bluuebunny/crossref_metadata_2025 huggingface dataset:
On the deformation and drag of a type-A multiple drop at low Reynolds number
Authors: Brunn P. O. , Roden T.
Published: April 2006

The dynamics of a perfectly symmetric type-A multiple drop is studied. Up to first order in Reynolds number a force balance predicts the size ratios of the two constituents of such a drop to be unique for each system. Inertial effects are shown (a) to be destabilizing and (b) to exclude the possibility of obtaining perfectly concentric type-A droplets in a diffusion column. This latter conclusion is strengthened further by the sedimentation results.
Synchronization in large directed networks of coupled phase oscillators
Authors: Restrepo Juan G. , Ott Edward , Hunt Brian R.
Published: April 2006

We study the emergence of collective synchronization in large directed networks of heterogeneous oscillators by generalizing the classical Kuramoto model of globally coupled phase oscillators to more realistic networks. We extend recent theoretical approximations describing the transition to synchronization in large undirected networks of coupled phase oscillators to the case of directed networks. We also consider the case of networks with mixed positive-negative coupling strengths. We compare our theory with numerical simulations and find good agreement.
Effective plasma confinement by applying multipolar magnetic fields in an internal linear inductively coupled plasma system
Authors: Kim Kyong Nam , Kim Mi Suk , Yeom Geun Young
Published: April 2006

A novel internal-type linear inductive antenna referred to as “double comb-type antenna” was used for a large-area plasma source with the substrate area of 880mm×660mm and the effect of plasma confinement by applying multi-polar magnetic field was investigated. High-density plasmas on the order of 3.18×1011cm−3, which is 50% higher than that obtained for the source without the magnetic field, could be obtained at the pressure of 15mTorr Ar and at the inductive power of 5000W with good plasma stability. The plasma uniformity less than 3% could also be obtained within the substrate area. When SiO2 film was etched using the double comb-type antenna, the average etch rate of about 2100Å∕min could be obtained with the etch uniformity of 5.4% on the substrate area using 15mTorr SF6, 5000W of rf power, and −34V of dc bias voltage.
Ultrafast carrier capture and relaxation in modulation-doped InAs quantum dots
Authors: Sun K. W. , Kechiantz A. , Lee B. C. , Lee C. P.
Published: April 2006

We report investigations on carrier capture and relaxation processes in undoped and modulation-doped InAs∕GaAs self-assembled quantum dots (QDs) by using time-resolved spectroscopy technique with a time resolution of ∼200fs. We find that carrier capture and relaxation in the ground state of the charged QD are faster compared to the undoped dots even at an excitation level as low as 1×1010cm−2. It is attributed to the triggering of the vibrating polarization field induced by the presence of cold carriers in the doped dots. The rate of an electron been captured by a positively charged QD is also calculated based on our proposed model.
Sustainable grazing systems for the Central Tablelands of New South Wales. 1. Agronomic implications of vegetation - environment associations within a naturalised temperate perennial grassland
Authors: King W. McG. , Dowling P. M. , Michalk D. L. , Kemp D. R. , Millar G. D. , Packer I. J. , Priest S. M. , Tarleton J. A.
Published: April 2006

Temperate perennial grass-based pastures dominate the high rainfall zone of south-eastern Australia and support a major livestock production industry. This area has experienced a recent change in overall pasture condition, however, typified by a reduction in the abundance of perennial grasses and an increasingly prominent winter-annual grass weed component. Improving the condition and productivity of these pastures can be achieved by improved management but this requires better knowledge of the interactions between management options and pasture species composition and of the interaction between pasture vegetation and the complex effects of a heterogeneous landscape. This paper reports the results of an intensive survey of a 60-ha paddock that was designed to identify the species present, determine their patterns of distribution and examine the relationships between pasture vegetation and the environment. The survey of species present in late summer was supplemented by the identification of seedlings that later emerged from extracted soil cores and by soil physical and chemical analyses. Data were analysed using ordination and interpreted with GIS software so that topographic features could be considered.
The most frequently identified taxa were Hypochaeris radicata, Austrodanthonia spp. and Bothriochloa spp. (in late summer) and Vulpia spp., Bromus molliformis and Trifolium subterraneum (winter-annual species). Austrodanthonia spp. were commonly found on the drier ridges and more acid soils with lower phosphate levels. These were also the areas dominated in spring by Vulpia spp. and were generally lower in plant species richness overall. The most species-rich areas occurred downslope where soil fertility was higher and less moisture stress was presumably experienced. The measured environmental factors explained a substantial proportion of the variation in the vegetation dataset, which underlined the importance of considering landscape effects in the management of typical tablelands pastures.
Sustainable grazing systems for the Central Tablelands of New South Wales. 2. Effect of pasture type and grazing management on pasture productivity and composition
Authors: Dowling P. M. , Michalk D. L. , Kemp D. R. , Millar G. D. , Priest S. M. , King W. McG. , Packer I. J. , Holst P. J. , Tarleton J. A.
Published: April 2006

This paper reports results from a large-scale field experiment conducted on a naturalised pasture at Carcoar, New South Wales, during the period 1997–2002. Here we describe the effect of pasture type and management on pasture productivity and composition, and discuss implications for long-term productivity. Four different pasture types (unfertilised naturalised, UN; fertilised naturalised, FN; fertilised introduced species, SP; and fertilised chicory, CH) were each subjected to 2 management strategies (continuously grazed, CG; and tactically grazed, TG). Stocking rate was set at a conservative level initially and then adjusted periodically based on ewe performance and minimum values of herbage mass (HM) in winter. TG involved a summer deferment when required and a lower stocking rate than on the CG treatment. CH was managed under a 4-paddock rotation. SP and CH also had 2.5 t/ha lime surface applied before introduced species being sod-sown.
Available herbage mass tended to peak during spring and summer and was lowest in late autumn–early winter. Under CG, application of superphosphate to the naturalised pasture increased herbage mass by up to 60%, but most of the response came from annual grasses (mainly vulpia and soft brome), and subterranean clover during spring. Fertiliser initially increased the herbage mass of perennial grasses relative to the unfertilised continuously grazed control, but this component decreased over time. TG increased the perennial grass content. Annual grass herbage mass was greater where fertilised and continuously grazed, but over time declined where unfertilised and/or tactically managed. Legumes were a minor component of these pastures, but were higher where fertilised and lower where tactically grazed. Net pasture growth rate (NGR) varied with seasonal conditions, and was higher where fertiliser was applied.
The data suggest that replanting perennial grasses is an effective process for increasing perenniality in this environment providing that it is economic. Further, the implementation of TG over summer has proved to be a useful approach for maintaining or increasing perennial content in existing pastures. However, there is a need to integrate TG with the timing of superphosphate application to maximise the effect on the perennial component and minimise dominance by annual species.
A Conserved Organization of Transcription during Embryonic Stem Cell Differentiation and in Cells with High C Value
Authors: Faro-Trindade Inês , Cook Peter R.
Published: April 2006

Although we have detailed information on the alterations occurring in steady-state levels of all cellular mRNAs during differentiation, we still know little about more global changes. Therefore, we investigated the numbers of molecules of RNA polymerase II that are active—and the way those molecules are organized—as two mouse cells (aneuploid F9 teratocarcinoma, and euploid and totipotent embryonic stem cells) differentiate into parietal endoderm. Quantitative immunoblotting shows the number of active molecules roughly halves. Transcription sites (detected by light and electron microscopy after allowing engaged polymerases to extend nascent transcripts in bromouridine-triphosphate) are uniformly distributed throughout the nucleoplasm. The numbers of such sites fall during differentiation as nuclei become smaller, but site density and diameter remain roughly constant. Similar site densities and diameters are found in salamander (amphibian) cells with 11-fold larger genomes, and in aneuploid HeLa cells. We conclude that active polymerases and their nascent transcripts are concentrated in a limited number of discrete nucleoplasmic sites or factories, and we speculate that the organization of transcription is conserved during both differentiation and evolution to a high C value.
Aneugenic Activity of Op18/Stathmin Is Potentiated by the Somatic Q18→E Mutation in Leukemic Cells
Authors: Holmfeldt Per , Brännström Kristoffer , Stenmark Sonja , Gullberg Martin
Published: April 2006

Op18/stathmin (Op18) is a phosphorylation-regulated microtubule destabilizer that is frequently overexpressed in tumors. The importance of Op18 in malignancy was recently suggested by identification of a somatic Q18→E mutation of Op18 in an adenocarcinoma. We addressed the functional consequences of aberrant Op18 expression in leukemias by analyzing the cell cycle of K562 cells either depleted of Op18 by expression of interfering hairpin RNA or induced to express wild-type or Q18E substituted Op18. We show here that although Op18 depletion increases microtubule density during interphase, the density of mitotic spindles is essentially unaltered and cells divide normally. This is consistent with phosphorylation-inactivation of Op18 during mitosis. Overexpression of wild-type Op18 results in aneugenic activities, manifest as aberrant mitosis, polyploidization, and chromosome loss. One particularly significant finding was that the aneugenic activity of Op18 was dramatically increased by the Q18→E mutation. The hyperactivity of mutant Op18 is apparent in its unphosphorylated state, and this mutation also suppresses phosphorylation-inactivation of the microtubule-destabilizing activity of Op18 without any apparent effect on its phosphorylation status. Thus, although Op18 is dispensable for mitosis, the hyperactive Q18→E mutant, or overexpressed wild-type Op18, exerts aneugenic effects that are likely to contribute to chromosomal instability in tumors.
Candida tibetensis sp. nov. and Candida linzhiensis sp. nov., novel anamorphic, ascomycetous yeast species from Tibet
Authors: Wu Zuo-Wei , Bai Feng-Yan
Published: April 2006

Three anamorphic, ascomycetous yeast strains isolated from plant samples collected in Linzhi District, Tibet, China, were revealed as representing two novel species by 26S rRNA gene D1/D2 domain sequence and physiological property comparisons. The names Candida tibetensis sp. nov. and Candida linzhiensis sp. nov. are proposed for these novel species, with XZ 41-6T (=AS 2.3072T=CBS 10298T) and XZ 92-1T (=AS 2.3073T=CBS 10299T) as the respective type strains. D1/D2 sequence analysis showed that C. tibetensis and C. linzhiensis are closely related to Candida caryicola and Candida sequanensis, respectively.
Newborn with pseudohypoaldosteronism and miliaria rubra
Authors: Akcakus Mustafa , Koklu Esad , Poyrazoglu Hakan , Kurtoglu Selim
Published: April 2006

Pseudohypoaldosteronism type 1 is a rare autosomal recessive disorder with salt‐wasting, hyperkalemia, metabolic acidosis, and multiorgan aldosterone unresponsiveness, which results in an excessive loss of sodium chloride through urine, sweat and saliva, among other secretions. Inflammation of and around the damaged eccrine glands has been attributed to the deleterious effects of excessive eccrine gland salt exposure. Such a high concentration of salt in the sweat causes cutaneous lesions similar to those appearing in miliaria rubra.
Controlled Cardiac Computed Tomography
Authors: Bai Erwei , Wang Chenglin , Liu Ying , Wang Ge
Published: April 2006

Cardiac computed tomography (CT) has been a hot topic for years because of the clinical importance of cardiac diseases and the rapid evolution of CT systems. In this paper, we propose a novel strategy for controlled cardiac CT that may effectively reduce image artifacts due to cardiac and respiratory motions. Our approach is radically different from existing ones and is based on controlling the X‐ray source rotation velocity and powering status in reference to the cardiac motion. We theoretically show that by such a control‐based intervention the data acquisition process can be optimized for cardiac CT in the cases of periodic and quasiperiodic cardiac motions. Specifically, we formulate the corresponding coordination/control schemes for either exact or approximate matches between the ideal and actual source positions, and report representative simulation results that support our analytic findings.
An Optimized Spline‐Based Registration of a 3D CT to a Set of C‐Arm Images
Authors: Jonic S. , Thévenaz P. , Zheng G. , Nolte L.-P. , Unser M.
Published: April 2006

We have developed an algorithm for the rigid‐body registration of a CT volume to a set of C‐arm images. The algorithm uses a gradient‐based iterative minimization of a least‐squares measure of dissimilarity between the C‐arm images and projections of the CT volume. To compute projections, we use a novel method for fast integration of the volume along rays. To improve robustness and speed, we take advantage of a coarse‐to‐fine processing of the volume/image pyramids. To compute the projections of the volume, the gradient of the dissimilarity measure, and the multiresolution data pyramids, we use a continuous image/volume model based on cubic B‐splines, which ensures a high interpolation accuracy and a gradient of the dissimilarity measure that is well defined everywhere. We show the performance of our algorithm on a human spine phantom, where the true alignment is determined using a set of fiducial markers.
A Stochastic‐Variational Model for Soft Mumford‐Shah Segmentation
Authors: Shen Jianhong (Jackie)
Published: April 2006

In contemporary image and vision analysis, stochastic approaches demonstrate great flexibility in representing and modeling complex phenomena, while variational‐PDE methods gain enormous computational advantages over Monte Carlo or other stochastic algorithms. In combination, the two can lead to much more powerful novel models and efficient algorithms. In the current work, we propose a stochastic‐variational model for soft (or fuzzy) Mumford‐Shah segmentation of mixture image patterns. Unlike the classical hard Mumford‐Shah segmentation, the new model allows each pixel to belong to each image pattern with some probability. Soft segmentation could lead to hard segmentation, and hence is more general. The modeling procedure, mathematical analysis on the existence of optimal solutions, and computational implementation of the new model are explored in detail, and numerical examples of both synthetic and natural images are presented.
The Effect of Human Growth Hormone on Superoxide Dismutase Activity, Glutathione and Malondialdehyde Levels of Hypoxic-Ischemic Newborn Rat Brain
Authors: Yapıcıoğlu Hacer , Satar Mehmet , Canacankatan Necmiye , Tutak Ercan , Sertdemir Yaşar , Antmen Efsun , Narlı Nejat
Published: April 2006

Objectives: We investigated the effect of human growth hormone (GH) on newborn rat brain superoxide dismutase, glutathione and malondialdehyde (MDA) levels in hypoxic-ischemic (H-I) newborn rats. Methods: Fourty-eight 7 days old newborn rats were randomized to a healthy (n: 15), H-I (n: 18) and GH administered H-I (GH-H-I, n: 15) group. Permanent, left common carotid ligation was performed in the H-I groups. In the GH-H-I group, 50 mg/kg human GH (Norditropin Simplex, Novo Nordisk A/S) was administered subcutaneously just before carotid artery ligation. Two hours after ligation, rats were subjected to 2 h of hypoxemia and then were decapitated. Right and left cerebral hemispheres (CHs) and cerebellum-brain stem (C-BS) were separated. Results: Glutathione levels of each region were not statistically different from each other in and between the groups. Superoxide dismutase levels were higher in C-BSs compared to CHs (for each comparison p < 0.01). CHs and C-BS MDA levels were similar in the control and H-I groups but MDA levels of both CHs of the GH-H-I group were significantly higher than the levels of the H-I group (p = 0.01; p = 0.024, respectively). Left CH MDA level of GH-H-I group was higher compared to left CH MDA of the control group (p = 0.045) while there was no difference between right CHs. In the GH-H-I group, left CH MDA level was higher than the C-BS (p = 0.03). MDA levels of the C-BSs did not differ between the groups (p > 0.05). Conclusion: Although we have not evaluated the effect of GH histopathologically, increased lipid peroxidation especially in the H-I (left) hemisphere of the GH treated rats might suggest that GH treatment may be harmful in H-I encephalopathy.
Outcome of Extremely Preterm Infants Randomized at Birth to Different PaCO2 Targets during the First Seven Days of Life
Authors: Thome Ulrich H. , Carroll William , Wu Tzong-Jin , Johnson Robert B. , Roane Claire , Young Daniel , Carlo Waldemar A.
Published: April 2006

Background: Ventilation with higher PaCO2 goals may reduce lung injury and bronchopulmonary dysplasia (BPD). The effect may be enhanced by using a higher PaCO2 goal than in previous trials. Objective: To determine the clinical benefits and safety of higher PaCO2 goals for ventilated preterm infants. Study Design: Preterm infants with a gestational age between 23 and 28 completed weeks receiving mechanical ventilation within 6 h of birth were randomized to be managed with either a PaCO2 target between 55 and 65 mm Hg (7.3– 8.7 kPa, minimal ventilation) or 35 and 45 mm Hg (4.7– 6.0 kPa, routine ventilation) for the first 7 days of life. The primary outcome measure was BPD, defined as need for mechanical ventilation or supplemental oxygen at 36 weeks postmenstrual age, or death. The neurodevelopmental status was assessed at 18–22 months corrected age. Results: The trial was stopped early after enrolling 31% of the projected sample size. Enrolled infants had a median birth weight of 640 g. BPD or death occurred in 21/33 (64%) infants after minimal ventilation and 19/32 (59%) infants after routine ventilation. Minimal ventilation was associated with trends towards higher mortality and higher incidence of neurodevelopmental impairment, and a significantly increased combined outcome of mental impairment or death (p < 0.05). Conclusion: Minimal ventilation as performed in this study did not improve clinical outcome, and may have been associated with a worse neurodevelopmental outcome.
Relation of Gallbladder Function and Helicobacter pylori Infection to Gastric Mucosa Inflammation in Patients with Symptomatic Cholecystolithiasis
Authors: Stathopoulos Panos , Zündt Benedikta , Spelsberg Fritz W. , Kolligs Lasse , Diebold Joachim , Göke Burkhard , Jüngst Dieter
Published: April 2006

Background: Inflammatory alterations of the gastric mucosa are commonly caused by Helicobacter pylori (Hp) infection in patients with symptomatic gallstone disease. However, the additional pathogenetic role of an impaired gallbladder function leading to an increased alkaline duodenogastric reflux is controversially discussed. Aim: To investigate the relation of gallbladder function and Hp infection to gastric mucosa inflammation in patients with symptomatic gallstones prior to cholecystectomy. Patients: Seventy-three patients with symptomatic gallstones were studied by endoscopy and Hp testing. Methods: Gastritis classification was performed according to the updated Sydney System and gallbladder function was determined by total lipid concentration of gallbladder bile collected during mainly laparoscopic cholecystectomy. Results: Fifteen patients revealed no, 39 patients mild, and 19 moderate to marked gastritis. No significant differences for bile salts, phospholipids, cholesterol, or total lipids in gallbladder bile were found between these three groups of patients. However, while only 1 out of 54 (<2%) patients with mild or no gastritis was found histologically positive for Hp, this infection could be detected in 14 (74%) out of 19 patients with moderate to marked gastritis. Conclusion: Moderate to marked gastric mucosa inflammation in gallstone patients is mainly caused by Hp infection, whereas gallbladder function is not related to the degree of gastritis. Thus, an increased alkaline duodenogastric reflux in gallstone patients seems to be of limited pathophysiological relevance.
Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock
Authors: Vilaprinyo Ester , Alves Rui , Sorribas Albert
Published: April 2006

Background

Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profile of changes to the expression levels of genes coding for enzymes of the glycolytic pathway and some of its branches. The experimental determination of changes in gene expression profiles provides a descriptive picture of the adaptive response to stress. However, it does not explain why a particular profile is selected for any given response.

Results

We used mathematical models and analysis of in silico gene expression profiles (GEPs) to understand how changes in gene expression correlate to an efficient response of yeast cells to heat shock. An exhaustive set of GEPs, matched with the corresponding set of enzyme activities, was simulated and analyzed. The effectiveness of each profile in the response to heat shock was evaluated according to relevant physiological and functional criteria. The small subset of GEPs that lead to effective physiological responses after heat shock was identified as the result of the tuning of several evolutionary criteria. The experimentally observed transcriptional changes in response to heat shock belong to this set and can be explained by quantitative design principles at the physiological level that ultimately constrain changes in gene expression.

Conclusion

Our theoretical approach suggests a method for understanding the combined effect of changes in the expression of multiple genes on the activity of metabolic pathways, and consequently on the adaptation of cellular metabolism to heat shock. This method identifies quantitative design principles that facilitate understating the response of the cell to stress.
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
Authors: Ebhardt H Alexander , Wiese Kay C , Unrau Peter J
Published: April 2006

Background

DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2–5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study.

Results

Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on http://bioinformatics.org/ebbie/

Conclusion

Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6–8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2, 3, 10, 11].
Classification of protein quaternary structure by functional domain composition
Authors: Yu Xiaojing , Wang Chuan , Li Yixue
Published: April 2006

Background

The number and the arrangement of subunits that form a protein are referred to as quaternary structure. Quaternary structure is an important protein attribute that is closely related to its function. Proteins with quaternary structure are called oligomeric proteins. Oligomeric proteins are involved in various biological processes, such as metabolism, signal transduction, and chromosome replication. Thus, it is highly desirable to develop some computational methods to automatically classify the quaternary structure of proteins from their sequences.

Results

To explore this problem, we adopted an approach based on the functional domain composition of proteins. Every protein was represented by a vector calculated from the domains in the PFAM database. The nearest neighbor algorithm (NNA) was used for classifying the quaternary structure of proteins from this information. The jackknife cross-validation test was performed on the non-redundant protein dataset in which the sequence identity was less than 25%. The overall success rate obtained is 75.17%. Additionally, to demonstrate the effectiveness of this method, we predicted the proteins in an independent dataset and achieved an overall success rate of 84.11%

Conclusion

Compared with the amino acid composition method and Blast, the results indicate that the domain composition approach may be a more effective and promising high-throughput method in dealing with this complicated problem in bioinformatics.
An analysis of the Sargasso Sea resource and the consequences for database composition
Authors: Tress Michael L , Cozzetto Domenico , Tramontano Anna , Valencia Alfonso
Published: April 2006

Background

The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences originate from a single marine environment and have been sequenced from species that are not easily obtainable by laboratory cultivation. The resource also contains very many fragments of whole protein sequences, a side effect of the shotgun sequencing method.

These sequences form a significant addendum to the current searchable databases but also present us with some intrinsic difficulties. While it is important to know whether it is possible to assign function to these sequences with the current methods and whether they will increase our capacity to explore sequence space, it is also interesting to know how current bioinformatics techniques will deal with the new sequences in the resource.

Results

The Sargasso Sea sequences seem to introduce a bias that decreases the potential of current methods to propose structure and function for new proteins. In particular the high proportion of sequence fragments in the resource seems to result in poor quality multiple alignments.

Conclusion

These observations suggest that the new sequences should be used with care, especially if the information is to be used in large scale analyses. On a positive note, the results may just spark improvements in computational and experimental methods to take into account the fragments generated by environmental sequencing techniques.
A FERM-adjacent (FA) region defines a subset of the 4.1 superfamily and is a potential regulator of FERM domain function
Authors: Baines Anthony J
Published: April 2006

Background

Proteins containing FERM domains comprise a diverse group of eukaryotic proteins that bind membrane proteins and lipids. In doing so, they organise membrane microstructure, and coordinate the disposition of signalling and cell adhesion complexes. In protein 4.1R, phosphorylation adjacent to the FERM domain regulates its activity, and membrane mechanical properties.

Results

A novel sequence domain has been detected in a subset of proteins that contain FERM domains. This subset includes the true 4.1 proteins, some tyrosine phosphatases, rho-GEF proteins and type II transmembrane proteins, as well as some uncharacterised FERM proteins. This FERM-adjacent region is always closely proximate to the C-terminal of the FERM domain. This sequence is likely to be folded with elements of α and β structure. The FERM-adjacent region of 4.1R contains serine residues phosphorylated by PKC and PKA; these appear conserved in about half of all other FERM-adjacent regions. Phylogenetic analyses indicate that all proteins containing a FERM-adjacent region arose from a single ancestor after FERM domains had started to proliferate in genomes of animals, plants and mycetozoa.

Conclusion

The FERM-adjacent region defines a subset of the FERM proteins in animals. The conservation of motifs in this region that are potential substrates for kinases together with the known regulatory phosphorylation of 4.1R in this region raises the possibility that the FERM-adjacent region is a regulatory adaptation in this subset of the FERM proteins.
Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis
Authors: Lista Florigio , Faggioni Giovanni , Valjevac Samina , Ciammaruconi Andrea , Vaissaire Josée , le Doujet Claudine , Gorgé Olivier , De Santis Riccardo , Carattoli Alessandra , Ciervo Alessandra , Fasanella Antonio , Orsini Francesco , D'Amelio Raffaele , Pourcel Christine , Cassone Antonio , Vergnaud Gilles
Published: April 2006

Background

The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary.

Results

Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats.

Conclusion

In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the B branch was described, and two new branches, D and E, are proposed. Owing to the upgrading achieved here, precise genotyping can now be produced either by automated capillary electrophoresis, or by the more accessible but slower and for some markers slightly less accurate agarose gel methodology.
A ketogenic diet as a potential novel therapeutic intervention in amyotrophic lateral sclerosis
Authors: Zhao Zhong , Lange Dale J , Voustianiouk Andrei , MacGrogan Donal , Ho Lap , Suh Jason , Humala Nelson , Thiyagarajan Meenakshisundaram , Wang Jun , Pasinetti Giulio M
Published: April 2006

Background

The cause of neuronal death in amyotrophic lateral sclerosis (ALS) is uncertain but mitochondrial dysfunction may play an important role. Ketones promote mitochondrial energy production and membrane stabilization.

Results

SOD1-G93A transgenic ALS mice were fed a ketogenic diet (KD) based on known formulations for humans. Motor performance, longevity, and motor neuron counts were measured in treated and disease controls. Because mitochondrial dysfunction plays a central role in neuronal cell death in ALS, we also studied the effect that the principal ketone body, D-β-3 hydroxybutyrate (DBH), has on mitochondrial ATP generation and neuroprotection. Blood ketones were > 3.5 times higher in KD fed animals compared to controls. KD fed mice lost 50% of baseline motor performance 25 days later than disease controls. KD animals weighed 4.6 g more than disease control animals at study endpoint; the interaction between diet and change in weight was significant (p = 0.047). In spinal cord sections obtained at the study endpoint, there were more motor neurons in KD fed animals (p = 0.030). DBH prevented rotenone mediated inhibition of mitochondrial complex I but not malonate inhibition of complex II. Rotenone neurotoxicity in SMI-32 immunopositive motor neurons was also inhibited by DBH.

Conclusion

This is the first study showing that diet, specifically a KD, alters the progression of the clinical and biological manifestations of the G93A SOD1 transgenic mouse model of ALS. These effects may be due to the ability of ketone bodies to promote ATP synthesis and bypass inhibition of complex I in the mitochondrial respiratory chain.
Crossmodal attention effects on brain responses to different stimulus classes
Authors: Nager Wido , Estorf Kaija , Münte Thomas F
Published: April 2006

Background

Attending to a point in space in one modality may facilitate processing to information from the same region in another modality. The involvement of sensory-specific cortical areas in intramodal and crossmodal selective spatial attention can be assessed with event-related brain potentials (ERPs).

ERPs were recorded in two groups of young participants (each n = 11). Stimulus sequences comprised visual standard stimuli (p = 0.4, a white square), visual deviant stimuli (p = 0.05, a white square with small black rectangle) and visual novel stimuli (p = 0.05, different multicolored checkerboards) as well as auditory standard (p = 0.4, 800 Hz tone), deviant (p = 0.05, 900 Hz tone), and novel (p = 0.05, random combination of three sine-wave tones) stimuli, occurring in random order at locations 30 degrees left and right of a fixation point. The "auditory group" of participants attended either to the left or to the right speaker in order to respond to the infrequent auditory deviants at that location by a speeded button press. Visual stimuli were irrelevant for this group. The "visual group" had the analogue task for the visual modality. For these participants auditory stimuli were irrelevant throughout the experiment.

Results

ERPs showed a typical enhancement of early sensory specific components by intramodal spatial attention (visual group: visual P1 and N1; auditory group: auditory Nd). Crossmodal spatial attention effects included a modulation of the Nd to auditory standards in the visual group and a modulation of the P1 to visual novels and N1 for visual standards for the auditory group. Similar to previous studies crossmodal spatial attention effects on visual standard and novel stimuli also included a frontocentral positivity in the 200–400 ms range that was not seen for intramodal spatial visual attention suggesting involvement of later supramodal areas.

Conclusion

These findings are consistent with an action of crossmodal spatial attention on early, sensory specific processing stages.
Percutaneous septal ablation for left mid-ventricular obstructive hypertrophic cardiomyopathy: a case report
Authors: Tengiz Istemihan , Ercan Ertugrul , Alioglu Emin , Turk Ugur O
Published: April 2006

Background

Mid-ventricular obstructive hypertrophic cardiomyopathy (MVOHC) is a rare type of cardiomyopathy. The diagnosis is based on the hourglass appearance on the left ventriculogram and the presence of pressure gradient between apical and basal chamber of the ventriculum on the hemodynamic assessment.

Case presentation

The present case represents successful percutaneous treatment with septal ablation to patient with MVOHC associated with systolic anterior motion of the mitral valve and obstruction at both the mid-ventricular and outflow levels.

Conclusion

Alcohol septal ablation has been proposed as less invasive alternatives to surgery in patients with MVOHC.
Endothelial nitric oxide synthase gene polymorphism (Glu298Asp) and development of pre-eclampsia: a case-control study and a meta-analysis
Authors: Yu Christina KH , Casas Juan P , Savvidou Makrina D , Sahemey Manpreet K , Nicolaides Kypros H , Hingorani Aroon D
Published: April 2006

Background

Pre-eclampsia is thought to have an important genetic component. Recently, pre-eclampsia has been associated in some studies with carriage of a common eNOS gene Glu298Asp polymorphism, a variant that leads to the replacement of glutamic acid by aspartic acid at codon 298.

Method

Healthy women with singleton pregnancies were recruited from 7 district general hospitals in London, UK. Women at high risk of pre-eclampsia were screened by uterine artery Doppler velocimetry at 22–24 weeks of gestation and maternal blood was obtained to genotype the eNOS Glu298Asp polymorphism. Odds ratios (OR) and 95%CI, using logistic regression methods, were obtained to evaluate the association between the Glu298Asp polymorphism and pre-eclampsia. A meta-analysis was then undertaken of all published studies up to November 2005 examining the association of eNOS Glu298Asp genotype and pre-eclampsia.

Results

89 women with pre-eclampsia and 349 controls were included in the new study. The Glu298Asp polymorphism in a recessive model was not significantly associated with pre-eclampsia (adjusted-OR: 0.83 [95%CI: 0.30–2.25]; p = 0.7). In the meta-analysis, under a recessive genetic model (1129 cases & 2384 controls) women homozygous for the Asp298 allele were not at significantly increased risk of pre-eclampsia (OR: 1.28 [95%CI: 0.76–2.16]; p = 0.34). A dominant model (1334 cases & 2894 controls) was associated with no increase of risk of pre-eclampsia for women carriers of the Asp298 allele (OR: 1.12 [95%CI: 0.84–1.49]; p = 0.42).

Conclusion

From the data currently available, the eNOS Glu298Asp polymorphism is not associated with a significant increased risk of pre-eclampsia. However, published studies have been underpowered, much larger studies are needed to confirm or refute a realistic genotypic risk of disease, but which might contribute to many cases of pre-eclampsia in the population.
Is comorbidity in adolescence a predictor for adult low back pain? A prospective study of a young population
Authors: Hestbaek Lise , Leboeuf-Yde Charlotte , Kyvik Kirsten O
Published: April 2006

Background

It has previously been shown that low back pain (LBP) often presents already in the teenage years and that previous LBP predicts future LBP. It is also well documented that there is a large degree of comorbidity associated with LBP, both in adolescents and adults. The objective of this study is to gain a deeper insight into the etiology of low back pain and to possibly develop a tool for early identification of high-risk groups. This is done by investigating whether different types of morbidity in adolescence are associated with LBP in adulthood.

Methods

Almost 10,000 Danish twins born between 1972 and 1982 were surveyed by means of postal questionnaires in 1994 and again in 2002. The questionnaires dealt with various aspects of general health, including the prevalence of LBP, classified according to number of days affected during the previous year (0, 1–7, 8–30, >30). The predictor variables used in this study were LBP, headache, asthma and atopic disease at baseline; the outcome variable was persistent LBP (>30 days during the past year) at follow-up. Associations between morbidity in 1994 and LBP in 2002 were investigated.

Results

LBP, headache and asthma in adolescence were positively associated with future LBP. There was no association between atopic disease and future LBP. Individuals with persistent LBP at baseline had an odds ratio of 3.5 (2.8–4.5) for future LBP, while the odds ratio for those with persistent LBP, persistent headache and asthma was 4.5 (2.5–8.1). There was a large degree of clustering of these disorders, but atopic disease was not part of this pattern.

Conclusion

Young people from 12 to 22 years of age with persistent LBP during the previous year have an odds ratio of 3.5 persistent LBP eight years later. Both headache and asthma are also positively associated with future LBP and there is a large clustering of LBP, headache and asthma in adolescence.
Linking community pharmacy dispensing data to prescribing data of general practitioners
Authors: Florentinus Stefan R , Souverein Patrick C , Griens Fabiënne AMG , Groenewegen Peter P , Leufkens Hubert GM , Heerdink Eibert R
Published: April 2006

Background

Databases are frequently used for pharmacoepidemiological research. However, most of these databases consist either of prescribing, dispensing or administrative data and therefore lack insight in the interaction between the several health professionals around the patient.

Methods

To determine the success rate of linking records from the dispensing database of the Foundation for Pharmaceutical Statistics to the prescribing database of the second Dutch national survey of general practice, conducted by NIVEL (Netherlands Institute for Health Services Research), a deterministic record linkage approach was used with patient and prescription characteristics as matching variables between the two databases.

Results

The catchment area included 123 community pharmacies, 90 GP practices and approximately 170,000 unique patients. Overall 110,102 (64.8%) unique patients were linked using the matching variables patient's gender, year of birth, the 4-digit part of the postal code, date of dispensing/prescribing and ATC-code. The final database contains of the 110,102 both prescribing data from 83 GP practices and dispensing data of 112 community pharmacies.

Conclusion

This study shows that linkage of dispensing to prescribing data is feasible with a combination of patient characteristics, such as gender, year of birth and postal code, and prescription characteristics like prescription date and ATC-code. We obtained a linkage proportion of 64.8% resulting in complete prescribing and dispensing history of 110,102 patients. This offers an opportunity to gain insight in the mechanisms and factors influencing drug utilisation in general practice.
Severity of self-reported diseases and symptoms in Denmark
Authors: Iburg Kim Moesgaard , Rasmussen Niels Kristian , Avlund Kirsten
Published: April 2006

Objective

To estimate and rank the relative severity of self-reported diseases and symptoms in Denmark.

Method

The 1994 Danish Health and Morbidity Survey collected data from 5,472 Danes older than 16 years of age. Interviews (response frequency: 79%) gave information on diseases and symptoms; a self-administered SF-36 questionnaire (response frequency: 64%) provided information on health-related quality of life. The severity of diseases and symptoms was represented by the health-related quality of life scores that individuals suffering from particular diseases and symptoms obtained on the single dimensions of the SF-36 and on a combined sum of all dimensions. We applied logistic regression to control for the influence of sex, age and socio-economic status on the SF-36 score. We also analysed the interaction between socio-economic status and diseases on the SF-36 score.

Results

Females, more frequently than males, reported on all symptoms and all disease groups except injuries. People with relatively low levels of education reported most diseases, especially musculoskeletal and cardiovascular diseases, more frequently than people with higher education. Age-adjusted mean SF-36 scores for all dimensions combined showed that the symptoms of melancholy/depression and breathing difficulties, psychiatric disorders and respiratory diseases scored lowest (i.e. were most often associated with worse health). Females had lower SF-36 combined scores (worse health) than males on all symptoms. We found interaction between socio-economic status and respiratory diseases and musculoskeletal diseases on the SF-36 score. SF-36 scores also indicated significantly worse health among Danes with low education and income levels compared to those with higher education and income.

Conclusion

In 1994 the Danes most frequently reported musculoskeletal symptoms and diseases. Psychiatric disorders and respiratory diseases were identified as the most severe reported diseases. Due to the interaction between socio-economic status and some diseases, severity estimates should be interpreted with caution or stratified by socio-economic groups.