bluuebunny/crossref_metadata_2025 huggingface dataset:
A short review on the aetiology and pathophysiology of alcoholism
Authors: Moussas George , Christodoulou Christos , Douzenis Athanassios
Published: May 2009

Alcoholism is a chronic remitting and relapsing condition; its aetiology and pathophysiology remains largely obscure despite recent advances. This review summarises the current knowledge about the causation (biological or psychological) of alcohol addiction. This involves heredity, candidate genes, alcohol metabolism regulation and the influence of alcohol in the pathophysiology of the different neurotransmitter systems. Alcohol addiction is a multifactorial phenomenon where personality structure, individual state of mind and social influences are in constant interaction with brain neurobiology and pathophysiology. This disorder influences different sexes in different ways and causes major problems, especially in developed societies.
Epidemiology of breast cancer subtypes in two prospective cohort studies of breast cancer survivors
Authors: Kwan Marilyn L , Kushi Lawrence H , Weltzien Erin , Maring Benjamin , Kutner Susan E , Fulton Regan S , Lee Marion M , Ambrosone Christine B , Caan Bette J
Published: May 2009

Introduction

The aim of this study was to describe breast tumor subtypes by common breast cancer risk factors and to determine correlates of subtypes using baseline data from two pooled prospective breast cancer studies within a large health maintenance organization.

Methods

Tumor data on 2544 invasive breast cancer cases subtyped by estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 (Her2) status were obtained (1868 luminal A tumors, 294 luminal B tumors, 288 triple-negative tumors and 94 Her2-overexpressing tumors). Demographic, reproductive and lifestyle information was collected either in person or by mailed questionnaires. Case-only odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using logistic regression, adjusting for age at diagnosis, race/ethnicity, and study origin.

Results

Compared with luminal A cases, luminal B cases were more likely to be younger at diagnosis (P = 0.0001) and were less likely to consume alcohol (OR = 0.74, 95% CI = 0.56 to 0.98), use hormone replacement therapy (HRT) (OR = 0.66, 95% CI = 0.46 to 0.94), and oral contraceptives (OR = 0.73, 95% CI = 0.55 to 0.96). Compared with luminal A cases, triple-negative cases tended to be younger at diagnosis (P ≤ 0.0001) and African American (OR = 3.14, 95% CI = 2.12 to 4.16), were more likely to have not breastfed if they had parity greater than or equal to three (OR = 1.68, 95% CI = 1.00 to 2.81), and were more likely to be overweight (OR = 1.82, 95% CI = 1.03 to 3.24) or obese (OR = 1.97, 95% CI = 1.03 to 3.77) if premenopausal. Her2-overexpressing cases were more likely to be younger at diagnosis (P = 0.03) and Hispanic (OR = 2.19, 95% CI = 1.16 to 4.13) or Asian (OR = 2.02, 95% CI = 1.05 to 3.88), and less likely to use HRT (OR = 0.45, 95% CI = 0.26 to 0.79).

Conclusions

These observations suggest that investigators should consider tumor heterogeneity in associations with traditional breast cancer risk factors. Important modifiable lifestyle factors that may be related to the development of a specific tumor subtype, but not all subtypes, include obesity, breastfeeding, and alcohol consumption. Future work that will further categorize triple-negative cases into basal and non-basal tumors may help to elucidate these associations further.
Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease
Authors: Dobrin Radu , Zhu Jun , Molony Cliona , Argman Carmen , Parrish Mark L , Carlson Sonia , Allan Mark F , Pomp Daniel , Schadt Eric E
Published: May 2009

Background

Obesity is a particularly complex disease that at least partially involves genetic and environmental perturbations to gene-networks connecting the hypothalamus and several metabolic tissues, resulting in an energy imbalance at the systems level.

Results

To provide an inter-tissue view of obesity with respect to molecular states that are associated with physiological states, we developed a framework for constructing tissue-to-tissue coexpression networks between genes in the hypothalamus, liver or adipose tissue. These networks have a scale-free architecture and are strikingly independent of gene-gene coexpression networks that are constructed from more standard analyses of single tissues. This is the first systematic effort to study inter-tissue relationships and highlights genes in the hypothalamus that act as information relays in the control of peripheral tissues in obese mice. The subnetworks identified as specific to tissue-to-tissue interactions are enriched in genes that have obesity-relevant biological functions such as circadian rhythm, energy balance, stress response, or immune response.

Conclusions

Tissue-to-tissue networks enable the identification of disease-specific genes that respond to changes induced by different tissues and they also provide unique details regarding candidate genes for obesity that are identified in genome-wide association studies. Identifying such genes from single tissue analyses would be difficult or impossible.
Phylogenetic classification of Escherichia coliO157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms
Authors: Clawson Michael L , Keen James E , Smith Timothy PL , Durso Lisa M , McDaneld Tara G , Mandrell Robert E , Davis Margaret A , Bono James L
Published: May 2009

Background

Cattle are a reservoir of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157), and are known to harbor subtypes not typically found in clinically ill humans. Consequently, nucleotide polymorphisms previously discovered via strains originating from human outbreaks may be restricted in their ability to distinguish STEC O157 genetic subtypes present in cattle. The objectives of this study were firstly to identify nucleotide polymorphisms in a diverse sampling of human and bovine STEC O157 strains, secondly to classify strains of either bovine or human origin by polymorphism-derived genotypes, and finally to compare the genotype diversity with pulsed-field gel electrophoresis (PFGE), a method currently used for assessing STEC O157 diversity.

Results

High-throughput 454 sequencing of pooled STEC O157 strain DNAs from human clinical cases (n = 91) and cattle (n = 102) identified 16,218 putative polymorphisms. From those, 178 were selected primarily within genomic regions conserved across E. coli serotypes and genotyped in 261 STEC O157 strains. Forty-two unique genotypes were observed that are tagged by a minimal set of 32 polymorphisms. Phylogenetic trees of the genotypes are divided into clades that represent strains of cattle origin, or cattle and human origin. Although PFGE diversity surpassed genotype diversity overall, ten PFGE patterns each occurred with multiple strains having different genotypes.

Conclusions

Deep sequencing of pooled STEC O157 DNAs proved highly effective in polymorphism discovery. A polymorphism set has been identified that characterizes genetic diversity within STEC O157 strains of bovine origin, and a subset observed in human strains. The set may complement current techniques used to classify strains implicated in disease outbreaks.
Worldwide patterns of haplotype diversity at 9p21.3, a locus associated with type 2 diabetes and coronary heart disease
Authors: Silander Kaisa , Tang Hua , Myles Sean , Jakkula Eveliina , Timpson Nicholas J , Cavalli-Sforza Luigi , Peltonen Leena
Published: May 2009

A 100 kb region on 9p21.3 harbors two major disease susceptibility loci: one for type 2 diabetes (T2D) and one for coronary heart disease (CHD). The single nucleotide polymorphisms (SNPs) associated with these two diseases in Europeans reside on two adjacent haplotype blocks with independent effects on disease. To help delimit the regions that likely harbor the disease-causing variants in populations of non-European origin, we studied the haplotype diversity and allelic history of the 9p21.3 region using 938 unrelated individuals from 51 populations (Human Genome Diversity Panel). We used SNP data from Illumina's 650Y SNP arrays supplemented with five additional SNPs within the region of interest. Haplotype frequencies were analyzed with the EM algorithm implemented in PLINK. For the T2D locus, the TT risk haplotype of SNPs rs10811661 and rs10757283 was present at similar frequencies in all global populations, while a shared 6-SNP haplotype that carries the protective C allele of rs10811661 was found at a frequency of 2.9% in Africans and 41.3% in East Asians and was associated with low haplotype diversity. For the CHD locus, all populations shared a core risk haplotype spanning >17.5 kb, which shows dramatic increase in frequency between African (11.5%) and Middle Eastern (63.7%) populations. Interestingly, two SNPs (rs2891168 and rs10757278) tagging this CHD risk haplotype are most strongly associated with CHD disease status according to independent clinical fine-mapping studies. The large variation in linkage disequilibrium patterns identified between the populations demonstrates the importance of allelic background data when selecting SNPs for replication in global populations. Intriguingly, the protective allele for T2D and the risk allele for CHD show an increase in frequency in non-Africans compared to Africans, implying different population histories for these two adjacent disease loci.
Fibroblast Growth Factor 21 Controls Glycemia via Regulation of Hepatic Glucose Flux and Insulin Sensitivity
Authors: Berglund Eric D. , Li Candice Y. , Bina Holly A. , Lynes Sara E. , Michael M. Dodson , Shanafelt Armen B. , Kharitonenkov Alexei , Wasserman David H.
Published: May 2009

Fibroblast growth factor 21 (FGF21) is a novel metabolic regulator shown to improve glycemic control. However, the molecular and functional mechanisms underlying FGF21-mediated improvements in glycemic control are not completely understood. We examined FGF21 effects on insulin sensitivity and glucose fluxes upon chronic (daily injection for 8 d) and acute (6 h infusion) administration in ob/+ and ob/ob mice. Results show that chronic FGF21 ameliorated fasting hyperglycemia in ob/ob mice via increased glucose disposal and improved hepatic insulin sensitivity. Acute FGF21 suppressed hepatic glucose production, increased liver glycogen, lowered glucagon, and improved glucose clearance in ob/+ mice. These effects were blunted in ob/ob mice. Neither chronic nor acute FGF21 altered skeletal muscle or adipose tissue glucose uptake in either genotype. In conclusion, FGF21 has potent glycemic effects caused by hepatic changes in glucose flux and improved insulin sensitivity. Thus, these studies define mechanisms underlying anti-hyperglycemic actions of FGF21 and support its therapeutic potential.
Apurinic/Apyrimidinic Endonuclease 1 Alters Estrogen Receptor Activity and Estrogen-Responsive Gene Expression
Authors: Curtis Carol D. , Thorngren Daniel L. , Ziegler Yvonne S. , Sarkeshik Ali , Yates John R. , Nardulli Ann M.
Published: May 2009

Apurinic/apyrimidinic endonuclease 1 or redox factor-1 (Ape1/Ref-1) is a pleiotropic cellular protein involved in DNA repair and, through its redox activity, enhances the binding of a select group of transcription factors to their cognate recognition sequences in DNA. Thus, we were intrigued when we identified Ape1/Ref-1 and a number of DNA repair and oxidative stress proteins in a complex associated with the DNA-bound estrogen receptor α (ERα). Because Ape1/Ref-1 interacts with a number of transcription factors and influences their activity, we determined whether it might also influence ERα activity. We found that endogenously expressed Ape1/Ref-1 and ERα from MCF-7 human breast cancer cells interact and that Ape1/Ref-1 enhances the interaction of ERα with estrogen-response elements (EREs) in DNA. More importantly, Ape1/Ref-1 alters expression of the endogenous, estrogen-responsive progesterone receptor and pS2 genes in MCF-7 cells and associates with ERE-containing regions of these genes in native chromatin. Interestingly, knocking down Ape1/Ref-1 expression or inhibiting its redox activity with the small molecule inhibitor E3330 enhances estrogen responsiveness of the progesterone receptor and pS2 genes but does not alter the expression of the constitutively active 36B4 gene. Additionally, the reduced form of Ape1/Ref-1 increases and E3330 limits ERα-ERE complex formation in vitro and in native chromatin. Our studies demonstrate that Ape1/Ref-1 mediates its gene-specific effects, in part, by associating with endogenous, estrogen-responsive genes and that the redox activity of Ape1/Ref-1 is instrumental in altering estrogen-responsive gene expression.
Down syndrome critical region protein 5 regulates membrane localization of Wnt receptors, Dishevelled stability and convergent extension in vertebrate embryos
Authors: Shao Ming , Liu Zhong-Zhen , Wang Cheng-Dong , Li Hong-Yan , Carron Clémence , Zhang Hong-Wei , Shi De-Li
Published: May 2009

The Glypican family of heparan sulfate proteoglycans regulates Wnt signaling and convergent extension (CE) in vertebrate embryos. They are predicted to be glycosylphosphatidylinositol (GPI)-tethered membrane-bound proteins, but there is no functional evidence of their regulation by the GPI synthesis complex. Down syndrome critical region protein 5 (Dscr5, also known as Pigp) is a component of the GPI-N-acetylglucosaminyltransferase (GPI-GnT)complex, and is associated with specific features of Down syndrome. Here we report that Dscr5 regulates CE movements through the non-canonical Wnt pathway. Both dscr5 overexpression and knockdown impaired convergence and extension movements. Dscr5 functionally interacted with Knypek/Glypican 4 and was required for its localization at the cell surface. Knockdown of dscr5 disrupted Knypek membrane localization and caused an enhanced Frizzled 7 receptor endocytosis in a Caveolin-dependent manner. Furthermore, dscr5 knockdown promoted specific Dishevelled degradation by the ubiquitin-proteosome pathway. These results reveal a functional link between Knypek/Glypican 4 and the GPI synthesis complex in the non-canonical Wnt pathway, and provide the new mechanistic insight that Dscr5 regulates CE in vertebrate embryos by anchoring different Wnt receptors at the cell surface and maintaining Dishevelled stability.
Alcohol dependence in public policy: towards its (re)inclusion
Authors: Williamson Laura
Published: May 2009

Public policy on alcohol in the UK relies on health promotion campaigns that encourage individuals who misuse alcohol to make healthier choices about their drinking. Individuals with alcohol-dependence syndrome have an impaired capacity to choose health. As a result, individuals with the worst alcohol misuse problems lie largely outside the reach of choice-based policy. However, such policy has been widely criticized and efforts to reform it are underway. This paper argues that the British Medical Association's recent attempt to improve policy on alcohol in the UK by introducing strategies which have been shown to control drinking within populations still gives insufficient attention to alcohol dependence. This is because it fails accurately and consistently to characterize alcohol dependence and gives insufficient attention to the social challenges it presents.
Ethical decision-making in two patients with locked-in syndrome on the intensive care unit
Authors: Kompanje E J O
Published: May 2009

Locked-in syndrome (LIS) is one of the most dramatic neurological outcomes and has a profound impact on patients and their families. Most patients have intact cognition and intellectual ability and perception. Communication is possible with eyelid and/or eyeball movement. According to the literature, the wish to die is not an important issue in acute and chronic LIS. This study describes and analyses the ethical decision-making process in two opposite cases of LIS in the intensive care unit. One patient expressed the wish to prolong her life for as long as possible; the other patient asked for deliberate termination of life. Both wishes were honoured. In conclusion, most patients with LIS are competent and intellectually intact. In The Netherlands the autonomy of the patient is respected by law. In respecting this autonomy, medical choices can be different in comparable patients.
Being ‘one cog in a bigger machine’: a qualitative study investigating ethical challenges perceived by junior doctors
Authors: McDougall R J
Published: May 2009

There is increasing recognition among bioethicists that health-care practitioners' everyday ethical challenges ought to be the focus of ethical analysis. Interviews were conducted with Australian junior doctors to identify some of the kinds of situations that they found ethically challenging, as a basis for this type of grounded philosophical analysis and for further empirical research into junior doctors' ethical issues. Fourteen doctors in their first to fourth year of work from six hospitals in Melbourne participated. Issues discussed included involvement in treatment perceived as inappropriate, seniors discouraging disclosure of errors, coping when requested help was not forthcoming, observing behaviour perceived as unethical, truth-telling and informed consent. The difficulties described often focused on interactions with colleagues and position in the health-care team. Although the results cannot be generalized to junior doctors as a population, these junior doctors' stories point to various issues warranting further investigation, both philosophical and empirical.
Hormone replacement therapy and cardiovascular disease revisited
Authors: Stevenson John C
Published: May 2009

Controversy still rages about whether hormone replacement therapy (HRT) confers cardiovascular benefit or harm. There is a wealth of biological evidence that estrogen has a beneficial effect, supporting a large body of epidemiological evidence demonstrating reduction in coronary events with HRT. A large randomized placebo-controlled clinical trial of preventive strategies for coronary heart disease (CHD) in postmenopausal women, the Women's Health Initiative (WHI), included HRT arms. The published preliminary findings of this trial showed a significant increase in coronary events, stroke, venous thromboembolism and breast cancer with estrogen–progestogen, leading to the conclusion that HRT was unsafe to use other than for short-term relief of menopausal symptoms. But subsequent publications of the more complete data from WHI have shown no significant increase in CHD, and a tendency to a reduction in those initiating HRT below age 60 years. This is important because other therapeutic strategies for the primary prevention of CHD, such as aspirin and statins, are not of proven benefit in women, in contrast to men. Subsequent WHI findings have not shown a clear increase in breast cancer, and any potential increase from HRT is similar to that seen with many lifestyle factors and other commonly used medications. The preliminary WHI results do not reflect accurately true benefits and risks, and HRT should remain a potential preventive treatment for CHD.
Acute unilateral cataract in a postpartum adolescent with poorly-controlled type 1 diabetes
Authors: Ahmad S S , Misra A , Glenn A , Temple R C
Published: May 2009

Acute cataract is recognized as a rare complication in adolescents with type 1 diabetes mellitus and may be associated with rapid improvement in glycaemia in patients with newly diagnosed diabetes. Transient cataracts, which resolve following improved metabolic control, and irreversible cataracts requiring surgery have also previously been documented. Development or progression of retinopathy may complicate pregnancy in women with diabetes. To our knowledge, we present the first case report of an acute cataract developing postpartum in a woman with type 1 diabetes.

This rare case serves to demonstrate a possible association between acute cataract and altered glycaemic control in pregnancy. Acute cataract should be considered in any woman with diabetes who develops sudden visual loss following pregnancy.
Pregnancy complicating Wegener's granulomatosis
Authors: Soh May Ching , Hart Hamish H , Bass Eileen , Wilkinson Lucille
Published: May 2009

Pregnancy associated with Wegener's granulomatosis is rare. Therapeutic options are limited. There is a paucity of published literature to guide clinical decision-making in these complex patients. Two cases are presented. Firstly, a 33-year-old woman with generalized Wegener's in remission and off all medications presented with a flare in the third trimester with haemoptysis, raised C-reactive protein and c-anti-neutrophilic cytoplasmic antibody (c-ANCA) levels. Her care was complicated by florid steroid-induced psychosis. With deteriorating disease control, she was treated with pulsed-intravenous cyclophosphamide with a good response. She delivered a healthy baby at 38 weeks. She had a severe postpartum flare. Secondly, a 37-year-old woman with limited Wegener's in remission for the last two years and off all treatment became pregnant after pre-conception counselling. A normal baby was delivered at term. An exhaustive review of all published literature on Wegener's activity in pregnancy is presented along with therapeutic options and recommendations.
Multiple pneumothoraces during second and third trimesters as first presentation of lymphangioleiomyomatosis
Authors: McCartney Ruth , Facey Nicola , Chalmers George , Mathers Alan , Roberts Fiona , Irvine Gill , Anderson Kenneth
Published: May 2009

A case of lymphangioleiomyomatosis presenting as multiple pneumothoraces during pregnancy is described below. Presentations, management and prognosis are discussed.
The angiotensin-converting enzyme gene insertion–deletion polymorphism in a white British patient cohort with obstetric cholestasis
Authors: Müllenbach Roman , Tetlow Natasha , Bennett Amanda , Pipkin Fiona Broughton , Morgan Linda , Williamson Catherine
Published: May 2009

The DD genotype of the angiotensin-converting enzyme (ACE) gene is over-represented in Finnish patients with obstetric cholestasis (OC). The purpose of this study was to establish whether this genotype is associated with cholestasis in UK cases. In a retrospective case-control study, we determined the ACE insertion/deletion frequencies in 166 British cases and 100 control women by polymerase chain reaction analysis. No significant difference in allele frequencies was found between these groups, but allele frequencies differed significantly between Finnish and UK OC cases ( P = 0.0005). The prevalence of the DD genotype is lower in UK cases than in controls (χ2 [1 d.f.] = 4.32, P = 0.05) and the odds ratio for OC associated with the DD genotypeis 0.54, 95% confidence interval 0.30–0.97. In contrast to Finnish OC cases, the DD genotype of the ACE is not increased in UK cases.
Obesity in pregnancy: risks and management
Authors: Fitzsimons Kate J , Modder Jo , Greer Ian A
Published: May 2009

Maternal obesity is now considered one of the most commonly occurring risk factors seen in obstetric practice. Compared with women with a healthy pre-pregnancy weight, women with obesity are at increased risk of miscarriage, gestational diabetes, preeclampsia, venous thromboembolism, induced labour, caesarean section, anaesthetic complications and wound infections, and they are less likely to initiate or maintain breastfeeding. Babies of obese mothers are at increased risk of stillbirth, congenital anomalies, prematurity, macrosomia and neonatal death. Intrauterine exposure to obesity is also associated with an increased risk of developing obesity and metabolic disorders in childhood. This article reviews the prevalence of obesity in pregnancy and the associated maternal and fetal complications. Recommendations and suggestions for pre-conception, antenatal and postnatal care of women with obesity are presented, and current research in the UK and future research priorities are considered.
Correlations of Free Thyroid Hormones Measured by Tandem Mass Spectrometry and Immunoassay with Thyroid-Stimulating Hormone across 4 Patient Populations
Authors: Jonklaas Jacqueline , Kahric-Janicic Natasa , Soldin Offie P , Soldin Steven J
Published: May 2009

Background: Accurate measurement of free thyroid hormones is important for managing thyroid disorders. Ultrafiltration liquid chromatography tandem mass spectrometry (LC-MS/MS) can reliably measure the concentrations of small molecules, including thyroid hormones. Our study was designed to compare free thyroid hormone measurements performed with immunoassay and LC-MS/MS.

Methods: We studied the performance of LC-MS/MS in 4 different populations comprising pediatric patients, euthyroid adults, and healthy nonpregnant and pregnant women. The samples obtained from each population numbered 38, 200, 28, and 128, respectively. Free thyroxine, free triiodothyronine, and thyroid-stimulating hormone (TSH) concentrations were documented.

Results: LC-MS/MS measurement of free thyroid hormones provided better correlation with log-transformed serum TSH in each population and also the populations combined. The correlations between free thyroxine measured by LC-MS/MS and log TSH in the pediatric outpatients and healthy adults were −0.90 and −0.77, respectively. The correlations for immunoassay were −0.82 and −0.48. The correlations between free triiodothyronine measured by LC-MS/MS and TSH for both pediatric and healthy adult populations were −0.72 and −0.68, respectively.

Conclusions: Free thyroid hormone concentrations measured by LC-MS/MS correlate to a greater degree with log TSH values compared to concentrations measured by immunoassay. This correlation was maintained across the patient populations we studied and may reflect the accuracy and specificity of LC-MS/MS. The superior ability of LC-MS/MS to enable documentation of the well-known thyroid hormone–TSH relationship supports the use of this measurement technique in a variety of clinical situations.
Impact of Left Ventricular End-Diastolic Wall Stress on Plasma B-Type Natriuretic Peptide in Heart Failure with Chronic Kidney Disease and End-Stage Renal Disease
Authors: Niizuma Shinichiro , Iwanaga Yoshitaka , Yahata Takaharu , Tamaki Yodo , Goto Yoichi , Nakahama Hajime , Miyazaki Shunichi
Published: May 2009

Background: Plasma B-type natriuretic peptide (BNP) is a diagnostic and prognostic marker in heart failure (HF). Although renal function is reported as an important clinical determinant, precise evaluations of the relationships of renal function with hemodynamic factors in determining BNP have not been performed. Therefore, we evaluated the association of plasma BNP concentrations with LV end-diastolic wall stress (EDWS) in a broad range of HF patients including those with chronic kidney disease (CKD) and end-stage renal disease (ESRD).

Methods: In 156 consecutive HF patients including those with CKD and ESRD, we measured plasma BNP and performed echocardiography and cardiac catheterization. LV EDWS was calculated as a crucial hemodynamic determinant of BNP.

Results: Plasma BNP concentrations increased progressively with decreasing renal function across the groups (P < 0.01) and were correlated with LV EDWS (r = 0.47) in the HF patients overall. This relationship was also present when patients were subdivided into systolic and diastolic HF (P < 0.01). In multivariable analysis, higher EDWS was associated with increased BNP concentration independently of renal dysfunction (P < 0.01). Anemia, systolic HF, and decreased BMI also contributed to increased BNP concentrations.

Conclusions: These results suggest that LV EDWS is a strong determinant of BNP even in patients with CKD and ESRD. Anemia, obesity, and HF type (systolic or diastolic) should also be considered in interpreting plasma BNP concentrations in HF patients. These findings may contribute to the clinical management of HF patients, especially those complicated with CKD and ESRD.
Briefing: ICE maritime panel November 2008
Authors: Marsh P.
Published: May 2009

This briefing note is the first in a series that will keep readers abreast of the work of the Institution of Civil Engineers' (ICE) maritime panel.
32nd America's Cup structures in Valencia, Spain
Authors: Gisbert Blanquer J. , Gras Navarro M.
Published: May 2009

This paper describes the maritime works performed by the Consorcio Valencia 2007 (Valencia 2007 Consortium), with a view to adapting the Port of Valencia facilities so that they would be suitable for hosting the 32nd America's Cup competition. The competition was the opportunity for the city to transform the inner basin into a new sports marina. The basin had lost its efficiency as a commercial port, and that is why it has changed its activity into recreational uses. The new uses created new infrastructure necessities, most of which were included in the 32nd Americas Cup contract. The maritime infrastructures were the new harbour entrance, the communication channel, the wharfs, the large yachts jetty and the new marina.
Reinforced concrete caissons for port structures in Spain
Authors: Esteban Lefler F. , Rey Romero V. D.
Published: May 2009

Reinforced concrete floating caissons are widely used for the construction of vertical breakwaters and gravity quay walls. This paper describes the caisson construction methods that are used most frequently in Spanish port structures, especially casting on floating dry docks. Determining factors in the selection of caisson type for breakwaters rely on technical and economic considerations. Environmental considerations emphasise the use of caissons when compared to alternatives that require large quantities of quarry stone materials such as rubble mound breakwaters. The main limiting factors are high stresses induced on the sea floor and the presence of complex dynamic wave–structure–soil interaction phenomena. Generalisation in the application of soil improvement techniques in the sea floor will extend the application of floating reinforced concrete caissons to soft-soil areas, which are very common in Spanish ports. There are also research programmes under development focusing on improving of the functional features of vertical wall structures, mainly determined by their high reflection. Technical and economic optimisation of marine structures based on floating reinforced concrete caissons is today an essential trend in the field of port structures in Spain.
Preparing for the future: teaching scenario planning at the graduate level
Authors: Biggs Reinette , Diebel Matthew W , Gilroy David , Kamarainen Amy M , Kornis Matthew S , Preston Nicholas D , Schmitz Jennifer E , Uejio Christopher K , Van De Bogert Matthew C , Weidel Brian C , West Paul C , Zaks David PM , Carpenter Stephen R
Published: May 2009

Are environmental science students developing the mindsets and obtaining the tools needed to help address the considerable challenges posed by the 21st century? Today's major environmental issues are characterized by high‐stakes decisions and high levels of uncertainty. Although traditional scientific approaches are valuable, contemporary environmental issues also require new tools and new ways of thinking. We provide an example of how such new, or “post‐normal”, approaches have been taught at the graduate level, through practical application of scenario planning. Surveyed students reported that they found the scenario planning course highly stimulating, thought‐provoking, and inspiring. Key learning points included recognizing the need for multiple points of view when considering complex environmental issues, and better appreciating the pervasiveness of uncertainty. Collaborating with non‐academic stakeholders was also particularly helpful. Most students left the course feeling more positive about the potential contribution they can make in addressing the environmental challenges that society faces.
Perfluorinated phosphonic acids in Canadian surface waters and wastewater treatment plant effluent: Discovery of a new class of perfluorinated acids
Authors: D'eon Jessica C. , Crozier Patrick W. , Furdui Vasile I. , Reiner Eric J. , Libelo E. Laurence , Mabury Scott A.
Published: May 2009

The environmental prevalence of a new class of perfluorinated acids, the perfluorinated phosphonic acids (PFPAs), was determined in Canadian surface waters and wastewater treatment plant (WWTP) effluent. For quality control and comparison, the C8- to C11-perfluorinated carboxylic acids and perfluorooctane sulfonic acid were included in the analysis. Water samples were extracted using weak anion-exchange solid-phase extraction cartridges. Perfluorinated phosphonic acids were observed in 80% of surface water samples and in six of the seven WWTP effluent samples. The C8-PFPA was observed at concentrations ranging from 88 ± 33 to 3,400 ± 900 pg/L in surface waters and from 760 ± 270 to 2,500 ± 320 pg/L in WWTP effluent. To our knowledge, this is the first observation of PFPAs in the environment. Given their structural similarities with perfluorinated carboxylic and sulfonic acids, PFPAs are expected to be persistent. The observation of PFPAs in the majority of samples analyzed here suggests they are prevalent environmental contaminants and should be considered in future environmental monitoring campaigns to better understand the total burden of fluorinated materials in the environment.
The Asian clam Corbicula fluminea as a biomonitor of trace element contamination: Accounting for different sources of variation using an hierarchical linear model
Authors: Shoults-Wilson W. Aaron , Peterson James T. , Unrine Jason M. , Rickard James , Black Marsha C.
Published: May 2009

In the present study, specimens of the invasive clam, Corbicula fluminea, were collected above and below possible sources of potentially toxic trace elements (As, Cd, Cr, Cu, Hg, Pb, and Zn) in the Altamaha River system (Georgia, USA). Bioaccumulation of these elements was quantified, along with environmental (water and sediment) concentrations. Hierarchical linear models were used to account for variability in tissue concentrations related to environmental (site water chemistry and sediment characteristics) and individual (growth metrics) variables while identifying the strongest relations between these variables and trace element accumulation. The present study found significantly elevated concentrations of Cd, Cu, and Hg downstream of the outfall of kaolin-processing facilities, Zn downstream of a tire cording facility, and Cr downstream of both a nuclear power plant and a paper pulp mill. Models of the present study indicated that variation in trace element accumulation was linked to distance upstream from the estuary, dissolved oxygen, percentage of silt and clay in the sediment, elemental concentrations in sediment, shell length, and bivalve condition index. By explicitly modeling environmental variability, the Hierarchical linear modeling procedure allowed the identification of sites showing increased accumulation of trace elements that may have been caused by human activity. Hierarchical linear modeling is a useful tool for accounting for environmental and individual sources of variation in bioaccumulation studies.
The Open-Air Treatment of PANDEMIC INFLUENZA
Authors: Hobday Richard A. , Cason John W.
Published: May 2009

The H1N1 “Spanish flu” outbreak of 1918–1919 was the most devastating pandemic on record, killing between 50 million and 100 million people. Should the next influenza pandemic prove equally virulent, there could be more than 300 million deaths globally. The conventional view is that little could have been done to prevent the H1N1 virus from spreading or to treat those infected; however, there is evidence to the contrary. Records from an “open-air” hospital in Boston, Massachusetts, suggest that some patients and staff were spared the worst of the outbreak. A combination of fresh air, sunlight, scrupulous standards of hygiene, and reusable face masks appears to have substantially reduced deaths among some patients and infections among medical staff. We argue that temporary hospitals should be a priority in emergency planning. Equally, other measures adopted during the 1918 pandemic merit more attention than they currently receive.
Distribution of Albian clastic deposits in the Benguela basin (Angola): evidence of a Benguela palaeocurrent?
Authors: Quesne Didier , Buta-Neto André , Benard Dominique , Guiraud Michel
Published: May 2009

The Albian clastic Tuenza Formation of the Benguela basin (south Angola) is described and its geographic distribution analysed in detail. From these observations, the existence of an Albian “PalaeoBenguela current” is proposed. This would imply that a marine longshore current reworked the sand transported by palaeorivers and settled it northward along the coast of the young Atlantic Ocean (during the Albian). A parallel between Albian clastic deposits and the modern sediments deposited by the Benguela current is drawn, focusing on the striking resemblance between the two currents, i.e. the actual Benguela current and the Albian marine current, and the associated sedimentary bodies.
Distribution of living benthic foraminifera in relation with environmental variables within the Aiguillon cove (Atlantic coast, France): improving knowledge for paleoecological interpretation
Authors: du Chatelet Eric Armynot , Degre Delphine , Sauriau Pierre-Guy , Debenay Jean-Pierre
Published: May 2009

Search for bioindicators in marine environments has provided new tools for monitoring global and local natural changes. Among these tools, benthic foraminifera play a central role. More accurate paleogeographical and paleoecological reconstructions become possible on the basis of the ecology of recent foraminifera. Nevertheless, factors acting on foraminiferal assemblages are still partially understood. The aim of this study is to correlate the distribution patterns of living (stained) benthic foraminifera with environmental variables such as tidal elevation, interstitial pore water salinity, organic matter content of the sediment, pheopigments, chlorophyll a, carbonate contents and grain size distribution of the sediment from 86 samples collected in the Aiguillon cove (France). In this paralic environment, sediment grain size, salinity and tidal elevation are fundamental factors that drive the distribution of the most abundant species i.e. Brizalina variabilis, Cribroelphidium excavatum and Haynesina germanica. Organic matter also influences the distribution patterns of benthic foraminifera: the relative abundance of Ammonia tepida is typically favored by an increase of total organic matter food resources. Chlorophyll a and pheopigments, as indicators of organic matter quality however may not be limiting in the proportion present in the Aiguillon cove. Carbonate proportions do not limit benthic foraminifera of the Aiguillon cove essentially with carbonaceous shells.
An Analysis of the Evaporation Method for Determining Interstitial Water
Authors: Dodd Charles G.
Published: May 2009

A theoretical study of the principles of evaporation of liquids from large pores in petroleum reservoir rock core samples has resulted in the development of a working hypothesis to explain the application of evaporation measurements to the determination of minimum interstitial-water content. Rate-determining factors that control kinetics of evaporation processes have been considered in evolving the new hypothesis. Variations in temperature during evaporation experiments are found to have a negligibly small effect on evaporation interstitial-water measurements. Determination of complete capillary-pressure curves by evaporation measurements is discussed briefly. Theoretical calculations indicate that minimum interstitial-water saturations determined by the evaporation method should correspond quantitatively with water saturations above transition zones in petroleum reservoirs. Experimental comparisons between the evaporation method and the well-accepted porous-disk method demonstrate excellent agreement.

Introduction

A new procedure for determining the "irreducible minimum"interstitial-water content of petroleum reservoir rock has been described recently by Messer. The essential novelty of Messer's experimental approach, as compared with methods previously proposed, lies in the displacement of a saturating liquid by evaporation rather than by the pressure of a second immiscible fluid or centrifugal force. Probably the major advantage of the evaporation process, especially when applied to routine core analyses, is its speed. In addition, it is applicable to drill cuttings. A third advantage, not suggested by Messer, results from using a saturating liquid known to wet the laboratory-extracted core with a zero contact angle.

Experience with the evaporation method has demonstrated that about 20 core samples may be run in eight hours. The porous-disk procedure of Rose and Bruce and the mercury pressuring method of Purcell permit the analysis of about two samples per day if the use of four cells each holding eight samples is assumed in the case of the former, and one piece of apparatus in the case of the latter. The centrifugal method of Slobod, Chambers, and Prehn is as rapid as the evaporation method when applied to "looser" cores of moderately high permeability, but is as slow as the other methods when relatively"tight" cores having permeabilities of a few millidarcys are analyzed.
Transport of Tritium Contamination to the Atmosphere in an Arid Environment
Authors: Garcia C. A. , Andraski B. J. , Stonestrom D. A. , Cooper C. A. , Johnson M. J. , Michel R. L. , Wheatcraft S. W.
Published: May 2009

Soil–plant–atmosphere interactions strongly influence water movement in desert unsaturated zones, but little is known about how such interactions affect atmospheric release of subsurface water‐borne contaminants. This 2‐yr study, performed at the U.S. Geological Survey's Amargosa Desert Research Site in southern Nevada, quantified the magnitude and spatiotemporal variability of tritium (3H) transport from the shallow unsaturated zone to the atmosphere adjacent to a low‐level radioactive waste (LLRW) facility. Tritium fluxes were calculated as the product of 3H concentrations in water vapor and respective evaporation and transpiration water‐vapor fluxes. Quarterly measured 3H concentrations in soil water vapor and in leaf water of the dominant creosote‐bush [Larrea tridentata (DC.) Coville] were spatially extrapolated and temporally interpolated to develop daily maps of contamination across the 0.76‐km2 study area. Maximum plant and root‐zone soil concentrations (4200 and 8700 Bq L−1, respectively) were measured 25 m from the LLRW facility boundary. Continuous evaporation was estimated using a Priestley–Taylor model and transpiration was computed as the difference between measured eddy‐covariance evapotranspiration and estimated evaporation. The mean evaporation/transpiration ratio was 3:1. Tritium released from the study area ranged from 0.12 to 12 μg d−1 and totaled 1.5 mg (8.2 × 1010 Bq) over 2 yr. Tritium flux variability was driven spatially by proximity to 3H source areas and temporally by changes in 3H concentrations and in the partitioning between evaporation and transpiration. Evapotranspiration removed and limited penetration of precipitation beneath native vegetation and fostered upward movement and release of 3H from below the root zone.
Untangling Diffusion from Advection in Unsaturated Porous Media: Experimental Data, Modeling, and Parameter Uncertainty
Authors: Stauffer Philip H. , Vrugt Jasper A. , Turin H. Jake , Gable Carl W. , Soll Wendy E.
Published: May 2009

We conducted a series of experimental and modeling tests using data from the Busted Butte Unsaturated Zone Transport Test. First, we conducted a suite of reactive (e.g., Li), nonreactive (Br), and colloidal tracer experiments. These tracers were injected for 190 d from two point sources at rates of 1 and 8 mL/h, respectively. We then used a numerical simulator (FEHM), populated with laboratory‐measured hydrologic properties, to verify that our conceptual model of the tracer test yielded a good fit to the tracer breakthrough data. Additionally, we used the AMALGAM‐SO and SCEM‐UA search algorithms to find optimal parameter estimates in our conceptual model and estimate their (nonlinear) uncertainty. To this end, the FEHM model was executed more than 50,000 times using parallel computing on a distributed computer cluster. The experimental and modeling results show that (i) no breakthrough of colloids was observed, low breakthroughs of Li were found, and significant and rapid breakthrough of Br was measured, (ii) measured hydraulic parameters from rock core samples provide a relatively accurate description of flow and transport at the scale and flow rates of the Busted Butte test, and (iii) the Millington–Quirk model of diffusion as a function of volumetric water content can fit the experimental breakthrough data well; however, (iv) a constant diffusion model with a much lower effective diffusion coefficient also fits the data well, and (v) numerous different optimized parameter combinations exist that fit the observed Br data acceptably well. This implies that one should be particularly careful in assigning values of the unsaturated subsurface flow and transport parameters without recourse to examining both parameter and model formulation uncertainty.
UZIG USGS Research: Advances through Interdisciplinary Interaction
Authors: Nimmo John R. , Andraski Brian J. , Muñoz-Carpena Rafael
Published: May 2009

Because vadose zone research relates to diverse disciplines, applications, and modes of research, collaboration across traditional operational and topical divisions is especially likely to yield major advances in understanding. The Unsaturated Zone Interest Group (UZIG) is an informal organization sponsored by the USGS to encourage and support interdisciplinary collaboration in vadose or unsaturated zone hydrologic research across organizational boundaries. It includes both USGS and non‐USGS scientists. Formed in 1987, the UZIG operates to promote communication, especially through periodic meetings with presentations, discussions, and field trips. The 10th meeting of the UZIG at Los Alamos, NM, in August 2007 was jointly sponsored by the USGS and Los Alamos National Laboratory. Presentations at this meeting served as the initial basis for selecting papers for this special section of Vadose Zone Journal, the purpose of which is to present noteworthy cutting‐edge unsaturated zone research promoted by, facilitated by, or presented in connection with the UZIG.
Early Adoption of SFAS No. 159: Lessons from Games (Almost) Played
Authors: Henry Elaine
Published: May 2009

SYNOPSIS: This paper examines instances of firms that early adopted SFAS No. 159, The Fair Value Option for Financial Assets and Financial Liabilities, and then rescinded or revised their early adoption of the standard because apparently their implementation was not in keeping with the “intent and spirit” of the standard. These reversals imply opportunistic use of the implementation provisions in SFAS No. 159 and, as such, provide a useful blueprint for understanding the effects of the standard, which became effective for all firms in November 2007. An analysis of the disclosures by the rescinding firms indicates the importance of informal mechanisms in helping firms interpret and implement new accounting standards, which is particularly relevant given the lesser amounts of detailed guidance provided by standard setters in principles-based compared with rules-based standards.