bluuebunny/crossref_metadata_2025 huggingface dataset:
Protecting Privacy Using k-Anonymity
Authors: El Emam Khaled , Dankar Fida Kamal
Published: June 2008

Objective: There is increasing pressure to share health information and even make it publicly available. However, such disclosures of personal health information raise serious privacy concerns. To alleviate such concerns, it is possible to anonymize the data before disclosure. One popular anonymization approach is k-anonymity. There have been no evaluations of the actual re-identification probability of k-anonymized data sets.

Design: Through a simulation, we evaluated the re-identification risk of k-anonymization and three different improvements on three large data sets.

Measurement: Re-identification probability is measured under two different re-identification scenarios. Information loss is measured by the commonly used discernability metric.

Results: For one of the re-identification scenarios, k-Anonymity consistently over-anonymizes data sets, with this over-anonymization being most pronounced with small sampling fractions. Over-anonymization results in excessive distortions to the data (i.e., high information loss), making the data less useful for subsequent analysis. We found that a hypothesis testing approach provided the best control over re-identification risk and reduces the extent of information loss compared to baseline k-anonymity.

Conclusion: Guidelines are provided on when to use the hypothesis testing approach instead of baseline k-anonymity.
Developmental plasticity and regenerative capacity in the renal ureteric bud/collecting duct system
Authors: Sweeney Derina , Lindström Nils , Davies Jamie A.
Published: June 2008

Branching morphogenesis of epithelia is an important mechanism in animal development, being responsible for the characteristic architectures of glandular organs such as kidney, lung, prostate and salivary gland. In these systems, new branches usually arise at the tips of existing branches. Recent studies, particularly in kidney, have shown that tip cells express a set of genes distinct from those in the stalks. Tip cells also undergo most cell proliferation, daughter cells either remaining in the tip or being left behind as the tips advance, to differentiate and contribute to new stalk. Published time-lapse observations have suggested, though, that new branches may be able to arise from stalks. This happens so rarely, however, that it is not clear whether this reflects true plasticity and reversal of differentiation, or whether it is just an occasional instance of groups of tip cells being `left behind' by error in a mainly stalk zone. To determine whether cells that have differentiated into stalks really do retain the ability to make new tips, we have removed existing tips from stalks, verified that the stalks are free of tip cells, and assessed the ability of tip-free stalks to initiate new branches. We find stalks to be fully capable of regenerating tips that express typical tip markers, with these tips going on to form epithelial trees, at high frequency. The transition from tip to stalk is therefore reversible, at least for early stages of development. This observation has major implications for models of pattern formation in branching trees, and may also be important for tissue engineering and regenerative medicine.
Stability of common biochemical analytes in serum gel tubes subjected to various storage temperatures and times pre-centrifugation
Authors: Tanner Melissa , Kent Neil , Smith Brian , Fletcher Stephen , Lewer Michelle
Published: June 2008

Background

Blood samples collected in rural and remote areas of Australasia are often exposed to a range of environmental conditions prior to analysis in a laboratory. The aim of this study was to determine analyte stability of venous blood specimens in serum gel tubes exposed to a range of storage temperatures and times prior to centrifugation.

Methods

Thirty healthy adult volunteers were enrolled in the study. Blood was collected into 11 serum gel separator tubes. All samples were allowed to clot at room temperature for 30 min. Two samples were centrifuged and analysed as controls. Nine samples were stored at 15, 25 or 35°C for 4, 8 or 24 h, respectively, before centrifugation. Thirty-five biochemical analytes were measured on each sample.

Results

Most analytes remained stable in all storage conditions including sodium, total protein, albumin, bilirubin, alanine transferase, aspartate aminotransferase, alkaline phosphatase, gamma glutamyl transferase, creatinine kinase, lipase, cholesterol, triglycerides, transferrin, urate, C-reactive protein, vitamin B12, thyroid-stimulating hormone, free thyroxine, free triiodothyronine, follicle-stimulating hormone, oestradiol, prostate-specific antigen, cortisol and vitamin D. Potassium, glucose, phosphate, creatinine, urea, ferritin, iron, lactate dehydrogenase, magnesium and calcium were not stable in at least one of the storage conditions.

Conclusions

These results can be used to determine which analytes produce valid results despite exposure to variable storage conditions for up to 24 h prior to centrifugation. The majority of analytes were unaffected by a delay in centrifugation at a variety of temperatures, however, some important analytes were significantly affected.
Plasma sphingosine-1-phosphate measurement in healthy subjects: close correlation with red blood cell parameters
Authors: Ohkawa Ryunosuke , Nakamura Kazuhiro , Okubo Shigeo , Hosogaya Shigemi , Ozaki Yukio , Tozuka Minoru , Osima Noriko , Yokota Hiromitsu , Ikeda Hitoshi , Yatomi Yutaka
Published: June 2008

Background

Since sphingosine-1-phosphate (Sph-1-P) plays an important role as an extracellular mediator through interaction with specific cell surface receptors, especially in the area of vascular biology and immunology/haematology, determination of its plasma concentration may become important from the clinical viewpoint. Thus, we attempted to develop a method of measuring the plasma Sph-1-P concentration for use in the clinical laboratory setting.

Methods

After two-step lipid extraction, Sph-1-P was coupled with o-phthaldialdehyde, and the resultant fluorescent derivative was separated by high-performance liquid chromatography. C17-Sph-1-P was used as the internal standard, instead of dihydrosphingosine-1-phosphate, which had been used previously for the same purpose but was actually detected in plasma.

Results

Our procedures for preparing the plasma samples and assay Sph-1-P were found to be satisfactory for clinical laboratory testing. The plasma Sph-1-P concentrations were significantly higher in men (413.1 ± 52.0 nmol/L; mean ± SD) than in women (352.4 ± 39.7 nmol/L). Unexpectedly, strong positive correlations were found between the plasma Sph-1-P concentration and red blood cell (RBC)-related parameters, rather than platelet-related parameters.

Conclusions

Our present study confirmed the possibility of the clinical introduction of plasma Sph-1-P measurement, and in addition, suggested that RBCs may be involved in the regulation of plasma Sph-1-P concentrations.
Discrepancies between qualitative and quantitative analysis of cerebrospinal fluid IgG: densitometric comparison of nephelometry-silver versus immuno-enzymes
Authors: Keir Geoffrey , Barrio Susana , Thompson Edward J
Published: June 2008

Background

Detection of local synthesis of IgG within the central nervous system is important for the diagnosis of brain inflammatory diseases such as multiple sclerosis. This is typically done by comparing the amounts of IgG in serum and parallel cerebrospinal fluid (CSF). Although there have been well-described problems with qualitative versus quantitative measurements of abnormal IgG, such as in myeloma paraproteins, similar difficulties are also found with CSF IgG.

Methods

Traditional quantitative analysis of IgG by rate nephelometry was followed by separation of the IgG using isoelectric focusing and then either silver stain or immunofixation. Finally, quantitative analysis was performed by scanning densitometry using public domain software downloaded from the National Institutes of Health.

Results

We report here the major discrepancies that can occur with CSF IgG between the silver stain versus the IgG stain.

Conclusions

We concur with the earlier recommendation that qualitative separation followed by densitometric estimation of enzyme-linked immunofixation is also more useful than simple quantitative nephelometric analysis followed by silver staining in the detection of local synthesis of IgG, analogous to the earlier work on paraproteins.
Protein S-100 is present in extracerebral fluids before and after cardiac surgery in children
Authors: Nagdyman Nicole , Ewert Peter , Schmitt Katharina , Hübler Michael , Stiller Brigitte , Müller Christian , Berger Felix
Published: June 2008

Background

Protein S-100 is found in extracerebral sources. The aim of our study was to examine the content of protein S-100 in native pericardial fluid as well as in postoperative extracerebral fluids after cardiac surgery in children.

Methods

We conducted a prospective study in 90 children measuring protein S-100 concentration in pericardial fluid directly after opening the pericardial sac before starting with cardiac surgery. Postoperatively, we examined pleural, peritoneal and pericardial fluid.

Results

Pericardial fluid sampled directly after opening the pericardial sac has a protein S-100 content of 3.2 (1.3–5.4) μg/L. Postoperatively, protein S-100 content was 0.89 (0.56–2.6) μg/L in pleural effusion, 0.14 (0.1–1.1) μg/L in peritoneal fluid and 2.75 (2.2–24.4) μg/L in pericardial fluid. The protein S-100 concentration in pericardial fluid before and after cardiac operation did not differ significantly. Pericardial protein S-100 concentrations were significantly higher than pleural and peritoneal protein S-100 concentrations.

Conclusions

Protein S-100 is present in extracerebral fluids before and after cardiac surgery in children. The time point of fluid withdrawal after the operation did not influence the protein S-100 concentration.
Plasma total homocysteine: instigator or indicator of cardiovascular disease?
Authors: Moat Stuart J
Published: June 2008

Cardiovascular disease (CVD) is a major cause of morbidity and mortality in developed countries. However, traditional risk factors cannot fully account for this. In the last 20 years, there has been an explosion of interest in plasma total homocysteine (tHcy) as a potential modifiable risk factor for CVD. Recent meta-analyses of epidemiological studies support the concept that increased tHcy concentrations are associated with CVD. This has led to the ‘homocysteine hypothesis’, which states that lowering plasma tHcy using folic acid and other B-vitamins will reduce the risk of CVD. In experimental studies, homocysteine has been shown to cause oxidative stress, endothelial cell dysfunction and promote thrombogenesis. However, data from recent large randomized controlled trials have shown that there is no clinical benefit to lowering plasma tHcy concentrations with folic acid and other B-vitamins. This lack of effect of tHcy lowering strongly suggests that homocysteine is not an instigator but merely an indicator of CVD.
Computational analysis of miRNA-mediated repression of translation: Implications for models of translation initiation inhibition
Authors: Nissan Tracy , Parker Roy
Published: June 2008

The mechanism by which miRNAs inhibit translation has been under scrutiny both in vivo and in vitro. Divergent results have led to the suggestion that miRNAs repress translation by a variety of mechanisms including blocking the function of the cap in stimulating translation. However, these analyses largely only examine the final output of the multistep process of translation. This raises the possibility that when different steps in translation are rate limiting, miRNAs might show different effects on protein production. To examine this possibility, we modeled the process of translation initiation and examined how the effects of miRNAs under different conditions might be explained. Our results suggest that different effects of miRNAs on protein production in separate experiments could be due to differences in rate-limiting steps. This analysis does not rule out that miRNAs directly repress the function of the cap structure, but it demonstrates that the observations used to argue for this effect are open to alternative interpretations. Taking all the data together, our analysis is consistent with the model that miRNAs may primarily repress translation initiation at a late step.
Fragile X mental retardation protein interactions with the microtubule associated protein 1B RNA
Authors: Menon Lakshmi , Mader Samantha Ann , Mihailescu Mihaela-Rita
Published: June 2008

Fragile X mental retardation syndrome, the most common form of inherited mental retardation, is caused by the absence of the fragile X mental retardation protein (FMRP). FMRP has been shown to use its arginine–glycine–glycine (RGG) box to bind to a subset of RNA targets that form a G quadruplex structure. We performed a detailed analysis of the interactions between the FMRP RGG box and the microtubule associated protein 1B (MAP1B) mRNA, a relevant in vivo FMRP target. We show that MAP1B RNA forms an intramolecular G quadruplex structure, which is bound with high affinity and specificity by the FMRP RGG box. We determined that hydrophobic interactions are important in the FMRP RGG box-MAP1B RNA association, with minor contributions from electrostatic interactions. Our findings that at low protein:RNA ratios the RNA G quadruplex structure is slightly stabilized, whereas at high ratios is unfolded, suggest a mechanism by which the FMRP concentration variation in response to a neurotransmitter stimulation event could act as a regulatory switch for the protein function, from translation repressor to translation activator.
Footprinting analysis demonstrates extensive similarity between eukaryotic RNase P and RNase MRP holoenzymes
Authors: Esakova Olga , Perederina Anna , Quan Chao , Schmitt Mark E. , Krasilnikov Andrey S.
Published: June 2008

Eukaryotic ribonuclease (RNase) P and RNase MRP are evolutionary related RNA-based enzymes involved in metabolism of various RNA molecules, including tRNA and rRNA. In contrast to the closely related eubacterial RNase P, which is comprised of an RNA component and a single small protein, these enzymes contain multiple protein components. Here we report the results of footprinting studies performed on purified Saccharomyces cerevisiae RNase MRP and RNase P holoenzymes. The results identify regions of the RNA components affected by the protein moiety, suggest a role of the proteins in stabilization of the RNA fold, and point to substantial similarities between the two evolutionary related RNA-based enzymes.
Long-term follow-up of prenatally treated children at risk for congenital adrenal hyperplasia: does dexamethasone cause behavioural problems?
Authors: Hirvikoski Tatja , Nordenström Anna , Lindholm Torun , Lindblad Frank , Ritzén E Martin , Lajic Svetlana
Published: June 2008

Objectives

To investigate the long-term effects of prenatal treatment of congenital adrenal hyperplasia (CAH) with emphasis on behavioural problems and temperament.

Design

A population-based long-term follow-up study of Swedish children at risk for virilising CAH, who had received treatment prenatally with dexamethasone (DEX). The questionnaire-based follow-up was performed when the children had reached school age.

Methods

Standardised parent-completed questionnaires were used to evaluate adaptive functioning, behavioural/emotional problems and psychopathology, social anxiety and temperament in DEX-exposed school-aged children (n=26) and matched controls (n=35). In addition, the association between parental questionnaires and children's self-ratings was investigated.

Results

There were no statistically significant differences between DEX-exposed children and controls in measures of psychopathology, behavioural problems and adaptive functioning. In a questionnaire on temperamental traits, DEX-exposed children were described by their parents as being more sociable than controls (P=0.042). The correlation analysis showed only modest parent–child agreement on social anxiety, i.e. the increased social anxiety in children's self-ratings was not confirmed by their parents.

Conclusions

DEX-treated children showed good overall adjustment. The parent–child agreement with respect to social anxiety was modest, highlighting the importance of multiple information sources and assessment methods. The clinical significance of the observed difference in sociability cannot be determined within the frameworks of this study. Additional studies of larger cohorts are essential to make more decisive conclusions on the safety of the treatment. Until then, it is important that parents are thoroughly informed about the benefits and potential risks and uncertainties of this controversial treatment.
Cytotype Regulation of P Transposable Elements in Drosophila melanogaster: Repressor Polypeptides or piRNAs?
Authors: Jensen Philip A , Stuart Jeremy R , Goodpaster Michael P , Goodman Joseph W , Simmons Michael J
Published: June 2008

The telomeric P elements TP5 and TP6 are associated with the P cytotype, a maternally inherited condition that represses P-element-induced hybrid dysgenesis in the Drosophila germ line. To see if cytotype repression by TP5 and TP6 might be mediated by the polypeptides they could encode, hobo transgenes carrying these elements were tested for expression of mRNA in the female germ line and for repression of hybrid dysgenesis. The TP5 and TP6 transgenes expressed more germ-line mRNA than the native telomeric P elements, but they were decidedly inferior to the native elements in their ability to repress hybrid dysgenesis. These paradoxical results are inconsistent with the repressor polypeptide model of cytotype. An alternative model based on the destruction of P transposase mRNA by Piwi-interacting (pi) RNAs was supported by finding reduced P mRNA levels in flies that carried the native telomeric P elements, which are inserted in a known major piRNA locus.
Histone H3 K56 Hyperacetylation Perturbs Replisomes and Causes DNA Damage
Authors: Celic Ivana , Verreault Alain , Boeke Jef D
Published: June 2008

Deacetylation of histone H3 K56, regulated by the sirtuins Hst3p and Hst4p, is critical for maintenance of genomic stability. However, the physiological consequences of a lack of H3 K56 deacetylation are poorly understood. Here we show that cells lacking Hst3p and Hst4p, in which H3 K56 is constitutively hyperacetylated, exhibit hallmarks of spontaneous DNA damage, such as activation of the checkpoint kinase Rad53p and upregulation of DNA-damage inducible genes. Consistently, hst3 hst4 cells display synthetic lethality interactions with mutations that cripple genes involved in DNA replication and DNA double-strand break (DSB) repair. In most cases, synthetic lethality depends upon hyperacetylation of H3 K56 because it can be suppressed by mutation of K56 to arginine, which mimics the nonacetylated state. We also show that hst3 hst4 phenotypes can be suppressed by overexpression of the PCNA clamp loader large subunit, Rfc1p, and by inactivation of the alternative clamp loaders CTF18, RAD24, and ELG1. Loss of CTF4, encoding a replisome component involved in sister chromatid cohesion, also suppresses hst3 hst4 phenotypes. Genetic analysis suggests that CTF4 is a part of the K56 acetylation pathway that converges on and modulates replisome function. This pathway represents an important mechanism for maintenance of genomic stability and depends upon proper regulation of H3 K56 acetylation by Hst3p and Hst4p. Our data also suggest the existence of a precarious balance between Rfc1p and the other RFC complexes and that the nonreplicative forms of RFC are strongly deleterious to cells that have genomewide and constitutive H3 K56 hyperacetylation.
Mutants Defective in Rad1-Rad10-Slx4 Exhibit a Unique Pattern of Viability During Mating-Type Switching in Saccharomyces cerevisiae
Authors: Lyndaker Amy M , Goldfarb Tamara , Alani Eric
Published: June 2008

Efficient repair of DNA double-strand breaks (DSBs) requires the coordination of checkpoint signaling and enzymatic repair functions. To study these processes during gene conversion at a single chromosomal break, we monitored mating-type switching in Saccharomyces cerevisiae strains defective in the Rad1-Rad10-Slx4 complex. Rad1-Rad10 is a structure-specific endonuclease that removes 3′ nonhomologous single-stranded ends that are generated during many recombination events. Slx4 is a known target of the DNA damage response that forms a complex with Rad1-Rad10 and is critical for 3′-end processing during repair of DSBs by single-strand annealing. We found that mutants lacking an intact Rad1-Rad10-Slx4 complex displayed RAD9- and MAD2-dependent cell cycle delays and decreased viability during mating-type switching. In particular, these mutants exhibited a unique pattern of dead and switched daughter cells arising from the same DSB-containing cell. Furthermore, we observed that mutations in post-replicative lesion bypass factors (mms2Δ, mph1Δ) resulted in decreased viability during mating-type switching and conferred shorter cell cycle delays in rad1Δ mutants. We conclude that Rad1-Rad10-Slx4 promotes efficient repair during gene conversion events involving a single 3′ nonhomologous tail and propose that the rad1Δ and slx4Δ mutant phenotypes result from inefficient repair of a lesion at the MAT locus that is bypassed by replication-mediated repair.
Migration Timing of Columbia River Spring Chinook Salmon: Effects of Temperature, River Discharge, and Ocean Environment
Authors: Keefer Matthew L. , Peery Christopher A. , Caudill Christopher C.
Published: June 2008

In an effort to improve run timing forecasts for Columbia River spring Chinook salmonOncorhynchus tshawytscha, we examined relationships among regional ocean climate indices, in‐river environmental conditions, and full run and stock‐specific migration timing metrics. Results consistently indicated that adult Chinook salmon arrived earliest in years with low river discharge or warm water temperatures and arrived latest in years of cold water temperatures and high flows. As single predictors, in‐river conditions generally explained more interannual variability in salmon return timing than did air temperature, the Pacific Decadal Oscillation, or the North Pacific Index. However, best‐fit multiple‐regression models included a combination of in‐river and climate predictors. While spatial and temporal scales of the analyses were relatively coarse (i.e., monthly values were used for all predictors), clear patterns emerged that can be used to improve pre‐ and in‐season run timing forecasting models for Columbia River spring Chinook salmon. We recommend continued refinement of climate‐based and environmental predictive tools to help manage anadromous fish stocks, including the threatened and endangered populations of the Columbia River basin.
Growth and Habitat Occupancy of Hatchery Coho Salmon in an Engineered Stream
Authors: Smith David L. , Brannon Ernest L.
Published: June 2008

We designed and constructed a natural channel (hereafter, engineered stream; length = 284 m, flow rate = 0.08 m3/s) and compared weight, length, and condition factor between hatchery coho salmon Oncorhynchus kisutch (brood years [BYs] 2000 and 2002) reared in the engineered stream and those reared at Dungeness Hatchery, Washington, under similar temperature regimes. In addition, we compared rearing density, egg‐to‐smolt survival, smolt density, and smolt capacity in the engineered stream with reported reference values for wild coho salmon in rivers. Mean weight and length of fish reared in the engineered stream were 8‐32% and 39‐154% less, respectively, than those of fish reared in the hatchery. Mean condition factor was 1.6‐3.1% greater for fish reared in the engineered stream than for fish reared in the hatchery. Mean monthly growth differed between the engineered stream and hatchery treatment groups; fish in the engineered stream lost weight during the winter, and those in the hatchery gained weight. Rearing density (245%), smolt density (93‐209%), egg‐to‐smolt survival (61‐158%), and smolt capacity (219‐411%) in the engineered stream were greater than reported reference values for wild coho salmon in natural systems. The BY 2000 return rate was 2.61% for hatchery‐reared fish versus 2.55% for fish from the engineered stream. The BY 2002 return was 0.38% for hatchery fish versus 0.12% for fish from the engineered stream. The most important findings of this study are that engineered streams (1) produce smaller fish exhibiting condition factors and smolt‐to‐adult return rates similar to those of fish produced by hatcheries, (2) have a greater rearing capacity than natural habitat, and (3) may be an important approach for restoring the rearing capacity of rivers.
Estuarine Recruitment, Growth, and First‐Year Survival of Juvenile Red Drum in North Carolina
Authors: Stewart Christopher B. , Scharf Frederick S.
Published: June 2008

For many marine and estuarine fishes, there is growing evidence that processes occurring during the juvenile life stage can contribute to determining the relative success of recruitment of annual cohorts into the fishery. We studied two consecutive annual cohorts of juvenile red drum Sciaenops ocellatus from estuarine arrival through age 1 in two estuarine systems of southeastern North Carolina. For age‐0 cohorts, relative abundance generally peaked in mid to late fall, and fish were present in shallow‐water habitats through December before presumably moving to deeper waters during winter. Reappearance of red drum in shallow‐water habitats during spring occurred between late March and late April depending on spring warming rates. Considerable differences in relative abundance of age‐0 red drum were observed between estuaries; such differences may be related to variations in estuarine hydrology and flushing rates, which probably affect larval delivery and distribution. Otolith‐derived hatch date distributions indicated that red drum juveniles in North Carolina were produced between July and October; interannual differences (of up to 30 d) in peak spawning times were correlated with variable nearshore water temperatures during summer. Juvenile growth rates during fall ranged from 0.45 to 0.75 mm/d, and mortality rates were between 1.6% and 4.1% per day; ratios of weight‐specific instantaneous growth to instantaneous mortality were greater than 1.0 for all cohorts during their first fall. Both growth and mortality varied between estuaries and years, suggesting local‐scale control of these vital rates. Discrete overwinter loss rates ranged from 35% to 67%, indicating that fall cohorts of juvenile red drum could be negatively affected by variable overwinter mortality. First‐year vital rates and demographics of red drum cohorts in North Carolina displayed considerable spatial and temporal variability that could potentially affect eventual year‐class success, highlighting the need for further understanding of the linkages between juvenile ecology and fishery recruitment.
A Rapid, Ethanol‐Free Fish Tissue Collection Method for Molecular Genetic Analyses
Authors: LaHood Eric S. , Miller Jason J. , Apland Chase , Ford Michael J.
Published: June 2008

Saving valuable time in genetics research has been thoroughly addressed by the biotechnical industry in the form of ever‐faster and safer DNA isolation and genotyping systems, such as solvent‐free robotic DNA isolation stations, fast polymerase chain reaction (PCR) machines, and semiautomated genetic analyzers. As a result, the time bottleneck has shifted to the tissue‐processing phase of many projects. We developed and tested a fish tissue collection method that reduces this bottleneck by replacing liquid preservative with chromatography paper, thus providing important time‐saving advantages and greater convenience while removing hazardous material constraints from tissue handling. The results show that genomic DNA isolated from caudal‐fin tissue samples collected on chromatography paper is similar in mean total yield, gel appearance, and PCR performance to DNA from tissues collected with ethanol in tubes. This collection method also reduces tissue‐processing time to a small fraction of the time traditionally required.
Regulation of proliferation and differentiation of adipocyte precursor cells in rainbow trout (Oncorhynchus mykiss)
Authors: Bouraoui L , Gutiérrez J , Navarro I
Published: June 2008

Here, we describe optimal conditions for the culture of rainbow trout (Oncorhynchus mykiss) pre-adipocytes obtained from adipose tissue and their differentiation into mature adipocytes, in order to study the endocrine control of adipogenesis. Pre-adipocytes were isolated by collagenase digestion and cultured on laminin or 1% gelatin substrate. The expression of proliferating cell nuclear antigen was used as a marker of cell proliferation on various days of culture. Insulin growth factor-I stimulated cell proliferation especially on days 5 and 7 of culture. Tumor necrosis factor α (TNFα) slightly enhanced cell proliferation only at a low dose. We verified the differentiation of cells grown in specific medium into mature adipocytes by oil red O (ORO) staining. Quantification of ORO showed an increase in triglycerides throughout culture. Immunofluorescence staining of cells at day 11 revealed the expression of CCAAT/enhancer-binding protein and peroxisome proliferator–activator receptor γ, suggesting that these transcriptional factors are involved in adipocyte differentiation in trout. We also examined the effect of TNFα on the differentiation of these adipocytes in primary culture. TNFα inhibited the differentiation of these cells, as indicated by a decrease in glycerol-3-phosphate dehydrogenase activity, an established marker of adipocyte differentiation. In conclusion, the culture system described here for trout pre-adipocytes is a powerful tool to study the endocrine regulation of adipogenesis in this species.
Stability of a loaded pile adjacent to a slurry-supported trench
Authors: Choy C. K. , Standing J. R. , Mair R. J.
Published: June 2008

Diaphragm walls are used to support the sides of deep excavations, and they are often installed close to existing buildings. Construction of these cast-in-place permanent retaining structures can result in substantial soil deformations and potential damage to adjacent structures. A better understanding of this soil–structure interaction problem would greatly benefit safe and economic design. There is particular uncertainty about the interaction and response of piled foundations to diaphragm wall construction, particularly where there could be trench instability at depth. A series of small-scale model tests has been conducted using the 8 m diameter geotechnical centrifuge at Cambridge University to study the installation effects of diaphragm walls on a single adjacent pile in dense fine sand. An instrumented model pile was installed and loaded at various offsets from a slurry-filled model trench. Two trench lengths were investigated. The tests have provided a detailed insight into the movements of the pile and the progressive redistribution of loads along the pile. A generalised mechanism for the pile–trench interaction is also proposed. The main factors affecting the severity of pile response are slurry level (trench pressure), pile offset distance (α) and trench length (L). The experiments showed that the risk of system instability reduced significantly with x/L values above 1·15.
Effects of subsurface cavity expansion in clays
Authors: Au S. K. A. , Yeung A. T. , Soga K. , Cheng Y. M.
Published: June 2008

Subsurface cavity expansion in clay induced by compaction grouting can generate upward displacement of clay and/or increase in effective stress leading to consolidation, resulting in settlement compensation and/or shear strength enhancement respectively. However, the two potential benefits of subsurface cavity expansion may offset each other. Experiments and numerical simulations on the engineering behaviour of E-grade kaolin induced by subsurface pressure-controlled cavity expansion were conducted to investigate the interrelationship between compensation effectiveness and shear strength enhancement. The results of numerical simulations are in reasonably good agreement with the experimental data, indicating that the numerical simulation procedure adopted is a plausible and reliable technique to describe the engineering behaviour of clays induced by pressure-controlled cavity expansion. Effects of cavity expansion rate, cavity expansion volume, injection point spacing, and stress history on compensation effectiveness and shear strength enhancement were studied. Practical applications of the results are also proposed.
The undrained cyclic behaviour of a carbonate sand
Authors: Qadimi A. , Coop M. R.
Published: June 2008

A series of undrained cyclic triaxial tests was carried out on a carbonate sand that had previously been the subject of extensive research for monotonic loading. It was found that the generation of pore pressures under cyclic loading depended on the same factors as they did for monotonic loading, so that the state of the soil in the plane of specific volume against logarithm of mean effective pressure was of particular significance. For states that were not initially on the normal compression line, the pore pressure changes were also found to be highly dependent on how the initial state was achieved: whether it was by compaction and first loading, or by overconsolidation. Failure was found to occur for a much lower number of cycles from states on the one-dimensional normal compression line than for states on the isotropic normal compression line, and cyclic loading to failure was found to be associated with much less particle breakage than monotonic loading. When the stiffnesses measured during cycling had been normalised for those factors that influence the monotonic stiffness of the soil tested, it was still found that for two-way cyclic loading there was a component of the reduction in stiffness that might be attributed to changes of fabric due to the alternation in the direction of the major principal stress.
Oxygen diffusion through partially hydrated geosynthetic clay liners
Authors: Bouazza A. , Rahman F.
Published: June 2008

One of the prime purposes of a cover system in sulphidic mine tailings is to limit oxygen intrusion into the waste deposits so that generation of acid mine drainage is minimised. In areas where humid climates tend to prevail, a resistive barrier is usually used, either as part of a conventional multi-component cover or as a capillary break cover. Geosynthetic clay liners (GCLs) can be used in either case because of their low saturated hydraulic conductivity, provided they can be kept close to saturation to minimise oxygen diffusion. This paper presents the results of a laboratory investigation into oxygen diffusion through partially hydrated needle-punched and stitch-bonded geosynthetic clay liners. It was observed that the diffusion coefficient decreased with an increase in the degree of saturation. The variations in diffusion coefficient followed the same trend for the GCLs investigated, with variation of up to four orders of magnitude for the conditions investigated, indicating that low oxygen diffusivity can be achieved if GCLs have a high degree of saturation. However, it was found that the way that GCLs are held together as a composite material has a significant effect on the variation of gas diffusivity. Finally, unique empirical relationships between the effective diffusion of needle-punched and stitch-bonded GCLs and degree of saturation appear to exist and can be used to obtain an estimate of the diffusion coefficient value for use in calculations of diffusive flux through cover systems containing stitch-bonded or needle-punched GCLs.
Soil layer response to pore pressure variations at the boundary
Authors: Conte E. , Troncone A.
Published: June 2008

A simple solution procedure is presented to obtain readily the transient response of saturated soil layers under one-dimensional conditions, when general pore pressure variations with time occur at the boundary. This procedure makes use of some analytical expressions derived in this study in conjunction with the Fourier series. The solution is used to analyse the experimental results from laboratory tests and field measurements concerning pore pressure and settlement rate, with the objective of evaluating representative values of the coefficient of swelling/consolidation of the soil.
Thermo-mechanical behaviour of a compacted swelling clay
Authors: Tang A.-M. , Cui Y.-J. , Barnel N.
Published: June 2008

Compacted unsaturated swelling clay is often considered as a possible buffer material for deep nuclear waste disposal. An isotropic cell permitting simultaneous control of suction, temperature and pressure was used to study the thermo-mechanical behaviour of this clay. Tests were performed at total suctions ranging from 9 to 110 MPa, temperatures ranging from 25°C to 80°C, and isotropic pressures from 0·1 to 60 MPa. It was observed that heating at constant suction and pressure induces either swelling or contraction. The results from compression tests at constant suction and temperature showed that, at lower suction, the yield pressure was lower, and the elastic compressibility and plastic compressibility parameters were higher. By contrast, at a similar suction, the yield pressure was slightly influenced by the temperature, and the compressibility parameters were insensitive to temperature changes. The thermal hardening phenomenon was equally evidenced by following a thermomechanical path of loading–heating–cooling–reloading.
Shear strength model for overconsolidated clay-infilled idealised rock joints
Authors: Indraratna B. , Jayanathan M. , Brown E. T.
Published: June 2008

Saturated infilled joints can contribute to the instability of rock masses during undrained shearing. This paper reports an experimental investigation into the effect of the overconsolidation of infilled rough joints on undrained shear behaviour. A revised model is presented for predicting the shear strength of rough infilled joints on the basis of experimental tests carried out on idealised sawtoothed joints with natural silty clay as the infill material. Tests were conducted under consolidated undrained conditions in a high-pressure triaxial apparatus on joints having a dip angle of 60°. Pore pressure development in the infill materials was monitored. The results show that the effect of asperities on shear strength is significant up to a critical asperity height to infill thickness ratio (t/a), whereas the shear behaviour is controlled by the infill alone beyond this critical value. The proposed model for predicting the shear strength of rough infilled joints describes how the OCR influences the shear strength, pore water pressure development, and critical t/a ratio.
Gas flow through clay barriers
Authors: Olivella S. , Alonso E. E.
Published: June 2008

A model for the simulation of gas flow in clayey rocks and clays is described. Gas migration is associated with the development of preferential paths along existing or pressure-dependent discontinuities. The model handles the combined phenomena of two-phase (air and liquid) flow and the generation of discrete paths. Aperture of discrete paths is the main variable to account for permeability and capillary pressure variations. The model, which has been implemented in a general thermo-hydro-mechanical code, is used to simulate two experiments (laboratory and field). The laboratory experiment involved gas flow through shale specimens tested in a triaxial cell. In the field experiment, gas flow was forced through a sand–bentonite barrier. Experimental results and model calculations are compared in the paper.
Compaction behaviour of clay
Authors: Tarantino A. , De Col E.
Published: June 2008

This paper presents an experimental study of the compaction behaviour of non-active clay. One-dimensional static compaction tests were carried out at high and medium water content with matric suction monitoring using Trento high-capacity tensiometers. At lower water contents, a transistor psychrometer was used to measure post-compaction suction. Samples were compacted on the dry side of optimum to cover a wide range of compaction water contents and vertical stresses. Three water content regions were identified in the compaction plane depending on whether post-compaction suction increased, decreased or remained constant as the degree of saturation was increased at constant water content. Hydraulic paths of specimens subjected to loading–unloading cycles at constant water content have clearly shown that post-compaction suction may increase as the degree of saturation increases. This non-intuitive behaviour was demonstrated to be associated with the coupling between mechanical and water retention behaviour. To this end, a coupled mechanical water retention model was formulated. Irreversible one-dimensional mechanical paths were modelled by a boundary surface in the space average skeleton vertical stress, modified suction and void ratio. Irreversible hydraulic ‘wetting’ paths were modelled by a boundary surface in the space suction, degree of saturation, and void ratio. This study was completed by investigating the pore size distribution of compacted samples through MIP tests.
Anisotropic creep model for soft soils
Authors: Leoni M. , Karstunen M. , Vermeer P. A.
Published: June 2008

In this paper a new anisotropic model for time-dependent behaviour of soft soils is presented. The formulation is based on a previously developed isotropic creep model, assuming rotated Modified Cam Clay ellipses as contours of volumetric creep strain rates. A rotational hardening law is adopted to account for changes in anisotropy due to viscous strains. Although this will introduce some new soil parameters, they do not need calibration as they can be expressed as functions of basic soil parameters through simple analytical expressions. To start with, the one-dimensional response of the model is discussed, making it possible to explore how the model is capable of capturing key features of viscous soft soil behaviour. Subsequently, the three-dimensional generalisation of the model is presented, followed by comparison with experimental data, showing good agreement in both triaxial undrained compression and extension. In the authors' opinion, the simple formulation of the model makes it attractive for use in engineering practice.
Spatial variation of void ratio and shear band thickness in sand using X-ray computed tomography
Authors: Alshibli K. A. , Hasan A.
Published: June 2008

A detailed study of spatial variation of void ratio and shear band thickness measurements is presented in this paper. A prismatic sand specimen that initially measured 57·4 mm wide × 120·5 mm long × 182·1 mm high was sheared under plane-strain (biaxial) loading conditions. The specimen was prepared at a relative density of 79% using F-75 Ottawa sand. X-ray computed tomography was used to scan the specimen before shearing and after the onset of the shear band. The specimen failed through a single shear band with an inclination angle of 65·6° measured from the direction of the minor principal stress. Computer algorithms were developed to calibrate CT images and quantify void ratio (e) variation within the specimen. CT data analysis revealed cross-sectional spatial variation in void ratio where density is higher in regions close to the edges of the specimen due to membrane effects and confining pressure with no significant variation in void ratio in the axial direction (top to bottom) before shearing. The shear band was easily identified from the CT images, and analysis of void ratio showed a noticeable jump in void ratio profile across the shear band. A detailed statistical summary of the thickness of the shear band and variation of void ratio across the shear band is presented and discussed.
Analysis of the shaft resistance of non-displacement piles in sand
Authors: Loukidis D. , Salgado R.
Published: June 2008

The paper examines, using numerical modelling, the problem of the limit shaft resistance of non-displacement piles installed in sands. The modelling makes use of an advanced, two-surface-plasticity constitutive model. The constitutive model predicts the soil response in both the small- and the large-strain range, while taking into account the effects of the intermediate principal effective stress and of the inherent anisotropy of the sand. Finite element analyses of shearing along the pile shaft are performed in order to examine the development of limit unit shaft resistance and the changes in stress state around the shaft upon axial loading of the pile. Special focus is placed on the operative value of the lateral earth pressure coefficient when limit shaft resistance is reached. The analyses offer useful insights regarding the factors controlling the value of unit shaft resistance in sands. The simulations predict a significant build-up of horizontal effective stress for dense sands. Based on these simulations, we propose a relationship between the lateral earth pressure coefficient for use in the calculation of the limit shaft resistance of the pile and the initial density and stress state of the sand.
Revised radiolarian ages for the sedimentary cover of the Balagne ophiolite (Corsica, France). Implications for the palaeoenvironmental evolution of the Balano-Ligurian margin
Authors: Danelian Taniel , De Wever Patrick , Durand-Delga Michel
Published: June 2008

The age of radiolarites covering the Balagne ophiolite is reassessed based on new and revised radiolarian fossil evidence. The oldest radiolarian cherts are dated as upper Bathonian-lower Callovian in two tectonic units: San Colombano and Novella. These are amongst the oldest ages available so far from ophiolites of the Ligurian ocean. An important stratigraphic gap, spanning the Callovian-early Kimmeridgian interval, is specified between radiolarites and the overlying (and locally gullying) San Colombano shallow-water limestones (sub-unit I). We can now specify that radiolarian ooze accumulated until the late Kimmeridgian in the distal parts of the Balagne margin (sub-unit SC III and Novella unit), while fragments of Hercynian basement fell into the Balagne basin during the late Kimmeridgian-Tithonian.
Surface processes versus kinematics of thrust belts: impact on rates of erosion, sedimentation, and exhumation – Insights from analogue models
Authors: Bonnet Cécile , Malavieille Jacques , Mosar Jon
Published: June 2008

The mechanical equilibrium of an orogenic wedge is maintained thanks to interactions between tectonic processes and surface processes. To better constrain the influence of erosion and sedimentation on the evolution of orogens, we performed a series of analogue models based on the tapered wedge principle, varying the amounts of erosion and sedimentation. The models develop by frontal accretion in the foreland basin and by simple underthrusting and subsequent underplating in the hinterland. The variations in rates of erosion and sedimentation strongly modify the extent, the morphology, the structures, the timing of development and the material paths in the different models. Under certain conditions, entire structural units can be formed and subsequently eroded out of the geological record, leading to important underestimations when restoring sections. Particles located in the converging lower-plate or in the upper-plate show complex uplift paths related to tectonic stages. The correlation between models and three Alpine tectonic cross-sections emphasizes the role of erosion and sedimentation on the dynamics and development of the orogen and adjacent Molasse basin. Along strike changes in the present structure of the orogen could be explained in part by differences in surface processes.