bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein motif extraction with neuro-fuzzy optimization
Authors: Chang Bill C.H. , Halgamuge Saman K.
Published: September 2002

Motivation: It is attempted to improve the speed and flexibility of protein motif identification. The proposed algorithm is able to extract both rigid and flexible protein motifs.

Results: In this work, we present a new algorithm for extracting the consensus pattern, or motif, from a group of related protein sequences. This algorithm involves a statistical method to find short patterns with high frequency and then neural network training to optimize the final classification accuracies. Fuzzy logic is used to increase the flexibility of protein motifs. C2H2 Zinc Finger Protein and epidermal growth factor protein sequences are used to demonstrate the capability of the proposed algorithm in finding motifs.

Availability: This program is freely available for academic use by request.

Contact: bcch@mame.mu.oz.ausam@mame.mu.oz.au
Probabilistic alignment of motifs with sequences
Authors: Gonnet Pedro , Lisacek Frédérique
Published: September 2002

Motivation: Motif detection is an important component of the classification and annotation of protein sequences. A method for aligning motifs with an amino acid sequence is introduced. The motifs can be described by the secondary (i.e. functional, biophysical, etc...) characteristics of a signal or pattern to be detected. The results produced are based on the statistical relevance of the alignment. The method was targeted to avoid the problems (i.e. over-fitting, biological interpretation and mathematical soundness) encountered in other methods currently available.

Results: The method was tested on lipoprotein signals in B. subtilis yielding stable results. The results of signal prediction were consistent with other methods where literature was available.

Availability: An implementation of the motif alignment, refining and bootstrapping is available for public use online at http://www.expasy.org/tools/patoseq/

Contact: pedro.gonnet@genebio.com

* To whom correspondence should be addressed.
Simplifying amino acid alphabets by means of a branch
and bound algorithm and substitution matrices
Authors: Cannata Nicola , Toppo Stefano , Romualdi Chiara , Valle Giorgio
Published: September 2002

Motivation: Protein and DNA are generally represented by sequences of letters. In a number of circumstances simplified alphabets (where one or more letters would be represented by the same symbol) have proved their potential utility in several fields of bioinformatics including searching for patterns occurring at an unexpected rate, studying protein folding and finding consensus sequences in multiple alignments. The main issue addressed in this paper is the possibility of finding a general approach that would allow an exhaustive analysis of all the possible simplified alphabets, using substitution matrices like PAM and BLOSUM as a measure for scoring.

Results: The computational approach presented in this paper has led to a computer program called AlphaSimp (Alphabet Simplifier) that can perform an exhaustive analysis of the possible simplified amino acid alphabets, using a branch and bound algorithm together with standard or user-defined substitution matrices. The program returns a ranked list of the highest-scoring simplified alphabets. When the extent of the simplification is limited and the simplified alphabets are maintained above ten symbols the program is able to complete the analysis in minutes or even seconds on a personal computer. However, the performance becomes worse, taking up to several hours, for highly simplified alphabets.

Availability: AlphaSimp and other accessory programs are available at http://bioinformatics.cribi.unipd.it/alphasimp

Contact: giorgio.valle@unipd.it
Prediction of Golgi Type II membrane proteins based on
their transmembrane domains
Authors: Yuan Zheng , Teasdale Rohan D.
Published: September 2002

Motivation: A major issue in cell biology today is how distinct intracellular regions of the cell, like the Golgi Apparatus, maintain their unique composition of proteins and lipids. The cell differentially separates Golgi resident proteins from proteins that move through the organelle to other subcellular destinations. We set out to determine if we could distinguish these two types of transmembrane proteins using computational approaches.

Results: A new method has been developed to predict Golgi membrane proteins based on their transmembrane domains. To establish the prediction procedure, we took the hydrophobicity values and frequencies of different residues within the transmembrane domains into consideration. A simple linear discriminant function was developed with a small number of parameters derived from a dataset of Type II transmembrane proteins of known localization. This can discriminate between proteins destined for Golgi apparatus or other locations (post-Golgi) with a success rate of 89.3% or 85.2%, respectively on our redundancy-reduced data sets.

Availability: See http://microarray.imb.uq.edu.au/golgi/

Contact: r.teasdale@imb.uq.edu.au

* To whom correspondence should be addressed.
MArray: analysing single, replicated or
reversed microarray experiments
Authors: Wang Junbai , Nygaard Vigdis , Smith-Sørensen Birgitte , Hovig Eivind , Myklebost Ola
Published: September 2002

Summary: MArray is a Matlab toolbox with a graphical user interface that allows the user to analyse single or paired microarray datasets by direct input of the raw data output file from image analysis packages, such as QuantArray or GenePiX. The application provides simple procedures to manually evaluate the quality of each measurement, multiple approaches to both ratio normalization (simple normalization, intensity dependent normalization) and evaluation of the reproducibility of paired experiments (using the techniques ‘simple statistical method’ and ‘quality control ellipse’ and ‘significance analysis of microarrays’). Specifically, interactive spot evaluation functions are available in MArray and an online gene information database (NCBI UniGene) is linked. The application may provide a valuable aid in selecting and optimizing experimental procedures, as well as serving as an analytical tool for two-state biological comparisons, such as a study of single-dose activation. It is entirely platform independent, and only requires Matlab installed.

Availability: http://matrise.uio.no/marray/marray.html

Contact: junbaiw@radium.uio.no

* To whom correspondence should be addressed.
Spatial Processes and Political Methodology: Introduction to the Special Issue
Authors: Ward Michael D. , O'Loughlin John
Published: September 2002

Recently in this journal, Gary Cox introduced a special issue by noting that “The spatial model is the workhorse theory of modern legislative studies” (Cox 2001, p. 189). In this special issue, the focus is on a different type of spatial model than that typically used in legislative studies. Specifically, we concentrate on models in which the data are dependent on one another as a result of geographic influences, broadly defined.
Spatial Effects and Ecological Inference
Authors: Anselin Luc , Tam Cho Wendy K.
Published: September 2002

This paper examines the role of spatial effects in ecological inference. Both formally and through simulation experiments, we consider the problems associated with ecological inference and cross-level inference methods in the presence of increasing degrees of spatial autocorrelation. Past assessments of spatial autocorrelation in aggregate data analysis focused on unidimensional, one-directional processes that are not representative of the full complexities caused by spatial autocorrelation. Our analysis is more complete and representative of true forms of spatial autocorrelation and pays particular attention to the specification of spatial autocorrelation in models with random coefficient variation. Our assessment focuses on the effects of this specification on the bias and precision of parameter estimates.
Conceptualizing Space: Reply
Authors: Anselin Luc , Cho Wendy K. Tam
Published: September 2002

We read with interest the sundry points raised by King in his comment (2002) on our article (Anselin and Cho 2002). Given the space and time constraints in this forum, it is impossible for us to address adequately all of the issues here. It is sufficient to say that we strongly disagree with King's claims that we are “missing the point.” We will pursue a more thorough and formal rebuttal elsewhere, but would like to set the record straight on a few issues in the limited space provided here.
Regulation and public‐private partnerships
Authors: Pongsiri Nutavoot
Published: September 2002

A public‐private partnership can be seen as an appropriate institutional means of dealing with particular sources of market failure by creating a perception of equity and mutual accountability in transactions between public and private organisations through co‐operative behaviour. The relative merit of the idea of public‐private partnership is oriented mainly around a mutual benefit. As the roles of government in public‐private partnerships are not only to provide services, but also to monitor the marketplace, a well‐defined regulation framework is essential. A sound regulatory framework will increase benefits to the government by ensuring that essential partnerships operate efficiently and optimise the resources available to them in line with broader policy objectives, ranging from social policy to environmental protection. In turn, it provides assurance to the private sector that the regulatory system includes protection from expropriation, arbitration of commercial disputes, respect for contract agreements, and legitimate recovery of costs and profit proportional to the risks undertaken.
The career choice of business graduates: SMEs or MNCs?
Authors: Moy Jane W. , Lee Sze M.
Published: September 2002

To promote SME growth, it is essential to attract young, educated minds to work for them. Recent graduates often view employment in small‐ and medium‐sized enterprises (SMEs) as a “second choice”, and prefer to work for multinational corporations )MNCs). This study uses a job attributes model to address the inability of SMEs to attract business graduates. The first part of the study investigates the importance of nine job attributes to graduates in initial job selections, and their perceptions of these attributes offered by SMEs and MNCs. The second part of the study reports that SME employer perceptions of the attractiveness of these attributes are very much different from those of the graduates. Finally, recruitment packages of SMEs and MNCs are compared, and attributes such as job security and long‐term career prospects are found to be better in SMEs, thus suggesting that SME owners must communicate more effectively with graduates.
Understanding willingness to accept domestic relocation: the example of French managers
Authors: Mignonac Karim
Published: September 2002

This article explores managers’ willingness to accept domestic geographical mobility within the company for which they are currently working. We examine the influence of managers’ work attitudes and career orientations on their willingness to relocate, posing a number of questions concerning these variables. Elements of answers to these questions are sought through an empirical research study with a sample of 203 private sector French managers. The results are interpreted within a theoretical perspective. We conclude with practical suggestions for developing company policies to facilitate internal managerial mobility.
Myofilament‐based relaxant effect of isoprenaline revealed during work‐loop contractions in rat cardiac trabeculae
Authors: Layland Joanne , Kentish Jonathan C.
Published: September 2002

In cardiac muscle, β‐adrenergic stimulation increases contractile force and accelerates relaxation. The relaxant effect is thought to be due primarily to stimulation of Ca2+ uptake into the sarcoplasmic reticulum (SR), although changes in myofilament properties may also contribute. The present study investigated the contribution of the myofilaments to the β‐adrenergic response in isolated rat cardiac trabeculae undergoing either isometric or work‐loop contractions (involving simultaneous force generation and shortening) at different stimulation frequencies (range 0.25‐4.5 Hz). SR‐dependent effects were eliminated by treatment with ryanodine (1 μM) and cyclopiazonic acid (30 μM). In isometric contractions during SR inhibition, isoprenaline increased the force but did not alter the time course of the twitch. In contrast, in work‐loop contractions, the positive inotropic effect was accompanied by a reduced diastolic force between beats, most apparent at higher frequencies (e.g. diastolic stress fell from 58.6 ± 5.5 to 28.8 ± 5.8 mN mm−2 at 1.5 Hz). This relaxant effect contributed to a β‐adrenoceptor‐mediated increase in net work and power output at higher frequencies, by reducing the amount of work required to re‐lengthen the muscle. Consequently, the frequency for maximum power output increased from 1.1 ± 0.1 to 1.6 ± 0.1 Hz. We conclude that the contribution of myofilament properties to the relaxant effect of β‐stimulation may be of greater significance when force and length are changing simultaneously (as occurs in the heart) than during force development under isometric conditions.
Length‐dependent activation in three striated muscle types of the rat
Authors: Konhilas John P. , Irving Thomas C. , de Tombe Pieter P.
Published: September 2002

The process whereby sarcomere length modulates the sensitivity of the myofilaments to Ca2+ is termed length‐dependent activation. Length‐dependent activation is a property of all striated muscles, yet the relative extent of length‐dependent activation between skeletal muscle and cardiac muscle is unclear. Although length‐dependent activation may be greater in fast skeletal muscle (FSM) than in slow skeletal muscle (SSM), there has not been a well controlled comparison of length‐dependent activation between skeletal muscle and cardiac muscle (CM). Accordingly, we measured sarcomere length‐dependent properties in skinned soleus (SSM), psoas (FSM) and ventricular trabeculae (CM) of the rat under carefully controlled conditions. The free Ca2+‐force relationship was determined at sarcomere lengths (SL) of 1.95 μm, 2.10 μm and 2.25 μm and fitted to a modified Hill equation. FSM and SSM were more sensitive to Ca2+ than CM. Length‐dependent activation was ordered as CM > FSM > SSM. Cooperativity as measured by the Hill coefficient of the Ca2+‐force relationship was not significantly different between CM and FSM, both of which exhibited greater cooperativity than SSM. SL did not significantly alter this parameter in each muscle type. To establish whether the observed differences can be explained by alterations in interfilament spacing, we measured myofilament lattice spacing (LS) by synchrotron X‐ray diffraction in relaxed, skinned muscle preparations. LS was inversely proportional to SL for each muscle type. The slope of the SL‐LS relationship, however, was not significantly different between striated muscle types. We conclude that (1) length‐dependent activation differs among the three types of striated muscle and (2) these differences in the length‐dependent properties among the striated muscle types may not solely be explained by the differences in the response of interfilament spacing to changes in muscle length in relaxed, skinned isolated muscle preparations.
Measurement of excitability of tonically firing neurones tested in a variable‐threshold model motoneurone
Authors: Matthews Peter B. C.
Published: September 2002

A new measure of excitability of tonically firing neurones termed the ‘estimated potential’ (EP) was tested on a model motoneurone (MN) with a voltage‐dependent threshold; the threshold followed the noisy membrane potential with an exponential delay. First, the model MN's after‐hyperpolarisation (AHP) was deduced from its interval histogram for tonic firing, using a recently described transform. This provided a ‘distance‐to‐threshold’ measure which underestimated the AHP's absolute size but had the same time course, thereby providing the time constant of the AHP's decay of conductance. The ‘estimated potential’ was then obtained from the classical ‘firing index’ (no. of responses/no. of stimuli) by using the estimated AHP to create a fixed threshold ‘daughter’ model MN to mimic its variable threshold parent and reproduce its input‐output non‐linearities. The EP gave a linear measure of the parent's stimulus‐evoked depolarisation for firing indices up to about 60 %, corresponding to depolarisations of three to four times the noise s.d. The EP was scaled in units of voltage whose absolute value will usually be unknown for real neurones, since it depended upon the details of the parent model. The EP's virtue is that, within its range, combining stimuli gives arithmetical addition and subtraction, thereby improving on the firing index which scales sigmoidally with the input. Moreover, with weak stimuli, the EP for a given input did not change on varying the parent model's firing rate. The estimated ‘distance‐to‐threshold’ AHP did not, however, give an accurate measure of the recovery of excitability following a spike during tonic firing. Excitability then depends upon the ‘survivors’ trajectory’ giving the mean membrane potential, relative to threshold, of those intervals which have ‘survived’ up to the time in question rather than upon the AHP per se; the survivors’ mean is more hyperpolarised because spiking preferentially eliminates trajectories with noise‐induced depolarisation.
Cortical spreading depression in the feline brain following sustained and transient stimuli studied using diffusion‐weighted imaging
Authors: Bradley Daniel P. , Smith Justin M. , Smith Martin I. , Bockhorst Kurt H.‐J. , Papadakis Nikolas G. , Hall Laurance D. , Parsons Andrew A. , James Michael F. , Huang Christopher L.‐H.
Published: September 2002

Cortical spreading depression (CSD) was induced by transient (10 min) applications of KCl in agar upon the cortical surface of α‐chloralose anaesthetised cats. Its features were compared with CSD resulting from sustained applications of crystalline KCl through a mapping of the apparent diffusion coefficient (ADC) using diffusion‐weighted echo planar imaging (DWI) over a poststimulus period of 60–100 min. Individual CSD events were computationally detected with the aid of Savitzky‐Golay smoothing applied to critically sampled data derived from regions of interest (ROIs) made up of 2 × 2 pixel matrices. The latter were consistently placed at three selected sites on the suprasylvian gyrus (SG) and six sites on the marginal gyrus (MG). The CSD events thus detected were then quantitatively characterised for each ROI using the original time series. Both stimuli consistently elicited similar spreading patterns of initial, primary CSD events that propagated over the SG and marginal MG and were restricted to the hemispheres on which the stimuli were applied. There followed secondary events over smaller extents of cortical surface. Sustained stimuli elicited primary and secondary CSD events with similar amplitudes of ADC deflection that were distributed around a single mean. The ADC deflections were also conserved in peak amplitude throughout the course of their propagation. The initial primary event showed a poststimulus latency of 1.1 ± 0.1 min. Successive secondary events followed at longer, but uniform, time intervals of around 10 min. Primary and secondary CSDs showed significantly different velocities of conduction (3.32 ± 0.43 mm min−1vs. 2.11 ± 0.21 mm min−1, respectively; n= 5) across the cerebral hemisphere. In contrast, transient stimuli produced significantly fewer numbers of CSD events (3.8 ± 0.5 events per animal, n= 5) than did sustained stimuli (7.4 ± 0.5 events per animal, mean ±s.e.m., n= 5, P= 0.002). The peak ADC deflection of their primary CSD events declined by ≈30 % as they propagated from their initiation site to the interhemispheric boundary. The primary CSD event following a transient stimulus showed a latency of 1.4 ± 0.1 min. It was followed by successive and smaller secondary ADC deflections that were separated by progressively longer time intervals. Conduction velocities of secondary events were similar to those of primary events. Conduction velocities of both primary and secondary events were slower than their counterparts following a sustained stimulus. ADC changes associated with CSD thus persist at times well after stimulus withdrawal and vary markedly with the nature of the initiating stimulus even in brain regions remote from the stimulus site.
Physiological origins of evoked magnetic fields and extracellular field potentials produced by guinea‐pig CA3 hippocampal slices
Authors: Murakami Shingo , Zhang Tongsheng , Hirose Akira , Okada Yoshio C.
Published: September 2002

This study examined whether evoked magnetic fields and intra‐ and extracellular potentials from longitudinal CA3 slices of guinea‐pig can be interpreted within a single theoretical framework that incorporates ligand‐ and voltage‐sensitive conductances in the dendrites and soma of the pyramidal cells. The 1991 CA3 mathematical model of R. D. Traub is modified to take into account the asymmetric branching patterns of the apical and basal dendrites of the pyramidal cells. The revised model accounts for the magnitude and waveform of the bi‐ and triphasic magnetic fields evoked by somatic and apical stimulations, respectively, in the slice in the absence of fast inhibition (blocked by 0.1 mm picrotoxin). The revised model also accounts for selective effects of 4‐aminopyridine (4‐AP) and tetraethylammonium (TEA), which block the potassium channels of A and C type, respectively, on the slow wave of the magnetic fields. Furthermore, the model correctly predicts the laminar profiles of field potential as well as intracellular potentials in the pyramidal cells produced by two classes of cells ‐ those directly activated and those indirectly (synaptically) activated by the applied external stimulus. The intracellular potentials in this validated model reveal that the spikes and slow waves of the magnetic fields are generated in or near the soma and apical dendrites, respectively. These results demonstrate that a single theoretical framework couched within the modern concepts of cellular physiology provides a unified account of magnetic fields outside the slice, extracellular potentials within the slice and intracellular potentials of the pyramidal cells for CA3.
Molecular correlates of the M‐current in cultured rat hippocampal neurons
Authors: Shah M. M. , Mistry M. , Marsh S. J. , Brown D. A. , Delmas P.
Published: September 2002

M‐type K+ currents (IK(M)) play a key role in regulating neuronal excitability. In sympathetic neurons, M‐channels are thought to be composed of a heteromeric assembly of KCNQ2 and KCNQ3 K+ channel subunits. Here, we have tried to identify the KCNQ subunits that are involved in the generation of IK(M) in hippocampal pyramidal neurons cultured from 5‐ to 7‐day‐old rats. RT‐PCR of either CA1 or CA3 regions revealed the presence of KCNQ2, KCNQ3, KCNQ4 and KCNQ5 subunits. Single‐cell PCR of dissociated hippocampal pyramidal neurons gave detectable signals for only KCNQ2, KCNQ3 and KCNQ5; where tested, most also expressed mRNA for the vesicular glutamate transporter VGLUT1. Staining for KCNQ2 and KCNQ5 protein showed punctate fluorescence on both the somata and dendrites of hippocampal neurons. Staining for KCNQ3 was diffusely distributed whereas KCNQ4 was undetectable. In perforated patch recordings, linopirdine, a specific M‐channel blocker, fully inhibited IK(M) with an IC50 of 3.6 ± 1.5 μM. In 70 % of these cells, TEA fully suppressed IK(M) with an IC50 of 0.7 ± 0.1 mm. In the remaining cells, TEA maximally reduced IK(M) by only 59.7 ± 5.2 % with an IC50 of 1.4 ± 0.3 mm; residual IK(M) was abolished by linopirdine. Our data suggest that KCNQ2, KCNQ3 and KCNQ5 subunits contribute to IK(M) in these neurons and that the variations in TEA sensitivity may reflect differential expression of KCNQ2, KCNQ3 and KCNQ5 subunits.
Risk of bladder cancer in foundry workers: a meta-analysis
Authors: Gaertner R R W , Thériault G P
Published: September 2002

To clarify the inconsistent reports of bladder cancer risk in foundry workers, a meta-analytic review of epidemiological studies was undertaken. Summary risk estimates (SRE) were calculated from 40 systematically extracted results. Weakly increased risks were observed overall, with an SRE of 1.11. Twenty three selected study results with better exposure information yielded an SRE of 1.16. This weak increase in risk is consistent with estimates obtained from dose-response trends of PAH exposures in aluminium smelter workers. Summary estimates did not vary substantially with exposure quality, study design, control for smoking, or when limiting the meta-analysis to large study results. Exposure-response findings showed significantly increased risks of about 1.6 to 1.7 after 20 or more years of employment, but this was based on few studies. Occupation specific SREs showed a 40–50% increased risk among moulders, casters, and unskilled foundry labourers. There was limited evidence that bladder cancer risk correlated with lung cancer risk, which is a more established risk among foundry workers. The small increased risk observed is prone to bias and confounding. Further studies of dose-response trends would greatly aid in determining whether this observed association is causal.
Personal exposure monitoring of particulate matter, nitrogen dioxide, and carbon monoxide, including susceptible groups
Authors: Harrison R M , Thornton C A , Lawrence R G , Mark D , Kinnersley R P , Ayres J G
Published: September 2002

Aims:To investigate the relation between personal exposures to nitrogen dioxide, carbon monoxide, and PM10, and exposures estimated from static concentrations of these pollutants measured within the same microenvironments, for healthy individuals and members of susceptible groups.

Methods:Eleven healthy adult subjects and 18 members of groups more susceptible to adverse health changes in response to a given level of exposure to nitrogen dioxide, carbon monoxide, and/or PM10than the general population (six schoolchildren, six elderly subjects, and six with pre-existing disease—two with chronic obstructive pulmonary disease (COPD), two with left ventricular failure (LVF), and two with severe asthma) were recruited. Daytime personal exposures were determined either directly or through shadowing. Relations between personal exposures and simultaneously measured microenvironment concentrations were examined.

Results:Correlations between personal exposures and microenvironment concentration were frequently weak for individual subjects because of the small range in measured concentrations. However, when all subjects were pooled, excellent relations between measured personal exposure and microenvironment concentration were found for both carbon monoxide and nitrogen dioxide, with slopes of close to one and near zero intercepts. For PM10, a good correlation was also found with an intercept of personal exposure (personal cloud) of 16.7 (SD 10.4) μg/m3. Modelled and measured personal exposures were generally in reasonably good agreement, but modelling with generic mean microenvironment data was unable to represent the full range of measured concentrations.

Conclusions:Microenvironment measurements of carbon monoxide and nitrogen dioxide can well represent the personal exposures of individuals within that microenvironment. The same is true for PM10with the addition of a personal cloud increment. Elderly subjects and those with pre-existing disease received generally lower PM10exposures than the healthy adult subjects and schoolchildren by virtue of their less active lifestyles.
Motor neurone disease
Authors: Talbot K
Published: September 2002

Motor neurone disease (MND), or amyotrophic lateral sclerosis (ALS), is a neurodegenerative disorder of unknown aetiology. Progressive motor weakness and bulbar dysfunction lead to premature death, usually from respiratory failure. Confirming the diagnosis may initially be difficult until the full clinical features are manifest. For all forms of the disease there is a significant differential diagnosis to consider, including treatable conditions, and therefore specialist neurological opinion should always be sought. Clear genetic inheritance has been demonstrated in a minority of patients with familial ALS but elucidation of the biological basis of genetic subtypes is also providing important information which may lead to treatments for sporadic forms of the disease. In the absence of curative or disease modifying therapy, management is supportive and requires a multidisciplinary approach. If, as seems likely, complex inherited and environmental factors contribute to the pathogenesis of MND, future treatment may involve a combination of molecular based treatments or restoration of cellular integrity using stem cell grafts.
Osteoporosis
Authors: Tuck S P , Francis R M
Published: September 2002

Osteoporosis is characterised by low bone mass and microarchitectural deterioration of bone tissue, leading to enhanced bone fragility and consequent increase in fracture risk. It is a common condition affecting one in three women and one in 12 men, resulting in substantial morbidity, excess mortality, and health and social services expenditure. It is therefore important to develop strategies to prevent and treat osteoporosis in both men and women. This paper reviews the pathogenesis of primary and secondary osteoporosis, as well as diagnosis, investigation, and management. This should include lifestyle changes to reduce bone loss and decrease the risk of falls, the identification and treatment of secondary causes of bone loss, and specific treatment for osteoporosis. Hormone replacement therapy, raloxifene, bisphosphonates, calcium and vitamin D, calcitonin, and parathyroid hormone have all been shown to improve bone density and decrease the risk of fracture in specific situations. It is important that treatment is tailored to the individual patient, to ensure compliance and optimise the potential benefits.
Investigation and management of iron deficiency anaemia in general practice: a cluster randomised controlled trial of a simple management prompt
Authors: Logan E C M , Yates J M , Stewart R M , Fielding K , Kendrick D
Published: September 2002

Background

Iron deficiency anaemia (IDA) remains the most common cause of anaemia and is frequently secondary to occult gastrointestinal blood loss requiring further investigation. The study was designed to prospectively assess the adequacy of investigation of IDA and to establish whether a simple computerised prompt would increase the completeness of investigation of patients presenting to their general practitioners.

Patients and methods

All men aged >20 and women aged >50 newly found to have a probable IDA (n=431) in primary care were randomised according to general practice (n=89) to one of two computer generated prompts, by the haematology laboratories in two large district general hospitals. Data were collected 12 months after the index date. The primary outcome measure was the adequacy of investigation of the cause of anaemia. Multiple logistic regression was used to analyse each binary outcome.

Results

Two hundred and three (47%) of 431 patients presenting to their general practitioner with an IDA were adequately managed and 140/357 (39%) of patients who were otherwise fit for investigation had no tests at all. Twenty one (17%) of 125 patients who did have adequate investigation at the time of presentation were found to have colorectal cancer. Only 30% of patients had a confirmed diagnosis within 12 months.

The prompt did not affect the level of investigation (odds ratio 0.88, 95% confidence interval (CI) 0.60 to 1.29, p=0.52). The initial prescribing of oral iron was improved (odds ratio 2.19, 95% CI 1.27 to 3.77, p=0.005), but not the documented prescribing of a full therapeutic course or the use of follow up blood counts.

Conclusions

The investigation and management of IDA presenting in general practice remains inadequate and is not improved by a simple management prompt.
Vaccination against hepatitis B infection in patients with end stage renal disease
Authors: Bel’eed K , Wright M , Eadington D , Farr M , Sellars L
Published: September 2002

Background

Experience of hepatitis B vaccination in a contemporary renal replacement programme is reported.

Methods

A total of 406 patients were involved: 214 on haemodialysis, 97 on continuous ambulatory peritoneal dialysis, 67 predialysis (serum creatinine >400 μmol/l), and 28 with a failing transplant. Primary vaccination comprised recombinant hepatitis B vaccine (Engerix B) 40 μg intramuscularly at 0, 1, 2, and 3 months. Booster doses were administered three monthly if anti-HBs titre was <100 IU/l.

Results

Uptake of vaccine was 61% (haemodialysis 70%, continuous ambulatory peritoneal dialysis 62%, predialysis 31%, transplant 61%, p<0.0001). Primary seroconversion occurred in 64% of vaccinated patients (anti-HBs; 10–100 U/l, 33%; >100 U/l, 31%). Booster doses led to further improvement in immunity in 66/115 (57%) patients after a first and 8/20 (40%) patients after a second booster dose, but uptake was again poor (first booster 74%, second 31%). Seroprotection declined unexpectedly rapidly; after a mean of 16 months 71/115 patients (62 %) had a significant fall in their anti-HBs titres; 30/115 (26%) lost detectable antibody.

Conclusions

Routine hepatitis B vaccination of patients with end stage renal failure is logistically difficult to administer on a large scale; primary seroconversion is relatively poor, but improves after repeated booster doses; protective anti-HBs titres decline rapidly, and yearly antibody checks with selective booster doses will be required to maintain seroprotection. The cost effectiveness of a vaccination programme will vary greatly depending on the prevalence of hepatitis B in the population at risk.
Emergency remediation of instability at Caudalosa tailings dam, Peru: a case history
Authors: Garga Vinod K , de la Torre Miguel
Published: September 2002

This paper describes the instability in the foundation of the Caudalosa tailings dam in Peru. The instability threatened collapse of the structure along with the risk of unacceptable contamination of the River Escalera, located immediately downstream of the toe of the dam. At the time of these investigations, large deformations were in progress. The head scarp of the potential slide, located in the stored tailings, had reached a height of 2 m. Visual observations, as well as subsurface investigations, indicated that the instability was due to the presence of soft to medium plastic clay in the foundation. Emergency stabilization was successfully achieved by the construction of large trenches at the downstream toe, allowing the low consistency clay to be removed and backfilled with compacted mine waste rock. Other secondary stabilizing measures that were undertaken are also described.Key words: clay, dam, instability, remediation, stabilization, slide, tailings.
Microfabric and mineralogical studies on the stabilization of an expansive soil using cement by-pass dust and some types of slags
Authors: Al-Rawas Amer Ali
Published: September 2002

This paper describes the microfabric and mineralogical aspects of the expansive soil of Al-Khod (northern Oman) treated with cement by-pass dust (CBPD), copper slag, slag-cement, and granulated blast furnace slag (GBFS). First, the engineering properties and chemical and mineralogical composition of the untreated soil were determined. The soil was then mixed with the additives at 3, 6, and 9% of the dry weight of the soil. The microfabric and mineralogical characteristics of the treated soil were determined. The high amounts of calcium ions and calcium oxide, which produces calcium ions, react with the clay particles through a cation exchange process resulting in the formation of aggregations and reduction of the swell potential of the soil. Mineralogical tests on the treated samples indicated a general reduction in all clay minerals peak intensities, particularly in the case of CBPD treated samples. The fabric of the untreated soil is composed of dense clay matrices with no appearance of aggregations or ped formations with increasing amounts of pore spaces. However, aggregations and few connectors were formed due to the addition of the stabilizers. Aggregations and bindings were formed for all of the soils treated with GBFS and for those with 9% additions of CBPD and slag-cement. The mineralogical and microfabric results were correlated with the swell percent and swell pressure of the treated samples. The formation of aggregations and reduction in clay minerals peak intensities resulted in the reduction of the swell pressure and swell percent values.Key words: microfabric, mineralogy, stabilization, expansive soils, SEM, XRD.
Behaviour of the stiff and sensitive Saint-Jean-Vianney clay in intact, destructured, and remoulded conditions
Authors: Saihi Faten , Leroueil Serge , Rochelle Pierre La , French Ivan
Published: September 2002

The role of the degree of microstructure on the behaviour of clayey soils has been the focus of many studies. However, none so far have quantified the evolution of the shear strength parameters for a given soil for degrees of microstructure going from an intact condition to complete remoulding. In the present study, a series of compression triaxial tests have been performed on specimens of the naturally highly structured Saint-Jean-Vianney clay under the following conditions: intact, destructured by straining outside the limit state curve, and reconstituted and reconsolidated after complete remoulding. The results show that the limit state curve is influenced by the level of destructuration reached before testing, and moreover, that the shear strength parameters at large deformation are influenced by the level of destructuration at the beginning of the test. The compression tests infer that the soil seems to retain the memory of its initial microstructure, at least for consolidation volumetric strains up to 14%. The observed behaviour has implications for the understanding and modelling of natural clays; it also explains to some extent the difference in strength parameters used in stability analyses of embankments on soft clays and natural slopes in clay.Key words: clay, microstructure, destructuration, shear strength, large deformation shear strength, triaxial test.
Geotechnical properties of Pusan clays
Authors: Chung S G , Giao P H , Kim G J , Leroueil S
Published: September 2002

The Nakdong River plain is one of the few areas in Korea where soft clays have been deposited. Although many site investigations related to large-scale reclamation works have been carried out over the past 10 years, soil profiles still need to be better characterized. The Pusan clays at this location constitute an interesting topic for researchers both in and outside Korea due to their geological complexity, unusually great thickness, very low overconsolidation (OCR) values, large consolidation settlement, and the effects of artesian pressure. This paper represents the first comprehensive review of Pusan clays and collates extensive existing and new geotechnical data. These data are then analyzed within the frameworks of both classical and new developments in soft clay engineering to address the problems mentioned above.Key words: Pusan, soft clay, intrinsic compression, geotechnical properties.
Geotechnical characterization of dewatered sewage sludge for landfill disposal
Authors: Lo Irene M.C , Zhou W W , Lee K M
Published: September 2002

The disposal of increased quantities of dewatered sewage sludge to landfills may cause geoenvironmental problems such as leachability, total and differential settlement, and slope stability of the waste during disposal. This study investigates the geotechnical properties of the dewatered sewage sludge generated from chemically enhanced primary treatment (CEPT) in Hong Kong. Compaction test results show that CEPT sludge exhibits compaction characteristics similar to those of clayey soils; however, the lowest hydraulic conductivity of CEPT sludge does not occur near the wet side of its optimum water content. The consolidation behavior of CEPT sludge does not follow the conventional Terzaghi's theory. Under an overburden pressure higher than 24 kPa, the relationship between the logarithm of the hydraulic conductivity (logk) and the void ratio (e) is linear. Results from direct shear tests reveal that, for CEPT sludge, slopes of 20° can probably be constructed during the landfill operation without causing sliding problems. Compared with the disposal of pure CEPT sludge, the co-disposal of dewatered sewage sludge with other solid wastes commonly found in Hong Kong results in lower compressibility, smaller settlement, but higher hydraulic conductivity.Key words: co-disposal, geotechnical properties, landfill disposal, sewage sludge.
Derivation of seismic cone interval velocities utilizing forward modeling and the downhill simplex method
Authors: Baziw Erick J
Published: September 2002

The seismic cone penetration test (SCPT) has proven to be a very valuable geotechnical tool in facilitating the determination of low strain (<104%) in situ compression (P) and shear (S) wave velocities. The P- and S-wave velocities are directly related to the soil elastic constants of Poisson's ratio, shear modulus, bulk modulus, and Young's modulus. The accurate determination of P- and S-wave velocities from the recorded seismic cone time series is of paramount importance to the evaluation of reliable elastic constants. Furthermore, since the shear and compression wave velocities are squared in deriving the elastic constants, small variations in the estimated velocities can cause appreciable errors. The standard techniques implemented in deriving SCPT interval velocities rely upon obtaining reference P- and S-wave arrival times as the probe is advanced into the soil profile. By assuming a straight ray travel path from the source to the SCPT seismic receiver and calculating the relative reference arrival time differences, interval SCPT velocities are obtained. The forward modeling  downhill simplex method (FMDSM) outlined in this paper offers distinct advantages over conventional SCPT velocity profile estimation methods. Some of these advantages consist of the allowance of ray path refraction, greater sophistication in interval velocity determination, incorporation of measurement weights, and meaningful interval velocity accuracy estimators.Key words: seismic cone penetration testing (SCPT), downhill simplex method (DSM), forward modeling, Fermat's principle, weighted least squares (l2 norm), cost function.
Dehn surgery on crosscap number two knots and projective planes
Authors: Teragaito Masakazu
Published: September 2002

In the present paper, we will study the creation of projective planes by Dehn surgery on knots in the 3-sphere. It is shown that a projective plane cannot be created by Dehn surgery on a crosscap number two knot. As a corollary, we will prove that crosscap number two knots satisfy the projective space conjecture, which asserts that the projective 3-space cannot be obtained by Dehn surgery on a non-trivial knot in the 3-sphere.
DEHN FILLINGS CREATING ESSENTIAL SPHERES AND TORI
Authors: LEE SANGYOP , OH SEUNGSANG , TERAGAITO MASAKAZU
Published: September 2002

Let M be a simple 3-manifold with a toral boundary component. It is known that if two Dehn fillings on M along the boundary produce a reducible manifold and a toroidal mainfold, then the distance between the filling slopes is at most three. This paper gives a remarkably short proof of this result.
KNOT THEORY IN HANDLEBODIES
Authors: HÄRING-OLDENBURG REINHARD , LAMBROPOULOU SOFIA
Published: September 2002

We consider oriented knots and links in a handlebody of genus g through appropriate braid representatives in S3, which are elements of the braid groups Bg,n. We prove a geometric version of the Markov theorem for braid equivalence in the handlebody, which is based on the L-moves. Using this we then prove two algebraic versions of the Markov theorem. The first one uses the L-moves. The second one uses the Markov moves and conjugation in the groups Bg,n. We show that not all conjugations correspond to isotopies.
COMPUTER AIDED KNOT THEORY USING MATHEMATICA AND MATHLINK
Authors: IMAFUJI NORIKO , OCHIAI MITSUYUKI
Published: September 2002

We introduce a computer tool called Knot2000(K2K) which was developed for the purpose of support for the research of knot theory. K2K is a package on Mathematica in which consists of 19 functions and it has already been opened to the public with other external programs and data files. In this paper, we will describe focusing on the usages of each functions and some examples of effective ways to use K2K, and show its availability.
Autonomic Neural Control of Dynamic Cerebral Autoregulation in Humans
Authors: Zhang Rong , Zuckerman Julie H. , Iwasaki Kenichi , Wilson Thad E. , Crandall Craig G. , Levine Benjamin D.
Published: September 2002

Background—

The purpose of the present study was to determine the role of autonomic neural control of dynamic cerebral autoregulation in humans.

Methods and Results—

We measured arterial pressure and cerebral blood flow (CBF) velocity in 12 healthy subjects (aged 29±6 years) before and after ganglion blockade with trimethaphan. CBF velocity was measured in the middle cerebral artery using transcranial Doppler. The magnitude of spontaneous changes in mean blood pressure and CBF velocity were quantified by spectral analysis. The transfer function gain, phase, and coherence between these variables were estimated to quantify dynamic cerebral autoregulation. After ganglion blockade, systolic and pulse pressure decreased significantly by 13% and 26%, respectively. CBF velocity decreased by 6% (
P
<0.05). In the very low frequency range (0.02 to 0.07 Hz), mean blood pressure variability decreased significantly (by 82%), while CBF velocity variability persisted. Thus, transfer function gain increased by 81%. In addition, the phase lead of CBF velocity to arterial pressure diminished. These changes in transfer function gain and phase persisted despite restoration of arterial pressure by infusion of phenylephrine and normalization of mean blood pressure variability by oscillatory lower body negative pressure.

Conclusions—

These data suggest that dynamic cerebral autoregulation is altered by ganglion blockade. We speculate that autonomic neural control of the cerebral circulation is tonically active and likely plays a significant role in the regulation of beat-to-beat CBF in humans.