bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing
Authors: Abdolrasouli Alireza , Rhodes Johanna , Beale Mathew A. , Hagen Ferry , Rogers Thomas R. , Chowdhary Anuradha , Meis Jacques F. , Armstrong-James Darius , Fisher Matthew C.
Published: June 2015

A rapid and global emergence of azole resistance has been observed in the pathogenic fungus
Aspergillus fumigatus
over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the
cyp51A
gene, which encodes a protein targeted by triazole antifungal drugs. Whole-genome sequencing (WGS) was performed for high-resolution single-nucleotide polymorphism (SNP) analysis of 24
A. fumigatus
isolates, including azole-resistant and susceptible clinical and environmental strains obtained from India, the Netherlands, and the United Kingdom, in order to assess the utility of WGS for characterizing the alleles causing resistance. WGS analysis confirmed that TR
34
/L98H (a mutation comprising a tandem repeat [TR] of 34 bases in the promoter of the
cyp51A
gene and a leucine-to-histidine change at codon 98) is the sole mechanism of azole resistance among the isolates tested in this panel of isolates. We used population genomic analysis and showed that
A. fumigatus
was panmictic, with as much genetic diversity found within a country as is found between continents. A striking exception to this was shown in India, where isolates are highly related despite being isolated from both clinical and environmental sources across >1,000 km; this broad occurrence suggests a recent selective sweep of a highly fit genotype that is associated with the TR
34
/L98H allele. We found that these sequenced isolates are all recombining, showing that azole-resistant alleles are segregating into diverse genetic backgrounds. Our analysis delineates the fundamental population genetic parameters that are needed to enable the use of genome-wide association studies to identify the contribution of SNP diversity to the generation and spread of azole resistance in this medically important fungus.

IMPORTANCE
Resistance to azoles in the ubiquitous ascomycete fungus
A. fumigatus
was first reported from clinical isolates collected in the United States during the late 1980s. Over the last decade, an increasing number of
A. fumigatus
isolates from the clinic and from nature have been found to show resistance to azoles, suggesting that resistance is emerging through selection by the widespread usage of agricultural azole antifungal compounds. Aspergillosis is an emerging clinical problem, with high rates of treatment failures necessitating the development of new techniques for surveillance and for determining the genome-wide basis of azole resistance in
A. fumigatus
.
Defining the Roles of TcdA and TcdB in Localized Gastrointestinal Disease, Systemic Organ Damage, and the Host Response during Clostridium difficile Infections
Authors: Carter Glen P. , Chakravorty Anjana , Pham Nguyen Tu Anh , Mileto Steven , Schreiber Fernanda , Li Lucy , Howarth Pauline , Clare Simon , Cunningham Bliss , Sambol Susan P. , Cheknis Adam , Figueroa Iris , Johnson Stuart , Gerding Dale , Rood Julian I. , Dougan Gordon , Lawley Trevor D. , Lyras Dena
Published: June 2015

Clostridium difficile
is a leading cause of antibiotic-associated diarrhea, a significant animal pathogen, and a worldwide public health burden. Most disease-causing strains secrete two exotoxins, TcdA and TcdB, which are considered to be the primary virulence factors. Understanding the role that these toxins play in disease is essential for the rational design of urgently needed new therapeutics. However, their relative contributions to disease remain contentious. Using three different animal models, we show that TcdA
+
TcdB
−
mutants are attenuated in virulence in comparison to the wild-type (TcdA
+
TcdB
+
) strain, whereas TcdA
−
TcdB
+
mutants are fully virulent. We also show for the first time that TcdB alone is associated with both severe localized intestinal damage and systemic organ damage, suggesting that this toxin might be responsible for the onset of multiple organ dysfunction syndrome (MODS), a poorly characterized but often fatal complication of
C. difficile
infection (CDI). Finally, we show that TcdB is the primary factor responsible for inducing the
in vivo
host innate immune and inflammatory responses. Surprisingly, the animal infection model used was found to profoundly influence disease outcomes, a finding which has important ramifications for the validation of new therapeutics and future disease pathogenesis studies. Overall, our results show unequivocally that TcdB is the major virulence factor of
C. difficile
and provide new insights into the host response to
C. difficile
during infection. The results also highlight the critical nature of using appropriate and, when possible, multiple animal infection models when studying bacterial virulence mechanisms.

IMPORTANCE
Clostridium difficile
is a leading cause of antibiotic-associated diarrhea and an important hospital pathogen. TcdA and TcdB are thought to be the primary virulence factors responsible for disease symptoms of
C. difficile
infections (CDI). However, the individual contributions of these toxins to disease remain contentious. Using three different animal models of infection, we show for the first time that TcdB alone causes severe damage to the gut, as well as systemic organ damage, suggesting that this toxin might be responsible for MODS, a serious but poorly understood complication of CDI. These findings provide important new insights into the host response to
C. difficile
during infection and should guide the rational development of urgently required nonantibiotic therapeutics for the treatment of CDI.
Bacteriophages Limit the Existence Conditions for Conjugative Plasmids
Authors: Harrison Ellie , Wood A. Jamie , Dytham Calvin , Pitchford Jonathan W. , Truman Julie , Spiers Andrew , Paterson Steve , Brockhurst Michael A.
Published: June 2015

Bacteriophages are a major cause of bacterial mortality and impose strong selection on natural bacterial populations, yet their effects on the dynamics of conjugative plasmids have rarely been tested. We combined experimental evolution, mathematical modeling, and individual-based simulations to explain how the ecological and population genetics effects of bacteriophages upon bacteria interact to determine the dynamics of conjugative plasmids and their persistence. The ecological effects of bacteriophages on bacteria are predicted to limit the existence conditions for conjugative plasmids, preventing persistence under weak selection for plasmid accessory traits. Experiments showed that phages drove faster extinction of plasmids in environments where the plasmid conferred no benefit, but they also revealed more complex effects of phages on plasmid dynamics under these conditions, specifically, the temporary maintenance of plasmids at fixation followed by rapid loss. We hypothesized that the population genetic effects of bacteriophages, specifically, selection for phage resistance mutations, may have caused this. Further mathematical modeling and individual-based simulations supported our hypothesis, showing that conjugative plasmids may hitchhike with phage resistance mutations in the bacterial chromosome.

IMPORTANCE
Conjugative plasmids are infectious loops of DNA capable of transmitting DNA between bacterial cells and between species. Because plasmids often carry extra genes that allow bacteria to live in otherwise-inhospitable environments, their dynamics are central to understanding bacterial adaptive evolution. The plasmid-bacterium interaction has typically been studied in isolation, but in natural bacterial communities, bacteriophages, viruses that infect bacteria, are ubiquitous. Using experiments, mathematical models, and computer simulations we show that bacteriophages drive plasmid dynamics through their ecological and evolutionary effects on bacteria and ultimately limit the conditions allowing plasmid existence. These results advance our understanding of bacterial adaptation and show that bacteriophages could be used to select against plasmids carrying undesirable traits, such as antibiotic resistance.
Inhibiting the Mammalian Target of Rapamycin Blocks the Development of Experimental Cerebral Malaria
Authors: Gordon Emile B. , Hart Geoffrey T. , Tran Tuan M. , Waisberg Michael , Akkaya Munir , Skinner Jeff , Zinöcker Severin , Pena Mirna , Yazew Takele , Qi Chen-Feng , Miller Louis H. , Pierce Susan K.
Published: June 2015

Malaria is an infectious disease caused by parasites of severalPlasmodiumspp. Cerebral malaria (CM) is a common form of severe malaria resulting in nearly 700,000 deaths each year in Africa alone. At present, there is no adjunctive therapy for CM. Although the mechanisms underlying the pathogenesis of CM are incompletely understood, it is likely that both intrinsic features of the parasite and the human host's immune response contribute to disease. The kinase mammalian target of rapamycin (mTOR) is a central regulator of immune responses, and drugs that inhibit the mTOR pathway have been shown to be antiparasitic. In a mouse model of CM, experimental CM (ECM), we show that the mTOR inhibitor rapamycin protects against ECM when administered within the first 4 days of infection. Treatment with rapamycin increased survival, blocked breakdown of the blood-brain barrier and brain hemorrhaging, decreased the influx of both CD4+and CD8+T cells into the brain and the accumulation of parasitized red blood cells in the brain. Rapamycin induced marked transcriptional changes in the brains of infected mice, and analysis of transcription profiles predicted that rapamycin blocked leukocyte trafficking to and proliferation in the brain. Remarkably, animals were protected against ECM even though rapamycin treatment significantly increased the inflammatory response induced by infection in both the brain and spleen. These results open a new avenue for the development of highly selective adjunctive therapies for CM by targeting pathways that regulate host and parasite metabolism.

IMPORTANCEMalaria is a highly prevalent infectious disease caused by parasites of severalPlasmodiumspp. Malaria is usually uncomplicated and resolves with time; however, in about 1% of cases, almost exclusively among young children, malaria becomes severe and life threatening, resulting in nearly 700,000 deaths each year in Africa alone. Among the most severe complications ofPlasmodium falciparuminfection is cerebral malaria with a fatality rate of 15 to 20%, despite treatment with antimalarial drugs. Cerebral malaria takes a second toll on African children, leaving survivors at high risk of debilitating neurological defects. At present, we have no effective adjunctive therapies for cerebral malaria, and developing such therapies would have a large impact on saving young lives in Africa. Here we report results that open a new avenue for the development of highly selective adjunctive therapies for cerebral malaria by targeting pathways that regulate host and parasite metabolism.
Holocene fluvial landforms and depositional environments of the Lower Mississippi Valley
Authors: Saucier Roger T.
Published: June 2015

Holocene fluvial land forms are exposed along a 46-mi (74 km) circuitous route west of Natchez, Mississippi, in Concordia Parish, northeastern Louisiana. The route encompasses U.S. 84 and Louisiana 129, 565, and 15 through the communities of Ferriday, Stacy, Monterey, and Deer Park (Fig. 1).

Road shoulders are adequate for safe temporary parking at al locations. All lands beyond highway rights-of-way are privately owned. Best observation is in winter to early spring due to an absence of foliage and crops.
Influence of adiposity on health-related quality of life in the Gateshead Millennium Study cohort: longitudinal study at 12 years
Authors: Parkinson Kathryn N , Adamson Ashley J , Basterfield Laura , Reilly Jessica K , Le Couteur Ann , Reilly John J
Published: June 2015

Objective

To examine whether adiposity is associated with an impaired quality of life (an individual's perception of their life) in general population samples in early adolescence.

Design and methods

Relationships between a direct measure of adiposity (fat mass index from bioimpedance) and a proxy measure (waist circumference), and a generic (KIDSCREEN-27) and a weight-specific measure of health-related quality of life (HRQoL, Impact of Weight on Quality of Life-Kids (IWQOL-Kids)) were examined in a longitudinal population-based cohort of young adolescents aged 12 years (n=519). The effects of change in adiposity over time (from 7 years and 9 years) were also examined (n=331–445 in longitudinal analyses).

Results

Impairment in HRQoL was associated with current adiposity but it was not predicted by earlier adiposity. At 12 years, higher adiposity was associated with lowerPhysical Well-Beingon KIDSCREEN-27, and with lowerTotal Scoreson the weight-specific IWQOL-Kids instrument, the latter particularly in girls.

Conclusions

Health and education professionals need to be aware in their clinical practice that higher adiposity impairs HRQoL in general populations of young adolescents. Further research would be useful to determine whether or not children of primary school age self-reporting lower HRQoL are more likely to develop higher adiposity later in adolescence or early adulthood.
Structured exercise improves mobility after hip fracture: a meta-analysis with meta-regression
Authors: Diong Joanna , Allen Natalie , Sherrington Catherine
Published: June 2015

Objectives

To determine the effect of structured exercise on overall mobility in people after hip fracture. To explore associations between trial-level characteristics and overall mobility.

Design

Systematic review, meta-analysis and meta-regression.

Data sources

MEDLINE, EMBASE, CINAHL, the Cochrane Central Register of Controlled Trials, the Cochrane Bone, Joint and Muscle Trauma Group Specialised Register and the Physiotherapy Evidence Database to May 2014.

Study eligibility criteria, participants and interventions

Randomised controlled trials of structured exercise, which aimed to improve mobility compared with a control intervention in adult participants after surgery for hip fracture were included.

Data extraction and synthesis

Data were extracted by one investigator and checked by an independent investigator. Standardised mean differences (SMD) of overall mobility were meta-analysed using random effects models. Random effects meta-regression was used to explore associations between trial-level characteristics and overall mobility.

Results

13 trials included in the meta-analysis involved 1903 participants. The pooled Hedges’ g SMD for overall mobility was 0.35 (95% CI 0.12 to 0.58, p=0.002) in favour of the intervention. Meta-regression showed greater treatment effects in trials that included progressive resistance exercise (change in SMD=0.58, 95% CI 0.17 to 0.98, p=0.008, adjusted R2=60%) and delivered interventions in settings other than hospital alone (change in SMD=0.50, 95% CI 0.08 to 0.93, p=0.024, adjusted R2=49%).

Conclusions and implications

Structured exercise produced small improvements on overall mobility after hip fracture. Interventions that included progressive resistance training and were delivered in other settings were more effective, although the latter may have been confounded by duration of interventions.
Strategic Assessment of Risk and Risk Tolerance (StARRT) framework for return-to-play decision-making
Authors: Shrier Ian
Published: June 2015

The sport medicine clinician is faced with return-to-play (RTP) decisions for every patient who wants to return to activity. The complex interaction of factors related to history, physical examination, testing, activity and baseline characteristics can make RTP decision-making challenging. Further, when reasoning is not explicit, unnecessary conflict can arise among clinicians themselves, or among clinicians and patients. This conflict can have negative health consequences for the patient. In 2010, a transparent framework for RTP decisions was proposed. However, some have identified limitations to the framework and found difficulties in its implementation. This paper presents a revised framework that addresses the limitations, and provides concrete examples of how to apply it in simple and complex cases.
Variations in Health-Related Quality of Life (HRQoL) and survival 1 year after stroke: five European population-based registers
Authors: Ayis Salma , Wellwood Ian , Rudd Anthony G , McKevitt Christopher , Parkin David , Wolfe Charles D A
Published: June 2015

Objective

There were two main objectives: to describe and compare clinical outcomes and Patient-Reported Outcome Measures (PROMs) collected using standardised procedures across the European Registers of Stroke (EROS) at 3 and 12 months after stroke; and to examine the relationship between patients’ Health-Related Quality of Life (HRQoL) at 3 months after stroke and survival up to 1 year across the 5 populations.

Design

Analysis of data from population-based stroke registers.

Setting

European populations in Dijon (France); Kaunas (Lithuania); London (UK); Warsaw (Poland) and Sesto Fiorentino (Italy).

Participants

Patients with ischaemic or intracerebral haemorrhage (ICH) stroke, registered between 2004 and 2006.

Outcome measures

(1) HRQoL, assessed by the physical component summary (PCS) and mental component summary (MCS) of the Short-Form Health Survey (SF-12), mapped into the EQ-5D to estimate responses on 5 dimensions (mobility, activity, pain, anxiety and depression, and self-care) and utility scores. (2) Mortality within 3 months and within 1 year of stroke.

Results

Of 1848 patients, 325 were lost to follow-up and 500 died within a year of stroke. Significant differences in mortality, HRQoL and utility scores were found, and remained after adjustments. Kaunas had an increased risk of death; OR 2.34, 95% CI (1.32 to 4.14) at 3 months after stroke in Kaunas, compared with London. Sesto Fiorentino had the highest adjusted PCS: 43.54 (SD=0.96), and Dijon had the lowest adjusted MCS: 38.67 (SD=0.67). There are strong associations between levels of the EQ-5D at 3 months and survival within the year. The trend across levels suggests a dose–response relationship.

Conclusions

The study demonstrated significant variations in survival, HRQoL and utilities across populations that could not be explained by stroke severity and sociodemographic factors. Strong associations between HRQoL at 3 months and survival to 1 year after stroke were identified.
Insulin treatment of maternal diabetes mellitus and respiratory outcome in late-preterm and term singletons
Authors: Becquet Odile , El Khabbaz Fares , Alberti Corinne , Mohamed Damir , Blachier Audrey , Biran Valérie , Sibony Olivier , Baud Olivier
Published: June 2015

Objectives

While the incidence of diabetes mellitus (DM) during pregnancy has been steadily increasing in recent years, the link between gestational DM and respiratory outcome in neonates has not been definitely established. We asked the question whether DM status and its treatment during pregnancy could influence the risk of neonatal respiratory distress.

Design

We studied in a large retrospective cohort the relationship between maternal DM status (non-DM, insulin-treated DM (IT-DM) and non-insulin-treated DM (NIT-DM)), and respiratory distress in term and near-term inborn singletons.

Results

Among 18 095 singletons delivered at 34 weeks of gestation or later, 412 (2.3%) were admitted to the neonatal intensive care unit (NICU) for respiratory distress within the first hours of life. The incidence of NICU admission due to respiratory distress groups was 2.2%, 5.7% and 2.1% in the non-DM, IT-DM and NIT-DM groups, respectively. Insulin treatment of DM, together with several other perinatal factors, was associated with a significant increased risk for respiratory distress. Several markers of the severity of respiratory illness, including durations of mechanical ventilation and supplemental oxygen, and hypertrophic cardiomyopathy were also found increased following IT-DM as compared with NIT-DM. In a multivariate model, we found that IT-DM, but not NIT-DM, was significantly associated with respiratory distress independent of gestational age and caesarean section, with an incidence rate ratio of 1.44 (1.00–2.08).

Conclusions

This study shows that the treatment of maternal DM with insulin during pregnancy is an independent risk factor for respiratory distress in term and near-term newborns.
A unit-based intervention aimed at improving patient adherence to pharmacological thromboprophylaxis
Authors: Baillie Charles Alexander , Guevara James P , Boston Raymond C , Hecht Todd E H
Published: June 2015

Background

Pharmacological thromboprophylaxis is necessary among many hospitalised patients to prevent venous thromboembolism (VTE). However, a significant number of clinician-ordered doses are not administered with many doses refused by patients. We aimed to assess the impact and sustainability of a multifaceted intervention to improve medication adherence to pharmacological thromboprophylaxis. The intervention included a standardised nursing response to patient refusal, daily assessment of VTE prophylaxis usage and regular feedback on refusal rates.

Methods

We conducted a quasi-experimental study of patients admitted between January 2010 and November 2012 to one of six hospital intervention units (three medical and three oncology units) or five control units. The primary outcome was the proportion of VTE prophylaxis doses missed for any reason.

Results

A total of 20 208 admissions occurred at the six hospital units during the study period. In the pre-post analysis, the rate of missed and refused doses decreased significantly after the intervention (24.7% to 14.7% and 18.3% to 9.4%, respectively; p value <0.01 for both comparisons). In multiple regression models with interrupted time series analysis, the intervention was associated with an immediate and sustained decrease in missed (adjusted OR 0.64; 95% CI 0.55 to 0.74 and 0.98; 95%CI 0.97 to 0.99) and refused doses (adjusted OR per month 0.58; 95% CI 0.48 to 0.71 and 0.97; 95%CI 0.96 to 0.98). No immediate or sustained reduction in missed or refused doses was observed in the control units.

Conclusions

Implementation of a multifaceted intervention resulted in an immediate and sustained decrease in the proportion of missed and refused doses of pharmacological thromboprophylaxis. Efforts aimed at increasing patient adherence are a promising approach to improve rates of VTE thromboprophylaxis administration.
Connecting cyto-nano-architectural attributes and epithelial molecular expression in oral submucous fibrosis progression to cancer
Authors: Bag Swarnendu , Pal Mousumi , Chaudhary Amrita , Das Raunak Kumar , Paul Ranjan Rashmi , Sengupta Sanghamitra , Chatterjee Jyotirmoy
Published: June 2015

Objective

Problems in pre-cancer diagnosis complicate cancer theragnosis as well as life expectancy. There is uncertainty regarding malignant transformation of oral submucous fibrosis (OSF), an oral pre-cancer with dysplastic (OSFWD) and non-dysplastic (OSFWT) subtypes. Understanding the structural, molecular and physical aspects of epithelial homeostasis may be useful.

Materials and methods

Histopathological grading of biopsy sections was performed using H&E staining. Alterations in epithelial surface architecture in different groups was evaluated using scanning electron microscopy (SEM). The expression of crucial epithelial genes (p63, CK-5/6, CK-10, E-cadherin and β-catenin) was studied by immunohistochemistry, Western blot and RT-PCR analysis.

Results

SEM observations revealed that the surface epithelial ridge pattern became thick and dense, and pit pattern gradually decreased in OSFWD and oral squamous cell carcinoma (OSCC). p63, ΔNp63 and CK-5/6 were up-regulated in OSFWD and OSCC but down-regulated in OSFWT. CK-10 was down-regulated in OSFWD compared to OSFWT. Cytoplasmic expression of E-cadherin and β-catenin was elevated in dysplastic and cancerous conditions. Moreover, statistical correlation between SEM features (ridges and pits) and molecular attributes demonstrated a significant positive relationship between the ridge-to-pit ratio and p63 population density (r=0.85) and the ridge-to-pit ratio and CK-5/6 intensity (r=0.63).

Conclusions

Molecular changes related to epithelial progressive maturation and cellular proliferation are correlated with concomitant alteration of epithelial surface architecture which helps to predict the malignant potentiality of OSF.
Enhanced regulation of cell cycle and suppression of osteoblast differentiation molecular signatures by prostate cancer stem-like holoclones
Authors: Gallagher Michael F , Salley Yvonne , Spillane Cathy D , Ffrench Brendan , El Baruni Salah , Blacksheilds Gordon , Smyth Paul , Martin Cara , Sheils Orla , Watson William , O'Leary John J
Published: June 2015

Aims

Targeting the stem cell properties of tumor-initiating cells is an avenue through which cancer treatment may be improved. Before this can be achieved, so-called ‘cancer stem cell’ (CSC) models must be developed and characterized in specific malignancies.

Methods

In this study, holoclone formation assays were used to characterise stem-like molecular signatures in prostate cancer (PCa) cells.

Results

LNCaP and PC3 parent cells were capable of responding to stem cell differentiation morphogen retinoic acid (RA), suggesting the presence of inherent stem-like properties. LNCaP cells, which represent early, androgen-responsive disease, formed holoclones after twenty six days. PC3 cells, which represent advanced, metastatic, castration-resistant disease, formed holoclones after only six days. Holoclones displayed decreased expression of RA-genes, suggesting a more immature, less differentiated phenotype. Gene and microRNA arrays demonstrated that holoclones downregulated a number of stem cell differentiation regulators while displaying enhanced regulation of G2 to M transition and the mitotic spindle checkpoint components of the cell cycle. PC3 holoclones displayed pronounced downregulation of known regulators of osteoblast differentiation from mesenchymal stem cells and Epithelial Mesenchymal Transition.

Conclusions

Our results suggest that some PCa cells retain the ability to transition to a more immature state in which differentiation and metastatic mechanisms are suppressed. The highlighting of osteoblast differentiation regulators in this mechanism is particularly notable, considering the propensity of PCa to metastasise to bone.
A brief histone in time: understanding the combinatorial functions of histone PTMs in the nucleosome context
Authors: Ng Marlee K. , Cheung Peter
Published: June 2015

It has been over 50 years since Allfrey et al. proposed that histone acetylation regulates RNA synthesis, and the study of histone modifications has progressed at an extraordinary pace for the past two decades. In this review, we provide a perspective on some key events and advances in our understanding of histone modifications. We also highlight reagents and tools from past to present that facilitated progress in this research field. Using histone H3 phosphorylation as an underlying thread, we review the rationale that led to the proposal of the histone code hypothesis, as well as examples that illustrate the concepts of combinatorial histone modifications and cross-talk pathways. We further highlight the importance of investigating these mechanisms in the context of nucleosomes rather than just at the histone level and present current and developing approaches for such studies. Overall, research on histone modifications has yielded great mechanistic insights into the regulation of genomic functions, and extending these studies using nucleosomes will further elucidate the complexity of these pathways in a more physiologically relevant context.
Microstructural study of deformation zones during cone penetration in silt at variable penetration rates
Authors: Paniagua P. , Fonseca J. , Gylland A.S. , Nordal S.
Published: June 2015

During conventional cone penetration testing in silt, the soil will normally be partially drained. If the penetration rate varies, time for drainage is altered and therefore the measured cone resistance and pore pressure will change. This paper studies the change in soil microstructure around the probe during cone penetration carried out at different penetration rates to investigate the failure mechanism and the processes controlling drainage in silt. Backscattered electron images of polished thin sections prepared from frozen samples at the end of penetration were used. Making use of advanced image-processing techniques, the statistical distribution of particle orientations and the local porosity were investigated for zones around the cone tip and shaft. The spatial distribution of the measured microscale parameters in the region near the probe indicates that the soil deformation during a piezometric cone penetration test (CPTU) in silt leads to the formation of both contractive and dilative zones. The macro response of the material, presented by the pore pressure and cone penetration resistance measured during the test, results from the competition between these zones during penetration, which is shown to be dependent on the penetration rate.
A GIS-based method for depicting the characteristics of mesoscale eddies: a case study in the Northern South China Sea
Authors: Li Ce , Du Yunyan , Liang Fuyuan , Yi Jiawei , Lakhan V. Chris
Published: June 2015

The paper presents a geographical information system (GIS)-based method for depicting the characteristics, particularly the internal structures and evolutionary processes, of mesoscale eddies. This was done by examining topologic relations among closed sea surface height (SSH) contours that were reconstructed from the Naval Research Laboratory Navy layered ocean model (NLOM). Different scenarios of the topological relations among the contour lines permitted the identification of the outermost outline of eddies and the depiction of the number of cores in each mesoscale oceanic eddy. With full consideration of the internal structure of the eddies, we then reconstructed the evolutionary processes of these eddies, and the results were compared with empirical observations on three long-lived mesoscale eddies in the northern South China Sea (SCS). Tracking results were similar, thereby validating our method as being efficient and robust in reconstructing mesoscale ocean eddies, especially their evolutionary processes based on their internal structures.
Impact of leaf retained water on tree transpiration
Authors: Lin Maosen , Guan Dexin , Wang Anzhi , Jin Changjie , Wu Jiabing , Yuan Fenghui
Published: June 2015

Water retained on tree leaves after rainfall, dew, or fog impacts transpiration. To determine the impact of leaf retained water (LRW) on the transpiration of trees, the difference between transpiration rates of different species with and without water sprayed on the leaves was measured. Results show that transpiration was inhibited by LRW. Both the inhibition extent and duration of LRW were higher on broadleaf species than on coniferous species. Under conditions of saturated LRW of the tree crown, mean transpiration inhibition rates of the test species were 0.32 (Quercus mongolica Fisch. ex Ledeb.), 0.25 (Acer mono), 0.37 (Tilia amurensis Rupr.), 0.31 (Fraxinus mandshurica Rupr.), 0.22 (Pinus koraiensis Siebold & Zucc.), 0.22 (Abies nephrolepis (Trautv. ex Maxim.) Maxim.), and 0.23 (Picea asperata Mast.). Mean inhibition rate and inhibition time for broadleaf species were 0.31 and 115 min, which were 40% higher and 27 min longer than those for coniferous species, respectively. The transpiration inhibition rate of LRW increased linearly with the LRW amount, and there was a higher transpiration inhibition rate in broadleaf species than in coniferous species for the same amount of LRW. Mean rising velocity of the inhibition with LRW amount for broadleaf species was 0.53%, whereas it was only 0.15% for the coniferous species.
Flexible chiral metamaterials with dynamically optical activity and high negative refractive index
Authors: Dincer Furkan , Karaaslan Muharrem , Unal Emin , Akgol Oguzhan , Sabah Cumali
Published: June 2015

We demonstrate numerically and experimentally chiral metamaterials (MTMs) based on gammadion-bilayer cross-wires that uniaxially create giant optical activity and tunable circular dichroism as a result of the dynamic design. In addition, the suggested structure gives high negative refractive index due to the large chirality in order to obtain an efficient polarization converter. We also present a numerical analysis in order to show the additional features of the proposed chiral MTM in detail. Therefore, a MTM sensor application of the proposed chiral MTM is introduced and discussed. The presented chiral designs offer a much simpler geometry and more efficient outlines. The experimental results are in a good agreement with the numerical simulation. It can be seen from the results that, the suggested chiral MTM can be used as a polarization converter, sensor, etc. for several frequency regimes.
Optical characterization of Ga2SeS layered crystals by transmission, reflection and ellipsometry
Authors: Isik Mehmet , Gasanly Nizami
Published: June 2015

Optical properties of [Formula: see text] crystals grown by Bridgman method were investigated by transmission, reflection and ellipsometry measurements. Analysis of the transmission and reflection measurements performed in the wavelength range of 400–1100 nm at room temperature indicated the presence of indirect and direct transitions with 2.28 eV and 2.38 eV band gap energies. Ellipsometry measurements were carried out in the 1.2–6.0 eV spectral region to get information about optical constants, real and imaginary parts of the pseudodielectric function. Moreover, the critical point (CP) analysis of the second derivative spectra of the pseudodielectric constant in the above band gap region was accomplished. The analysis revealed the presence of five CPs with energies of 3.87, 4.16, 4.41, 4.67 and 5.34 eV.
Optical solitons in DWDM system with spatio-temporal dispersion
Authors: Mirzazadeh M. , Eslami Mostafa , Savescu Michelle , Bhrawy A. H. , Alshaery A. A. , Hilal E. M. , Biswas Anjan
Published: June 2015

This paper obtains bright, dark and singular soliton solutions to dense wavelength division multiplexed (DWDM) system, with spatio-temporal dispersion. There are two types of nonlinear media that are considered and they are Kerr law and parabolic law. Four integration algorithms are applied to retrieve these solitons. They are G′/G-expansion scheme, extended tanh function approach, Kudryashov's algorithm and finally the ansatz method. The results follow with respective constraints that guarantees the existence of solitons.
Setting Cournot Versus Lyapunov Games Stability Conditions and Equilibrium Point Properties
Authors: Clempner Julio B.
Published: June 2015

In potential games, the best-reply dynamics results in the existence of a cost function such that each player's best-reply set equals the set of minimizers of the potential given by the opponents' strategies. The study of sequential best-reply dynamics dates back to Cournot and, an equilibrium point which is stable under the game's best-reply dynamics is commonly said to be Cournot stable. However, it is exactly the best-reply behavior that we obtain using the Lyapunov notion of stability in game theory. In addition, Lyapunov theory presents several advantages. In this paper, we show that the stability conditions and the equilibrium point properties of Cournot and Lyapunov meet in potential games.
Component Acquisition Games
Authors: Curiel Imma
Published: June 2015

This paper focuses on situations in several companies each of which has a set of jobs that it has to complete. Each job has a specific starting and ending time and a specific starting and ending point. In order to complete its jobs a company needs to acquire components. There are several types of components. Each job requires exactly one component but not all components are suitable for all jobs. By cooperating, the companies can reduce the costs of acquisition. A component can be used by several companies as long as there is no overlap in the time-intervals of usage by different companies and there is enough time to move the component from where a company has stopped using it to where the next company needs it. A cooperative component acquisition game is constructed to model the cooperation between the companies. This game need not be balanced. Additional properties are introduced that guarantee the game to be totally balanced. We construct an element of the core by using the integer programming formulation of the characteristic function. These games have some relationship with coloring games but we show that results that are valid for coloring games do not hold for them.
Computation of Nonunique Solutions for Trusses Undergoing Large Deflections
Authors: Cengiz Toklu Yusuf , Temür Rasim , Bekdaş Gebrail
Published: June 2015

Determination of nonunique configurations of structures is a problem which cannot be treated readily using classical methods of analysis. In the literature, these kinds of problems are tackled for some simple problems, like trusses with a small number of joints and members, and with specially designed approaches. The recent method of analysis called Total Potential Optimization using Metaheuristic Algorithms (TPO/MA), on the other hand, provides an efficient tool for dealing with these kinds of problems, practically without recourse to any special arrangement. In this analysis, using Harmony Search as the metaheuristic algorithm, large truss structures with linear elastic members are investigated under large deflections as to the existence of more than one solution. The results have shown that for the two examples investigated, a tower truss with 25 members and a dome truss with 24 members, nonunique configurations do exist at quite unexpected levels of loads, and that only one of them can be found with normal applications of the well-known Finite Element method.
DETERMINANTS OF INNOVATION INTENSITY IN DEVELOPED AND IN DEVELOPING ECONOMIES: THE CASE OF FRANCE AND CROATIA
Authors: PEKOVIC SANJA , LOJPUR ANDJELKO , PEJIC-BACH MIRJANA
Published: June 2015

Motivated by differences in the intensity of innovation across national economies, this paper presents an empirical examination of the determinants of a firm's likelihood to invest in different innovation intensity levels in both France and Croatia which represent developed and developing countries, respectively. We used a theoretical framework, which considers the firm's characteristics, internal strategic behaviours and external strategic features, to guide an empirical exploration into the determinants of innovation performance across two countries. The comparison between results from France and Croatia indicates that the incentives of the innovation activities differ between two countries mainly due to a firm's characteristics (size) and external strategic features (export and firm performance). On the other hand, firm's internal strategic behaviours (quality strategy, environmental strategy, R&D and training) have the same role in innovation performance improvement in both developed and developing countries. Consequently, we conclude that managers of firms should customise strategies which aim to improve innovation performance according to the specificities of national economies.
WOULD CLIMATE POLICY IMPROVE THE EUROPEAN ENERGY SECURITY?
Authors: GUIVARCH CÉLINE , MONJON STÉPHANIE , ROZENBERG JULIE , VOGT-SCHILB ADRIEN
Published: June 2015

Energy security improvement is often presented as a co-benefit of climate policies. This paper evaluates this claim. It investigates whether climate policy would improve energy security, while accounting for the difficulties entailed by the many-faceted nature of the concept and the large uncertainties on the determinants of future energy systems. A multi-dimension analysis grid is used to capture the energy security concept, and a database of scenarios allows us to explore the uncertainty space. The results, focusing on Europe, reveal there is no unequivocal effect of climate policy on all the perspectives of energy security. Moreover, time significantly matters: the impact of climate policies is mixed in the short term and globally good in the medium term. In the long term, there is a risk of degradation of the energy security. Lastly, we examine the robustness of our results to uncertainties on drivers of economic growth, availability of fossil fuels and the potentials and low-carbon technologies, and find that they are sensitive mainly to fossil fuels availability, low carbon technologies in the energy sector and improvements in energy efficiency.
FORECASTING VALUE-AT-RISK WITH TIME-VARYING VARIANCE, SKEWNESS AND KURTOSIS IN AN EXPONENTIAL WEIGHTED MOVING AVERAGE FRAMEWORK
Authors: GABRIELSEN ALEXANDROS , KIRCHNER AXEL , LIU ZHUOSHI , ZAGAGLIA PAOLO
Published: June 2015

This paper provides an insight to the time-varying dynamics of the shape of the distribution of financial return series by proposing an exponential weighted moving average (EWMA) model that jointly estimates volatility, skewness and kurtosis over time using a modified form of the Gram–Charlier density in which skewness and kurtosis appear directly in the functional form of this density. In this setting, Value-at-Risk (VaR) can be described as a function of the time-varying higher moments by applying the Cornish-Fisher expansion series of the first four moments. An evaluation of the predictive performance of the proposed model in the estimation of 1-day and 10-day VaR forecasts is performed in comparison with the historical simulation, filtered historical simulation and generalized autoregressive conditional heteroscedasticity (GARCH) model. The adequacy of the VaR forecasts is evaluated under the unconditional, independence and conditional likelihood ratio tests as well as Basel II regulatory tests. The results presented have significant implications for risk management, trading and hedging activities as well as in the pricing of equity derivatives.
ON THE IMPACT OF THE BOUNDARY ON DYNAMICS: ANTI-PERSISTENCE IN THE CASE OF THE HKD EXCHANGE RATE CORRIDOR
Authors: YEE HONG BEN
Published: June 2015

This paper studies the features of the USD/HKD exchange rate process by assessing the conformity of its dynamics to that of a random walk. This is not a trivial task since we consider the period within which the rate is confined to a specified corridor. This is achieved via analysis of its fractal dimension by means of the Hurst exponent as estimated using the rescaled range method. The conformity can be quantified by the difference between the estimated Hurst exponent and the random walk Hurst exponent of ½. At least two distinct Hurst exponents are identified, one corresponding to a random walk while the other, to an anti-persistent process. Partitioning the rate in state space associates the anti-persistence with proximity to the lower boundary of the corridor so the rate can be modeled using a random walk when sufficiently distant from the boundary.
Optimizing the production of activated carbon from fast pyrolysis char
Authors: del-Campo B.G. , Morris M.D. , Laird D.A. , Kieffer M.M. , Brown R.C.
Published: June 2015

Fast pyrolysis of red oak wood yields approximately 10–30 wt% biochar, which is considered a low value co-product. Production of high value activated carbon using steam was investigated at different activation conditions. The relationship between activation parameters, surface area and revenue was evaluated using response surface methodology. A second degree model showed a maximum economic benefit at 800°C with 5 minutes of steam activation, resulting in $907 of net revenue per metric ton of biochar.
Seismicity of the central Afar rift and implications for Tendaho dam hazards
Authors: Ayele Atalay , Ebinger Cynthia J. , van Alstyne Carolyn , Keir Derek , Nixon Casey W. , Belachew Manahloh , Hammond James O. S.
Published: June 2015

Temporary broadband seismic networks deployed from 2007 to 2011 around the Afar triple junction of the East African Rift System provide insights into seismicity patterns of the actively deforming crust around the 1.86 km
3
impounded lake system behind the Tendaho dam. The observed seismicity correlates well with the active magmatic centres around central Afar. The area around the dam site is characterized by a network of intersecting NNE- and NW-trending faults. Seismicity clusters observed in the specified time interval indicate that both fault sets are active and are potential sources of seismogenic hazards. The dam neighbourhood is naturally active and it is a challenge to associate the observed seismic activity to either a change in magmato-tectonic conditions or attribute it to the influence of reservoir load. It is evident that the dam region experiences high levels of seismic and volcano-tectonic unrest, regardless of the origin of the activity. The spatial overlap of narrow zones of crustal seismicity and upper mantle low velocity zones observed in S-wave tomography models suggests that melt production zones guide the distribution of strain during continental rupture. Given its volcanically and seismically active setting, the Tendaho dam site and the surrounding region require continuous monitoring for the safety of downstream populations and development infrastructures in the Afar National Regional State of Ethiopia.
Demystifying Casualties of Evictions in Big Data Priority Scheduling
Authors: Rosà Andrea , Chen Lydia Y. , Birke Robert , Binder Walter
Published: June 2015

The ever increasing size and complexity of large-scale datacenters enhance the difficulty of developing efficient scheduling policies for big data systems, where priority scheduling is often employed to guarantee the allocation of system resources to high priority tasks, at the cost of task preemption and resulting resource waste. A large number of related studies focuses on understanding workloads and their performance impact on such systems; nevertheless, existing works pay little attention on evicted tasks, their characteristics, and the resulting impairment on the system performance. In this paper, we base our analysis on Google cluster traces, where tasks can experience three diffierent types of unsuccessful events, namely eviction, kill and fail. We particularly focus on eviction events, i.e., preemption of task execution due to higher priority tasks, and rigorously quantify their performance drawbacks, in terms of wasted machine time and resources, with particular focus on priority. Motivated by the high dependency of eviction on underlying scheduling policies, we also study its statistical patterns and its dependency on other types of unsuccessful events. Moreover, by considering co-executed tasks and system load, we deepen the knowledge on priority scheduling, showing how priority and machine utilization affect the eviction process and related tasks.