bluuebunny/crossref_metadata_2025 huggingface dataset:
A daily homogenized temperature data set for Australia
Authors: Trewin Blair
Published: June 2012

A new homogenized daily maximum and minimum temperature data set, the Australian Climate Observations Reference Network—Surface Air Temperature data set, has been developed for Australia. This data set contains data from 112 locations across Australia, and extends from 1910 to the present, with 60 locations having data for the full post‐1910 period.

These data have been comprehensively analysed for inhomogeneities and data errors ensuring a set of station temperature data which are suitable for the analysis of climate variability and trends. For the purposes of merging station series and correcting inhomogeneities, the data set has been developed using a technique, the percentile‐matching (PM) algorithm, which applies differing adjustments to daily data depending on their position in the frequency distribution. This method is intended to produce data sets that are homogeneous for higher‐order statistical properties, such as variance and the frequency of extremes, as well as for mean values. The PM algorithm is evaluated and found to have clear advantages over adjustments based on monthly means, particularly in the homogenization of temperature extremes. Copyright © 2012 Royal Meteorological Society
Determination of amatoxins in different tissues and development stages of Amanita exitialis
Authors: Hu Jinsong , Zhang Ping , Zeng Jun , Chen Zuohong
Published: June 2012

BACKGROUND: Mushroom poisoning is the main cause of human death by food poisoning in China. Most lethal mushrooms belong to the Amanita genus, whose amatoxins are responsible for the death of humans. Amanita exitialis is a lethal white mushroom commonly found in Guangdong Province, China. In this study the contents and distribution of the major amatoxins in different tissues and development stages of A. exitialis were systematically analysed.

RESULTS: The amatoxin contents and distribution in six different mushroom tissues of A. exitialis were analysed by reverse phase high‐performance liquid chromatography. The highest concentrations of amatoxins were found in the gills and pileus, followed by the stipe and annulus, with the lowest concentrations in the volva and spores. Further analysis of mushrooms in different development stages showed that the amatoxin content was relatively high and steady during early development, reached its peak when the fruit body was in the vigorous growth stage and then decreased sharply when the mushroom entered its mature stage. Furthermore, the α‐amanitin/β‐amanitin ratio varied significantly in different tissues but remained constant within a specific tissue throughout development.

CONCLUSION: The contents and distribution of amatoxins in different tissues and development stages of A. exitialis are markedly different. The distribution of α‐amanitin and β‐amanitin varies in different tissues but remains constant throughout development. Copyright © 2012 Society of Chemical Industry
Lycium barbarum polysaccharide inhibits the proliferation of HeLa cells by inducing apoptosis
Authors: Zhu Cai‐Ping , Zhang Sheng‐Hua
Published: June 2012

BACKGROUND: Lycium barbarum polysaccharide (LBP), isolated with boiling water from the famous Chinese medicinal herb Lycium barbarum fruits, is one of the most important functional constituents in Lycium barbarum. In this study the effects of LBP on cell proliferation, cell cycle and apoptosis in human cervical carcinoma cells (HeLa cells) were investigated.

RESULTS: LBP could inhibit the proliferation of HeLa cells by changing cell cycle distribution and inducing apoptosis. In addition, the loss of mitochondrial transmembrane potential (Δψm) was observed by flow cytometry and the increase of intracellular Ca2+ concentration was detected by laser scanning confocal microscope in apoptotic cells. At the same time, the nitric oxide content, nitric oxide synthase and inducible nitric oxide synthase activities were also increased.

CONCLUSION: The inhibitory effect of LBP on the proliferation of HeLa cells was caused by inducing apoptosis through the mitochondrial pathway. The results showed that LBP can be developed as a potential chemotherapeutic agent candidate against human cervical cancer. Copyright © 2012 Society of Chemical Industry
Microalgae as an alternative source of omega‐3 long chain polyunsaturated fatty acids
Authors: Ryckebosch Eline , Bruneel Charlotte , Muylaert Koenraad , Foubert Imogen
Published: June 2012

The health benefits of omega‐3 long chain polyunsaturated fatty acids (omega‐3 LC‐PUFA) are recognized worldwide. The traditional source of omega‐3 LC‐PUFA is fish. However, global consumer needs cannot be supplied by the current global fish harvest. Therefore, new sources of omega‐3 LC‐PUFA have to be found. Microalgae are producers of omega‐3 LC‐PUFA and a potential alternative for seafood. Other sources of omega‐3 LC‐PUFA include krill oil, calamari oil and genetically engineered land plant crops.
Frying oil use in China
Authors: Fan Liuping , Eskin N.A. Michael
Published: June 2012

The rapid development of China's economy has resulted in a dramatic increase in the production and purchase of instant fried food products by consumers. China's food industry has relied largely on the importation of soybean oil and palm oil. Palm oil is widely used by the commercial food industry because of its high oxidative stability and low cost. In contrast, the demand for rapeseed oil and peanut oil has gradually increased but only for domestic frying. In the future, specialized frying oils with improved stability and function will be developed for industrial and domestic frying in China.
Novel Thermally Conductive Thermoplastic/Ceramic Composite Foams
Authors: Chan Ellen , Leung Siu N. , Khan Muhammad O. , Naguib Hani E. , Dawson Francis , Adinkrah Vincent
Published: June 2012

Multifunctional materials that are lightweight and thermally conductive but electrically insulating are important for modern electronics, computer, and telecommunication technologies. Here, a novel foam structure of a polymer/matrix composite filled with ceramic platelets with improved thermal conductivity is reported. Such improvement is caused by the stress‐induced alignment of thermally conductive fillers in the cell wall of the plastic foam. The foam structure is very promising for use as a lightweight electronic packaging material owing to its light weight, thermal conduction ability, electrical insulation, and good processability.

magnified image
Mark Krein's method of directing functionals and singular potentials
Authors: Fulton Charles , Langer Heinz , Luger Annemarie
Published: June 2012

It is shown that M. Krein's method of directing functionals can be used to prove the existence of a scalar spectral measure for certain Sturm–Liouville equations with two singular endpoints. The essential assumption is the existence of a solution of the equation that is square integrable at one singular endpoint and depends analytically on the eigenvalue parameter.
Kinetic Study of 1,5‐Hydrogen Transfer Reactions of Methyl Acrylate and Butyl Acrylate Using Quantum Chemistry
Authors: Yu Xinrui , Broadbelt Linda J.
Published: June 2012

1,5‐Hydrogen transfer reactions in methyl acrylate and butyl acrylate free‐radical polymerization are studied using quantum chemistry and transition state theory to estimate the kinetic parameters (ktr, Ea, and A) with tetrameric radicals, requiring a number of atoms that ranks among the largest polymeric mimics to date. A two‐step transformation accounted for the overall reaction: rotation from an extended conformation to a coiled conformation and abstraction of the fifth hydrogen atom by the end‐chain radical. UB3LYP/6‐31G(d) was used for geometry optimization, validation of the transition states, and calculation of frequencies that were used to obtain thermodynamic properties. The more computationally demanding level of theory, MPWB1K/6‐31G(d,p), was used for calculation of the electronic energy.

magnified image
Nonstationary flow for the Navier–Stokes equations in a cylindrical pipe
Authors: Rencławowicz Joanna , Zajączkowski Wojciech M.
Published: June 2012

In cylindrical domain, we consider the nonstationary flow with prescribed inflow and outflow, modelled with Navier–Stokes equations under the slip boundary conditions. Using smallness of some derivatives of inflow function, external force and initial velocity of the flow, but with no smallness restrictions on the inflow, initial velocity neither force, we prove existence of solutions in . Copyright © 2012 John Wiley & Sons, Ltd.
The Impact of a Nurse‐Led Chronic Musculoskeletal Pain Clinic on Healthcare Utilization
Authors: Ryan S. , Packham J. C. , T Dawes P. , Jordan K. P.
Published: June 2012

Aims and objectives

To determine whether a nurse‐led chronic musculoskeletal pain clinic for fibromyalgia patients can reduce utilization of healthcare services.

Background

People with fibromyalgia often consult multiple specialities due to the vast nature of their symptoms but receive little or no help in managing their symptoms.

Design

A retrospective evaluation of a nurse consultant‐led chronic pain management clinic.

Methods

The frequency of hospital attendances in the five years before and three years after pain clinic attendance was evaluated. General practitioner (GP) attendances in the 12‐month period before and after pain clinic attendance were compared with attendances for two groups of patients from an established GP cohort: (i) patients referred to rheumatology new patient clinics and (ii) all patients with fibromyalgia referred to any hospital new patient clinic.

Results

In the three years following attendance at the pain clinic, the mean number of hospital appointments fell significantly from 2.8 to 1.4 per annum (p < 0.001). The mean reduction seen in hospital clinic attendances in the first year (0.8/annum) improved in the second (1.2/annum) and third (2.1/annum) years. Seventy‐eight per cent of pain clinic patients reduced their visits to their GP in the 12 months following treatment in the pain service, compared with 53% of patients referred to rheumatology clinics and 46% of patients with fibromyalgia.

Conclusion

A nurse‐led chronic pain clinic for fibromyalgia patients can have a positive impact on primary and secondary healthcare utilization.

Relevance to clinical practice

Having a designated nurse‐led pain clinic can enable patients to access the appropriate service at an earlier stage in their condition and receive the support needed to manage the impact of their pain. Copyright © 2012 John Wiley & Sons, Ltd.
A multi‐asperity plastic‐contact crack plane model for geomaterials
Authors: Mihai I. C. , Jefferson A. D.
Published: June 2012

A mechanistic constitutive model for fully formed cracks in geomaterials, such as concrete and rock, is presented. A three‐dimensional characterisation of the crack morphology is employed in which the crack surface is idealised as a series of conical teeth and corresponding recesses of variable height and slope. Based on this geometrical characterisation, an effective contact function is derived to relate the contact stresses that develop on the sides of the teeth to the net stresses on a crack plane. Plastic embedment and frictional sliding are simulated using a local plasticity model in which the plastic surfaces are expressed in terms of the contact surface function in cylindrical relative displacement space. Finally, the performance of the model is assessed against several sets of experimental data from direct shear tests, and it is concluded that the model is able to capture key characteristics of the behaviour of fully formed cracks in geomaterials. Copyright © 2012 John Wiley & Sons, Ltd.
An analytical solution for rainfall infiltration into an unsaturated infinite slope and its application to slope stability analysis
Authors: Zhan Tony L. T. , Jia G. W. , Chen Y.‐M. , Fredlund D. G. , Li H.
Published: June 2012

Surficial slope failures in residual soils are common in tropical and subtropical regions as a result of rainfall infiltration. This study develops an analytical solution for simulating rainfall infiltration into an infinite unsaturated soil slope. The analytical solution is based on the general partial differential equation for water flow through unsaturated soils. It can accept soil–water characteristic curve and unsaturated permeability function of the exponential form into account. Numerical simulations are conducted to verify the assumptions of the analytical solution and demonstrate that the proposed analytical solution is acceptable for the coarse soils with low air entry values. The pore‐water pressure (pwp) distributions obtained from the analytical solution can be incorporated into a limit equilibrium method to do infinite slope stability analysis for a rain‐induced shallow slip. The analysis method takes into account the influence of the water content change on unit weight and hence on factor of safety. A series of analytical parametric analyses have been performed using the developed model. The analyses indicate that when the residual soil slope, consisting of a completely decomposed granite layer underlain by a less permeable layer, is subjected to a continuous heavy rainfall, the loss of negative pwp and the reduction in factor of safety were found to be most significant for the shallow soil layer and during the first 12 h. The antecedent and subsequent rainfall intensity, depth of a less permeable layer and slope angle all have a significant influence on the pwp response and hence the slope stability. Copyright © 2012 John Wiley & Sons, Ltd.
Fetal ovarian cysts: an early manifestation of McCune–Albright syndrome?
Authors: Gaspari Laura , Paris Françoise , Nicolino Marc , Hameury Frédéric , Bonnaure Hélène , Pienkowski Catherine , Servant Nadège , Kalfa Nicolas , Sultan Charles
Published: June 2012

Objective

Beyond the classic triad of peripheral precocious puberty, café‐au‐lait skin pigmentation and polyostotic fibrous dysplasia, partial presentation McCune–Albright syndrome (MAS) has been reported, including the association of isolated recurrent ovarian cysts in early infancy. The aims of this study were to determine whether isolated voluminous fetal unilateral ovarian cysts (diameter > 4 cm) may be associated with a Gsα activating mutation, suggestive of MAS.

Design

We followed five female fetuses presenting with voluminous unilateral ovarian cysts by ultrasonography until delivery. At birth, all patients underwent percutaneous cyst aspiration and two patients later underwent ovariectomy. A sensitive PCR‐based method was used to analyze the Gsα activating mutation in DNA obtained from ovarian cystic fluids or tissue.

Results

Among the five cases, one Gsα mutation (R201C) was identified in the ovarian tissue.

Conclusions

We demonstrate for the first time that voluminous fetal unilateral ovarian cysts may be suggestive of MAS. Systematic search for the Gsα mutation should be performed in all newborns with voluminous fetal unilateral ovarian cysts requiring percutaneous cyst aspiration, because early diagnosis of MAS prevents unnecessary oophorectomy to eliminate questions of malignancy and imposes long‐term clinical, biological, and imaging follow‐up to detect other early manifestations of MAS. © 2012 John Wiley & Sons, Ltd.
Adverse drug reactions to anthroposophic and homeopathic solutions for injection: a systematic evaluation of German pharmacovigilance databases
Authors: Jong Miek C. , Jong Mats U. , Baars Erik W.
Published: June 2012

Purpose

Medicinal solutions for injection are frequently applied in anthroposophic medicine and homeopathy. Despite their extensive use, there is little data published on the safety of these products. Therefore, we investigated the safety of anthroposophic and homeopathic solutions for injection through a systematic evaluation of adverse drug reactions (ADRs).

Methods

ADRs were extracted from the pharmacovigilance databases of eight German manufacturers. Analysed ADRs included case reports in humans only, (spontaneous) case reports from post‐marketing surveillance, literature and clinical/safety trials.

Results

Between 2000 and 2009, in total, 303 million ampoules for injection were sold, and 486 case reports were identified, corresponding to a total number of 1180 ADRs. Of all case reports, 71.8% (349/486) included ADRs that were listed (e.g. stated in package leaflet), and 9.5% (46/486) of the reports were classified as serious. The most frequently reported ADRs were pruritus, followed by angioedema, diarrhoea and erythema. A total of 27.3% (322/1180) were localized reactions for example; application or injection site erythema, pain, swelling and inflammation. The overall reporting rate of ADRs associated with injections was less than 4 per 1 million sold ampoules and classified as very rare.

Conclusions

Our systematic evaluation demonstrated that the reporting rate of ADRs associated with anthroposophic and homeopathic solutions for injection is very low. Most reported ADRs were listed, and one quarter consisted of local reactions. These findings suggest a low risk profile for solutions for injection as therapeutically applied in anthroposophic medicine and homeopathy. Copyright © 2012 John Wiley & Sons, Ltd.
Are two antidepressants always better than one?
Authors: Feetam Celia
Published: June 2012

Up to a third of patients do not respond to their first antidepressant and many remain depressed despite multiple treatments. Combining antidepressants is one strategy recommended for patients who respond inadequately to initial treatment and in this article Celia Feetam discusses the evidence for this approach.
Classifying and treating personality disorders: back to the future?
Authors: Titmarsh Steve
Published: June 2012

Current diagnostic criteria proposals for personality disorder in what will become the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM‐5), due to be published in May 2013, are, to paraphrase Professor Peter Tyrer, misguided. Steve Titmarsh reports on Professor Tyrer's excellent Keynote Lecture at the Latest Advances in Psychiatry Symposium in March on the problems personality disorder presents to psychiatrists and how some of the issues surrounding diagnosis might be resolved by taking a not‐so‐new approach to the problem.
Synthesis and rotation barriers in 2, 6‐Di‐(o‐anisyl) anisole
Authors: Yamamoto Takuhei , Chen Pi‐Yu , Lin Guangxin , Błoch‐Mechkour Anna , Jacobsen Neil E. , Bally Thomas , Glass Richard S.
Published: June 2012

Variable temperature 1H NMR spectroscopic studies of 2, 6‐di(o‐anisyl) anisole show syn and anti atropisomers at low temperature. The barrier for interconverting these isomers by rotation about the aryl‐aryl bond, found by fitting the experimental data, is 41.2 kJ/mol. Copyright © 2012 John Wiley & Sons, Ltd.
Effect of metal doping on highly efficient photovoltaics and switchable photovoltage in bismuth ferrite nanotubes
Authors: Gopal Khan Gobinda , Das Rajasree , Mukherjee Nillohit , Mandal Kalyan
Published: June 2012

We report enhanced anomalous photovoltaic effects and switchable photovoltage generation in pure and Pr–Cr co‐doped BiFeO3 (BFO) nanotubes (NTs). Influence of metal doping on short circuit current, open circuit voltage, power conversion efficiency and fill factor are investigated. The power conversion efficiency of pure BFO NTs (∼0.207%) is found to be enhanced by several orders of magnitude in comparison with the reported bulk effect. Pr‐doped NTs provide highest values of power conversion efficiency (∼0.5%).

magnified image

(© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Testing bioequivalence for multiple formulations with power and sample size calculations
Authors: Zheng Cheng , Wang Jixian , Zhao Lihui
Published: June 2012

Bioequivalence (BE) trials play an important role in drug development for demonstrating the BE between test and reference formulations. The key statistical analysis for BE trials is the use of two one‐sided tests (TOST), which is equivalent to showing that the 90% confidence interval of the relative bioavailability is within a given range. Power and sample size calculations for the comparison between one test formulation and the reference formulation has been intensively investigated, and tables and software are available for practical use. From a statistical and logistical perspective, it might be more efficient to test more than one formulation in a single trial. However, approaches for controlling the overall type I error may be required. We propose a method called multiplicity‐adjusted TOST (MATOST) combining multiple comparison adjustment approaches, such as Hochberg's or Dunnett's method, with TOST. Because power and sample size calculations become more complex and are difficult to solve analytically, efficient simulation‐based procedures for this purpose have been developed and implemented in an R package. Some numerical results for a range of scenarios are presented in the paper. We show that given the same overall type I error and power, a BE crossover trial designed to test multiple formulations simultaneously only requires a small increase in the total sample size compared with a simple 2 × 2 crossover design evaluating only one test formulation. Hence, we conclude that testing multiple formulations in a single study is generally an efficient approach. The R package MATOST is available at https://sites.google.com/site/matostbe/. Copyright © 2012 John Wiley & Sons, Ltd.
Seasonal dependence of WRF model biases and sensitivity to PBL schemes over Europe
Authors: García‐Díez M. , Fernández J. , Fita L. , Yagüe C.
Published: June 2012

The seasonal dependence of Weather Research and Forecasting (WRF) model surface temperature biases and sensitivity to planetary boundary layer (PBL) schemes are jointly explored. For this purpose, the year 2001 was simulated using three different PBL schemes in a domain covering all Europe. The simulations were compared with gridded observations, upper‐air data and high‐frequency station data. Seasonal and daily cycles were analysed, aimed at providing a link between long‐term biases and restricted case studies. The results show that the model mean bias significantly depends on the season, being warm in winter and cold in summer. The winter warm bias is related to misrepresented cold extremes, while a systematic cold bias dominates the whole temperature range in summer. Regarding PBL schemes, an overall underestimation of the entrainment is found, with the non‐local Yonsei University scheme producing systematically warmer temperatures. It is shown that the opposite seasonal biases and systematic behaviour of the PBL schemes during the year lead to a different best‐performing scheme in winter and summer. Moreover, the best‐performing PBL scheme in an average sense is a result of the compensation of errors. The average summer results can be partially explained by a detailed case study. It is concluded that short‐term studies should be used with caution to decide on the parametrizations to be used in long‐term simulations. Copyright © 2012 Royal Meteorological Society
CT‐guided robotic needle biopsy of lung nodules with respiratory motion – experimental system and preliminary test
Authors: Zhou Yu , Thiruvalluvan Kaarvannan , Krzeminski Lukasz , Moore William H. , Xu Zhigang , Liang Zhengrong
Published: June 2012

Background

CT‐guided needle biopsy of lung nodules requires breath holding during needle placement, and is thus inapplicable to patients with difficulty in holding breath.

Methods

A robotic needle biopsy technique is introduced, adapting to the patient respiratory pattern and using a robot manipulator to drive the needle towards a moving lung nodule. Based on the nodule respiratory motion model, needle placement is planned to follow an optimal timing and path, and is triggered based on the respiratory phase tracking. An experimental system has been created to study robotic needle placement.

Results

Preliminary phantom tests were conducted based on three representative clinically‐collected lung nodule motion paths, using an 18‐gauge coaxial needle set. 300 needle paths were implemented. Robotic needle driving was accomplished within 0.4 s (a typical respiratory phase), and resulted in a needle placement accuracy of 0.5 mm with a standard deviation about 0.1 mm over the non‐resistance paths.

Conclusion

The proposed robotic needle placement technique is promising for accurately biopsying lung nodules under respiratory motion and those with very small sizes. Copyright © 2012 John Wiley & Sons, Ltd.
One-loop BPS amplitudes as BPS-state sums
Authors: Angelantonj Carlo , Florakis Ioannis , Pioline Boris
Published: June 2012

Abstract

Recently, we introduced a new procedure for computing a class of one-loop BPS-saturated amplitudes in String Theory, which expresses them as a sum of one-loop contributions of all perturbative BPS states in a manifestly T-duality invariant fashion. In this paper, we extend this procedure toallBPS-saturated amplitudes of the form ∫FΓd+k,dΦ, withΦbeing a weak (almost) holomorphic modular form of weight − k/2. We use the fact that any suchΦcan be expressed as a linear combination of certain absolutely convergent Poincaré series, against which the fundamental domain F can be unfolded. The resulting BPS-state sum neatly exhibits the singularities of the amplitude at points of gauge symmetry enhancement, in a chamber-independent fashion. We illustrate our method with concrete examples of interest in heterotic string compactifications.
Synthetic biology, inspired by synthetic chemistry
Authors: Malinova V. , Nallani M. , Meier W.P. , Sinner E.K.
Published: June 2012

We like to give an overview about the developments in the field of synthetic biology, regarding polymer‐based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell.
The Association Between H3K4me3 and Antisense Transcription
Authors: Cui Peng , Liu Wanfei , Zhao Yuhui , Lin Qiang , Ding Feng , Xin Chengqi , Geng Jianing , Song Shuhui , Sun Fanglin , Hu Songnian , Yu Jun
Published: June 2012

Histone H3 lysine 4 trimethylation (H3K4me3) is well known to occur in the promoter region of genes for transcription activation. However, when investigating the H3K4me3 profiles in the mouse cerebrum and testis, we discovered that H3K4me3 also has a significant enrichment at the 3′ end of actively transcribed (sense) genes, named as 3′-H3K4me3. 3′-H3K4me3 is associated with ∼15% of protein-coding genes in both tissues. In addition, we examined the transcriptional initiation signals including RNA polymerase II (RNAPII) binding sites and 5′-CAGE-tag that marks transcriptional start sites. Interestingly, we found that 3′-H3K4me3 is associated with the initiation of antisense transcription. Furthermore, 3′-H3K4me3 modification levels correlate positively with the antisense expression levels of the associated sense genes, implying that 3′-H3K4me3 is involved in the activation of antisense transcription. Taken together, our findings suggest that H3K4me3 may be involved in the regulation of antisense transcription that initiates from the 3′ end of sense genes. In addition, a positive correlation was also observed between the expression of antisense and the associated sense genes with 3′-H3K4me3 modification. More importantly, we observed the 3′-H3K4me3 enrichment among genes in human, fruitfly and Arabidopsis, and found that the sequences of 3′-H3K4me3-marked regions are highly conserved and essentially indistinguishable from known promoters in vertebrate. Therefore, we speculate that these 3′-H3K4me3-marked regions may serve as potential promoters for antisense transcription and 3′-H3K4me3 appear to be a universal epigenetic feature in eukaryotes. Our results provide a novel insight into the epigenetic roles of H3K4me3 and the regulatory mechanism of antisense transcription.
Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers
Authors: Wajid Bilal , Serpedin Erchin
Published: June 2012

In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.
Spatiotemporal instability of a variable-density Batchelor vortex
Authors: Di Pierro Bastien , Abid Malek
Published: June 2012

Linear and nonlinear impulse responses are computed, using three-dimensional numerical simulations, for an incompressible and variable density (inhomogeneous) Batchelor vortex at a moderately high Reynolds number, $\mathit{Re}= 667$. In the linear framework, the computed wavepacket is decomposed into azimuthal modes whose growth rates are determined along each spatiotemporal ray, in the laboratory frame. It is found that the Batchelor vortex undergoes a convective/absolute transition when the density ratio (inner/ambient), $s$, is varied solely (there is no need for an external counter flow to trigger this transition like that needed in the constant density case). More precisely, it is shown that the transition occurs for heavy vortices when the density ratio reaches a critical value, ${s}_{c} \simeq 1. 08$. For light vortices ($s\lt 1$) no transition was found. It is also shown that the first azimuthal mode that transits have an azimuthal wavenumber $m= \ensuremath{-} 2$ and the transition occurs for a swirl number (a measure of the azimuthal to axial velocity ratio), $q= 0. 57$. It is followed by $m= \ensuremath{-} 1$, then by $m= \ensuremath{-} 3$. When nonlinearities are allowed, it is found that they saturate the amplitude within the linear-response wavepacket, leaving the wavepacket fronts unaffected. The conclusions should thus be the same as those obtained in the linear case: the linear convective/absolute transition should coincide with the nonlinear one for the variable-density Batchelor vortex.
Aeroacoustic power generated by a compact axisymmetric cavity: prediction of self-sustained oscillation and influence of the depth
Authors: Nakı̇boğlu G. , Manders H. B. M. , Hirschberg A.
Published: June 2012

Aeroacoustic power generation due to a self-sustained oscillation by an axisymmetric compact cavity exposed to a low-Mach-number grazing flow is studied both experimentally and numerically. The feedback effect is produced by the velocity fluctuations resulting from a coupling with acoustic standing waves in a coaxial pipe. A numerical methodology that combines incompressible flow simulations with vortex sound theory is used to predict the time-averaged acoustic source power generated by the cavity. The effect of cavity depth on the whistling is addressed. It is observed that the whistling occurs around a peak-whistling Strouhal number which depends on the cavity depth to width ratio. The proposed numerical method provides excellent predictions of the peak-whistling Strouhal number as a function of cavity depth. Given the oscillation amplitude, the numerical method predicts the time-averaged acoustic source power within a factor of two for moderate fluctuation amplitudes. For deep cavities the time-averaged acoustic source power appears to be independent of the cavity depth.
Boundary layer structure in turbulent Rayleigh–Bénard convection
Authors: Shi Nan , Emran Mohammad S. , Schumacher Jörg
Published: June 2012

The structure of the boundary layers in turbulent Rayleigh–Bénard convection is studied by means of three-dimensional direct numerical simulations. We consider convection in a cylindrical cell at aspect ratio one for Rayleigh numbers of $\mathit{Ra}= 3\ensuremath{\times} 1{0}^{9} $ and $3\ensuremath{\times} 1{0}^{10} $ at fixed Prandtl number $\mathit{Pr}= 0. 7$. Similar to the experimental results in the same setup and for the same Prandtl number, the structure of the laminar boundary layers of the velocity and temperature fields is found to deviate from the prediction of Prandtl–Blasius–Pohlhausen theory. Deviations decrease when a dynamical rescaling of the data with an instantaneously defined boundary layer thickness is performed and the analysis plane is aligned with the instantaneous direction of the large-scale circulation in the closed cell. Our numerical results demonstrate that important assumptions of existing classical laminar boundary layer theories for forced and natural convection are violated, such as the strict two-dimensionality of the dynamics or the steadiness of the fluid motion. The boundary layer dynamics consists of two essential local dynamical building blocks, a plume detachment and a post-plume phase. The former is associated with larger variations of the instantaneous thickness of velocity and temperature boundary layer and a fully three-dimensional local flow. The post-plume dynamics is connected with the large-scale circulation in the cell that penetrates the boundary region from above. The mean turbulence profiles taken in localized sections of the boundary layer for each dynamical phase are also compared with solutions of perturbation expansions of the boundary layer equations of forced or natural convection towards mixed convection. Our analysis of both boundary layers shows that the near-wall dynamics combines elements of forced Blasius-type and natural convection.
Transverse instability and low-frequency flapping in incompressible separated boundary layer flows: an experimental study
Authors: Passaggia Pierre-Yves , Leweke Thomas , Ehrenstein Uwe
Published: June 2012

The unstable dynamics of a transitional laminar separation bubble behind a two-dimensional bump geometry is investigated experimentally using dye visualizations and particle image velocimetry measurements. For Reynolds numbers above a critical value, the initially two-dimensional recirculation bubble is subject to modulations in the spanwise direction which can trigger vortex shedding. Increasing the Reynolds number further, the unstable behaviour is dominated by a low-frequency flapping motion, well known in transonic flows, and here investigated for the first time experimentally in an incompressible flow regime. These phenomena are characterized by non-intrusive measurements of the spatial structure and the frequencies of the unsteady motion. The results are in excellent agreement with previous numerical and theoretical predictions for the same geometry.
Computationally efficient methods for modelling laser wakefield acceleration in the blowout regime
Authors: COWAN B. M. , KALMYKOV S. Y. , BECK A. , DAVOINE X. , BUNKERS K. , LIFSCHITZ A. F. , LEFEBVRE E. , BRUHWILER D. L. , SHADWICK B. A. , UMSTADTER D. P.
Published: June 2012

Electron self-injection and acceleration until dephasing in the blowout regime is studied for a set of initial conditions typical of recent experiments with 100-terawatt-class lasers. Two different approaches to computationally efficient, fully explicit, 3D particle-in-cell modelling are examined. First, the Cartesian code vorpal (Nieter, C. and Cary, J. R. 2004 VORPAL: a versatile plasma simulation code. J. Comput. Phys.196, 538) using a perfect-dispersion electromagnetic solver precisely describes the laser pulse and bubble dynamics, taking advantage of coarser resolution in the propagation direction, with a proportionally larger time step. Using third-order splines for macroparticles helps suppress the sampling noise while keeping the usage of computational resources modest. The second way to reduce the simulation load is using reduced-geometry codes. In our case, the quasi-cylindrical code calder-circ (Lifschitz, A. F. et al. 2009 Particle-in-cell modelling of laser-plasma interaction using Fourier decomposition. J. Comput. Phys.228(5), 1803–1814) uses decomposition of fields and currents into a set of poloidal modes, while the macroparticles move in the Cartesian 3D space. Cylindrical symmetry of the interaction allows using just two modes, reducing the computational load to roughly that of a planar Cartesian simulation while preserving the 3D nature of the interaction. This significant economy of resources allows using fine resolution in the direction of propagation and a small time step, making numerical dispersion vanishingly small, together with a large number of particles per cell, enabling good particle statistics. Quantitative agreement of two simulations indicates that these are free of numerical artefacts. Both approaches thus retrieve the physically correct evolution of the plasma bubble, recovering the intrinsic connection of electron self-injection to the nonlinear optical evolution of the driver.
The current state of play on the molecular genetics of depression
Authors: Cohen-Woods S. , Craig I. W. , McGuffin P.
Published: June 2012

Background

It has been well established that both genes and non-shared environment contribute substantially to the underlying aetiology of major depressive disorder (MDD). A comprehensive overview of genetic research in MDD is presented.

Method

Papers were retrieved from PubMed up to December 2011, using many keywords including: depression, major depressive disorder, genetics, rare variants, gene–environment, whole genome, epigenetics, and specific candidate genes and variants. These were combined in a variety of permutations.

Results

Linkage studies have yielded some promising chromosomal regions in MDD. However, there is a continued lack of consistency in association studies, in both candidate gene and genome-wide association studies (GWAS). Numerous factors may account for variable results including the use of different diagnostic approaches, small samples in early studies, population stratification, epigenetic phenomena, copy number variation (CNV), rare variation, and phenotypic and allelic heterogeneity. The conflicting results are also probably, in part, a consequence of environmental factors not being considered or controlled for.

Conclusions

Each research group has to identify what issues their sample may best address. We suggest that, where possible, more emphasis should be placed on the environment in molecular behavioural genetics to identify individuals at environmental high risk in addition to genetic high risk. Sequencing should be used to identify rare and alternative variation that may act as a risk factor, and a systems biology approach including gene–gene interactions and pathway analyses would be advantageous. GWAS may require even larger samples with reliably defined (sub)phenotypes.
The association between social stress and global cognitive function in a population-based study: the European Prospective Investigation into Cancer (EPIC)-Norfolk study
Authors: Leng Y. , Wainwright N. W. J. , Hayat S. , Stephan B. C. M. , Matthews F. E. , Luben R. , Surtees P. G. , Khaw K.-T. , Brayne C.
Published: June 2012

Background

Stress is thought to exert both positive and negative effects on cognition, but the precise cognitive effects of social stress and individuals' response to stress remain unclear. We aimed to investigate the association between different measures of social stress and cognitive function in a middle- to older-aged population using data from the European Prospective Investigation into Cancer (EPIC)-Norfolk study.

Method

Participants completed a comprehensive assessment of lifetime social adversity between 1993 and 1997 and the short form of the Mini Mental State Examination (SF-MMSE), an assessment of global cognitive function, during the third health check between 2004 and 2011 (a median of 10.5 years later). A low MMSE score was defined as a score in the bottom quartile (20–26).

Results

Completed MMSE scores and stress measures were available for 5129 participants aged 48–90 years. Participants who reported that their lives had been more stressful over the previous 10 years were significantly more likely to have low MMSE scores [odds ratio (OR) 1.14, 95% confidence interval (CI) 1.04–1.24 per unit increase in perceived stress], independently of sociodemographic factors, physical and emotional health. The effects were restricted to the highest level of stress and the association was stronger among participants with a lower educational level. Adaptation following life event experiences also seemed to be associated with MMSE scores after adjusting for sociodemographic factors, but the association was attenuated with further adjustment.

Conclusions

In this generally high-functioning population, individuals' interpretations and responses to stressful events, rather than the events themselves, were associated with cognitive function.
Pausanias and the temple of Hera at Olympia
Authors: Arafat K. W.
Published: June 2012

This article considers the contents of the temple of Hera at Olympia in the light of Pausanias' account and of excavation reports. Of all the temples Pausanias describes, the Heraion is the most crowded, and it is argued that by his day it was acting as a storeroom, primarily for objects from nearby buildings. The implications are assessed for the history of the attribution of the Heraion, and for the use of temples in Pausanias' day.
Fungal spore concentrations in two haematopoietic stem cell transplantation (HSCT) units containing distinct air control systems
Authors: BRUN C. P. , MIRON D. , SILLA L. M. R. , PASQUALOTTO A. C.
Published: June 2012

Invasive fungal diseases have emerged as important causes of morbidity and mortality in haematological patients. In this study air samples were collected in two haematopoietic stem cell transplantation (HSCT) units, in which distinct air-control systems were in place. In hospital 1 no high-efficiency particulate air (HEPA) filter was available whereas in hospital 2 HSCT rooms were equipped with HEPA filters, with positive air pressure in relation to the corridor. A total of 117 samples from rooms, toilets and corridors were obtained during December 2009 to January 2011, using a six-stage Andersen sampler. In both hospitals, the concentration of potentially pathogenic fungi in the air was reduced in patients' rooms compared to corridors (P < 0·0001). Despite the presence of a HEPA filter in hospital 2, rooms in both hospitals showed similar concentrations of potentially pathogenic fungi (P = 0·714). These findings may be explained by the implementation of additional protective measures in hospital 1, emphasizing the importance of such measures in protected environments.
SO THAT THE BABY NOT BE FORMED LIKE A POTTERY RATTLE: AZTEC RATTLE FIGURINES AND HOUSEHOLD SOCIAL REPRODUCTIVE PRACTICES
Authors: Overholtzer Lisa
Published: June 2012

This paper examines the materiality—or the mutually constitutive relationships between people and things—of Aztec rattle figurines in order to shed light on household ritual life in Postclassic central Mexico. By examining iconographic, archaeological, and ethnohistoric evidence, I argue that these figurines were actively used in household healing rituals concerning successful biological and social reproduction, comprised of the work, relationships, and attitudes that perpetuate human life. I then consider the physical experience of that ritual use by exploring the visual, tactile, auditory, and physiological aspects of these figurines. I contend that their visibility in workshops, markets, and the home presented an image of the female body that reinforced women's important roles in the production and reproduction of the household and society. Finally, the material qualities of these figurines reveal ancient discourses on the human body and experimentation with bodily representation in terms of scale, form, and material.
GREAT DEVELOPMENT IN TROUBLED TIMES: THE TERMINAL CLASSIC AT THE MAYA SITE OF NAKUM, PETEN, GUATEMALA
Authors: Źrałka Jarosław , Hermes Bernard
Published: June 2012

Recent investigations carried out at the Maya site of Nakum, located in the northeastern part of Guatemala, revealed traces of very intense Terminal Classic period occupation and architectural construction and renovation. Archaeological excavations in the site's core and its periphery indicate that the apogee of Nakum's cultural prosperity and demographic increase occurred during the Terminal Classic period when many new structures were constructed and almost all old constructions were rebuilt. The growth and prosperity of Terminal Classic Nakum stands in stark contrast to the prevailing pattern of collapse and abandonment seen at many other lowland Maya sites during this turbulent period. Archaeological and epigraphic data suggest that Nakum survived the collapse of other major cities such as Tikal or Naranjo by at least a century. Nakum's success can be attributed to its role as a fluvial port that controlled commercial activities within this region. Its advantageous location on the banks of the Holmul River, combined with weakened competition from formerly more powerful neighbors such as Tikal and Naranjo, apparently permitted Nakum's ruling elite to actively expand its trade relationships in spite of the broad economic and political crisis that profoundly affected the Southern Maya Lowlands. However, its success was relatively brief, for by the end of the Terminal Classic (ca.a.d.950) Nakum apparently succumbed to the same forces that had caused the collapse and abandonment of most Southern Maya Lowland cities.
FINDING A BALANCE
Authors: Spence Michael W.
Published: June 2012

The invitation to do this autobiographical article reached me on my seventieth birthday, catching me in an unusually reflective mood, so I decided to take a stab at it. If nothing else, I could honor my mentors, especially James Anderson and René Millon. Without them I might still be doing archaeology but it would be a very different sort of archaeology, probably not as good and certainly not as much fun. But I don't find this kind of writing easy. Social scientists are not used to having “I” as the main subject of a sentence, an analogy perhaps to the difficulty we have in maintaining a balance between our professional and personal lives. However, I seem to have overcome that academic modesty, as this paragraph demonstrates. So here we go.
Towards a New History of European Law
Authors: DAVIES BILL , RASMUSSEN MORTEN
Published: June 2012

This article introduces the special issue on the new history of European law. Its intention is to provide our audience with the intellectual context that the contributions seek to address and some of the underlying conclusions from the fields of political science and legal scholarship that the archive material synthesised here will recast. Each of the individual contributions will be described and located in the new field of scholarship, and the intentions and current limitations of our findings will be delineated.
Negotiating the Foundations of European Law, 1950–57: The Legal History of the Treaties of Paris and Rome
Authors: BOERGER-DE SMEDT ANNE
Published: June 2012

This article analyses how the seeds for the development of European law from the 1960s onwards were sown in the foundational treaties. It argues that despite the fact that both European treaties embodied a conscious choice by the majority of the governments not to establish the European Communities on a constitutional basis, a small number of politicians and jurists managed nonetheless to insert the potential for the constitutional practice. Following a chronological account of each set of negotiations, the article untangles the complex ideas and decisions, which crafted both the legal shape of the treaties and the jurisdiction of the new European Court of Justice.