bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-scale structure of genomic methylation patterns
Authors: Rollins Robert A. , Haghighi Fatemeh , Edwards John R. , Das Rajdeep , Zhang Michael Q. , Ju Jingyue , Bestor Timothy H.
Published: December 2005

The mammalian genome depends on patterns of methylated cytosines for normal function, but the relationship between genomic methylation patterns and the underlying sequence is unclear. We have characterized the methylation landscape of the human genome by global analysis of patterns of CpG depletion and by direct sequencing of 3073 unmethylated domains and 2565 methylated domains from human brain DNA. The genome was found to consist of short (<4 kb) unmethylated domains embedded in a matrix of long methylated domains. Unmethylated domains were enriched in promoters, CpG islands, and first exons, while methylated domains comprised interspersed and tandem-repeated sequences, exons other than first exons, and non-annotated single-copy sequences that are depleted in the CpG dinucleotide. The enrichment of regulatory sequences in the relatively small unmethylated compartment suggests that cytosine methylation constrains the effective size of the genome through the selective exposure of regulatory sequences. This buffers regulatory networks against changes in total genome size and provides an explanation for the C value paradox, which concerns the wide variations in genome size that scale independently of gene number. This suggestion is compatible with the finding that cytosine methylation is universal among large-genome eukaryotes, while many eukaryotes with genome sizes <5 × 108 bp do not methylate their DNA.
Design optimization methods for genomic DNA tiling arrays
Authors: Bertone Paul , Trifonov Valery , Rozowsky Joel S. , Schubert Falk , Emanuelsson Olof , Karro John , Kao Ming-Yang , Snyder Michael , Gerstein Mark
Published: December 2005

A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central issue in designing tiling arrays is that of arriving at a single-copy tile path, as significant sequence cross-hybridization can result from the presence of non-unique probes on the array. Due to the fragmentation of genomic DNA caused by the widespread distribution of repetitive elements, the problem of obtaining adequate sequence coverage increases with the sizes of subsequence tiles that are to be included in the design. This becomes increasingly problematic when considering complex eukaryotic genomes that contain many thousands of interspersed repeats. The general problem of sequence tiling can be framed as finding an optimal partitioning of non-repetitive subsequences over a prescribed range of tile sizes, on a DNA sequence comprising repetitive and non-repetitive regions. Exact solutions to the tiling problem become computationally infeasible when applied to large genomes, but successive optimizations are developed that allow their practical implementation. These include an efficient method for determining the degree of similarity of many oligonucleotide sequences over large genomes, and two algorithms for finding an optimal tile path composed of longer sequence tiles. The first algorithm, a dynamic programming approach, finds an optimal tiling in linear time and space; the second applies a heuristic search to reduce the space complexity to a constant requirement. A Web resource has also been developed, accessible at http://tiling.gersteinlab.org, to generate optimal tile paths from user-provided DNA sequences.
Transposon-free regions in mammalian genomes
Authors: Simons Cas , Pheasant Michael , Makunin Igor V. , Mattick John S.
Published: December 2005

Despite the presence of over 3 million transposons separated on average by ∼500 bp, the human and mouse genomes each contain almost 1000 transposon-free regions (TFRs) over 10 kb in length. The majority of human TFRs correlate with orthologous TFRs in the mouse, despite the fact that most transposons are lineage specific. Many human TFRs also overlap with orthologous TFRs in the marsupial opossum, indicating that these regions have remained refractory to transposon insertion for long evolutionary periods. Over 90% of the bases covered by TFRs are noncoding, much of which is not highly conserved. Most TFRs are not associated with unusual nucleotide composition, but are significantly associated with genes encoding developmental regulators, suggesting that they represent extended regions of regulatory information that are largely unable to tolerate insertions, a conclusion difficult to reconcile with current conceptions of gene regulation.
STARS: Space–Time Analysis of Regional Systems
Authors: Rey Sergio J. , Janikas Mark V.
Published: December 2005

Space–Time Analysis of Regional Systems (STARS) is an open‐source package designed for the dynamic exploratory analysis of data measured for areal units at multiple points in time. STARS consists of four core analytical modules:Anselin (1995)exploratory spatial data analysis;Anselin (2003)inequality measures;Carlino and Mills (1993)mobility metrics; andChristakos, Bogaert, and Serre (2001)spatial Markov. Developed using the Python object‐oriented scripting language, STARS lends itself to three main modes of use. Within the context of a command line interface (CLI), STARS can be treated as a package which can be called from within customized scripts for batch‐oriented analyses and simulation. Alternatively, a graphical user interface (GUI) integrates most of the analytical modules with a series of dynamic graphical views containing brushing and linking functionality to support the interactive exploration of the spatial, temporal, and distributional dimensions of socioeconomic and physical processes. Finally, the GUI and CLI modes can be combined for use from the Python shell to facilitate interactive programming and access to the many libraries contained within Python. This article provides an overview of the design of STARS, its implementation, functionality, and future plans. A selection of its analytical capabilities are also illustrated that highlight the power and flexibility of the package.
Extending the SAND Spatial Database System for the Visualization of Three‐Dimensional Scientific Data
Authors: Samet Hanan , Webber Robert E.
Published: December 2005

The three‐dimensional extension of the SAND (Spatial and Nonspatial Data) spatial database system is described as is its use for data found in scientific visualization applications. The focus is on surface data. Some of the principal operations supported by SAND involve locating spatial objects in the order of their distance from other spatial objects in an incremental manner so that the number of objects that are needed is not known a priori. These techniques are shown to be useful in enabling users to visualize the results of certain proximity queries without having to execute algorithms to completion as is the case when performing a nearest‐neighbor query where a Voronoi diagram (i.e., Thiessen polygon) would be computed as a preprocessing step before any attempt to respond to the query could be made. This is achieved by making use of operations such as the spatial join and the distance semijoin. Examples of the utility of such operations is demonstrated in the context of posing meteorological queries to a spatial database with a visualization component.
A phylogeny of ranid frogs (Anura: Ranoidea: Ranidae), based on a simultaneous analysis of morphological and molecular data
Authors: Scott Elizabeth
Published: December 2005

During the last two decades, major taxonomic rearrangements were instituted in the anuran family Ranidae. Most of these changes were not based on phylogenetic analysis, and many are controversial. Addressing the phylogeny of Ranidae requires broader taxon sampling within the superfamily Ranoidea, the phylogenetic relationships and higher classification of which are also in a state of flux. No comprehensive attempt has yet been made to reconstruct ranid phylogeny using both morphological and molecular data. In the present contribution, data from 178 organismal characters were collated for 74 exemplar species representing the families Arthroleptidae, Hemisotidae, Hyperoliidae, Mantellidae Microhylidae, Petropedetidae, Rhacophoridae, Sooglossidae, and most subfamilies of Ranidae. These were combined with ∼1 kb of DNA sequence from the mitochondrial 12S rDNA and 16S rDNA gene regions in a simultaneous parsimony analysis with direct optimization. Results support the classification of Hemisus with the brevicipitine microhylids, confirm that Arthroleptidae (and its two component subfamilies Astylosterninae and Arthroleptinae) are monophyletic, and advocate the recognition of Leptopelidae. Monophyly of Ranidae is compromised by recognition of Petropedetidae, Rhacophoridae and Mantellidae, which should be recognized as subfamilies of Ranidae at present. Furthermore, Petropedetidae was found to be grossly paraphyletic, comprising three clades which are all considered separate subfamilies of Ranidae, i.e., Petropedetinae, Phrynobatrachinae and Cacosterninae. Three well defined subfamilies of Ranidae were consistently retrieved as monophyletic in a sensitivity analysis, i.e., Tomopterninae, Ptychadeninae and Pyxicephalinae. However, Ptychadeninae and Pyxicephalinae were embedded in Raninae and Dicroglossinae, respectively. Ceratobatrachinae is removed from Dicroglossinae. Dicroglossinae is synonymized with Pyxicephalinae. A new subfamily Strongylopinae is proposed. Raninae should be conservatively treated as a “metataxon” (sensuFord and Cannatella, 1993) until such time as it is fully revised. Tomopterninae is removed from synonymy with Cacosterninae. Morphological synapomorphies are reported for major monophyletic clades retrieved in the simultaneous analysis with equal weights. The present study found that many Old World clades appear to contain both African and Asian taxa, contrary to the findings of some recent biogeographical analyses. This study demonstrates the value of broad taxonomic sampling in ranid phylogeny, and highlights the immense contribution that can be made from detailed morphological data.

© The Willi Hennig Society 2005.
Phylogeny ofMysis(Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data
Authors: Audzijonytė Asta , Damgaard Jakob , Varvio Sirkka‐Liisa , Vainio Jouni K. , Väinölä Risto
Published: December 2005

We studied the phylogenetic history of opossum shrimps of the genusMysisLatreille, 1802 (Crustacea: Mysida) using parsimony analyses of morphological characters, DNA sequence data from mitochondrial (16S, COI and CytB) and nuclear genes (ITS2, 18S), and eight allozyme loci. With these data we aimed to resolve a long‐debated question of the origin of the non‐marine (continental) taxa in the genus, i.e., “glacial relicts” in circumpolar postglacial lakes and “arctic immigrants” in the Caspian Sea. A simultaneous analysis of the data sets gave a single tree supporting monophyly of all continental species, as well as monophyly of the taxa from circumpolar lakes and from the Caspian Sea. A clade of three circumarctic marine species was sister group to the continental taxa, whereas Atlantic species had more distant relationships to the others. Small molecular differentiation among the morphologically diverse endemic species from the Caspian Sea suggested their recent speciation, while the phenotypically more uniform “glacial relict” species from circumpolar lakes (Mysis relictagroup) showed deep molecular divergences. For the length‐variable ITS2 region both direct optimization anda priorialignment procedures gave similar topologies, although the former approach provided a better overall resolution. In terms of partitioned Bremer support (PBS), mitochondrial protein coding genes provided the largest contribution (83%) to the total tree resolution. This estimate however, appears to be partly spurious, due to the concerted inheritance of mitochondrial characters and probable cases of introgression or ancestral polymorphism.

© The Willi Hennig Society 2005.
The PhyloCode, types, ranks and monophyly: a response to Pickett
Authors: Laurin Michel , de Queiroz Kevin , Cantino Phil , Cellinese Nico , Olmstead Richard
Published: December 2005

A report from the First International Phylogenetic Nomenclature Meeting recently published in Cladistics conveys several misconceptions about the PhyloCode and presents an erroneous interpretation of discussions that took place at that meeting. Contrary to Pickett's assertions, the PhyloCode is designed to name clades, not paraphyletic groups; the rejection of ranks has never been a fundamental principle of phylogenetic nomenclature; and specifiers under the PhyloCode differ in several ways from types under rank‐based nomenclature.

© The Willi Hennig Society 2005.
A Bayesian approach for population pharmacokinetic modelling of sirolimus
Authors: Dansirikul Chantaratsamon , Morris Raymond G. , Tett Susan E. , Duffull Stephen B.
Published: December 2005

Aims

To explore a Bayesian approach for the pharmacokinetic analysis of sirolimus concentration data arising from therapeutic drug monitoring (poorly informative concentration‐time point design), and to explore possible covariate relationships for sirolimus pharmacokinetics.

Methods

Sirolimus concentration‐time data were available as part of routine clinical care from 25 kidney transplant recipients. Most samples were taken at or near the trough time point at steady state. The data were analyzed using a fully conditional Bayesian approach with PKBUGS (v 1.1)/WinBUGS (v 1.3). Features of the data included noncompliance and missing concentration measurements below the limit of sensitivity of the assay. Informative priors were used.

Results

A two‐compartment model with proportional residual error provided the best fit to the data (consisting of 315 sirolimus concentration‐time points). The typical value for the apparent clearance (CL/F ) was 12.5 l h−1 at the median age of 44 years. Apparent CL was found to be inversely related to age with a posterior probability of a clinically significant effect of 0.734.

Conclusions

A population pharmacokinetic model was developed for sirolimus using a novel approach. Bayesian modelling with informative priors allowed interpretation of a significant covariate relationship, even using poorly informative data.
Absence of an interaction between iron and mycophenolate mofetil absorption
Authors: Ducray Patricia Sanwald , Banken Ludger , Gerber Marianne , Boutouyrie Bruno , Zandt Hagen
Published: December 2005

Aim

To determine whether concomitant iron affects the absorption of mycophenolate mofetil.

Methods

An open‐label, single centre, randomized, crossover trial was conducted in 16 healthy males. Fasting subjects received mycophenolate mofetil alone (treatment A) or co‐administered with iron (treatment B).

Results

The mycophenolic acid AUC(0,24 h) for treatments A and B were 42.5 ± 10.5 and 44.7 ± 12.4 µg ml−1 h, respectively. anova modelling showed the relative bioavailability of mycophenolate mofetil to be similar for the two treatments (90% confidence interval 0.92, 1.19).

Conclusions

There was no interaction between mycophenolate mofetil and iron supplements administered concomitantly to healthy fasting subjects.
Genetic polymorphisms in KCNQ1, HERG, KCNE1 and KCNE2 genes in the Chinese, Malay and Indian populations of Singapore
Authors: Koo Seok Hwee , Ho Woon Fei , Lee Edmund Jon Deoon
Published: December 2005

Aims

To determine the genetic variability of long QT syndrome (LQTS)‐associated genes (KCNQ1, HERG, KCNE1 and KCNE2) among three distinct ethnic groups in the Singapore population.

Methods

Genomic DNA samples from up to 265 normal healthy Chinese, 118 Malay and 139 Indian volunteer subjects were screened for genetic variations in the coding region of the LQTS‐associated genes using denaturing high‐performance liquid chromatography and sequencing analyses.

Results

In total, 37 single nucleotide polymorphisms (SNPs) were identified in the coding exons of the LQTS‐associated potassium ion channel genes, seven of which were novel nonsynonymous polymorphisms. SNPs 356G→A (exon 1 of KCNQ1), 2624C→T and 2893G→A (exon 11 of HERG), 3164G→A, 3322C→G and 3460G→A (exon 14 of HERG), and 79C→T (exon 3 of KCNE2) resulted in Gly119Asp, Thr875Met, Gly965Arg, Arg1055Gln, Leu1108Val, Gly1154Ser and Arg27Cys amino acid substitutions, respectively. In addition, 16 intronic variants were detected. The functional consequence of these variants has not been studied and their association with risk of LQTS is unclear.

Conclusions

There exist multiple genetic polymorphisms of the LQTS‐associated genes in the three distinct Asian populations. Though the functional significance of many of these SNPs is unknown, this interindividual and interethnic genetic variability may underlie the different susceptibilities of individuals to developing LQTS.
A placebo‐controlled study of retinal blood flow changes by pentoxifylline and metabolites in humans
Authors: Magnusson Marie , Bergstrand Ingar C. , Björkman Sven , Heijl Anders , Roth Bodil , Höglund Peter
Published: December 2005

Aim

To investigate the possible effects of pentoxifylline metabolites on retinal blood flow in humans.

Methods

A randomized, placebo‐controlled, four‐period cross‐over study that was observer blinded and partly blinded for the eight participants. On one occasion a placebo was given as an intravenous (i.v.) infusion over 100 min. On the other three occasions pentoxifylline was administered as i.v. infusions over 100 min at a rate of 3 mg min−1. Before two of the pentoxifylline infusions the subjects were pretreated with either ciprofloxacin or rifampicin. Retinal blood flow was measured by scanning laser doppler flowmetry (SLDF) in a selected area of the central temporal retina before, during and until 5 h after the end of infusion. Blood samples for concentration analyses of pentoxifyllin, R‐M1, S‐M1, M4 and M5 were taken serially and areas under the curves (AUCs) were calculated. Linear mixed models were used for the statistical analyses.

Results

Mean AUCs (ng h ml−1) were significantly increased for pentoxifylline (1964 vs. 1453) and S‐M1 (5804 vs. 4227), but not R‐M1 when pentoxifylline was co‐administered with ciprofloxacin. The mean AUC for M5 was significantly reduced when subjects were pretreated with rifampicin (2041 vs. 3080). Pentoxifylline with and without pretreatment with rifampicin significantly increased retinal blood flow assessed as mean flow, pulsation (i.e. 1‐systole/diastole), and diastolic flow (but not during systole), compared with placebo. The increases over placebo were more pronounced on diastolic flow, 9.7% (95% confidence interval 4.2, 15.5) than on mean flow, 4.6% (1.1, 8.3) after pentoxifylline administration. With pentoxifylline after rifampicin pretreatment the corresponding differences were 11.7% (5.8, 17.9) and 5.1% (1.4, 7.8) over placebo, respectively. After co‐administration of pentoxifylline and ciprofloxacin we saw only a nonsignificant trend towards increased flow during diastole, but a significant decrease in pulsation. When AUCs for pentoxifylline and its metabolites were used as regressor variables to retinal mean flow we found that pentoxifylline, R‐M1 and M5 had coefficients with a positive sign indicating that they enhanced the retinal blood flow. In contrast, S‐M1 and M4 had coefficients with negative sign and thus appeared to decrease the blood flow in subjects treated with pentoxifylline.

Conclusion

The R‐M1 and M5 metabolites of pentoxifylline contributed significantly to the effects of pentoxifylline on retinal blood flow.
Tadalafil pharmacokinetics in healthy subjects
Authors: Forgue S. Thomas , Patterson Beverley E. , Bedding Alun W. , Payne Christopher D. , Phillips Diane L. , Wrishko Rebecca E. , Mitchell Malcolm I.
Published: December 2005

Aims

To characterize tadalafil plasma pharmacokinetics in healthy subjects following single and multiple doses.

Methods

Noncompartmental parameters were calculated for healthy subjects receiving a single 2.5–20‐mg tadalafil dose in 13 clinical pharmacology studies. An integrated statistical analysis of results in 237 subjects provided global averages and an assessment of effects of body mass index (BMI), age, gender and smoking status. Diurnal variation, food effects and proportionality of exposure to dose were analysed in three studies. Multiple‐dose pharmacokinetics were evaluated in a separate study in which parallel groups of 15 subjects received 10 or 20 mg tadalafil once daily for 10 days.

Results

Tadalafil was absorbed rapidly with mean Cmax (378 µg l−1 for 20 mg) observed at 2 h; thereafter, concentrations declined nearly monoexponentially with a mean (5th, 95th percentiles) t1/2 of 17.5 (11.5, 29.6) hours. Mean oral clearance (CL/F) was 2.48 (1.35, 4.35) l h−1 and apparent volume of distribution (Vz/F) was 62.6 (39.5, 92.1) l. No clinically meaningful effect of BMI, age, gender or smoking was identified. Exposure was not substantially affected by time of dosing. Food had negligible effects on bioavailability as assessed by 90% confidence intervals for Cmax and AUC mean ratios. Parameters were proportional to dose, indicating that doubling the dose doubled exposure. Steady state was attained by day 5 following once‐daily administration, and accumulation (1.6‐fold) was consistent with the t1/2.

Conclusions

Tadalafil pharmacokinetics are linear with respect to dose and time, and are not affected by food. Systemic clearance is low relative to other phosphodiesterase 5 inhibitors.
Reduction of oxidative stress and modulation of autoantibodies against modified low‐density lipoprotein after rosuvastatin therapy
Authors: Resch Ulrike , Tatzber Franz , Budinsky Alexandra , Sinzinger Helmut
Published: December 2005

Aims

To examine the effect of 24 weeks’ rosuvastatin treatment on oxidative stress and changes in immune response to oxidized low‐density lipoprotein (LDL).

Methods

This was an open‐label study of patients in Austria receiving 10 or 40 mg rosuvastatin daily alternately during 12 and 24 weeks. Circulating concentrations of antibodies to malondialdehyde‐oxidized LDL (MDA‐LDL), both IgG and IgM type, to copper‐oxidized LDL (Cu‐OxLDL‐IgG), concentrations of oxidized LDL complexed to IgG (OxLDL‐IC) and markers of oxidative stress and systemic inflammation in subjects with plasma LDL cholesterol concentrations between 130 mg dl−1 and 250 mg dl−1 and triglycerides ≤ 400 mg dl−1 were determined.

Results

During statin therapy, plasma endogenous peroxides (POX‐ACT) concentrations and peroxidase activity were significantly decreased, associated with a modest increase in total antioxidant capacity (TAC). Antibody titres to MDA‐LDL‐IgM, Cu‐OxLDL‐IgG and OxLDL‐IC decreased, whereas MDA‐LDL‐IgG concentrations were increased after therapy. These changes were dose‐ and LDL‐independent. POX‐ACT concentrations were significantly positively correlated with inflammation markers before and after therapy and inversely with high‐density lipoprotein‐cholesterol concentrations after therapy.

Conclusion

This study provides in vivo evidence that rosuvastatin significantly reduces oxidative stress and has immunomodulatory properties in a dose‐ and LDL‐independent manner.
Initial phase of chronic medication use; patients’ reasons for discontinuation
Authors: Hugtenburg J. G. , Blom A. Th. G. , Kisoensingh S. U.
Published: December 2005

Aim The aim of this study was to gain more insight into patients’ reasons for discontinuing chronic medication.

Methods Electronic medication overviews recorded by a pharmacy were analysed with respect to patients’ return behaviour during 3 months following their first prescription. Patients who did not return in time were interviewed by telephone to find out their reasons for either returning too late or not returning at all to the pharmacy to collect their repeat medication.

Results Of 232 first‐time chronic medication prescriptions, 132 were not collected at all (46.1%) or too late (11%). These prescriptions involved 121 patients, 113 (93.4%) of whom participated in the telephone interview. Twenty patients returned too late to collect their repeat prescriptions, largely because they had forgotten to take their medication according to schedule (n = 13). Ninety‐three patients did not return to the pharmacy at all because of side‐effects (24.5%), inefficacy (16.4%), medication not intended for chronic use (15.3%) and absence of need for continued use (14.3%).

Conclusions About 50% of patients who have been prescribed chronic medication for the first time stop using their drugs within a matter of months. Perceived drug side‐effects, drug ineffectiveness and personal considerations related to use and a lack of need of treatment were the main reasons for discontinuing chronic drug therapy. This kind of noncompliance may result in an increased health risk as well as constituting a waste of a large amount of money. Adequate patient counselling and shared decision‐making between doctors and patients are needed to prevent the unnecessary cessation of chronic drug therapy.
The influence of CYP2D6 genotype on trough plasma perhexiline and cis‐OH‐perhexiline concentrations following a standard loading regimen in patients with myocardial ischaemia
Authors: Davies Benjamin J. , Coller Janet K. , James Heather M. , Somogyi Andrew A. , Horowitz John D. , Sallustio Benedetta C.
Published: December 2005

Aims

CYP2D6 protein expression is determined by the number of functional CYP2D6 alleles. It is also higher in individuals with at least one CYP2D6*2 allele. This study has investigated the effect of the number of functional CYP2D6 alleles and the influence of CYP2D6*2 alleles on plasma perhexiline concentrations in patients administered a standard loading regimen over 3 days.

Methods

Eighteen patients with myocardial ischaemia who were not taking any drugs known to inhibit CYP2D6 metabolism in vivo commenced treatment with 200 mg of perhexiline twice per day. On the fourth day, blood was drawn for genotyping and the measurement of trough plasma concentrations of perhexiline and its major metabolite, cis‐OH‐perhexiline.

Results

The only genotypic CYP2D6 poor metabolizer had a trough plasma perhexiline concentration of 2.70 mg l−1 and no detectable cis‐OH‐perhexiline. The mean ± SD trough plasma perhexiline concentration in patients with one functional allele was significantly higher (0.63 ± 0.31 mg l−1, n = 8, P = 0.05) than in patients with two functional alleles (0.37 ± 0.17 mg l−1, n = 9). Conversely, the mean metabolic ratio was significantly lower in patients with one functional allele (2.90 ± 1.76, P < 0.01) compared with patients with two functional alleles (6.52 ± 3.26). Patients with at least one CYP2D6*2 allele had a lower plasma perhexiline concentration (0.20 ± 0.09 mg l−1, n = 5, P < 0.001) and a higher metabolic ratio (7.86 ± 2.51, P < 0.01) than the non‐poor metabolizer patients with no CYP2D6*2 alleles (0.62 ± 0.23 mg l−1 and 3.55 ± 2.54, respectively, n = 12).

Conclusion

Patients with only one functional allele and not CYP2D6*2 have diminished CYP2D6 metabolic capacity for perhexiline.
Curriculum development in pharmacotherapy: testing the ability of preclinical medical students to learn therapeutic problem solving in a randomized controlled trial
Authors: Vollebregt J. A. , Metz J. C. M. , De Haan M. , Richir M. C. , Hugtenburg J. G. , De Vries T. P. G. M.
Published: December 2005

Aims

To determine whether preclinical medical students are able to learn therapeutic problem solving simultaneously with gaining knowledge of pharmacology.

Methods

A randomized controlled pre/post‐test study among 85 3rd year preclinical medical students from two medical faculties in Amsterdam. In addition to the normal curriculum, the study group followed a course, which was a copy of the obligatory training in cognitive therapeutic skills for 5th year students who had gained knowledge first, followed by applying the knowledge. Before, immediately after and 9 months after the training both the study group and a control group took a test (T0, T1, T2). The level of knowledge and cognitive therapeutic skills were assessed. As a reference, 38 5th year students also took the tests.

Results

On T0 the levels of cognitive therapeutic skills of the study and control groups were similar (26.7% and 27.4% of the required level for graduation, respectively). On T1 and T2, the study group scored significantly higher compared with the control group: 46.0/36.7% and 41.3/36.3%, respectively (P < 0.05). In comparison with T0, the scores of the study group on T1 increased significantly and showed no significant decline on T2. There were no differences between the groups with respect to the level of knowledge in any of the three tests. The level of cognitive therapeutic skills in the 5th year reference group increased slightly but not significantly from 40.3% to 44.5% after the training; the level of knowledge increased significantly from 48.8% to 68.0%.

Conclusions

Preclinical medical students are able to learn cognitive therapeutic skills simultaneously with gaining knowledge of pharmacology.
Low incidence of hypertensive disorders of pregnancy in women treated with spiramycin for toxoplasma infection
Authors: Todros T. , Verdiglione P. , Oggè G. , Paladini D. , Vergani P. , Cardaropoli S.
Published: December 2005

Aims

Toxoplasma infection in pregnancy is usually treated with long‐term administration of the macrolide spiramycin to prevent fetal malformations. We had empirically observed that treated patients seldom developed pregnancy‐induced hypertension (PIH), a common and severe disorder of pregnancy whose aetiology and pathogenesis are still debated. Some clinical and experimental data suggest that infection could play a role in its development.

Methods

To test this hypothesis, we studied a cohort of 417 pregnant women treated with spiramycin because of seroconversion for Toxoplasma gondii and 353 low‐risk women who did not take any antibiotic during pregnancy. PIH was defined as blood pressure >140/90 mmHg on two or more occasions, occurring after 20 weeks of gestational age.

Results

Seventeen (5.2%) women in the control group developed PIH compared with two (0.5%) in the case group. The odds of developing the disease were significantly lower in the treated subjects (odds ratio = 0.092, 95% confidence interval 0.021, 0.399; P < 0.001).

Conclusions

Our results suggest that antibiotic treatment during pregnancy can reduce the incidence of PIH, thus opening new perspectives in its prevention and therapy.
Differentialin vitroinhibition of M3G and M6G formation from morphine by (R)‐ and (S)‐methadone and structurally related opioids
Authors: Morrish Glynn A. , Foster David J. R. , Somogyi Andrew A.
Published: December 2005

AimsTo determine thein vitrokinetics of morphine‐3‐glucuronide (M3G) and morphine‐6‐glucuronide (M6G) formation and the inhibition potential by methadone enantiomers and structurally related opioids.

MethodsM3G and M6G formation kinetics from morphine were determined using microsomes from five human livers. Inhibition of glucuronide formation was investigated with eight inhibitors (100 µm) and the mechanism of inhibition determined for (R)‐ and (S)‐methadone (70–500 µm) using three microsomal samples.

ResultsGlucuronide formation displayed single enzyme kinetics. The M3GVmax(mean ± SD) was 4.8‐fold greater than M6GVmax(555 ± 110vs.115 ± 19 nmol mg−1protein h−1;P = 0.006, mean of difference 439; 95% confidence interval 313, 565 nmol mg−1protein h−1).Kmvalues for M3G and M6G formation were not significantly different (1.12 ± 0.37vs.1.11 ± 0.31 mm;P = 0.89, 0.02; − 0.29, 0.32 mm). M3G and M6G formation was inhibited (P < 0.01) with a significant increase in the M3G/M6G ratio (P < 0.01) for all compounds tested. Detailed analysis with (R)‐ and (S)‐methadone revealed noncompetitive inhibition with (R)‐methadoneKiof 320 ± 42 µmand 192 ± 12 µmfor M3G and M6G, respectively, and (S)‐methadoneKiof 226 ± 30 µmand 152 ± 20 µmfor M3G and M6G, respectively.Kivalues for M3G inhibition were significantly greater than for M6G for (R)‐methadone (P = 0.017, 128; 55, 202 µm) and (S)‐methadone (P = 0.026, 75; 22, 128 µm).

ConclusionsBoth methadone enantiomers noncompetitively inhibited the formation of morphine's primary metabolites, with greater inhibition of M6G formation compared with M3G. These findings indicate a mechanism for reduced morphine clearance in methadone‐maintained patients and reduced relative formation of the opioid active M6G compared with M3G.
A randomised control trial of patient self‐management of oral anticoagulation compared with patient self‐testing
Authors: Gardiner Chris , Williams Karen , Longair Ian , Mackie Ian J. , Machin Samuel J. , Cohen Hannah
Published: December 2005

Several studies suggest that patient self‐management (PSM) may improve the quality of oral anticoagulation therapy as measured by time spent within the international normalised ratio (INR) target range. We performed a prospective randomised control trial to determine whether the improvement in quality of treatment afforded by PSM is greater than that achieved by patient self‐testing (PST) alone. A total of 104 of 800 eligible patients aged 22–88 years (median = 59·8), attending our hospital anticoagulant clinic and receiving long‐term warfarin for >8 months agreed to participate. Patients were randomised to PSM (n = 55) or PST (n = 49). Both groups measured their INR using the CoaguChek S every 2 weeks or more frequently if required, for a period of 6 months. Seventy‐seven of 104 (74%) patients completed the study (PSM = 41 and PST = 36). The ‘drop out’ rates for both groups were similar. There was no significant difference between the percentage time in target therapeutic range for PSM (69·9%) and PST (71·8%). Both groups combined showed a significant improvement over the previous 6 months (71·0% vs. 62·5%; P = 0·04). Changes in time within the therapeutic range in individual patients (+5·86) also showed a significant difference. The quality of warfarin control in both PST and PSM may be superior to that achieved by conventional management in a specialised hospital anticoagulation clinic.
Increased levels of soluble flt‐3 ligand in serum and long‐term bone marrow culture supernatants in patients with chronic idiopathic neutropenia
Authors: Papadaki Helen A. , Damianaki Athina , Pontikoglou Charalampos , Pyrovolaki Katerina , Eliopoulos Dimitris G. , Stavroulaki Emily , Eliopoulos George D.
Published: December 2005

The levels of serum and long‐term bone marrow culture supernatant soluble flt‐3 ligand (sFL) were determined in 54 patients with chronic idiopathic neutropenia (CIN) and 16 normal controls. Both serum and supernatant sFL levels were significantly increased in the patients compared with controls. Individual sFL values inversely correlated with the number of circulating neutrophils and the proportion of bone marrow CD34+ cells. Supernatant sFL values positively correlated with the levels of supernatant G‐CSF. These findings suggest that the impaired myelopoiesis in CIN patients is accompanied by a compensatory mechanism attempting to increase the neutrophil production at the myeloid progenitor cell level.
Analysis of immunoglobulin VH genes suggests cutaneous marginal zone B‐cell lymphomas recognise similar antigens
Authors: Bahler David W. , Kim Bong K. , Gao Aili , Swerdlow Steven H.
Published: December 2005

Extranodal marginal zone B‐cell lymphomas (EMZL) are thought to develop from reactive infiltrates that represent immune responses to external or auto‐antigens. Except for gastric EMZL, the antigenic triggers of EMZL development are mostly unknown, although a subset of cutaneous EMZL have been associated with Borrelia burgdorferi infections. To further evaluate whether a common antigen may be promoting the development of cutaneous EMZL, the immunoglobulin heavy chain variable (VH) genes from eight USA cases were sequenced and analysed. All used VH3 family gene segments, with 2/8 using the same V3–30 segment, 2/8 using the closely related V3–30·3 or V3–33 segments, 6/8 containing mutations and 2/7 showing evidence of ongoing mutation. Many of the complimentarity‐determining region 3s (CDR3s) also showed similarities in length and displayed conserved amino acid motifs in the non‐templated areas between the diversity and joining segments. The use of similar VH gene segments and conserved CDR3 amino acid motifs suggests that some of these cutaneous EMZL may bind the same or similar antigen via their surface immunoglobulin receptor. Analysis of the somatic mutations present in many of the VH genes was also consistent with antigen directly stimulating the growth of cutaneous EMZL.
Correction of severe anaemia using immuno‐regulated gene therapy is achieved by restoring the early erythroblast compartment
Authors: Du  Roure Camille , Takács Katalin , Maxwell Patrick H. , Roberts Irene , Dazzi Francesco , Cannella Laura , Merkenschlager Matthias , Fisher Amanda G.
Published: December 2005

Patients with chronic renal failure usually require exogenous erythropoietin (epo) to alleviate anaemia resulting from inadequate epo production by the kidneys. We have recently shown that severe anaemia in genetically manipulated epo‐deficient mice (EpoTAg) can be corrected by adoptively transferred epo‐producing lymphocytes. The aim of this study was to investigate the precise effects of human epo administration by this route on erythropoietic development in epo‐deficient mice. The erythroblast compartments of untreated and treated EpoTAg mice were analysed in comparison with wild‐type mice. The early erythroblast population was reduced in the bone marrow of epo‐deficient mice, whilst the number of erythroid colony‐forming units (CFU‐E) was not significantly compromised. This paucity in marrow early erythroblasts was restored to normal values in treated mutant mice. In addition, the early erythroblast population was expanded in the spleens of treated animals. These findings show that the early erythroblasts are important targets of epo and that epo corrects anaemia of epo‐deficient mice by restoring marrow function and splenic erythropoiesis.
Treatment for myeloid leukaemia of Down syndrome: population‐based experience in the UK and results from the Medical Research Council AML 10 and AML 12 trials
Authors: Rao Anupama , Hills Robert K. , Stiller Charles , Gibson Brenda E. , de Graaf Siebold S.N. , Hann Ian M. , O'Marcaigh Aengus , Wheatley Keith , Webb David K.H.
Published: December 2005

Down syndrome (DS) children are at an increased risk of developing myelodysplasia and acute myeloid leukaemia (AML). We retrospectively analysed the population‐based data on 81 children with myeloid leukaemia of Down syndrome (ML‐DS) from the UK National Registry of Childhood Tumours and experience in the Medical Research Council (MRC) AML 10 and AML 12 trials, which enrolled 46 children with ML‐DS from 1988 to 2002. Eight per cent of UK children with AML had DS, but DS children comprised only 5% of children registered in MRC trials. The unique clinical characteristics of ML‐DS were confirmed. Overall survival (OS) of ML‐DS at 5 years increased from 47% in UK children diagnosed from 1988 to 1995 to 75% in children diagnosed from 1996 to 2002. OS for DS children registered in AML 10 and AML 12 was 74% in 5 years and improved from AML 10 to AML 12 (56% vs. 83%) There was no significant difference in OS between DS and non‐DS children (OS: 74% vs. 62%, P = 0·4) in the trials, but this result masked a significant increase in early death amongst DS children, with a significant reduction in mortality later on. Relapse was significantly reduced (3% vs. 39%, P = 0·0003), leading to the improved disease‐free survival (83% vs. 56%, P = 0·02). Given the increased number of earl treatment‐related deaths, future treatment protocols should aim to reduce chemotherapy dosage or intensity whilst maintaining low rates of resistant and recurrent disease.
Oxindole alkaloids from Uncaria tomentosa induce apoptosis in proliferating, G0/G1‐arrested and bcl‐2‐expressing acute lymphoblastic leukaemia cells
Authors: Bacher Nicole , Tiefenthaler Martin , Sturm Sonja , Stuppner Hermann , Ausserlechner Michael J. , Kofler Reinhard , Konwalinka Günther
Published: December 2005

Natural products are still an untapped source of promising lead compounds for the generation of antineoplastic drugs. Here, we investigated for the first time the antiproliferative and apoptotic effects of highly purified oxindole alkaloids, namely isopteropodine (A1), pteropodine (A2), isomitraphylline (A3), uncarine F (A4) and mitraphylline (A5) obtained from Uncaria tomentosa, a South American Rubiaceae, on human lymphoblastic leukaemia T cells (CCRF‐CEM‐C7H2). Four of the five tested alkaloids inhibited proliferation of acute lymphoblastic leukaemia cells. Furthermore, the antiproliferative effect of the most potent alkaloids pteropodine (A2) and uncarine F (A4) correlated with induction of apoptosis. After 48 h, 100 μmol/l A2 or A4 increased apoptotic cells by 57%. CEM‐C7H2 sublines with tetracycline‐regulated expression of bcl‐2, p16ink4A or constitutively expressing the cowpox virus protein crm‐A were used for further studies of the apoptosis‐inducing properties of these alkaloids. Neither overexpression of bcl‐2 or crm‐A nor cell‐cycle arrest in G0/G1 phase by tetracycline‐regulated expression of p16INK4A could prevent alkaloid‐induced apoptosis. Our results show the strong apoptotic effects of pteropodine and uncarine F on acute leukaemic lymphoblasts and recommend the alkaloids for further studies in xenograft models.
Involvement of 4-1BB (CD137)−4-1BBligand interaction in the modulation of CD4+ T cell-mediated inflammatory colitis
Authors: Maerten P , Kwon B S , Shen C , De Hertogh G , Cadot P , Bullens D M A , Overbergh L , Mathieu C , Van Assche G , Geboes K , Rutgeerts P , Ceuppens J L
Published: December 2005

4-1BB ligand (4-1BBL) expressed on antigen-presenting cells interacts with 4-1BB on activated T cells (especially CD8+ cells) and co-stimulates the latter to secrete cytokines and to proliferate. The role of 4-1BB−4-1BBL interaction was studied here in a model of colitis based on naive CD4+ T cell transfer to SCID mice, a disease model in which CD8 cells do not take part. We found that CD4+ T cells from 4-1BB-deficient mice, after transfer in SCID mice, proliferated more rapidly compared to wild-type CD4+ T cells. Mice reconstituted with naive CD4+ T cells from 4-1BB-deficient mice developed colitis, however, with a mixed Th1/Th2 response, in contrast to the Th1-type response in mice reconstituted with wild-type naive CD4+ T cells. Importantly, this altered cytokine response did not temper colitis severity. Although it has been reported previously that 4-1BB co-stimulation may contribute to regulatory T cell functioning, we found that CD4+CD25+ regulatory T cells from 4-1BB-deficient mice were perfectly able to prevent naive CD4+ T cell-induced colitis. In conclusion, our data provide evidence that 4-1BB−4-1BBL interaction modulates the effector CD4+ T cell-driven immune response and cytokine production in experimental colitis without affecting regulatory T cell function.
Immunomodulation using the recombinant monoclonal human B7-DC cross-linking antibody rHIgM12
Authors: Van Keulen V P , Ciric B , Radhakrishnan S , Heckman K L , Mitsunaga Y , Iijima K , Kita H , Rodriguez M , Pease L R
Published: December 2005

A patient with Waldenstrom’s macroglobulinaemia expresses a high titre IgM antibody in serum that binds both mouse and human dendritic cells (DC) in a B7-DC (PD-L2)-dependent manner. We have reported previously that purified antibody from patient serum activates immature and mature DC in vitro, enhancing the ability of these professional antigen-presenting cells to activate naive T cells, take up antigen, resist a cytokine-depleted environment and secrete immunomodulatory cytokines, such as interkeukin (IL)-6 and tumour necrosis factor (TNF)-α. Systemic treatment of experimental animals with this antibody induces potent anti-melanoma immunity and modulates protectively the recall response against antigen challenge through the airway in an experimental model of inflammatory airway disease. Here we describe a monoclonal IgM antibody derived from this serum immunoglobulin that recapitulates each of these earlier observations, providing direct evidence that M protein from the Waldenstrom’s patient mediates these potent immunomodulatory effects. Furthermore, cell lines expressing this recombinant form of the human antibody provide the basis for developing this reagent for clinical application.
Oral administration of CpG-ODNs suppresses antigen-induced asthma in mice
Authors: Kitagaki K , Businga T R , Kline J N
Published: December 2005

Oligodeoxynucleotides containing CpG motifs (CpG-ODNs) can protect against eosinophilic airway inflammation in asthma. Previously we have found that parenteral or mucosal administration of CpG-ODNs is effective in preventing (as well as reversing established) disease. In this study, we examined the effect of oral CpG-ODNs on the development of immune tolerance. Using an ovalbumin (OVA)-induced murine model of asthma, we found that CpG-ODNs, administered orally around the time of sensitization, prevented eosinophilic airway inflammation in a dose-dependent manner. Although oral co-administration of CpG-ODNs with OVA (known to induce tolerance) did not significantly change the inhibition of OVA-induced airway eosinophilia, it did modulate OVA-specific immunoglobulin responses: oral administration of OVA alone suppressed OVA-specific IgG1 production, but only mice that received CpG-ODNs demonstrated enhanced levels of OVA-specific IgG2c. Finally, we examined whether oral administration of CpG-ODNs, alone or with OVA, could reverse established eosinophilic airway inflammation. Again, neither OVA nor CpG-ODNs alone modulated established eosinophilic airway inflammation, but a combination of the OVA and CpG-ODNs successfully desensitized the mice. This desensitization was associated with suppression of OVA-specific IgE and enhancement of OVA-specific IgG2c production. These findings provide the first indication that oral administration of CpG-ODNs is effective in preventing and reversing antigen-induced eosinophilic airway inflammation. CpG-ODNs may be useful as a component of oral immunotherapy to promote tolerance in established asthma.
NK cells, displaying early activation, cytotoxicity and adhesion molecules, are associated with mild dengue disease
Authors: Azeredo E L , De Oliveira-Pinto L M , Zagne S M , Cerqueira D I S , Nogueira R M R , Kubelka C F
Published: December 2005

During the innate immune response against infections, Natural Killer (NK) cells are as important effector cells as are Cytotoxic T lymphocytes (CTL) generated after antigenic stimulation in the adaptative response. NK cells increase in numbers, after viral infection or vaccination. We investigated the NK cell and CD8 T lymphocyte status in 55 dengue infected patients. The NK (CD56+CD3-) and CD56+ T cell (CD56+CD3+) rates rise during the acute phase of disease. The majority of NK cells from dengue patients display early markers for activation (CD69, HLA-DR, and CD38) and cell adhesion molecules (CD44, CD11a) during the acute phase of disease. The intracellular cytotoxic granule, TIA-1, is also up-regulated early in NK cells. Most of these markers appear also on CD8+ T lymphocytes but during the late acute phase. Circulating IL-15 is elevated in a significant number of patients during early acute infection and its values were statistically correlated with NK frequencies and cytotoxic markers on NKs. We have therefore shown that dengue virus infection is very likely stimulating a cytotoxic response that may be efficient in controlling the virus in synergism with CD8+ T lymphocytes. Interestingly, the heightened CD56+CD3-, CD56+CD3+, CD56+TIA-1+ and CD56+CD11a+ cell rates are associated with mild dengue clinical manifestations and might indicate a good prognosis of the disease.