. The Cambridge Risk Score is a practical first step in a screening procedure to identify individuals with these disorders who might benefit from diagnostic testing or to direct preventive interventions.