bluuebunny/crossref_metadata_2025 huggingface dataset:
Analyzing the growth of InxGa1−xN/GaN superlattices in self-induced GaN nanowires by x-ray diffraction
Authors: Wölz M. , Kaganer V. M. , Brandt O. , Geelhaar L. , Riechert H.
Published: June 2011

Self-induced GaN nanowires are grown by plasma-assisted molecular beam epitaxy, with InxGa1−xN quantum wells inserted to form an axial superlattice. From the ω−2θ scans of a laboratory x-ray diffraction experiment, we obtain the superlattice period, the thickness of the quantum wells, and the In content in this layer. The axial growth rate of the InxGa1−xN quantum wells is significantly enhanced, which we attribute to increased Ga diffusion along the nanowire sidewalls in the presence of In.
Site-specific characterization of threonine, serine, and tyrosine glycosylations of amyloid precursor protein/amyloid β-peptides in human cerebrospinal fluid
Authors: Halim Adnan , Brinkmalm Gunnar , Rüetschi Ulla , Westman-Brinkmalm Ann , Portelius Erik , Zetterberg Henrik , Blennow Kaj , Larson Göran , Nilsson Jonas
Published: June 2011

The proteolytic processing of human amyloid precursor protein (APP) into shorter aggregating amyloid β (Aβ)-peptides, e.g., Aβ1-42, is considered a critical step in the pathogenesis of Alzheimer’s disease (AD). Although APP is a well-known membrane glycoprotein carrying both N- and O-glycans, nothing is known about the occurrence of released APP/Aβ glycopeptides in cerebrospinal fluid (CSF). We used the 6E10 antibody and immunopurified Aβ peptides and glycopeptides from CSF samples and then liquid chromatography—tandem mass spectrometry for structural analysis using collision-induced dissociation and electron capture dissociation. In addition to 33 unglycosylated APP/Aβ peptides, we identified 37 APP/Aβ glycopeptides with sialylated core 1 like O-glycans attached to Thr(−39, −21, −20, and −13), in a series of APP/Aβ
X
-15 glycopeptides, where
X
was −63, −57, −52, and −45, in relation to Asp1 of the Aβ sequence. Unexpectedly, we also identified a series of 27 glycopeptides, the Aβ1-
X
series, where
X
was 20 (DAEFRHDSGYEVHHQKLVFF), 19, 18, 17, 16, and 15, which were all uniquely glycosylated on Tyr10. The Tyr10 linked O-glycans were (Neu5Ac)
1-2
Hex(Neu5Ac)HexNAc-
O
- structures with the disialylated terminals occasionally O-acetylated or lactonized, indicating a terminal Neu5Acα2,8Neu5Ac linkage. We could not detect any glycosylation of the Aβ1-38/40/42 isoforms. We observed an increase of up to 2.5 times of Tyr10 glycosylated Aβ peptides in CSF in six AD patients compared to seven non-AD patients. APP/Aβ sialylated O-glycans, including that of a Tyr residue, the first in a mammalian protein, may modulate APP processing, inhibiting the amyloidogenic pathway associated with AD.
Paired-end RAD-seq forde novoassembly and marker design without available reference
Authors: Willing Eva-Maria , Hoffmann Margarete , Klein Juliane D. , Weigel Detlef , Dreyer Christine
Published: June 2011

Motivation: Next-generation sequencing technologies have facilitated the study of organisms on a genome-wide scale. A recent method called restriction site associated DNA sequencing (RAD-seq) allows to sample sequence information at reduced complexity across a target genome using the Illumina platform. Single-end RAD-seq has proven to provide a large number of informative genetic markers in reference as well as non-reference organisms.

Results: Here, we present a method for de novo assembly of paired-end RAD-seq data in order to produce extended contigs flanking a restriction site. We were able to reconstruct one-tenth of the guppy genome represented by 200–500 bp contigs associated to EcoRI recognition sites. In addition, these contigs were used as reference allowing the detection of thousands of new polymorphic markers that are informative for mapping and population genetic studies in the guppy.

Availability: A perl and C++ implementation of the method demonstrated in this article is available under http://guppy.weigelworld.org/weigeldatabases/radMarkers/ as package RApiD.

Contact:  christine.dreyer@tuebingen.mpg.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Vertebrate palaeontology of Australasia into the twenty-first century
Authors: Nguyen Jacqueline M. T. , Molak Martyna , Black Karen H. , Fitzgerald Erich M. G. , Travouillon Kenny J. , Ho Simon Y. W.
Published: June 2011

The 13th Conference on Australasian Vertebrate Evolution Palaeontology and Systematics (CAVEPS) took place in Perth, Western Australia, from 27 to 30 April 2011. This biennial meeting was jointly hosted by Curtin University, the Western Australian Museum, Murdoch University and the University of Western Australia. Researchers from diverse disciplines addressed many aspects of vertebrate evolution, including functional morphology, phylogeny, ecology and extinctions. New additions to the fossil record were reported, especially from hitherto under-represented ages and clades. Yet, application of new techniques in palaeobiological analyses dominated, such as dental microwear and geochronology, and technological advances, including computed tomography and ancient biomolecules. This signals a shift towards increased emphasis in interpreting broader evolutionary patterns and processes. Nonetheless, further field exploration for new fossils and systematic descriptions will continue to shape our understanding of vertebrate evolution in this little-studied, but most unusual, part of the globe.
Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza
Authors: Truscott James , Fraser Christophe , Cauchemez Simon , Meeyai Aronrag , Hinsley Wes , Donnelly Christl A. , Ghani Azra , Ferguson Neil
Published: June 2011

Seasonal influenza has considerable impact around the world, both economically and in mortality among risk groups, but there is considerable uncertainty as to the essential mechanisms and their parametrization. In this paper, we identify a number of characteristic features of influenza incidence time series in temperate regions, including ranges of annual attack rates and outbreak durations. By constraining the output of simple models to match these characteristic features, we investigate the role played by population heterogeneity, multiple strains, cross-immunity and the rate of strain evolution in the generation of incidence time series. Results indicate that an age-structured model with non-random mixing and co-circulating strains are both required to match observed time-series data. Our work gives estimates of the seasonal peak basic reproduction number,
R
0
, in the range 1.6–3. Estimates of
R
0
are strongly correlated with the timescale for waning of immunity to current circulating seasonal influenza strain, which we estimate is between 3 and 8 years. Seasonal variation in transmissibility is largely confined to 15–30% of its mean value. While population heterogeneity and cross-immunity are required mechanisms, the degree of heterogeneity and cross-immunity is not tightly constrained. We discuss our findings in the context of other work fitting to seasonal influenza data.
Interactive Exploration of Protein Cavities
Authors: Krone M. , Falk M. , Rehm S. , Pleiss J. , Ertl T.
Published: June 2011

We present a novel application for the interactive exploration of cavities within proteins in dynamic data sets. Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens up to the environment, making the binding site accessible to the surrounding substrate. Our user‐driven approach enables expert users to select a certain cavity and track its evolution over time. The user is supported by different visualizations of the extracted cavity to facilitate the analysis. The boundary of the protein and its cavities is obtained by means of volume ray casting, where the volume is computed in real‐time for each frame, therefore allowing the examination of time‐dependent data sets. A fast, partial segmentation of the volume is applied to obtain the selected cavity and trace it over time. Domain experts found our method useful when they applied it exemplarily on two trajectories of lipases from Rhizomucor miehei and Candida antarctica. In both data sets cavities near the active center were easily identified and tracked over time until they reached the surface and formed an open substrate channel.
Visual Recommendations for Network Navigation
Authors: Crnovrsanin Tarik , Liao Isaac , Wu Yingcai , Ma Kwan‐Liu
Published: June 2011

Understanding large, complex networks is important for many critical tasks, including decision making, process optimization, and threat detection. Existing network analysis tools often lack intuitive interfaces to support the exploration of large scale data. We present a visual recommendation system to help guide users during navigation of network data. Collaborative filtering, similarity metrics, and relative importance are used to generate recommendations of potentially significant nodes for users to explore. In addition, graph layout and node visibility are adjusted in real‐time to accommodate recommendation display and to reduce visual clutter. Case studies are presented to show how our design can improve network exploration.
Diagnostic specificity of an equine influenza blocking ELISA estimated from New South Wales field data from the Australian epidemic in 2007
Authors: Sergeant ESG , Cowled BD , Bingham P
Published: June 2011

This observational study was undertaken in order to evaluate the diagnostic specificity of the blocking enzyme‐linked immunosorbent assay (bELISA) for serum antibodies to influenza A virus nucleoprotein during the equine influenza (EI) outbreak response in New South Wales, Australia, in 2007. Using data collected during the outbreak response, bELISA testing data were collated for assumed uninfected horses from areas where EI infection was never recorded. Diagnostic specificity of the bELISA used during the EI response was high, but varied significantly between some regions, although the reason(s) for this variation could not be determined.
Overview of the epidemiology of equine influenza in the Australian outbreak
Authors: Moloney BJ
Published: June 2011

This overview of the equine influenza (EI) epidemic as it occurred in two Australian states, New South Wales and Queensland, in 2007 describes the functions and activities of the epidemiology teams that were engaged during the outbreak and also identifies key features of the epidemiology of EI during the outbreak.
Significant features of the epidemiology of equine influenza in New South Wales, Australia, 2007
Authors: Moloney B , Sergeant ESG , Taragel C , Buckley P
Published: June 2011

Equine influenza (EI) was first diagnosed in the Australian horse population on 24 August 2007 at Centennial Park Equestrian Centre (CPEC) in Sydney, New South Wales (NSW), Australia. By then, the virus had already spread to many properties in NSW and southern Queensland. The outbreak in NSW affected approximately 6000 premises populated by approximately 47,000 horses. Analyses undertaken by the epidemiology section, a distinct unit within the planning section of the State Disease Control Headquarters, included the attack risk on affected properties, the level of under‐reporting of affected properties and a risk assessment of the movement of horses out of the Special Restricted Area. We describe the epidemiological features and the lessons learned from the outbreak in NSW.
The August 2007 equine influenza response management framework
Authors: Webster WR
Published: June 2011

This section outlines the most important issues addressed in the management of the response in the two infected states, New South Wales and Queensland. There were differences in the management of the response between the states for logistic, geographic and organisation structural reasons. Issues included the use of control centres, information centres, the problems associated with the lack of trained staff to undertake all the roles, legislative issues, controls of horse movements, the availability of resources for adequate surveillance, the challenges of communication between disparate groups and tracing the movements of both humans and horses.
Industry liaison officers in the infected states of Australia during the 2007 equine influenza outbreak
Authors: Hoare R , Paxton D
Published: June 2011

We describe the activities of persons who were formally employed as industry liaison officers (ILOs) in the infected states of Australia during the 2007 equine influenza outbreak. The knowledge and communication skills of ILOs allowed them to function very effectively, despite most of them having received no prior training. It is arguable, however, that if ILOs had received prior training, they would have performed more effectively sooner. We suggest that more individuals need ILO training in ‘peacetime’ and that ‘just‐in‐time’ training packages require preparation and trial prior to outbreaks to be effective.
Factors associated with high psychological distress in horse industry participants during the 2007 Australian equine influenza outbreak and evidence of recovery after 1 year
Authors: Taylor M , Agho K , Stevens G , Raphael B
Published: June 2011

This short report summarises data on the prevalence of high psychological distress in horse industry participants during the 2007 Australian equine influenza (EI) outbreak and the statistical analysis undertaken to identify the factors associated with this high psychological distress. In addition, follow‐up data collected 1 year later are reported briefly.
Demonstrating freedom from equine influenza in New South Wales, Australia, following the 2007 outbreak
Authors: Sergeant ESG , Wilson G
Published: June 2011

Objective

To quantify the probability of freedom from equine influenza (EI) in New South Wales (NSW), Australia, based on analysis of polymerase chain reaction (PCR) testing.

Methods  Testing in the infected areas of NSW during the period 1 January to 30 April 2008.

Results  Data from the random survey were collated and analysed to provide estimates of the probability of detecting EI if it was present at a prevalence ranging from 0.01% to 0.5%. The sensitivity estimates were then combined with a prior estimate of the probability of freedom in a simulation model, to estimate the posterior probability of freedom from EI (given the negative results of the random survey).

Conclusions  The very large volume of PCR tests performed provided a very high level of confidence that EI had been successfully eradicated from NSW.
Oxygen consumption test to evaluate the diffusive flux into reactive tailings: interpretation and numerical assessment
Authors: Mbonimpa Mamert , Aubertin Michel , Bussière Bruno
Published: June 2011

The oxygen consumption (OC) test is conducted on sulphide tailings by measuring the decline of oxygen concentration in a closed headspace, at the top of a cylinder, as a result of diffusion and oxidation reactions. For a short-duration test, the measurements may be interpreted using a simplified analytical method based on modified Fick’s laws, which provides the combined value of the effective oxygen diffusion (De) and reaction rate (Kr) coefficients of the tailings. This lump value can be used to evaluate the steady-state oxygen flux entering the exposed sulphide tailings. In this paper, a numerical parametric study is performed to investigate the effect of test duration and headspace height, h, on results obtained from OC tests. The assessment also considers tailings with different values of De and Kr. The results indicate that the simplified interpretation method usually tends to underestimate the surface oxygen flux, in proportions that depend on the testing conditions. Results from this study can be used to estimate the relative precision of the oxygen flux for specific conditions, thus helping practitioners decide how to best interpret testing measurements for a given application.
In vitroAntioxidation Activity and Genoprotective Effect of Selected Chinese Medicinal Herbs
Authors: Szeto Yim Tong , Wong Shirley Ching Yee , Wong Julia Wai Ming , Kalle Wouter , Pak Sok Cheon
Published: June 2011

Some traditional Chinese medicinal seeds and fruits are well known for their antioxidant properties. This research aims to investigate whether Fructus Lycii, Fructus Schisandrae Chinensis, Fructus Ligustri Lucidi and Semen Cuscutae protect DNA from oxidant challenge by hydrogen peroxide ( H2O2). The standard comet assay was used to assess the genoprotective effect of these medicinal herbs. Blood was taken from three healthy adults, aged from 36 to 42. Lymphocytes were isolated and treated with different concentrations of aqueous herbal extracts, while controls were treated with phosphate buffered saline. The lymphocytes were stressed with 50 μ M H2O2. Treated cells were embedded in agarose and layered on slides. These sandwiched lymphocytes were lysed and afterwards subjected to an electric field in an alkaline environment. Damaged DNA was pulled out from the nucleus towards the positive electrode as a comet tail; its density was related to the degree of DNA damage. Finally, the slides were stained with fluorescence dye and tails were visually scored for 100 cells. The experiment was repeated three times and DNA damage in treated cells was compared to the controls. There was no statistical difference in DNA damage among the herb treated cells and untreated cells in the comet assay. Our data demonstrated that the selected medicinal herbs did not show in vitro DNA protection in the comet assay against oxidant challenge.
DIRECTED RANDOM WALK ON THE LATTICES OF GENUS TWO
Authors: NAZARENKO A. V.
Published: June 2011

The object of the present investigation is an ensemble of self-avoiding and directed graphs belonging to eight-branching Cayley tree (Bethe lattice) generated by the Fuchsian group of a Riemann surface of genus two and embedded in the Poincaré unit disk. We consider two-parametric lattices and calculate the multifractal scaling exponents for the moments of the graph lengths distribution as functions of these parameters. We show the results of numerical and statistical computations, where the latter are based on a random walk model.
SCHEME FOR GENERATION OF GREENBERGER-HORNE-ZEILINGER STATES OF REMOTE ATOMS TRAPPED IN SEPARATE OPTICAL CAVITIES
Authors: XIONG WEI , YE LIU
Published: June 2011

We propose a scheme for generating maximally entangled states for three atoms trapped in three distant cavities connected by two identical single-mode fibers. During the operation, neither the atomic system nor the fibers are excited, which is important in view of decoherence. Under certain conditions, the probability of the excited cavities can be negligible. Taking advantage of adiabatic passage, the GHZ state can be generated deterministically, and the fidelity of entanglement is insensitive to fluctuation of experimental parameters. Compared to the previous schemes, the significant advantage of the proposed scheme is that each cavity can interact with the other two directly, which can avoid the effect of indirect interaction brought about using only local quantum operator and nonlocal resources.
SCALING PROPERTIES OF MULTIPARTITE ENTANGLEMENT IN PARAMETRIC DOWN-CONVERSION
Authors: PATERA GIUSEPPE , KOLOBOV MIKHAIL I.
Published: June 2011

We quantify and compare the quantum multipartite entanglement generated in two different physical systems involving parametric down-conversion of a multimode pumping field. In particular, we focus our attention on its scaling properties with respect to the number N of modes involved in the processes.
THE QUANTUM CAPACITY BOUNDS OF A LOSSY GAUSSIAN QUANTUM CHANNEL
Authors: CHEN XIAO-YU , JIANG LI-ZHEN
Published: June 2011

Quantum capacity of the lossy Gaussian quantum channel remains an open problem in quantum information theory, although the upper and lower bounds are well-known. We show that for the n-use of the channel, the input of entangled commutative Gaussian state does not improve the lower bound of the capacity. When the total energy is limited, an unfair distribution of the energy among the n-use will improve the lower bound.
Increased adiposity in DNA binding-dependent androgen receptor knockout male mice associated with decreased voluntary activity and not insulin resistance
Authors: Rana Kesha , Fam Barbara C. , Clarke Michele V. , Pang Tammy P. S. , Zajac Jeffrey D. , MacLean Helen E.
Published: June 2011

In men, as testosterone levels decrease, fat mass increases and muscle mass decreases. Increased fat mass in men, in particular central obesity, is a major risk factor for type 2 diabetes, cardiovascular disease, and all-cause mortality. Testosterone treatment has been shown to decrease fat mass and increase fat-free mass. We hypothesize that androgens act directly via the DNA binding-dependent actions of the androgen receptor (AR) to regulate genes controlling fat mass and metabolism. The aim of this study was to determine the effect of a global DNA binding-dependent (DBD) AR knockout (DBD-ARKO) on the metabolic phenotype in male mice by measuring body mass, fat mass, food intake, voluntary physical activity, resting energy expenditure, substrate oxidation rates, serum glucose, insulin, lipid, and hormone levels, and metabolic gene expression levels and second messenger protein levels. DBD-ARKO males have increased adiposity despite a decreased total body mass compared with wild-type (WT) males. DBD-ARKO males showed reduced voluntary activity, decreased food intake, increased serum leptin and adiponectin levels, an altered lipid metabolism gene profile, and increased phosphorylated CREB levels compared with WT males. This study demonstrates that androgens acting via the DNA binding-dependent actions of the AR regulate fat mass and metabolism in males and that the increased adiposity in DBD-ARKO male mice is associated with decreased voluntary activity, hyperleptinemia and hyperadiponectinemia and not with insulin resistance, increased food intake, or decreased resting energy expenditure.
Comment on “Carbon in Trees in Tasmanian State Forest”
Authors: Dean Christopher
Published: June 2011

Moroni et al. (2010) reported extant, spatially representative carbon stocks for Tasmania's State forest. Their disputation of earlier work, contextual setting, redefinition of carbon carrying capacity (CCC), methods, adoption of ecological concepts and consequent conclusions on carbon flux were investigated. Their reported data was very useful; however, the absence of sufficient context and fundamental equations was atypical of scientific publications; old-growth should have been differentiated from mature forests and wet-sclerophyll from mixed-forest, redefinition of CCC was unwarranted, and several of their arguments and conclusions appeared unwarranted. From their graphs and tables, I estimated that the carbon deficit in State forest biomass (the amount below CCC) due to commercial forestry was conservatively 29(±4) Tg (or 106(±13) Mtonnes CO2-eq; with couped-production forests 29(±6)% below CCC) a greenhouse gas mitigation opportunity—indicating the usefulness of the existing definition of CCC. Also, using their data, earlier work on long-term fluxes accompanying conversion of wet-eucalypt forests to harvesting cycles was found to correspond to 0.56(±0.01) Mha (i.e., >1/3 of State forest), 76(±2)% of which is in the commercial production area—in contrast to their claim that earlier work referred to a small and atypical proportion.
Adult Height in Girls with Delayed Pubertal Growth
Authors: Wehkalampi Karoliina , Päkkilä Katarina , Laine Tiina , Dunkel Leo
Published: June 2011

Background/Aims: Boys with constitutional delay of growth and puberty (CDGP) with early reduction in relative height before the onset of puberty will have adult height (AH) clearly below their target height (TH). Characteristics of growth in girls with CDGP are poorly known. We examined whether girls with CDGP attain their TH and whether early reduction in height SDS influences their AH. We also investigated effects of low-dose estrogen on AH. Methods: We investigated growth of 39 women (7 treated with low-dose estrogen) with CDGP history. We compared AH between estrogen-treated and untreated subjects, and used multiple linear regression to investigate the influence of various growth characteristics, e.g. height SDS changes between different ages in childhood, on AH. Results: AH was similar in estrogen-treated and untreated subjects. Reduction of height SDS between 3 and 8 years was significantly associated with the difference between AH and TH (regression coefficient 0.8, 95% confidence interval 0.1–1.5). Overall, 49% of subjects had AH >0.50 SDS below TH. Conclusion: A proportion of CDGP girls do not attain AH consistent with their TH. Reduction in height SDS in childhood predicts smaller AH. Low-dose estrogen treatment does not seem to influence AH in girls with CDGP.
Cross-Shelf and Out-of-Bay Transport Driven by an Open-Ocean Current
Authors: Zhang Yu , Pedlosky Joseph , Flierl Glenn R.
Published: June 2011

This paper studies the interaction of an Antarctic Circumpolar Current (ACC)–like wind-driven channel flow with a continental slope and a flat-bottomed bay-shaped shelf near the channel’s southern boundary. Interaction between the model ACC and the topography in the second layer induces local changes of the potential vorticity (PV) flux, which further causes the formation of a first-layer PV front near the base of the topography. Located between the ACC and the first-layer slope, the newly formed PV front is constantly perturbed by the ACC and in turn forces the first-layer slope with its own variability in an intermittent but persistent way. The volume transport of the slope water across the first-layer slope edge is mostly directly driven by eddies and meanders of the new front, and its magnitude is similar to the maximum Ekman transport in the channel. Near the bay’s opening, the effect of the topographic waves, excited by offshore variability, dominates the cross-isobath exchange and induces a mean clockwise shelf circulation. The waves’ propagation is only toward the west and tends to be blocked by the bay’s western boundary in the narrow-shelf region. The ensuing wave–coast interaction amplifies the wave amplitude and the cross-shelf transport. Because the interaction only occurs near the western boundary, the shelf water in the west of the bay is more readily carried offshore than that in the east and the mean shelf circulation is also intensified along the bay’s western boundary.
Discrimination of grade 2 and 3 cervical intraepithelial neoplasia by means of analysis of water soluble proteins recovered from cervical biopsies
Authors: Uleberg Kai-Erik , Munk Ane Cecilie , Brede Cato , Gudlaugsson Einar , van Diermen Bianca , Skaland Ivar , Malpica Anais , Janssen Emiel AM , Hjelle Anne , Baak Jan PA
Published: June 2011

Background

Cervical intraepithelial neoplasia (CIN) grades 2 and 3 are usually grouped and treated in the same way as "high grade", in spite of their different risk to cancer progression and spontaneous regression rates. CIN2-3 is usually diagnosed in formaldehyde-fixed paraffin embedded (FFPE) punch biopsies. This procedure virtually eliminates the availability of water-soluble proteins which could have diagnostic and prognostic value.

Aim

To investigate whether a water-soluble protein-saving biopsy processing method followed by a proteomic analysis of supernatant samples using LC-MS/MS (LTQ Orbitrap) can be used to distinguish between CIN2 and CIN3.

Methods

Fresh cervical punch biopsies from 20 women were incubated in RPMI1640 medium for 24 hours at 4°C for protein extraction and subsequently subjected to standard FFPE processing. P16 and Ki67-supported histologic consensus review CIN grade (CIN2, n = 10, CIN3, n = 10) was assessed by independent gynecological pathologists. The biopsy supernatants were depleted of 7 high abundance proteins prior to uni-dimensional LC-MS/MS analysis for protein identifications.

Results

The age of the patients ranged from 25-40 years (median 29.7), and mean protein concentration was 0.81 mg/ml (range 0.55 - 1.14). After application of multistep identification criteria, 114 proteins were identified, including proteins like vimentin, actin, transthyretin, apolipoprotein A-1, Heat Shock protein beta 1, vitamin D binding protein and different cytokeratins. The identified proteins are annotated to metabolic processes (36%), signal transduction (27%), cell cycle processes (15%) and trafficking/transport (9%). Using binary logistic regression, Cytokeratin 2 was found to have the strongest independent discriminatory power resulting in 90% overall correct classification.

Conclusions

114 proteins were identified in supernatants from fresh cervical biopsies and many differed between CIN2 and 3. Cytokeratin 2 is the strongest discriminator with 90% overall correct classifications.
Development of a microplate coagulation assay for Factor V in human plasma
Authors: Tilley Derek , Levit Irina , Samis John A
Published: June 2011

Background

Factor V (FV) in its activated form, FVa, is a critical regulator of thrombin generation during fibrin clot formation. There is a need of a simple, fast, and inexpensive microplate-based coagulation assay to measure the functional activity of FV in human plasma. The objective of this study was to develop a microplate-based assay that measures FV coagulation activity during clot formation in human plasma, which is currently not available.

Methods

The FV assay requires a kinetic microplate reader to measure the change in absorbance at 405nm during fibrin formation in human plasma. The FV assay accurately measures the time, initial rate, and extent of fibrin clot formation in human plasma.

Results

The FV microplate assay is simple, fast, economical, sensitive to approx 24-80pM, and multiple samples may be analyzed simultaneously. All the required materials are commercially available. Standard curves of time or initial rate of fibrin clot formation vs FV activity in the 1-stage assay (Without activation by thrombin) may be used to measure FV activity in samples of human plasma. The assay was used to demonstrate that in nine patients with disseminated intravascular coagulation (DIC), the FV 1-stage, 2-stage (With activation by thrombin), and total (2-stage activity - 1-stage activity) activities were decreased, on average, by approximately 54%, 44%, and 42%, respectively, from prolonged clot times when compared to normal pooled human reference plasma (NHP). The results indicate that the FV in the DIC patient plasmas supported both a delayed and slower rate of fibrin clot formation compared with NHP; however, the extent of fibrin clot formation in the DIC patients remained largely unchanged from that observed with NHP.

Conclusions

The FV microplate assay may be easily adapted to measure the activity of any coagulation factor using the appropriate factor-deficient plasma and clot initiating reagent. The microplate assay will find use in both research and clinical laboratories to provide measurement of the functional coagulation activity of FV in human plasma.
Inhibition of cyclophilins alters lipid trafficking and blocks hepatitis C virus secretion
Authors: Anderson Leah J , Lin Kai , Compton Teresa , Wiedmann Brigitte
Published: June 2011

Host cyclophilin (cyp) inhibitors, such as NIM811, efficiently inhibit replication of hepatitis C virus (HCV) and have shown significant promise in recent clinical trials for the treatment of chronic HCV. It is therefore important to fully understand the mechanism of action of these therapeutic agents. Data obtained from comprehensive systems biology approaches have led to the hypothesis that the antiviral activity of cyclophilin inhibitors is mediated through impairing the cellular machinery on which HCV relies to traffic cofactors necessary for formation of the replication complex. Indeed, our results demonstrate when cyclophilins are inhibited by NIM811, lipid and protein trafficking within the VLDL pathway is impaired. Following treatment of replicon or HCV infected cells with NIM811, intracellular lipid droplets (LD) more than double in size and decrease in number. Changes in the LDs in response to cyclophilin inhibition are dependent upon expression of viral proteins. Additionally, in cells treated with NIM811, apoB accumulates in a crescent or ring shaped structure surrounding the enlarged LDs and is no longer secreted. Silencing of cypA or cyp40 using siRNA had a similar effect on LD size and apoB localization as compound treatment, suggesting these cyclophilins may play an important role in lipid and apoB trafficking. Interestingly, the decrease in apoB secretion correlates with a decrease in release of viral particles in HCV infected cells. Altogether, these results add a new level of complexity to the mechanism of action of cyclophilin inhibition, and suggest the role for cyclophilins in the virus life cycle extends beyond replication to virus release.
IFN-γ production by lung NK cells is critical for the natural resistance to pulmonary metastasis of B16 melanoma in mice
Authors: Takeda Kazuyoshi , Nakayama Masafumi , Sakaki Masashi , Hayakawa Yoshihiro , Imawari Michio , Ogasawara Kouetsu , Okumura Ko , Smyth Mark J
Published: June 2011

NK cells are effector lymphocytes playing a critical role in the natural resistance against tumors. However, the precise mechanisms underlying NK cell-mediated natural resistance against tumor metastasis are still unrevealed. B16 cells, mouse melanoma cells, were resistant to freshly isolated NK cell-mediated killing; nevertheless, NK cells were critical for natural resistance against experimental lung metastasis of B16 cells. We found that lung metastasis was increased significantly in IFN-γ–/– mice but not pfp–/–, IFN-αR–/–, or IL-12/IL-18–/– mice. Interestingly, freshly isolated lung NK cells, but not spleen or liver NK cells, displayed augmented IFN-γ production after B16 inoculation. Adoptive transfer of pfp–/– NK cells, but not IFN-γ–/– NK cells, significantly decreased B16 lung metastasis in IFN-γ–/– and pfp/IFN-γ–/–mice. Lung metastases of IFN-γRDN B16 was also increased in NK cell-depleted or IFN-γ–/– mice, suggesting that the IFN-γ response of host cells was required in the NK cell and IFN-γ-mediated antimetastatic effect. Our results demonstrate that IFN-γ production from lung resident NK cells is a key response in the natural resistance to the experimental lung metastasis of NK cell-resistant tumor cells.
Maximal representation dimension of finite p-groups
Authors: Cernele Shane , Kamgarpour Masoud , Reichstein Zinovy
Published: June 2011

The representation dimension rdim(G) of a finite group G is the smallest positive integer m for which there exists an embedding of G in GL
m
(ℂ). In this paper we find the largest value of rdim(G), as G ranges over all groups of order pn
, for a fixed prime p and a fixed exponent n ⩾ 1.
Src kinase activity coordinates cell adhesion and spreading with activation of mammalian target of rapamycin in pancreatic endocrine tumour cells
Authors: Di Florio Alessia , Adesso Laura , Pedrotti Simona , Capurso Gabriele , Pilozzi Emanuela , Corbo Vincenzo , Scarpa Aldo , Geremia Raffaele , Delle Fave Gianfranco , Sette Claudio
Published: June 2011

Pancreatic endocrine tumours (PETs) are rare and heterogeneous neoplasms, often diagnosed at metastatic stage, for which no cure is currently available. Recently, activation of two pathways that support proliferation and invasiveness of cancer cells, the Src family kinase (SFK) and mammalian target of rapamycin (mTOR) pathways, was demonstrated in PETs. Since both pathways represent suitable targets for therapeutic intervention, we investigated their possible interaction in PETs. Western blot and immunofluorescence analyses indicated that SFK and mTOR activity correlate in PET cell lines. We also found that SFKs coordinate cell adhesion and spreading with activation of the mTOR pathway in PET cells. Live cell metabolic labelling and biochemical studies demonstrated that SFK activity enhance mTOR-dependent translation initiation. Furthermore, microarray analysis of the mRNAs associated with polyribosomes revealed that SFKs regulate mTOR-dependent translation of specific transcripts, with an enrichment in mRNAs encoding cell cycle proteins. Importantly, a synergic inhibition of proliferation was observed in PET cells concomitantly treated with SFK and mTOR inhibitors, without activation of the phosphatidylinositol 3-kinase/AKT pro-survival pathway. Tissue microarray analysis revealed activation of Src and mTOR in some PET samples, and identified phosphorylation of 4E-BP1 as an independent marker of poor prognosis in PETs. Thus, our work highlights a novel link between the SFK and mTOR pathways, which regulate the translation of mRNAs for cell cycle regulators, and suggest that crosstalk between these pathways promotes PET cell proliferation.
Thermal insulation performance of aerated lightweight concrete
Authors: Ng Soon-Ching , Low Kaw-Sai , Lim Siong-Kang
Published: June 2011

Building envelopes that insulate buildings against heat and cold are receiving increasing attention as a promising passive energy-efficient measure in building construction. The experimental study reported here evaluates the thermal insulation performance of aerated lightweight concrete of different densities produced by incorporating either 100% sand or 100% soil as filler. Experimental aerated lightweight concrete wall panels (750 mm long, 750 mm wide and 40 mm thick) were cast and tested. Both soil-based and sand-based (control) aerated lightweight concrete panels were cured in a room with a prevailing temperature of approximately 29°C. The temperature gradient for soil-based aerated lightweight concrete panels was found to be superior to that of control aerated lightweight concrete panels of comparable density. The results indicate the potential improvement of soil-based aerated lightweight concrete in terms of thermal insulation compared with sand-based aerated lightweight concrete.
Briefing: Globalisation, innovation and collaboration
Authors: Dryden David
Published: June 2011

Globalisation has revolutionised the methods of conducting business; creating new challenges in effectively operating across multiple cultures and time zones to serve a global customer base on a 24 h basis. This has acted as a catalyst for the development of distributed and dynamic agile working teams; the equivalent of corporate ‘special forces’, that can react immediately to customer demands to deliver specific projects anywhere in the world, and at any time in order to meet the demands of globalisation. The author explains his organisation’s approach to operating in today’s global marketplace.
Evaluation of workplace drug testing the UK civil engineering construction
Authors: Wamuziri Sam
Published: June 2011

The legal position regarding workplace drug testing in the UK is assessed. Workplace drug testing in construction appears to be legally defensible provided the procedures meet certain criteria. The various forms of employment-related drug testing programmes are outlined. These include pre-employment testing, random testing, post-accident testing, and post-treatment testing. Previous research on the influence of workplace drug testing on occupational safety is reviewed. Results of a survey to evaluate the extent to which workplace drug testing has been implemented by UK contractors are analysed. Reasons that have led contractors to introduce workplace drug testing include: to promote the safety of their employees; because drug testing is seen as an effective deterrent; and company concerns about their liability for drug-related incidents. The factors that have influenced the decision for some companies not to implement workplace drug testing include: concerns for increased legal liability and employee opposition to drug testing. There is also the belief that drug testing is an invasion of privacy and that it is not effective in reducing occupational accidents. The effectiveness of workplace drug testing in construction remains debatable.
Life-cycle planning methodology for ancillary highway assets
Authors: Costello Seosamh Benedict , Moss William Frank , Read Christopher John , Grayer Steve
Published: June 2011

Central to the development of highway asset management plans is the creation of life-cycle plans for all highway assets. Understandably, significant effort has been focused to date on the condition and performance of the carriageway and structures stock, given their overall asset value. However, an understanding of current asset condition and future asset performance is lacking in most authorities for their ancillary highway assets, such as road markings or road lighting columns. A number of life-cycle planning tools are available to develop life-cycle plans, both deterministic and stochastic in nature. The challenge in including ancillary highway assets in a stochastic modelling process is the determination of the current condition of the assets, represented by a distribution of condition, and the modelling of deterioration, represented by a transition probability matrix. The methodology outlined in this paper allows for the current condition of the assets to be assessed either visually, through walked surveys or from video survey footage, or using data collection devices, where appropriate. The current condition of the assets is then translated into distributions of condition for onward use in the model. The asset lives were captured using expert engineering opinion and, through some simple assumptions, translated into transition probability matrices. A pilot study was undertaken on a London borough's principal road network, as a proof of concept, and road markings have been used throughout to demonstrate the methodology. In this pilot study, video survey footage was used to assess asset condition. Lessons learned and recommendations are included for other authorities wishing to follow a similar methodology.
The Ants of the Genus Lasius (Hymenoptera, Formicidae) from Late Eocene European Ambers
Authors: Dlussky G.
Published: June 2011

The Ants of the GenusLasius(Hymenoptera, Formicidae) from Late Eocene European Ambers

Finds of the genusLasiusFabricius in the Baltic, Bitterfeldian, Rovno, and Scandinavian Ambers (Late Eocene) are revised. Neotypes ofL. pumilusMayr, 1868 andL. punctulatusMayr, 1868 are designated. A key to workers and gynes ofLasiusspecies from the Late Eocene European ambers is compiled. AllLasiusspecies from these ambers belong to the subgenusLasiuss. str.L. schiefferdeckeriMayr, 1868 is one of most abundant ant species in the Late Eocene European ambers: it consists 15.2-19.5% of all ant specimens in Baltic Amber, 24.5% in Bitterfeldian Amber, 23.8% in Rovno Amber, and 23.6% in Scandinavian Amber of the examined collections. Based on the features of fossilization of this species, it is possible to assume that at least in part it constructed arboreal nests and made roads to aphids' colonies. The list of nine ant species found in syninclusions withL. schiefferdeckeriis provided.
New Species and New Records of Mites of the Genus Pediculaster (Acari, Heterostigmata, Pygmephoridae) from Ukraine
Authors: Khaustov A.
Published: June 2011

New Species and New Records of Mites of the GenusPediculaster(Acari, Heterostigmata, Pygmephoridae) from Ukraine

A new speciesPediculaster dudinskyiKhaustov, sp. n. is described from Transcarpatian region of Ukraine.Pediculaster hungaricusMahunka et Zaki, 1982 andP. rugosusMahunka, 1973 are recorded from Ukraine for the first time.
Training Students to Appraise the Quality of Scientific Literature
Authors: Arlt Sebastian P. , Heuwieser Wolfgang
Published: June 2011

Implementing evidence-based veterinary medicine (EBVM) into clinical practice requires not only the ability to retrieve, interpret, and apply the results of published scientific studies, but also the ability to critically evaluate the quality of the literature. These skills, however, are not widely taught in the veterinary curriculum. The objective of this study was to test a literature evaluation form (LEF) designed to assist veterinary students in appraising the quality of literature on animal reproduction and to compare their ability to do so with that of students who were provided with a control form (CF). The 68 participants were in their fifth year of study and attended a clinical rotation at the Clinic for Animal Reproduction. Students in the LEF group determined the quality of two scientific papers, considering statements about study design, information content, and objectivity, and determined rating points to obtain an overall score. Participants using the CF ranked the quality of the article without the assistance of the quality assessment form. The LEF group was able to more correctly assess the quality of the literature and the variability of the chosen evidence levels was higher in the CF group. The questionnaire was found to be a useful tool for the systematic assessment of the quality of publications within a reasonable period of time. Seventy-eight per cent of the participants agreed that the LEF helps them evaluate the quality and validity of biomedical scientific information. We conclude that courses that introduce EBVM should be taught in the first semesters of the veterinary curriculum so that students can develop competence in defining a clinical problem, retrieving information from the literature, and developing independent critical thinking.
Quantified Surface Improvement Using Temperature Cycle Injection Moulding
Authors: Wlodarski P. G. , Pittman J. F. T. , Sienz J. , Crow K. , Foad R.
Published: June 2011

In temperature cycle injection moulding (TCIM) of thermoplastics, the mould cavity surface is heated rapidly to a temperature close to the glass transition or crystalline melting point of the resin before melt injection, and then cooled after injection is complete. A range of important benefits of the process are listed, among which is surface improvement, and results are presented that quantify in detail the improvements achhieved. Weldline dimensions and surface roughness are determined using white light inteferometry, with a scale of inspection below 5 nm. For a qualitative comparison of the surface finish, photography and stereomicroscopy are used. Weld lines on conventional ABS/PMMA parts are up to 17 μm deep and 70 μm wide, hence clearly visible, whereas they are not detectable on TCIM parts. Surface roughness, Ra, on these parts is found to be 37 nm for conventional parts, reducing to 20 nm using TCIM. Surface roughness is compared for conventional and TCIM mouldings in chemically foamed ABS, foamed PP with and without talc, and long-fibre-glass filled PP. For the conventionally produced foamed parts, Ra is approximately 1500 nm. Using TCIM, Ra reduces to 30 nm for ABS, 70 nm for unfilled PP and 130 nm for PP with talc. Visually, this corresponds to a change from a heavily patterned, striated appearance to a uniform glossy surface. The parts in long-fibre (11 mm) filled PP show a reduction in Ra from 1600 nm to 150 nm using TCIM. The conventionally moulded parts have a rough, pitted surface; the TCIM parts are smooth and glossy.