bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of Au–silica core–shell particles by sol–gel process
Authors: Kobayashi Y , Inose H , Nakagawa T , Gonda K , Takeda M , Ohuchi N , Kasuya A
Published: March 2012

This paper describes an amine free sol–gel method for silica coating of Au nanoparticles and shows an X-ray image of a colloid solution of the silica coated Au (Au–SiO2) particles. The Au nanoparticles that had a size of 16·9±1·2 nm were prepared through a conventional citrate reduction method. The silica coating was performed with a sol–gel reaction of tetraethylorthosilicate (TEOS) catalysed with NaOH in the presence of Au nanoparticles. The silica shell thickness was varied from 37 to 68 nm for TEOS concentrations of 1×10−3–20×10−3M at 4·3×10−5M of Au, 10·7M of H2O and 1·0×10−3M of NaOH. The optical properties of the Au–SiO2 particle colloid solution were related to the refractive index around the Au particles and the intensity of scattering from silica shells. The as prepared colloid solution could be concentrated up to an Au concentration of 4·3×10−2M with salting out. The concentrated colloid solution showed a high contrast X-ray image.
Electron beam physical vapour deposited zirconia based ceramics for developments of solar surface coatings
Authors: Bhattacharyya D , Targa M , Nicholls J R
Published: March 2012

Infrared radiative properties of thermal barrier coatings have been investigated for developments of solar absorbing surface coatings. Various types of multilayer broadband optical filters were designed incorporating 7 wt-% yttria stabilised zirconia (7YSZ) and aluminium oxide (Al2O3). Electron beam physical vapour deposition method was employed to deposit 7YSZ thin films on quartz substrates to study their optical properties. The refractive index and thickness of 7YSZ films were estimated using spectroscopic ellipsometry technique, giving the index as 1·95 at 633 nm. Multilayer thermal barrier coating structures were fabricated by depositing alternate layers of 7YSZ and Al2O3 on quartz using electron beam physical vapour deposition. The spectral characteristics of multilayer 7YSZ–Al2O3 coatings were evaluated using a spectrometer in the visible and near infrared range. Preliminary results obtained from multilayer 7YSZ–Al2O3 coatings had exhibited 75% transmission over a wide band of 0·4–1·0 μm.
Effects of carbon and nitrogen ion implantations on surface and tribological properties of Ti–Al–Si–N coatings
Authors: Shum P W , Xu Y F , Zhou Z F , Li K Y
Published: March 2012

The post-treatment of ion implantation on hard coatings attracts a great deal of attention because of the improvement in coating surface properties. The present research investigates the effect of nitrogen (N), carbon (C) and carbon followed with nitrogen (C+N) ion implantations on the structural and mechanical properties of the Ti–Al–Si–N coatings. Ion implantations were performed at an energy of 50 keV and different doses. The surface properties of the implanted layer were identified by a variety of analytic techniques, such as cross-sectional transmission electron microscopy, energy dispersive spectroscopy, Raman spectroscopy, X-ray photoelectron spectroscopy and nanoindentation measurement. Additionally, the wear performance of the samples was evaluated by a typical ball on disc tribometer in dry conditions. The results showed that the surface properties depended strongly on the implanted species and doses. In addition, a great improvement in the wear was observed on the samples with the post-treatment process of C and C+N ion implantations.
Effect of duty cycle on residual stress and tribology behaviour of TiCx nanostructure coating deposited by PACVD method
Authors: Shanaghi A , Rouhaghdam A R Sabour , Ahangarani S
Published: March 2012

In this paper, nanostructured TiCx was coated onto H11 hot working steel by pulsed dc plasma assisted chemical vapour deposition method, and various duty cycles were carried out in order to observe the influence of this parameter on residual stress and tribology behaviours. The duty cycles were 33, 40 and 50% at 510°C operating temperature. Therefore, wear behaviour, hardness and chemical analyses of TiCx nanostructure coating were characterised, and it was found that the residual stresses in the coating were compressive, which were −1·1516, −0·1323 and −0·1752 MPa at three different duty cycles, i.e. 33, 40 and 50% respectively. According to the results, the coating that was applied at 40% exhibited superior wear resistance and possessed the lowest friction coefficient of ∼0·06 in a pin-on-disc test against WC–Co.
Improved corrosion protection of aluminium alloy AA 2024 by sol–gel hybrid coatings after surface pretreatment by silanisation
Authors: Basu B J , Srinivasan A , Manasa J , Grips V K W
Published: March 2012

Sol–gel derived organic–inorganic hybrid coatings have been investigated as a potential replacement for the environmentally hazardous chromate conversion coatings for corrosion protection of aerospace aluminium alloy AA 2024. Sol–gel hybrid coatings were prepared using a sol mixture (1∶1 volume ratio) of 3-glycidoxypropyl trimethoxysilane and tetraethoxysilane and doped with cerium nitrate and deposited on AA 2024 by dip coating and spray coating techniques. The effect of surface pretreatment on the corrosion protection efficiency of the sol–gel hybrid coatings was studied. The corrosion resistance of the coatings in 3·5% sodium chloride solution was evaluated by potentiodynamic polarisation measurements, electrochemical impedance spectroscopy and salt spray tests. The results showed that a sol–gel coating system with a simple silanisation as surface pretreatment exhibited improved corrosion protection for AA 2024.
Synthesis and phase transformation of Al–Cu–Fe coatings by various processes
Authors: Ji X , Zhou X Y , Mi Y M , Zhang C M , Zhao X X
Published: March 2012

Despite considerable advances in co-sputtering deposition process optimisation, there is rather limited work reported on the effects of process variables on the final deposit characteristics. This article considers the effects of process parameters on the deposition of Al–Cu–Fe quasi-crystalline coatings on silicon (100) substrates. A magnetron co-sputtering system was used to produce a series of deposits. The process variables of parameters, such as sputtering powers and annealing temperatures and times, are correlated and discussed. Scanning electron microscopy, atomic force microscopy and X-ray diffraction are used to analyse the deposited coatings in terms of elemental composition and structure characteristics in the deposition. Sputtering powers are found to be a vital parameter in determining the surface roughness and the maximum grain width of the coatings. An inverse relation between the annealing temperatures and the phase transformations of the β and i phases is observed.
Wear and corrosion resistance of pack chromised carbon steel
Authors: Fernandes F A P , Heck S C , Picon C A , Totten G E , Casteletti L C
Published: March 2012

Pack chromising treatment is an environmentally friendly alternative to hard chromium to form wear and corrosion resistant surface layers. In this work, samples of AISI 1060 steel were pack chromised for 6 and 9 h at 1000 and 1050°C using different activator concentrations. Wear tests were performed in dry conditions and corrosion tests in natural sea water for the pack chromised samples and hard chromium. Pack chromising yielded the formation of layers with high chromium concentrations, high hardness and wear resistance. Increasing activator concentration causes no significant change on the morphology and thickness of the layers. The layers produced at 1050°C yielded only a (Cr,Fe)2N1−x phase, and those obtained at 1000°C are composed of a carbide mixture with (Cr,Fe)2N1−x. The sample treated at 1050°C for 9 h resulted in an optimum condition by means of better wear resistance and corrosion properties, which were close to that exhibited by the hard chrome, indicating that pack chromising is a promising alternative.
Comparison between tribological behaviour of HVOF coatings produced from conventional Ni+TiC powder mixture and Ni–TiC, Ni–(Ti,W)C composite powders
Authors: Karbasi M , Ghavidel M R Zamanzad , Saidi A , Sabooni S
Published: March 2012

The specification of the powder mixtures used in any thermal spray process has a significant effect on the coating properties. In this research work, Ni–TiC and Ni–(Ti,W)C composite powders, synthesised by self-propagation high temperature synthesis process, were used to prepare coatings by high velocity oxygen fuel (HVOF) method. The coatings were characterised and compared with that produced from conventional Ni+TiC powder mixture. Using the composite powders resulted in homogeneous coatings with no carbide oxidation during the HVOF process, while a significant oxidation of TiC occurred when conventional powders were used. The coatings produced from composite powders also show superior wear resistance over that of conventional powders. Details of the wear mechanism when using different powders as feedstock were explained.
Morphostasis in a novel eukaryote illuminates the evolutionary transition from phagotrophy to phototrophy: description of Rapaza viridis n. gen. et sp. (Euglenozoa, Euglenida)
Authors: Yamaguchi Aika , Yubuki Naoji , Leander Brian S
Published: March 2012

Background

Morphostasis of traits in different species is necessary for reconstructing the evolutionary history of complex characters. Studies that place these species into a molecular phylogenetic context test hypotheses about the transitional stages that link divergent character states. For instance, the transition from a phagotrophic mode of nutrition to a phototrophic lifestyle has occurred several times independently across the tree of eukaryotes; one of these events took place within the Euglenida, a large group of flagellates with diverse modes of nutrition. Phototrophic euglenids form a clade that is nested within lineages of phagotrophic euglenids and that originated through a secondary endosymbiosis with green algae. Although it is clear that phototrophic euglenids evolved from phagotrophic ancestors, the morphological disparity between species representing these different nutritional modes remains substantial.

Results

We cultivated a novel marine euglenid, Rapaza viridis n. gen. et sp. ("green grasper"), and a green alga, Tetraselmis sp., from the same environment. Cells of R. viridis were comprehensively characterized with light microscopy, SEM, TEM, and molecular phylogenetic analysis of small subunit rDNA sequences. Ultrastructural and behavioral observations demonstrated that this isolate habitually consumes a specific strain of Tetraselmis prey cells and possesses a functional chloroplast that is homologous with other phototrophic euglenids. A novel feeding apparatus consisting of a reduced rod of microtubules facilitated this first and only example of mixotrophy among euglenids. R. viridis also possessed a robust photoreception apparatus, two flagella of unequal length, euglenoid movement, and a pellicle consisting of 16 strips and one (square-shaped) whorl of posterior strip reduction. The molecular phylogenetic data demonstrated that R. viridis branches as the nearest sister lineage to phototrophic euglenids.

Conclusions

The unusual combination of features in R. viridis combined with its molecular phylogenetic position completely conforms to the expected transitional stage that occurred during the early evolution of phototrophic euglenids from phagotrophic ancestors. The marine mixotrophic mode of nutrition, the preference for green algal prey cells, the structure of the feeding apparatus, and the organization of the pellicle are outstanding examples of morphostasis that clarify pivotal stages in the evolutionary history of this diverse group of microbial eukaryotes.
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana
Authors: Chen Yi-An , Wen Ying-Chi , Chang Wen-Chi
Published: March 2012

Background

Construction of transcriptional regulatory networks (TRNs) is of priority concern in systems biology. Numerous high-throughput approaches, including microarray and next-generation sequencing, are extensively adopted to examine transcriptional expression patterns on the whole-genome scale; those data are helpful in reconstructing TRNs. Identifying transcription factor binding sites (TFBSs) in a gene promoter is the initial step in elucidating the transcriptional regulation mechanism. Since transcription factors usually co-regulate a common group of genes by forming regulatory modules with similar TFBSs. Therefore, the combinatorial interactions of transcription factors must be modeled to reconstruct the gene regulatory networks.

Description For systems biology applications, this work develops a novel database called Arabidopsis thaliana Promoter Analysis Net (AtPAN), capable of detecting TFBSs and their corresponding transcription factors (TFs) in a promoter or a set of promoters in Arabidopsis. For further analysis, according to the microarray expression data and literature, the co-expressed TFs and their target genes can be retrieved from AtPAN. Additionally, proteins interacting with the co-expressed TFs are also incorporated to reconstruct co-expressed TRNs. Moreover, combinatorial TFs can be detected by the frequency of TFBSs co-occurrence in a group of gene promoters. In addition, TFBSs in the conserved regions between the two input sequences or homologous genes in Arabidopsis and rice are also provided in AtPAN. The output results also suggest conducting wet experiments in the future.

Conclusions

The AtPAN, which has a user-friendly input/output interface and provide graphical view of the TRNs. This novel and creative resource is freely available online at http://AtPAN.itps.ncku.edu.tw/.
Osseointegration and biocompatibility of different metal implants - a comparative experimental investigation in sheep
Authors: Plecko Michael , Sievert Christine , Andermatt Daniel , Frigg Robert , Kronen Peter , Klein Karina , Stübinger Stefan , Nuss Katja , Bürki Alexander , Ferguson Stephen , Stoeckle Ulrich , von Rechenberg Brigitte
Published: March 2012

Background

In the present study, 4 different metallic implant materials, either partly coated or polished, were tested for their osseointegration and biocompatibility in a pelvic implantation model in sheep.

Methods

Materials to be evaluated were: Cobalt-Chrome (CC), Cobalt-Chrome/Titanium coating (CCTC), Cobalt-Chrome/Zirconium/Titanium coating (CCZTC), Pure Titanium Standard (PTST), Steel, TAN Standard (TANST) and TAN new finish (TANNEW). Surgery was performed on 7 sheep, with 18 implants per sheep, for a total of 63 implants. After 8 weeks, the specimens were harvested and evaluated macroscopically, radiologically, biomechanically (removal torque), histomorphometrically and histologically.

Results

Cobalt-Chrome screws showed significantly (p = 0.031) lower removal torque values than pure titanium screws and also a tendency towards lower values compared to the other materials, except for steel. Steel screws showed no significant differences, in comparison to cobalt-chrome and TANST, however also a trend towards lower torque values than the remaining materials. The results of the fluorescence sections agreed with those of the biomechanical test. Histomorphometrically, there were no significant differences of bone area between the groups. The BIC (bone-to-implant-contact), used for the assessment of the osseointegration, was significantly lower for cobalt-chrome, compared to steel (p = 0.001). Steel again showed a lower ratio (p = 0.0001) compared to the other materials.

Conclusion

This study demonstrated that cobalt-chrome and steel show less osseointegration than the other metals and metal-alloys. However, osseointegration of cobalt-chrome was improved by zirconium and/or titanium based coatings (CCTC, TANST, TAN, TANNEW) being similar as pure titanium in their osseointegrative behavior.
MicroRNAs in B cell development and malignancy
Authors: Fernando Thilini R , Rodriguez-Malave Norma I , Rao Dinesh S
Published: March 2012

MicroRNAs are small RNA molecules that regulate gene expression and play critical roles in B cell development and malignancy. miRNA expression is important globally, as B cell specific knockouts of Dicer show profound defects in B cell development; and is also critical at the level of specific miRNAs. In this review, we discuss miRNAs that are involved in normal B cell development in the bone marrow and during B cell activation and terminal differentiation in the periphery. Next, we turn to miRNAs that are dysregulated during diseases of B cells, including malignant diseases and autoimmunity. Further study of miRNAs and their targets will lead to a better understanding of B cell development, and should also lead to the development of novel therapeutic strategies against B cell diseases.
Auto-titrating versus fixed continuous positive airway pressure for the treatment of obstructive sleep apnea: a systematic review with meta-analyses
Authors: Ip Stanley , D'Ambrosio Carolyn , Patel Kamal , Obadan Ndidiamaka , Kitsios Georgios D , Chung Mei , Balk Ethan M
Published: March 2012

Background

Obstructive sleep apnea is a relatively common disorder that can lead to lost productivity and cardiovascular disease. The form of positive airway treatment that should be offered is unclear.

Methods

MEDLINE and the Cochrane Central Trials registry were searched for English language randomized controlled trials comparing auto-titrating positive airway pressure (APAP) with continuous positive airway pressure (CPAP) in adults with obstructive sleep apnea (inception through 9/2010). Six researchers extracted information on study design, potential bias, patient characteristics, interventions and outcomes. Data for each study were extracted by one reviewer and confirmed by another. Random effects model meta-analyses were performed for selected outcomes.

Results

Twenty-four randomized controlled trials met the inclusion criteria. In individual studies, APAP and fixed CPAP resulted in similar changes from baseline in the apnea-hypopnea index, most other sleep study measures and quality of life. By meta-analysis, APAP improved compliance by 11 minutes per night (95% CI, 3 to 19 minutes) and reduced sleepiness as measured by the Epworth Sleepiness Scale by 0.5 points (95% CI, 0.8 to 0.2 point reduction) compared with fixed CPAP. Fixed CPAP improved minimum oxygen saturation by 1.3% more than APAP (95% CI, 0.4 to 2.2%). Studies had relatively short follow-up and generally excluded patients with significant comorbidities. No study reported on objective clinical outcomes.

Conclusions

Statistically significant differences were found but clinical importance is unclear. Because the treatment effects are similar between APAP and CPAP, the therapy of choice may depend on other factors such as patient preference, specific reasons for non-compliance and cost.
The Transparent Dead Leaves Model
Authors: Galerne B. , Gousseau Y.
Published: March 2012

In this paper we introduce the transparent dead leaves (TDL) random field, a new germ-grain model in which the grains are combined according to a transparency principle. Informally, this model may be seen as the superposition of infinitely many semitransparent objects. It is therefore of interest in view of the modeling of natural images. Properties of this new model are established and a simulation algorithm is proposed. The main contribution of the paper is to establish a central limit theorem, showing that, when varying the transparency of the grain from opacity to total transparency, the TDL model ranges from the dead leaves model to a Gaussian random field.
Percolation and Connectivity in AB Random Geometric Graphs
Authors: Iyer Srikanth K. , Yogeshwaran D.
Published: March 2012

Given two independent Poisson point processes Φ(1), Φ(2) in , the AB Poisson Boolean model is the graph with the points of Φ(1) as vertices and with edges between any pair of points for which the intersection of balls of radius 2r centered at these points contains at least one point of Φ(2). This is a generalization of the AB percolation model on discrete lattices. We show the existence of percolation for all d ≥ 2 and derive bounds for a critical intensity. We also provide a characterization for this critical intensity when d = 2. To study the connectivity problem, we consider independent Poisson point processes of intensities n and τn in the unit cube. The AB random geometric graph is defined as above but with balls of radius r. We derive a weak law result for the largest nearest-neighbor distance and almost-sure asymptotic bounds for the connectivity threshold.
An Sir Epidemic Model on a Population with Random Network and Household Structure, and Several Types of Individuals
Authors: Ball Frank , Sirl David
Published: March 2012

We consider a stochastic SIR (susceptible → infective → removed) epidemic model with several types of individuals. Infectious individuals can make infectious contacts on two levels, within their own ‘household’ and with their neighbours in a random graph representing additional social contacts. This random graph is an extension of the well-known configuration model to allow for several types of individuals. We give a strong approximation theorem which leads to a threshold theorem for the epidemic model and a method for calculating the probability of a major outbreak given few initial infectives. A multitype analogue of a theorem of Ball, Sirl and Trapman (2009) heuristically motivates a method for calculating the expected size of such a major outbreak. We also consider vaccination and give some short numerical illustrations of our results.
Limiting Distributions for a Class Of Diminishing Urn Models
Authors: Kuba Markus , Panholzer Alois
Published: March 2012

In this work we analyze a class of 2 × 2 Pólya-Eggenberger urn models with ball replacement matrix and c = pa with . We determine limiting distributions by obtaining a precise recursive description of the moments of the considered random variables, which allows us to deduce asymptotic expansions of the moments. In particular, we obtain limiting distributions for the pills problem a = c = d = 1, originally proposed by Knuth and McCarthy. Furthermore, we also obtain limiting distributions for the well-known sampling without replacement urn, a = d = 1 and c = 0, and generalizations of it to arbitrary and c = 0. Moreover, we obtain a recursive description of the moment sequence for a generalized problem.
Joint Vertex Degrees in the Inhomogeneous Random Graph Model ℊ(n,{pij})
Authors: Lin Kaisheng , Reinert Gesine
Published: March 2012

In a random graph, counts for the number of vertices with given degrees will typically be dependent. We show via a multivariate normal and a Poisson process approximation that, for graphs which have independent edges, with a possibly inhomogeneous distribution, only when the degrees are large can we reasonably approximate the joint counts as independent. The proofs are based on Stein's method and the Stein-Chen method with a new size-biased coupling for such inhomogeneous random graphs, and, hence, bounds on the distributional distance are obtained. Finally, we illustrate that apparent (pseudo-)power-law-type behaviour can arise in such inhomogeneous networks despite not actually following a power-law degree distribution.
The Coupon Collector's Problem Revisited: Asymptotics of the Variance
Authors: Doumas Aristides V. , Papanicolaou Vassilis G.
Published: March 2012

We develop techniques for computing the asymptotics of the first and second moments of the number TN of coupons that a collector has to buy in order to find all N existing different coupons as N → ∞. The probabilities (occurring frequencies) of the coupons can be quite arbitrary. From these asymptotics we obtain the leading behavior of the variance V[TN] of TN (see Theorems 3.1 and 4.4). Then, we combine our results with the general limit theorems of Neal in order to derive the limit distribution of TN (appropriately normalized), which, for a large class of probabilities, turns out to be the standard Gumbel distribution. We also give various illustrative examples.
Extinction Probability of Interacting Branching Collision Processes
Authors: Chen Anyue , Li Junping , Chen Yiqing , Zhou Dingxuan
Published: March 2012

We consider the uniqueness and extinction properties of the interacting branching collision process (IBCP), which consists of two strongly interacting components: an ordinary Markov branching process and a collision branching process. We establish that there is a unique IBCP, and derive necessary and sufficient conditions for it to be nonexplosive that are easily checked. Explicit expressions are obtained for the extinction probabilities for both regular and irregular cases. The associated expected hitting times are also considered. Examples are provided to illustrate our results.
The Distribution of Foschini's Lower Bound for Channel Capacity
Authors: Withers Christopher S. , Nadarajah Saralees
Published: March 2012

Foschini gave a lower bound for the channel capacity of anN-transmitM-receive antenna system in a Raleigh fading environment with independence at both transmitters and receivers. We show that this bound is approximately normal.
Asymptotic Conditional Distribution of Exceedance Counts
Authors: Falk Michael , Tichy Diana
Published: March 2012

We investigate the asymptotic distribution of the number of exceedances amongdidentically distributed but not necessarily independent random variables (RVs) above a sequence of increasing thresholds, conditional on the assumption that there is at least one exceedance. Our results enable the computation of thefragility index, which represents the expected number of exceedances, given that there is at least one exceedance. Computed from the firstdRVs of a strictly stationary sequence, we show that, under appropriate conditions, the reciprocal of the fragility index converges to the extremal index corresponding to the stationary sequence asdincreases.
Twenty Questions with Noise: Bayes Optimal Policies for Entropy Loss
Authors: Jedynak Bruno , Frazier Peter I. , Sznitman Raphael
Published: March 2012

We consider the problem of twenty questions with noisy answers, in which we seek to find a target by repeatedly choosing a set, asking an oracle whether the target lies in this set, and obtaining an answer corrupted by noise. Starting with a prior distribution on the target's location, we seek to minimize the expected entropy of the posterior distribution. We formulate this problem as a dynamic program and show that any policy optimizing the one-step expected reduction in entropy is also optimal over the full horizon. Two such Bayes optimal policies are presented: one generalizes the probabilistic bisection policy due to Horstein and the other asks a deterministic set of questions. We study the structural properties of the latter, and illustrate its use in a computer vision application.
Approximating Multivariate Tempered Stable Processes
Authors: Baeumer Boris , Kovács Mihály
Published: March 2012

We give a simple method to approximate multidimensional exponentially tempered stable processes and show that the approximating process converges in the Skorokhod topology to the tempered process. The approximation is based on the generation of a random angle and a random variable with a lower-dimensional Lévy measure. We then show that if an arbitrarily small normal random variable is added, the marginal densities converge uniformly at an almost linear rate, providing a critical tool to assess the performance of existing particle tracking codes.
A Note on the Dependence Structure of the Two-State Markovian Arrival Process
Authors: Ramírez-Cobo Pepa , Carrizosa Emilio
Published: March 2012

The Markovian arrival process generalizes the Poisson process by allowing for dependent and nonexponential interarrival times. We study the autocorrelation function of the two-state Markovian arrival process. Our findings show that the correlation structure of such a process has a very specific pattern, namely, it always converges geometrically to zero. Moreover, the signs of the autocorrelation coefficients are either constant or alternating.
Separating planar cell polarity and Hippo pathway activities of the protocadherins Fat and Dachsous
Authors: Matakatsu Hitoshi , Blair Seth S.
Published: March 2012

The giant Drosophila protocadherin Fat (Ft) affects planar cell polarity (PCP). Ft also inhibits the overgrowth of imaginal discs via the Hippo pathway, repressing the activity of the transcription co-factor Yorkie (Yki). Much of Ft activity is likely to be mediated by its intracellular domain (Ft ICD). However, the links between the Ft ICD and either PCP or Hippo activity are poorly understood, and the role of the Hippo pathway in PCP is ambiguous. We have performed a structure-function analysis of the Ft ICD. We found that the effects of the Ft ICD on PCP and the Hippo pathway are largely separable. Surprisingly, the domains required for PCP and Hippo activities do not map to any of the previously identified protein interaction domains, nor, with one exception, to the regions that are highly conserved in mammalian Fat4. We also found that the extracellular domain of Ft can act independently of the Ft ICD in PCP and can trigger dominant-negative and boundary effects on Hippo activity, probably via binding to the protocadherin Dachsous.
Adenylyl cyclase AC8 directly controls its micro-environment by recruiting the actin cytoskeleton in a cholesterol-rich milieu
Authors: Ayling Laura J. , Briddon Stephen J. , Halls Michelle L. , Hammond Gerald R. V. , Vaca Luis , Pacheco Jonathan , Hill Stephen J. , Cooper Dermot M. F.
Published: March 2012

The central and pervasive influence of cAMP on cellular functions underscores the value of stringent control of the organization of adenylyl cyclases (ACs) in the plasma membrane. Biochemical data suggest that ACs reside in membrane rafts and could compartmentalize intermediary scaffolding proteins and associated regulatory elements. However, little is known about the organization or regulation of the dynamic behaviour of ACs in a cellular context. The present study examines these issues, using confocal image analysis of various AC8 constructs, combined with fluorescence recovery after photobleaching and fluorescence correlation spectroscopy. These studies reveal that AC8, through its N-terminus, enhances the cortical actin signal at the plasma membrane; an interaction that was confirmed by GST pull-down and immunoprecipitation experiments. AC8 also associates dynamically with lipid rafts; the direct association of AC8 with sterols was confirmed in Förster resonance energy transfer experiments. Disruption of the actin cytoskeleton and lipid rafts indicates that AC8 tracks along the cytoskeleton in a cholesterol-enriched domain, and the cAMP that it produces contributes to sculpting the actin cytoskeleton. Thus, an adenylyl cyclase is shown not just to act as a scaffold, but also to actively orchestrate its own micro-environment, by associating with the cytoskeleton and controlling the association by producing cAMP, to yield a highly organized signalling hub.
Rad9B responds to nucleolar stress through ATR and JNK signalling, and delays the G1–S transition
Authors: Pérez-Castro Antonio Jesús , Freire Raimundo
Published: March 2012

The complex formed by Rad9, Rad1 and Hus1 (9-1-1) protects against genomic instability by activating DNA damage checkpoint and DNA damage repair pathways, mainly in response to replication fork collapse and UV lesions. Here we compare the role of Rad9A (also known as Rad9) with the human paralogue Rad9B. Unlike Rad9A, overexpression of Rad9B delays cells in G1 phase. Moreover, Rad9B migrates to nucleoli after nucleolar stress in an ATR- and JNK-dependent manner, in a newly described nucleolar domain structure containing p21. Analysis of chimeras of Rad9A and Rad9B demonstrate that localisation to nucleoli and the block in G1 phase upon overexpression crucially depend on the Rad9B C-terminal tail. Taken together, data presented here show a relationship between Rad9B and pathways for checkpoints, stress response and nucleolar function.
A short Gfi-1B isoform controls erythroid differentiation by recruiting the LSD1–CoREST complex through the dimethylation of its SNAG domain
Authors: Laurent Benoît , Randrianarison-Huetz Voahangy , Frisan Emilie , Andrieu-Soler Charlotte , Soler Eric , Fontenay Michaela , Dusanter-Fourt Isabelle , Duménil Dominique
Published: March 2012

Gfi-1B is a transcriptional repressor essential for the regulation of erythropoiesis and megakaryopoiesis. Here we identify Gfi-1B p32, a Gfi-1B isoform, as essential for erythroid differentiation. Gfi-1B p32 is generated by alternative splicing and lacks the two first zinc finger domains of the protein. Selective knock down of Gfi-1B p32 compromises erythroid differentiation, whereas its ectopic expression induces erythropoiesis in the absence of erythropoietin. Gfi-1B p32 isoform binds to Gfi-1B target gene promoters and associates with the LSD1–CoREST repressor complex more efficiently than the major Gfi-1B p37 isoform. Furthermore, we show that Gfi-1B includes a KSKK motif in its SNAG domain, which recruits the repressor complex only when dimethylated on lysine 8. Mutation of lysine 8 prevents Gfi-1B p32-induced erythroid development. Our results thus highlight a key role for the alternatively spliced Gfi-1B p32 isoform in erythroid development.
A motif of eleven amino acids is a structural adaptation that facilitates motor capability of eutherian prestin
Authors: Tan Xiaodong , Pecka Jason L. , Tang Jie , Lovas Sándor , Beisel Kirk W. , He David Z. Z.
Published: March 2012

Cochlear outer hair cells (OHCs) alter their length in response to transmembrane voltage changes. This so-called electromotility is the result of conformational changes of membrane-bound prestin. Prestin-based OHC motility is thought to be responsible for cochlear amplification, which contributes to the exquisite frequency selectivity and sensitivity of mammalian hearing. Prestin belongs to an anion transporter family, the solute carrier protein 26A (SLC26A). Prestin is unique in this family in that it functions as a voltage-dependent motor protein manifested by two hallmarks, nonlinear capacitance and motility. Evidence suggests that prestin orthologs from zebrafish and chicken are anion exchangers or transporters with no motor function. We identified a segment of 11 amino acid residues in eutherian prestin that is extremely conserved among eutherian species but highly variable among non-mammalian orthologs and SLC26A paralogs. To determine whether this sequence represents a motif that facilitates motor function in eutherian prestin, we utilized a chimeric approach by swapping corresponding residues from the zebrafish and chicken with those of gerbil. Motility and nonlinear capacitance were measured from chimeric prestin-transfected human embryonic kidney 293 cells using a voltage-clamp technique and photodiode-based displacement measurement system. We observed a gain of motor function with both of the hallmarks in the chimeric prestin without loss of transport function. Our results show, for the first time, that the substitution of a span of 11 amino acid residues confers the electrogenic anion transporters of zebrafish and chicken prestins with motor-like function. Thus, this motif represents the structural adaptation that assists gain of motor function in eutherian prestin.
The endonuclease Ankle1 requires its LEM and GIY-YIG motifs for DNA cleavage in vivo
Authors: Brachner Andreas , Braun Juliane , Ghodgaonkar Medini , Castor Dennis , Zlopasa Livija , Ehrlich Veronika , Jiricny Josef , Gotzmann Josef , Knasmüller Siegfried , Foisner Roland
Published: March 2012

The LEM domain (for lamina-associated polypeptide, emerin, MAN1 domain) defines a group of nuclear proteins that bind chromatin through interaction of the LEM motif with the conserved DNA crosslinking protein, barrier-to-autointegration factor (BAF). Here, we describe a LEM protein annotated in databases as ‘Ankyrin repeat and LEM domain-containing protein 1’ (Ankle1). We show that Ankle1 is conserved in metazoans and contains a unique C-terminal GIY-YIG motif that confers endonuclease activity in vitro and in vivo. In mammals, Ankle1 is predominantly expressed in hematopoietic tissues. Although most characterized LEM proteins are components of the inner nuclear membrane, ectopic Ankle1 shuttles between cytoplasm and nucleus. Ankle1 enriched in the nucleoplasm induces DNA cleavage and DNA damage response. This activity requires both the catalytic C-terminal GIY-YIG domain and the LEM motif, which binds chromatin via BAF. Hence, Ankle1 is an unusual LEM protein with a GIY-YIG-type endonuclease activity in higher eukaryotes.
A Review of Mechanisms of Contrast for Diffuse Optical Imaging of Cancer
Authors: Enfield Louise C. , Gibson Adam P.
Published: March 2012

Diffuse optical imaging and spectroscopy have been extensively used to detect, diagnose and monitor cancer. This paper is a review not of cancer in general, but of the biological changes that occur that can provide contrast for near infrared (NIR) techniques. Cancer is defined by characteristics such as the development of new blood vessels, changes in metabolism and the ability to invade surrounding tissue. The sensitivity of NIR techniques to haemoglobin, water and lipid concentrations, tissue oxygen saturation and cell density means that the pathological changes that occur in malignant tissues can provide contrast between healthy and pathological tissue. Each of these contrast mechanisms are discussed in turn, with a short introduction to the physiological changes that occur, and then a review of the NIR techniques that can be used to investigate these changes and findings from published papers. The role of exogenous contrast agents with NIR techniques in cancer diagnosis and assessment are also discussed. By understanding the characteristics of cancer and the changes that occur, we can interpret our results from NIR with greater confidence and accuracy and develop new techniques that target these characteristics. Information on angiogenesis or hypoxia can be clinically useful, especially when planning treatment (hypoxia) or predicting outcome to chemotherapy (haemoglobin concentration can be used as a measure of vessel density). By understanding the characteristics of cancer and the changes that occur, we can interpret our results from NIR with greater confidence and accuracy and develop new techniques that target these characteristics.
Functional near Infrared Spectroscopy in Psychiatry: A Critical Review
Authors: Ernst Lena H. , Schneider Sabrina , Ehlis Ann-Christine , Fallgatter Andreas J.
Published: March 2012

This review deals with the utilisation of functional near infrared (fNIR) spectroscopy for an in vivo assessment of activation changes in brain tissue, which has broadened the range of non-invasive functional imaging methods within the field of neuroscientific research. Due to its simple and quick applicability as well as the absence of side effects, fNIR spectroscopy is particularly well tolerated by psychiatric patients and can hence markedly contribute to the understanding of the neurobiological basis of psychiatric disorders. The optical, light-based method emits near infrared wavelengths of about 700–1000 nm, which are able to penetrate the scalp and skull, into the head. Because near infrared light is distinctively absorbed by the chromophores oxy-haemoglobin (O2Hb) and deoxy-haemoglobin (HHb), the measured relative amount of reflected NIR light can indicate regional oxygenation patterns in cortical brain tissue with a depth resolution of, on average, 1.5 cm and a spatial resolution of about 2–3 cm. Validity and reliability of fNIR spectroscopy measurements to assess task-related cognitive activation have been repeatedly confirmed among healthy subjects. Beyond that, the application of fNIR spectroscopy to detect altered cortical oxygenation in psychiatric patients during cognitive tasks has been greatly intensified over the last two decades. In this context, hypo-frontality, a decrease in frontal lobe activity that is associated with a number of clinical symptoms and psychiatric disorders, has been demonstrated in a wide range of fNIR spectroscopy studies with psychiatric patients. Despite its variety of beneficial properties, the most apparent disadvantages of NIR spectroscopy compared to other imaging techniques are its limited spatial as well as depth resolution and its restriction to cortical areas. Although multimodal approaches based on simultaneous application of NIR spectroscopy combined with other imaging techniques initially revealed promising results, further technical development and a broadened implementation of combined measurements are necessary in order to uncover distinct brain activity alterations in different psychiatric disorders. In addition to the need for further technical improvement of the method, broad and longitudinal applications of fNIR spectroscopy measurements in psychiatric research are required in order to identify robust diagnostic markers which are required to establish NIR spectroscopy as a valid inter-individual screening instrument in psychiatry.
An ABC of near Infrared Photon Migration in Tissues: The Diffusive Regime of Propagation
Authors: Martelli Fabrizio
Published: March 2012

In this paper, the theories commonly used for the study of photon migration through biological tissues and for biomedical applications are reviewed. The concepts of absorption and scattering are introduced with particular reference to biological tissues and to the near infrared wavelength range. In particular, the basic definitions of optical properties and their statistical meaning, the Beer–Lambert law, the modified Beer–Lambert law, the radiative transfer equation and the diffusion equation are examined and described. The main frame of the theories is provided in the time domain, in the continuous wave domain and in the frequency domain and the principal solutions of the radiative transfer equation and of the diffusion equation are reviewed. The propagation of photons through biological tissue can be accurately described with solutions of the radiative transfer equation, while solutions of the diffusion equation are subjected to intrinsic approximations that limit their range of validity. Whenever the solutions of the diffusion equation provide a sufficiently accurate description of photon migration, we have a diffusive regime of propagation and the media where this happens can be denoted as diffusive as well. A rule to identify the diffusive regime of propagation has been provided. For many biological tissues, the diffusive regime of propagation can be established, even near the source, provided the photons have travelled trajectories with lengths greater than four times the transport mean free path.
Near Infrared Spectroscopy in Optical Coherence Tomography
Authors: Wang Chenyu , Kim Jinman , Jin Craig T. , Leong Philip H.W. , McEwan Alistair
Published: March 2012

Optical coherence tomography (OCT) is a technique that is able to provide cross section views of tissue layers. This fast and non-invasive method is widely used in clinical applications for the diagnosis and treatment of certain diseases. Although conventional OCT is derived from the theory of interferometric imaging, emerging developments, including spectroscopic OCT and related techniques such as dual-band OCT and Raman spectroscopy–OCT, have resulted in significantly improved clinical capabilities for observing the tissue layers through enhanced tissue definition, image resolution, image contrast and scanning speed. This paper reviews the state-of-the-art developments of OCT. It starts with a general introduction of conventional interferometric OCT imaging methods including the time-domain and frequency-domain techniques. The second section explores the advances introduced from spectroscopy techniques in OCT, especially with spectroscopic OCT, dual-band OCT and Raman spectroscopy combined OCT. The final section discusses the current challenges in the application of approaches based on computer-aided diagnosis (CAD) for retinal imaging, for example automated segmentation of tissue layers and tracking disease progression. This task is currently limited by the quality of the recorded data from OCT systems but will be improved by adopting spectroscopic techniques. Finally, we analyse and discuss the improvements that are expected in retinal CAD from the adoption of newly emerging near infrared spectroscopy OCT at multiple wavelengths.
Some Options for Making Non-Invasive Measurements on the Human Body with near Infrared Spectroscopy
Authors: Norris Karl H.
Published: March 2012

The most widely used non-invasive spectroscopic measurements on the human body are related to the oxygen level of the blood, and the pulse oximeter is now used in all hospitals. This device uses wavelengths in the cross-over region between visible and infrared radiation, so it may be classed as a visible light-measuring instrument or as a near infrared (NIR) instrument. Much research has been aimed at possible medical applications of NIR spectroscopy and recent developments are covered by others in this special medical issue. This paper discusses the problems in making spectroscopic measurements on the human body and presents some novel spectra which indicate opportunities for non-invasive assessments on the human body.
Causes of obesity in captive cynomolgus macaques: influence of body condition, social and management factors on behaviour around feeding
Authors: Bauer S A , Pearl D L , Leslie K E , Fournier J , Turner P V
Published: March 2012

Similar to other primate species, captive cynomolgus macaques ( Macaca fascicularis) are prone to becoming overweight. The relationship between body condition and feeding behaviour in group-housed animals has not been reported. This study evaluated the effect of daily feeding routines on behaviour patterns in cynomolgus macaques to determine whether overweight macaques displayed different behaviours and activity levels. In this prospective observational study, 16 macaques ( m = 4, f = 12) from four separate troops ( n = 4 per troop) were selected from a colony of 165 animals. Observational data were collected over six months during morning and afternoon feedings by scan sampling. Behaviours of interest included foraging, eating, aggressive and positive social interactions, inactivity and physical activities. Multivariable mixed logistic regression modelling was used for data analysis. Results indicated that overweight animals were more likely to be inactive, dominant animals had increased probabilities of eating compared with non-dominants, and aggressive behaviours were more likely to occur in the morning and before feeding, suggesting feeding anticipation. Positive social interaction before feeding was seen and may be a strategy used to avoid aggressive encounters around food resources. Individual animal caregivers had an unintentional impact on behaviour, as decreased eating and an increase in inactivity were noted when certain individuals fed animals. These findings illustrate the complexities of feeding group-housed cynomolgus macaques to avoid overweight body condition. Feeding routines may require more care and attention to distribute food in a way that ensures equitable food intake among troop animals, while not disturbing group cohesion.