bluuebunny/crossref_metadata_2025 huggingface dataset:
A Role for Site-Specific Phosphorylation of Mouse Progesterone Receptor at Serine 191 in Vivo
Authors: Grimm Sandra L. , Ward Robert D. , Obr Alison E. , Franco Heather L. , Fernandez-Valdivia Rodrigo , Kim Jung-Sun , Roberts Justin M. , Jeong Jae-Wook , DeMayo Francesco J. , Lydon John P. , Edwards Dean P. , Weigel Nancy L.
Published: October 2014

Progesterone receptors (PRs) are phosphorylated on multiple sites, and a variety of roles for phosphorylation have been suggested by cell-based studies. Previous studies using PR-null mice have shown that PR plays an important role in female fertility, regulation of uterine growth, the uterine decidualization response, and proliferation as well as ductal side-branching and alveologenesis in the mammary gland. To study the role of PR phosphorylation in vivo, a mouse was engineered with homozygous replacement of PR with a PR serine-to-alanine mutation at amino acid 191. No overt phenotypes were observed in the mammary glands or uteri of PR S191A treated with progesterone (P4). In contrast, although PR S191A mice were fertile, litters were 19% smaller than wild type and the estrous cycle was lengthened slightly. Moreover, P4-dependent gene regulation in primary mammary epithelial cells (MECs) was altered in a gene-selective manner. MECs derived from wild type and PR S191A mice were grown in a three-dimensional culture. Both formed acinar structures that were morphologically similar, and proliferation was stimulated equally by P4. However, P4 induction of receptor activator of nuclear factor-κB ligand and calcitonin was selectively reduced in S191A cultures. These differences were confirmed in freshly isolated MECs. Chromatin immunoprecipitation analysis showed that the binding of S191A PR to some of the receptor activator of nuclear factor-κB ligand enhancers and a calcitonin enhancer was substantially reduced. Thus, the elimination of a single phosphorylation site is sufficient to modulate PR activity in vivo. PR contains many phosphorylation sites, and the coordinate regulation of multiple sites is a potential mechanism for selective modulation of PR function.
edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
Authors: Dai Zhiyin , Sheridan Julie M. , Gearing Linden J. , Moore Darcy L. , Su Shian , Wormald Sam , Wilcox Stephen , O'Connor Liam , Dickins Ross A. , Blewitt Marnie E. , Ritchie Matthew E.
Published: October 2014

Pooled library sequencing screens that perturb gene function in a high-throughput manner are becoming increasingly popular in functional genomics research. Irrespective of the mechanism by which loss of function is achieved, via either RNA interference using short hairpin RNAs (shRNAs) or genetic mutation using single guide RNAs (sgRNAs) with the CRISPR-Cas9 system, there is a need to establish optimal analysis tools to handle such data. Our open-source processing pipeline in edgeR provides a complete analysis solution for screen data, that begins with the raw sequence reads and ends with a ranked list of candidate genes for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, genes in the rows) with options for allowing mismatches and small shifts in sequence position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or generalized linear modeling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.
Metabolomics in psoriatic disease: pilot study reveals metabolite differences in psoriasis and psoriatic arthritis
Authors: Armstrong April W. , Wu Julie , Johnson Mary Ann , Grapov Dmitry , Azizi Baktazh , Dhillon Jaskaran , Fiehn Oliver
Published: October 2014

Importance:While “omics” studies have advanced our understanding of inflammatory skin diseases, metabolomics is mostly an unexplored field in dermatology.

Objective:We sought to elucidate the pathogenesis of psoriatic diseases by determining the differences in metabolomic profiles among psoriasis patients with or without psoriatic arthritis and healthy controls.

Design:We employed a global metabolomics approach to compare circulating metabolites from patients with psoriasis, psoriasis and psoriatic arthritis, and healthy controls.

Setting:Study participants were recruited from the general community and from the Psoriasis Clinic at the University of California Davis in United States.

Participants:We examined metabolomic profiles using blood serum samples from 30 patients age and gender matched into three groups: 10 patients with psoriasis, 10 patients with psoriasis and psoriatic arthritis and 10 control participants.

Main outcome(s) and measures(s):Metabolite levels were measured calculating the mean peak intensities from gas chromatography time-of-flight mass spectrometry.

Results:Multivariate analyses of metabolomics profiles revealed altered serum metabolites among the study population. Compared to control patients, psoriasis patients had a higher level of alpha ketoglutaric acid (Pso: 288 ± 88; Control: 209 ± 69; p=0.03), a lower level of asparagine (Pso: 5460 ± 980; Control: 7260 ± 2100; p=0.02), and a lower level of glutamine (Pso: 86000 ± 20000; Control: 111000 ± 27000; p=0.02). Compared to control patients, patients with psoriasis and psoriatic arthritis had increased levels of glucuronic acid (Pso + PsA: 638 ± 250; Control: 347 ± 61; p=0.001). Compared to patients with psoriasis alone, patients with both psoriasis and psoriatic arthritis had a decreased level of alpha ketoglutaric acid (Pso + PsA: 186 ± 80; Pso: 288 ± 88; p=0.02) and an increased level of lignoceric acid (Pso + PsA: 442 ± 280; Pso: 214 ± 64; p=0.02).

Conclusions and relevance:The metabolite differences help elucidate the pathogenesis of psoriasis and psoriatic arthritis and they may provide insights for therapeutic development.
Strategy for reduction of medical costs and growth of the healthcare industry after establishment of the national health insurance system in Japan: lessons for the Indonesian health care reform system -II-
Authors: Sawada Tokihiko , Kawahara Hirohisa
Published: October 2014

Japan has long operated a government-based health insurance system covering the entire population, and has been focusing on strategies for balancing viable national health care services with the need to minimize national health care expenditure. Hemodialysis (HD) is a representative form of medical treatment that is expected to expand in Indonesia in the near future, and which will require sustained financial support from the national health insurance system. In this report, consecutive to our previous one, we describe how the Japanese government has attempted to minimize medical expenditure in the past, focusing especially on HD.
Effect of extracorporeal irradiation on segmental bone autograft incorporation in Sprague-Dawley rats
Authors: Wahyudi Muhammad , Kamal Achmad F. , Siregar Nurjati C. , Prasetyo Marcel
Published: October 2014

Background: Bone graft has been widely used in bone tumor reconstructive surgery. Extracorporeal irradiation (ECI) is commonly used to eliminate malignant cells before bone autograft. However, it may have negative effects on autograft incorporation. This study aimed to evaluate the ability of bone autograft incorporation after extra corporeal irradiation.Methods: 24 Sprague-Dawley rats underwent 7-mm en bloc resection of tibial diaphysis, and were divided into 4 groups. The first group did not receive irradiation; the 2nd, 3rd, and 4th groups received 50, 150 and 300 Gy bone irradiation respectively, and then reimplanted. Radiologic score were evaluated at week-6 and -8, while histopathology, osteoblast count and BMP-2 expression were examined at week-8. Data were analyzed with ANOVA or Kruskal-Wallis tests.Results: At week-6, radiologic scores in group 150 and 300 Gy were significantly lower compared to control group (4 vs 6 dan 4 vs 6; p = 0.011; p = 0.01). The same results were also obtained at week-8 (5.40 vs 7.14; p = 0.009 in the group 150 Gy and 5.60 vs 7.14; p = 0.018 in the group 300 Gy. Histopathological scores of the groups receiving 50, 150 and 300 Gy were significantly lower compared to the control group (6 vs 7, p = 0.017; 4 vs 7, p = 0.005; 6 vs 7, p = 0.013). Osteoblast count and BMP-2 expression were not significantly different among all groups.Conclusion: ECI with the dose of 50 to 300 Gy is associated with delayed bone autograft incorporation. However, the osteoinductive and osteogenesis capacity for autograft incorporation were maintained.
Central nervous system lymphoma: a description and analysis of patients’ clinical and radiological features
Authors: July Julius , Wijaya Andy , Muliantara Priscilla , Yuniarti Mira
Published: October 2014

Background: Central nervous system (CNS) lymphoma is a rare brain neoplasm. Its incidence has increased these years, so it should be considered in the differential diagnosis for mass lesions in the CNS. The aim of the study was to describe the radiological and clinical features of patients with CNS lymphoma.Methods: The study was a retrospective study. All patients histopathologically confirmed to have CNS lymphoma from November 2008 to December 2013 in Siloam Hospital Lippo Village were included in the study. Medical records and patients’ MRI results were retrieved to be analyzed.Results: 32 patients were histopathologically diagnosed to have CNS lymphoma. The patients, mean age was 54 ± 15.01 years with slight male predominance. No patient was immuno compromised (CD4 > 500 cells/µL and leukocyte 5,000-11,000 cells/µL). The median interval between the onset of the initial symptoms and diagnosis is 7 weeks. The most common presenting symptoms were headache, mental changes, and neurological deficits related to the location of lesion. MR images show that most lesions were enhanced with contrast, iso-hypointense in T1 weighted imaging (T1WI), iso- to hypointense with perifocal edema in T2 weighted imaging (T2WI), hyperintense in diffusion weighted imaging (DWI), with the most common location was white matter of cerebral hemisphere on one or more lobes and periventricular area, and the tumor could be single or multiple (24%) without clear edges.Conclusion: Short course of neurological worsening (within weeks) should lead a suspicion toward lymphoma. The characteristics of MR images are markedly enhanced by contrast, iso- to hypointense on T1WI and T2WI, and hyperintense in DWI, involving white matter of cerebral hemisphere and periventricular area.
Survival of cervical cancer patients and its prognostic factors at Cipto Mangunkusumo Hospital, Jakarta
Authors: Nuranna Laila , Prastasari Rahma , Sutrisna Bambang
Published: October 2014

Background: Cervical cancer is the second most common cancer among Indonesian women. Information concerning survival probability is very important for the patient and institution. Our last data about cervical cancer survival was studied for more than 10 years ago. This study aimed to know the latest cervical cancer survival and its prognostic factors.Methods: This is a retrospective cohort study which enrolled cervical cancer patients treated at Cipto Mangunkusumo Hospital in 2005-2006. Subjects were followed-up for minimum of 5 years. Kaplan-Meier and Cox regression analysis was used to determine the survival probability and to assess prognostic factors.Results: A total of 447 patients who met the study criteria were selected. Stage III was the largest proportion on the study (41.6%). Most of the histopathology type was squamous cell carcinoma (71.6%). This study revealed that median survival was 63 months with the overall 5-years survival probability to be 52%. Tumor size did not influence overall survival rate. Stage III and IV had lower survival probability (HR 3.27 and 6.44). Poor differentiation and uncompleted therapy also had lower survival probability (HR 2.26 and 2.22). Histopathology of others (neuroendocrine) had lower survival probability (HR 2.85). However, it was not statistically significant on multivariate analysis.Conclusion: Median survival time for cervical cancer patients at Cipto Mangunkusumo Hospital was 63 months. There were improvement in the survival rate comparing from the study in 1997. In this study, the independent prognostic factors for survival were tumor staging, tumor differentiation, and completion of therapy.
IFNγ modulates human immunoglobulin receptor expression in lipoaspirate-derived mesenchymal stem cells
Authors: Laksmitawati Dian R. , Pawitan Jeanne A. , Sadikin Mohamad , Sardjono Caroline T. , Utomo Ahmad R.
Published: October 2014

Background: Mesenchymal stem cell (MSC) has been reported to have immunomodulator capacity against autoimmune diseases and to prevent allogenic tissue rejection. Many studies revealed that MSC’s inhibit T cell proliferation and induce immunosuppressive condition through the production of prostaglandins, and interleukin-10. In addition, MSC was reported to reduce circulating autoantibody in autoimmune patients following MSC transfusion. So far, there has been no report stating the presence of Fc receptors (receptors for immunoglobulin) on MSCs. The aim of this study was to reveal the expression of FcγRs in lipoaspirate-derived MSCs by measuring transcription of FcγR mRNA and whether the expression can be modulated.Methods: Lipoaspirate-derived MSCs were cultured in suitable medium and confirmed to be MSCs according to the criteria published by International Society for Cellular Therapy. Total mRNA of MSCs was isolated, and detection of human FcγRI, FcγRIIA and FcγRIIB mRNA was performed. Further, modulation of the expression was tested using heat aggregated gamma globulin (HAGG) and interferon (IFN)γ.Results: FcγRs mRNA was detected in the first passage of MSCs. However, the expression was no longer present after more than 4 passages. Further, increased level of FcγRI and FcγRIIA mRNA expression was detected with the addition of IFNγ in the culture. This preliminary finding opens a new insight for the understanding of interaction between MSCs and immunoglobulin G through FcγRs.Conclusion: Lipoaspirate-derived MSCs express FcγRs, and the expression is modulated by IFNγ.
Gender and poverty in Britain: changes and continuities between 1999 and 2012
Authors: Dermott Esther , Pantazis Christina
Published: October 2014

Drawing on nationally representative surveys, this paper describes the contemporary relationship between gender and poverty in Britain and changes between 1999 and 2012. Poverty rates between men and women have converged: women today are only marginally poorer than men. Our analysis reveals that female lone parents‘ poverty rates remain exceptionally high, the situation of older women has markedly improved, and there is an emerging poor group of solo-living men. We therefore argue that gendered analysis of poverty needs to consider the circumstances of men as well as women, and that some of the standard feminisation of poverty arguments require revision.
Excavating evidence from experience
Authors: Byrne Libby
Published: October 2014

This article addresses the challenge of excavating the evidence from our lived experience with arts and health, describing the impact of direct personal experience with art making on health, and of an inter-subjective aesthetic experience. This material, derived from a studio practice of painting that explored the experience of multiple sclerosis (MS), was presented as a case story at the Evidence in a Different Form Conference in 2013, and the kinds of evidence noted by the group are reported.
Producing the evidence we need and validating the evidence we have
Authors: Robinson Priscilla , Daly Jeanne
Published: October 2014

If health policy-makers are to fund arts/health programmes, they need evidence that there is a benefit. For some, the best research evidence is to be derived from blinded clinical trials that have been synthesized into a systematic review. Clearly, however, there are questions which cannot be answered with clinical trials. In this article we discuss how high-quality evidence can be derived from many kinds of research. Clinical trials are useful in some settings but we need to know about the full range of research methods in the emerging field of arts and public health. Researchers can use their own specialist knowledge and forge research collaborations to strengthen the use of arts-based methods for evidence for health improvement at a population level.
The Internet as Teacher
Authors: Thorgersen Ketil , Zandén Olle
Published: October 2014

Social media has led to new opportunities for learning music. In less formalized settings, a whole new arena for learning music has developed. The aim of this article is to investigate student teachers’ experiences of learning to play an instrument with the Internet as a teacher. The investigation was done as an action research study where twelve beginning teacher-training students were given the task to use the Internet to learn how to play an instrument. The students were organized in peer groups to help each other. Documentation of the progress happened through logbooks. The project lasted for half a year in 2011 and had a triple intention: to provide the students with experience about learning how to play by help of the Internet, for the students to learn to play a second instrument, and to investigate if and how learning practices for learning an instrument aided by the Internet could be useful in music teacher training.
Optimización en las estrategias de seguridad ambiental
Authors: Saravia Martínez Arq. María
Published: October 2014

La presente investigación se propone indagar en la utilización de formas tipológicas replicables de saneamiento alternativo que resuelven el problema de la gestión de los desagües domésticos dentro del propio predio individual en determinados sectores suburbanos del país. Toma el tratamiento, reciclaje y reutilización de las aguas primarias y grises como estrategia de seguridad ambiental. Pretende de esta manera mostrar a usuarios y autoridades públicas, ejemplos acabados de soluciones técnicas adecuadas desde el punto de vista ambiental, y apropiadas para los privados, resolviendo problemas que hoy no tienen solución en el Uruguay suburbano y rural.
An Ostrowski type inequality for derivatives of q-th power of s-convex functions via fractional integrals
Authors: Özdemir Muhamet Emin , Yildiz Çetin
Published: October 2014

In this paper, we establish several new inequalities for s-convex mappings
that are connected with the Riemann–Liouville fractional integrals. Our
results have some relationships with an Ostrowski type integral inequality in
the literature.
Lewisian Time Travel in a Relativistic Setting
Authors: Daniels Paul R.
Published: October 2014

I argue that David Lewis’s philosophically dominant conception of time travel cannot straightforwardly handle what we might call cases of relativistic time travel – that is, the sort of time travel which could only plausibly occur in a relativistic setting. I evaluate whether or not the Lewisian account can be successfully adapted such that it would able to analyse potential cases of relativistic time travel satisfactorily while still being employable in the analysis of those cases that make no mention of physics or the structure of spacetime. This is primarily an analytical and explanatory exercise, rather than a polemical one.
Must Naturalism Lead to a Deflationary Meta-Ontology?
Authors: Haug Matthew
Published: October 2014

Huw Price has argued that naturalistic philosophy inevitably leads to a deflationary approach to ontological questions. In this paper, I rebut these arguments. A more substantive, less language-focused approach to metaphysics remains open to naturalists. However, rebutting one of Price’s main arguments requires rejecting Quine’s criterion of ontological commitment. So, even though Price’s argument is unsound, it reveals that naturalists cannot rest content with broadly Quinean, “mainstream metaphysics,” which, I suggest, naturalists also have independent reasons to reject.
Combined deletion of Pten and p53 in mammary epithelium accelerates triple‐negative breast cancer with dependency on eEF2K
Authors: Liu Jeff C , Voisin Veronique , Wang Sharon , Wang Dong‐Yu , Jones Robert A , Datti Alessandro , Uehling David , Al‐awar Rima , Egan Sean E , Bader Gary D , Tsao Ming , Mak Tak W , Zacksenhaus Eldad
Published: October 2014

The tumor suppressors Pten and p53 are frequently lost in breast cancer, yet the consequences of their combined inactivation are poorly understood. Here, we show that mammary‐specific deletion of Pten via WAP‐Cre, which targets alveolar progenitors, induced tumors with shortened latency compared to those induced by MMTV‐Cre, which targets basal/luminal progenitors. Combined Pten‐p53 mutations accelerated formation of claudin‐low, triple‐negative‐like breast cancer (TNBC) that exhibited hyper‐activated AKT signaling and more mesenchymal features relative to Pten or p53 single‐mutant tumors. Twenty‐four genes that were significantly and differentially expressed between WAP‐Cre:Pten/p53 and MMTV‐Cre:Pten/p53 tumors predicted poor survival for claudin‐low patients. Kinome screens identified eukaryotic elongation factor‐2 kinase (eEF2K) inhibitors as more potent than PI3K/AKT/mTOR inhibitors on both mouse and human Pten/p53‐deficient TNBC cells. Sensitivity to eEF2K inhibition correlated with AKT pathway activity. eEF2K monotherapy suppressed growth of Pten/p53‐deficient TNBC xenografts in vivo and cooperated with doxorubicin to efficiently kill tumor cells in vitro. Our results identify a prognostic signature for claudin‐low patients and provide a rationale for using eEF2K inhibitors for treatment of TNBC with elevated AKT signaling.
Predictors of Neurological Deficit after Endovascular Treatment of Cerebral Arteriovenous Malformations and Functional Repercussions in Prospective Follow-Up
Authors: Jordan Jose , Llibre Juan Carlos , Vazquez Frank
Published: October 2014

Endovascular therapy is a well-established approach to the treatment of cerebral arteriovenous malformations (AVMs). The objective of this study was to determine the predictive factors of neurological deficit following endovascular procedures. Seventy-one patients with cerebral AVMs who underwent 147 embolization sessions from 2006 to 2011 were followed up prospectively (average 31.1 ± 17.5 months). Functional neurological condition was documented by means of the modified Rankin scale. Factors found to be predictors of neurological deficit were the partial obstruction of drainage veins (OR = 197.6; IC = 2.76 – 1416.0; P = 0.015), a positive result in the Propofol test (OR = 50.2; IC = 6.18 – 566.5; P = 0.000), AVM diameter under 3 cm (OR = 21.3; IC: 1.71 265.6; P = 0.018), the presence of intranidal aneurysms (OR = 11.2; IC = 1.09 114.2; P = 0.042), the absence of post-procedure hypotension (OR = 10.2; IC = 1.35 77.7; P = 0.003), deep venous drainage (OR = 7.14; IC = 1.15 44.4; P = 0.035), and devascularization in excess of 40% per session (OR = 3.3; IC = 1.11 – 16.8; P = 0.056). Fifty-six patients (78.9%) did not experience changes in their neurological condition after the treatment and 13 patients (18.3%) showed a new neurological deficit related to the treatment; 95.8% of the patients did not show significant long-term incapacity. Partial obstruction of drainage veins, small AVMs, intranidal aneurysms, faulty hemodynamic control and extensive devascularization were found to be predictors of neurological deficit. A significant number of patients with neurological deficit improved in the long term.
320-Row Detector Dynamic 4D-CTA for the Assessment of Brain and Spinal Cord Vascular Shunting Malformations
Authors: D'Orazio Federico , Splendiani Alessandra , Gallucci Massimo
Published: October 2014

Shunting vascular malformations of the brain and spinal cord are traditionally studied using digital subtraction angiography (DSA), the current gold standard imaging method routinely used because of its favourable combination in terms of spatial and temporal resolution. Because DSA is relatively expensive, time-consuming and carries a risk of silent embolic events and a small risk of transient or permanent neurologic deterioration, a non-invasive alternative angiographic method is of interest. New 320 row-detector CT scanners allow volumetric imaging of the whole brain with temporal resolution up to ≅ 3 Hz. Those characteristics make computed tomography angiography (CTA) an affordable imaging method to study the haemodynamics of the whole brain and can also be applied to the study of limited portions of the spinal cord. The aim of this paper is to make a brief summary of our experience in studying shunting vascular malformation of the brain and spinal cord using dynamic 4D-CTA, explaining the technical details of the studies performed at our institution, and the state-of-the-art major advantages and drawbacks of this new technique. We found that dynamic 4D-CTA is able to depict the main architectural characteristics of previously untreated vascular shunting malformations both in brain and spinal cord (i.e. their main arterial feeders and draining veins) allowing their correct diagnosis and exhaustive classification, limiting the use of DSA for therapeutic purposes.
Out-of-Hospital Medication Errors Among Young Children in the United States, 2002–2012
Authors: Smith Maxwell D. , Spiller Henry A. , Casavant Marcel J. , Chounthirath Thiphalak , Brophy Todd J. , Xiang Huiyun
Published: October 2014

OBJECTIVE:

To investigate out-of-hospital medication errors among young children in the United States.

METHODS:

Using data from the National Poison Database System, a retrospective analysis of out-of-hospital medication errors among children <6 years old from 2002 through 2012 was conducted.

RESULTS:

During 2002–2012, 696 937 children <6 years experienced out-of-hospital medication errors, averaging 63 358 episodes per year, or 1 child every 8 minutes. The average annual rate of medication errors was 26.42 per 10 000 population. Cough and cold medication errors decreased significantly, whereas the number (42.9% increase) and rate (37.2% increase) of all other medication errors rose significantly during the 11-year study period. The number and rate of medication error events decreased with increasing child age, with children <1 year accounting for 25.2% of episodes. Analgesics (25.2%) were most commonly involved in medication errors, followed by cough and cold preparations (24.6%). Ingestion accounted for 96.2% of events, and 27.0% of medication errors were attributed to inadvertently taking or being given medication twice. Most (93.5%) cases were managed outside of a health care facility; 4.4% were treated and released from a health care facility; 0.4% were admitted to a non–critical care unit; 0.3% were admitted to a critical care unit; and 25 children died.

CONCLUSIONS:

This is the first comprehensive study to evaluate the epidemiologic characteristics of out-of-hospital medication errors among children <6 years of age on a national level. Increased efforts are needed to prevent medication errors, especially those involving non–cough and cold preparations, among young children.
Influence of Strain Rate on the Load-Strain Characteristics of Geosynthetics
Authors: Sawicki A. , Kazimierowicz-Frankowska K.
Published: October 2014

Experimental results dealing with the influence of strain rate on the load-strain characteristics of five different geosynthetics are presented and discussed, including the load-strain curves and the strength of these materials. Theoretical and empirical formulae are proposed to describe the observed behaviour of the geosynthetics investigated. Particular attention is devoted to complex loading histories, for example, loading at a constant strain rate followed by creep or stress relaxation and then subsequent loading at the same strain rate. Such loading programmes reveal interesting features of the geosynthetics’ behaviour, which can be designated as the isotach properties. This problem is discussed in detail and a simple method of describing these properties is proposed.
Strain Induced Changes in Geomembrane Surface Topography
Authors: Frost J.D. , Zettler T.E. , DeJong J.T. , Lee S.W. , Kagbo S.
Published: October 2014

Textured geomembranes are commonly used in field applications to increase the strength of geomembrane-soil and geomembrane-geosynthetic interfaces. Under normal operating conditions, geomembranes within landfill liner systems are subjected to both multiaxial and uniaxial strains induced by anchorage in trenches, differential settlements, and thermal changes. The existence of strain may alter the geomembrane surface, thereby affecting the strength of the interface. This paper presents the results of an investigation into changes in surface topography of geomembranes subjected to uniaxial strain. An integrated strain profilometer device was developed to permit quantification of geomembrane surfaces while they were subjected to strain. Geomembranes manufactured using various texturing processes were subjected to increasing uniaxial strain levels ranging from 1 to 25%. Results show that the effect of strain on the surface topography is dependent on the geomembrane manufacturing process. The implications of changes in surface topography are linked to potential changes in the interface strength.
Filtration Performance of Woven Geotextiles With Wastewater Treatment Sludge
Authors: Aydilek A.H. , Edil T.B.
Published: October 2014

Capping of contaminated soft sediments and sludges for in situ containment provides an efficient remediation alternative. Capping design typically involves the use of geosynthetics for multiple functions, e.g., reinforcement, separation, and filtration. Filtration performance becomes a decisive factor for proper long-term performance of a cap. Because of multiple functions required, woven geotextiles are often the choice geosynthetic in such applications. A research program concerning the filtration behavior of contaminated wastewater treatment sludges was conducted. The laboratory portion of the program included a series of filtration tests with different woven geotextiles. Filtration performance of the sludge-woven geotextile systems was also observed in field test cells. Geotextile samples were exhumed from the cells after exposure and analyzed in the laboratory. The results indicate that the sludges can be filtered using woven geotextiles and the selection of a proper filter can be made on the basis of geotextile pore structure parameters, i.e. percent open area and pore opening size distribution. The standard gradient ratio test did not always reflect the filtration performance and, therefore, other clogging ratios need to be considered. A commonly used geotextile pore opening size-to-soil particle ratio in the existing filter criteria, O95/D85, did not predict the filtration behavior displayed by the sludge; however, another ratio, O50/D 50 , showed general correlation to clogging and retention.
Monitored Displacements of Unique Geosynthetic-Reinforced Soil Bridge Abutments
Authors: Abu-Hejleh N. , Zornberg J.G. , Wang T. , Watcharamonthein J.
Published: October 2014

A geosynthetic-reinforced soil (GRS) system was constructed to support the shallow footings of a two-span bridge and the approaching roadway structures. Construction of this system, the Founders/Meadows bridge abutments, was completed in 1999 near Denver, Colorado, USA. This unique system was selected with the objectives of alleviating the “bump at the bridge” problem often noticed when using traditional deep foundations, allowing for a small construction working area, and facilitating construction in stages. The primary focus of the paper is to evaluate the deformation response of this structure under service loads based on displacement data collected through surveying, inclinometer, strain gages, and digital road profiler. The overall short- and long-term performance of the Founders/Meadows structure was excellent, suggesting that GRS walls are a viable alternative to support both bridge and approaching roadway structures.
Limit Equilibrium Method Back Analyses of Geotextile-Reinforced Embankments on Soft Bangkok Clay – A Case Study
Authors: Bergado D.T. , Lorenzo G.A. , Long P.V.
Published: October 2014

The limit equilibrium method (LEM) was used to back analyze the performance of three full-scale test embankments constructed over soft Bangkok clay. The control embankment was unreinforced while the other two embankments were reinforced with multiple layers of low-strength geotextile and with a single layer of high-strength geotextile, respectively. The analyses results confirmed the embankment performance indicating a two-stage failure mode of the reinforced embankments, namely: (i) the critical stage followed by (ii) the collapse stage. The critical stage occurred at the onset of plastic deformation of the soft clay foundation. The collapse stage occurred at the onset of embankment collapse when the reinforcement was on the verge of experiencing tensile failure or rupture. The critical reinforcement strain at the critical stage was independent of geotextile stiffness and on subsoil conditions and was 2.5 to 3%. The localized strain corresponds to the mobilized strain at the collapse stage in excess of the critical strain and can be estimated using a new method requiring two parameters: the in-soil stiffness and the reinforcement inclination factor. Back-analyses confirmed the horizontal and bisectional directions of reinforcement tensile force corresponding to the critical and collapse heights, respectively.
Geomembrane Research Needs
Authors: Elton D.J. , Peggs I.
Published: October 2014

A US National Science Foundation/Auburn University Workshop was held in Summer 2000 to identify geomembrane-related topics that require research. Three publications were produced: a geomembrane state-of-practice paper, a paper on research needs, and a final paper on organizing similar workshops. The present paper focuses on geomembrane research needs, with the intent of moving the profession forward by identifying what new knowledge/research is needed and how to get it. Stimulating discussion on the subject is a secondary purpose of the paper. Ten professionals, selected for their expertise and experience, attended the Workshop. Most facets of the geomembrane/waste disposal industry were represented. The participants almost exclusively represented United States geomembrane practice. Most of the discussions related to high-density polyethylene, linear low-density polyethylene, polyvinyl chloride, and polypropylene geomembranes. The Workshop considered seventeen topics related to geomembranes in waste, water, and product containment systems. The topics were seam tests, seam strength, wrinkles, lifetime predictions, seams types, geomembranes on steep walls, thermal seams in PVC geomembranes, geomembranes in bioreactors, durability, remote leak repair, defect significance, shear displacements, seams in different geomembrane types, leak location and significance, puncture protection, and multiaxial testing.
Peak Versus Residual Shear Strength in Geosynthetic-Reinforced Soil Design
Authors: Zornberg J.G.
Published: October 2014

Current design guidelines for geosynthetic-reinforced soil structures disagree over the shear strength parameters that should be selected to characterize the backfill material. Most geosynthetic reinforcing materials are classified as extensible inclusions for almost all practical applications. The extensible nature of geosynthetic reinforcements has led to the recommendation by several agencies and reinforced soil designers toward the use of the residual shear strength instead of the peak shear strength for design. However, common practice in the US has been the use of the peak shear strength. The main purpose of this paper is to provide experimental evidence regarding selection of either peak or residual shear strength to characterize the backfill material for the design of geosynthetic-reinforced soil structures. Specifically, experimental results from reduced-scale models tested in a geotechnical centrifuge indicate that the stability of geosynthetic-reinforced slopes is governed by the peak soil shear strength.
Short-Term Strain and Deformation Behavior of Geosynthetic Walls at Working Stress Conditions
Authors: Bathurst R.J. , Allen T.M. , Walters D.L.
Published: October 2014

The paper reviews geosynthetic reinforcement strain measurement techniques that have been reported in a database of well-documented case studies and more recent full-scale laboratory test walls. Interpretation of strain measurements, accuracy of readings, and advantages and disadvantages of different techniques are discussed. In general, properly calibrated strain gauges have proven useful to estimate reinforcement strains at low strain levels (0.02 to 2%). Extensometers are shown to be accurate at strains greater than 2% and to have marginal reliability at strains between 0.5 and 2%. A strategy to improve confidence with interpretation of strain readings is to use strain gauges and extensometers in the field and to adjust strain gauge calibration factors based on in situ measurements from both devices. Corrected reinforcement strains can be used together with appropriately selected reinforcement stiffness values to estimate reinforcement loads. Estimated loads can then be compared to predicted values using current and proposed design methods for the internal stability of geosynthetic-reinforced soil walls.
Soil Reinforcement Loads in Geosynthetic Walls at Working Stress Conditions
Authors: Allen T.M. , Bathurst R.J.
Published: October 2014

Knowing the load in geosynthetic reinforcement layers in full-scale walls is an important step to improving internal stability design methods. Interpretation of empirical reinforcement load data enables analytical models to be properly calibrated. High-quality empirical data also provides a baseline against which new design methods can be validated. In this paper, loads in soil reinforcement layers from 16 full-scale geosynthetic wall case histories were estimated from strain measurements and converted to load through the stiffness of the reinforcement material. The paper summarizes these estimated peak loads, describes general trends in the data, and compares these reinforcement loads to predictions using current design practice applied to the wall case histories. It was found that reinforcement loads derived from strain measurements are, in general, much lower than would be predicted based on current limit equilibrium design methods that use classical earth pressure theory. The low reinforcement strains and loads measured to date in geosynthetic walls point to the desirability of using peak soil shear strength rather than constant volume shear strength for design. This approach will help to reduce design conservatism and will be consistent with the philosophy of preventing failure of a major component of the reinforced soil system, the soil. Once the soil has failed, for all practical purposes, the wall has failed as well.
Observed Long-Term Performance of Geosynthetic Walls and Implications for Design
Authors: Allen T.M. , Bathurst R.J.
Published: October 2014

Geosynthetic-reinforced walls have been viewed by the civil engineering profession as a new technology whose acceptable long-term performance is yet to be established. Nevertheless, geosynthetic walls have been in use for almost 25 years. Much of the uncertainty associated with acceptance of geosynthetic-reinforced wall technologies is related to time-dependent deformation. This paper summarizes the creep rates measured in full-scale walls and compares them to creep rates measured in-isolation in the laboratory where the applied load level matches values estimated for the same structures in the field. In the majority of cases, the laboratory in-isolation creep rates were the same as or greater than the measured reinforcement creep rates in full-scale walls, corroborating that reinforcement load levels can be estimated from measured strain data. At the end of wall construction, it appears that the reinforcement is primarily exhibiting creep, with only minor stress relaxation. However, in the long-term, there is a trend toward reinforcement stress relaxation. Furthermore, the long-term behavior observed in the full-scale walls indicates that the reinforcement loads are well below values required to cause creep rupture over the design life of the structures and, in some cases, creep appears to have stopped completely. Finally, the paper offers quantitative guidelines to delineate anticipated poor and good long-term wall performance based largely on level of reinforcement strains and magnitude of post-construction wall deformations.
Soil strength estimation and pore pressure dissipation for free-fall piezocone in soft clay
Authors: CHOW S.H. , O'LOUGHLIN C.D. , RANDOLPH M.F.
Published: October 2014

This paper considers centrifuge modelling of free-fall piezocones in soft clay, and interprets the test data to estimate the undrained shear strength and coefficient of consolidation. Data from the free-fall piezocones, which involved dynamic embedment in a normally consolidated kaolin clay sample from various drop heights, were compared with equivalent data from piezocone tests. The undrained shear strength, as interpreted from the acceleration trace of the free-fall piezocone, was found to be in good agreement with that derived from the piezocone penetration tests. The free-fall piezocone is also found to produce identical pore pressure dissipation behaviour as for a statically penetrated piezocone, despite a significant rise in the pore pressure at the start of the dissipation phase.
Cross‐taxon congruence in lake plankton largely independent of environmental gradients
Authors: Özkan Korhan , Jeppesen Erik , Davidson Thomas A. , Søndergaard Martin , Lauridsen Torben L. , Bjerring Rikke , Johansson Liselotte S. , Svenning Jens-Christian
Published: October 2014

Groups of organisms often have congruent patterns of diversity or community structure due to similar environmental requirements. However, ecological interactions across trophic levels may also promote congruence independent of environmental drivers through selective predation, niche partitioning, or facilitation. We examined congruence between phytoplankton and zooplankton communities using 20 years of monitoring data from 17 Danish lakes, most of which were subject to external nutrient loading reduction after a period of eutrophication. Linear mixed effect models and partial Mantel tests were used to elucidate the extent to which congruence in genus richness and composition was driven by environmental factors. Congruence not explained by environmental controls might indicate ecological interactions across trophic levels of lake plankton. Genus richness and composition of phyto‐ and zooplankton were significantly congruent. Environmental factors had limited power to explain the genus richness of phyto‐ and zooplankton (R2: 6% and 12%, respectively). Including richness of the reciprocal group among the predictors markedly improved each respective model and explanatory power (R2: 11% and 17%, respectively). Similarly, a large proportion of the congruence in genus composition was independent of environmental dissimilarity (Mantel r: 0.29 and partial Mantel r after accounting for environmental control: 0.17). The strength of the congruence varied among different groups of phyto‐ and zooplankton, likely reflecting that the different zooplankton groups differ in their grazing size spectra and thus in the strength of their coupling with the phytoplankton assemblages. Remarkably, congruence with phytoplankton was strongest for the smallest group of zooplankton, rotifers, which graze on a limited size spectrum of phytoplankton. Moreover, congruence was stronger in low‐nutrient lakes, suggesting that the strength of the interactions between the two groups weakens with eutrophication. This is likely due to changes in trophic dynamics, where enhanced fish predation on large‐bodied zooplankton with increasing nutrient levels results in reduced zooplankton grazing control of phytoplankton assemblages.
Ecological speciation and phenotypic plasticity affect ecosystems
Authors: Lundsgaard-Hansen Bänz , Matthews Blake , Seehausen Ole
Published: October 2014

Phenotypic differences among closely related populations and species can cause contrasting effects on ecosystems; however, it is unknown whether such effects result from genetic divergence, phenotypic plasticity, or both. To test this, we reared sympatric limnetic and benthic species of whitefish from a young adaptive radiation in a common garden, where the benthic species was raised on two distinct food types. We then used these fish in a mesocosm experiment to test for contrasting ecosystem effects of closely related species and of plastically induced differences within a species. We found that strong contrasting ecosystem effects resulted more frequently from genetic divergence, although they were not stronger overall than those resulting from phenotypic plasticity. Overall, our results provide evidence that genetically based differences among closely related species that evolved during a young adaptive radiation can affect ecosystems, and that phenotypic plasticity can modify the ecosystem effects of such species.
Fire alters ecosystem carbon and nutrients but not plant nutrient stoichiometry or composition in tropical savanna
Authors: Pellegrini Adam F. A. , Hedin Lars O. , Staver A. Carla , Govender Navashni
Published: October 2014

Fire and nutrients interact to influence the global distribution and dynamics of the savanna biome, but the results of these interactions are both complex and poorly known. A critical but unresolved question is whether short‐term losses of carbon and nutrients caused by fire can trigger long‐term and potentially compensatory responses in the nutrient stoichiometry of plants, or in the abundance of dinitrogen‐fixing trees. There is disagreement in the literature about the potential role of fire on savanna nutrients, and, in turn, on plant stoichiometry and composition. A major limitation has been the lack of fire manipulations over time scales sufficiently long for these interactions to emerge. We use a 58‐year, replicated, large‐scale, fire manipulation experiment in Kruger National Park (South Africa) in savanna to quantify the effect of fire on (1) distributions of carbon, nitrogen, and phosphorus at the ecosystem scale; (2) carbon : nitrogen : phosphorus stoichiometry of above‐ and belowground tissues of plant species; and (3) abundance of plant functional groups including nitrogen fixers. Our results show dramatic effects of fire on the relative distribution of nutrients in soils, but that individual plant stoichiometry and plant community composition remained unexpectedly resilient. Moreover, measures of nutrients and carbon stable isotopes allowed us to discount the role of tree cover change in favor of the turnover of herbaceous biomass as the primary mechanism that mediates a transition from low to high soil carbon and nutrients in the absence of fire. We conclude that, in contrast to extra‐tropical grasslands or closed‐canopy forests, vegetation in the savanna biome may be uniquely adapted to nutrient losses caused by recurring fire.