Cross-linking of collagen I by tissue transglutaminase provides a promising biomaterial for promoting bone healing

Transglutaminases (TGs) stabilize proteins by the formation of ε(γ-glutamyl)lysine cross-links. Here, we demonstrate that the cross-linking of collagen I (COL I) by tissue transglutaminase (TG2) causes an alteration in the morphology and rheological properties of the collagen fibers. Human osteoblasts (HOB) attach, spread, proliferate, differentiate and mineralize more rapidly on this cross-linked matrix compared to native collagen. When seeded on cross-linked COL I, HOB are more resistant to the loss of cell spreading by incubation with RGD containing peptides and with α1, α2 and β1 integrin blocking antibodies. Following adhesion on cross-linked collagen, HOB show increased phosphorylation of the focal adhesion kinase, and increased expression of β1 and β3 integrins. Addition of human bone morphogenetic protein to HOB seeded on TG2 cross-linked COL I enhanced the expression of the differentiation marker bone alkaline phosphatase when compared to cross-linked collagen alone. In summary, the use of TG2-modified COL I provides a promising new scaffold for promoting bone healing. © 2014 Springer-Verlag.

Price discovery for Chinese shares cross-listed in multiple markets

In this article we study the relationship between security returns cross-listed on the A share market of China and the H share market at the Stock Exchange of Hong Kong (SEHK). Most of these securities are also cross-listed on other markets. An important feature of this article is that we focus on the multilateral relationships between all cross-listed markets rather than concentrating only on the bi-lateral relationship between A and Hong Kong H shares. Using the impulse response functions and the variance decompositions from a Vector Autoregressive (VAR) process we show that the returns to the A share market are almost exclusively determined by domestic factors. In contrast, we find that the H share market is influenced by both the A share market within China and foreign stock markets elsewhere in the world. Impulse response functions suggest that innovations to the A share market and the Hong Kong H share market are partly transmitted to each other and to stock markets outside China. We show that liquidity has an important role to play in determining the impact that the home market has on cross-listed variance decompositions. © 2012 Copyright Taylor and Francis Group, LLC.

Achievable performance gain of IEEE 802.11 multi-rate link adaptation algorithm with cross-layer design

Link quality-based rate adaptation has been widely used for IEEE 802.11 networks. However, network performance is affected by both link quality and random channel access. Selection of transmit modes for optimal link throughput can cause medium access control (MAC) throughput loss. In this paper, we investigate this issue and propose a generalised cross-layer rate adaptation algorithm. It considers jointly link quality and channel access to optimise network throughput. The objective is to examine the potential benefits by cross-layer design. An efficient analytic model is proposed to evaluate rate adaptation algorithms under dynamic channel and multi-user access environments. The proposed algorithm is compared to link throughput optimisation-based algorithm. It is found rate adaptation by optimising link layer throughput can result in large performance loss, which cannot be compensated by the means of optimising MAC access mechanism alone. Results show cross-layer design can achieve consistent and considerable performance gains of up to 20%. It deserves to be exploited in practical design for IEEE 802.11 networks.

Representing spray zone with cross flow as a well-mixed compartment in a high shear granulator

The spray zone is an important region to control nucleation of granules in a high shear granulator. In this study, a spray zone with cross flow is quantified as a well-mixed compartment in a high shear granulator. Granulation kinetics is quantitatively derived at both particle-scale and spray zone-scale. Two spatial decay rates, DGSDR (droplet-granule spatial decay rate) ζDG and DPSDR (droplet-primary particle spatial decay rate) ζDP, which are functions of volume fraction and diameter of particulate species within the powder bed, are defined to simplify the deduction. It is concluded that in cross flow, explicit analytical results show that the droplet concentration is subject to exponential decay with depth which produces a numerically infinite depth of spray zone in a real penetration process. In a well-mixed spray zone, the depth of the spray zone is 4/(ζDG + ζDP) and π2/3(ζDG + ζDP) in cuboid and cylinder shape, respectively. The first-order droplet-based collision rates of, nucleation rate B0 and rewetting rate RW0 are uncorrelated with the flow pattern and shape of the spray zone. The second-order droplet-based collision rate, nucleated granule-granule collision rate RGG, is correlated with the mixing pattern. Finally, a real formulation case of a high shear granulation process is used to estimate the size of the spray zone. The results show that the spray zone is a thin layer at the powder bed surface. We present, for the first time, the spray zone as a well-mixed compartment. The granulation kinetics of a well-mixed spray zone could be integrated into a Population Balance Model (PBM), particularly to aid development of a distributed model for product quality prediction.

Costs and benefits of orthographic inconsistency in reading:evidence from a cross-linguistic comparison

We compared reading acquisition in English and Italian children up to late primary school analyzing RTs and errors as a function of various psycholinguistic variables and changes due to experience. Our results show that reading becomes progressively more reliant on larger processing units with age, but that this is modulated by consistency of the language. In English, an inconsistent orthography, reliance on larger units occurs earlier on and it is demonstrated by faster RTs, a stronger effect of lexical variables and lack of length effect (by fifth grade). However, not all English children are able to master this mode of processing yielding larger inter-individual variability. In Italian, a consistent orthography, reliance on larger units occurs later and it is less pronounced. This is demonstrated by larger length effects which remain significant even in older children and by larger effects of a global factor (related to speed of orthographic decoding) explaining changes of performance across ages. Our results show the importance of considering not only overall performance, but inter-individual variability and variability between conditions when interpreting cross-linguistic differences.

Periphyton responses to eutrophication in the Florida Everglades: Cross-system patterns of structural and compositional change

We examined periphyton along transects in five Everglades marshes and related compositional and functional aspects to phosphorus(P ) gradients caused by enriched inflows. Results were compared to those of a P-addition experiment in a pristine Everglades marsh. While the water total P (TP) concentration was not related to P load in the marshes or experiment the concentration of TP in periphyton was strongly correlated with the distance from the P source. Increased P concentration in periphyton was associated with a loss of biomass,p articularly of the calcifying mat-forming matrix, regardless of the growth form of the periphyton (epiphytic, floating,or epilithic). Diatom species composition was also strongly related to P availability, but the TP optima of many species varied among marshes. Enriched periphyton communities were found 14 km downstream of P inputs to one marsh that has been receiving enhanced P loads for decades, where other studies using different biotic indicators show negligible change in the same marsh. Although recovery trajectories are unknown, periphyton indicators should serve as excellent metrics for the progression or amelioration of P-related effects in the Everglades.

Investigation of PHY, MAC and APP layers for adaptive and cross-layer optimization in IEEE802.11 WLAN

Due to huge popularity of portable terminals based on Wireless LANs and increasing demand for multimedia services from these terminals, the earlier structures and protocols are insufficient to cover the requirements of emerging networks and communications. Most research in this field is tailored to find more efficient ways to optimize the quality of wireless LAN regarding the requirements of multimedia services. Our work is to investigate the effects of modulation modes at the physical layer, retry limits at the MAC layer and packet sizes at the application layer over the quality of media packet transmission. Interrelation among these parameters to extract a cross-layer idea will be discussed as well. We will show how these parameters from different layers jointly contribute to the performance of service delivery by the network. The results obtained could form a basis to suggest independent optimization in each layer (an adaptive approach) or optimization of a set of parameters from different layers (a cross-layer approach). Our simulation model is implemented in the NS-2 simulator. Throughput and delay (latency) of packet transmission are the quantities of our assessments. © 2010 IEEE.

RNA Virus Evolution: a Cross-scale, Disease Dynamic Perspective

RNA viruses are an important cause of global morbidity and mortality. The rapid evolutionary rates of RNA virus pathogens, caused by high replication rates and error-prone polymerases, can make the pathogens difficult to control. RNA viruses can undergo immune escape within their hosts and develop resistance to the treatment and vaccines we design to fight them. Understanding the spread and evolution of RNA pathogens is essential for reducing human suffering. In this dissertation, I make use of the rapid evolutionary rate of viral pathogens to answer several questions about how RNA viruses spread and evolve. To address each of the questions, I link mathematical techniques for modeling viral population dynamics with phylogenetic and coalescent techniques for analyzing and modeling viral genetic sequences and evolution. The first project uses multi-scale mechanistic modeling to show that decreases in viral substitution rates over the course of an acute infection, combined with the timing of infectious hosts transmitting new infections to susceptible individuals, can account for discrepancies in viral substitution rates in different host populations. The second project combines coalescent models with within-host mathematical models to identify driving evolutionary forces in chronic hepatitis C virus infection. The third project compares the effects of intrinsic and extrinsic viral transmission rate variation on viral phylogenies.

A Bayesian Dirichlet-Multinomial Test for Cross-Group Differences

Testing for differences within data sets is an important issue across various applications. Our work is primarily motivated by the analysis of microbiomial composition, which has been increasingly relevant and important with the rise of DNA sequencing. We first review classical frequentist tests that are commonly used in tackling such problems. We then propose a Bayesian Dirichlet-multinomial framework for modeling the metagenomic data and for testing underlying differences between the samples. A parametric Dirichlet-multinomial model uses an intuitive hierarchical structure that allows for flexibility in characterizing both the within-group variation and the cross-group difference and provides very interpretable parameters. A computational method for evaluating the marginal likelihoods under the null and alternative hypotheses is also given. Through simulations, we show that our Bayesian model performs competitively against frequentist counterparts. We illustrate the method through analyzing metagenomic applications using the Human Microbiome Project data.

Colloquial Finnish in Subtitles – a Survey on the British Situation Comedy Peep Show

The use of dialects in audiovisual texts is increasing, but the use of standard language in Finnish subtitles is still the prevalent norm and seldom flouted. This may not be in the best interest of the audience as the way the characters speak – their idiolects – is very important for the atmosphere of the audiovisual text and widely used to give the characters personalities and background. This thesis studies whether the viewing experience could be enhanced by taking the characters’ idiolects into account in subtitling. The study was executed as a survey, and the respondents were recruited from social media and an university of applied sciences. A total of 113 respondents were divided into two groups: the experimental group (n=59) and the control group (n=54). Both groups were shown an excerpt of the British situation comedy Peep Show, but with different subtitles. In the experimental subtitles, three characters were given a written idiolect with a level of colloquial language corresponding to the spoken idiolect of the character, while the control subtitles followed the norm of using standard language. The questionnaire contained background questions, a Likert-scale question and open questions. The quantitative responses were analysed statistically through cross tabulation and Mann–Whitney U test or Kruskal-Wallis test (CI=95%, α=0,05). The results showed a statistically significant difference in keeping track on which of the characters was speaking for the benefit of the experimental subtitles. In the other items no statistically significant difference was found between the groups. In the open questions the use of colloquial language was mostly commented favourably.

Effects of efficient fronto-temporal circuitry on lexical ambiguity resolution: converging evidence from cross-age comparisons in eye-tracking and ERP data

Eye-tracking was used to examine how younger and older adults use syntactic and semantic information to disambiguate noun/verb (NV) homographs (e.g., park). We find that young adults exhibit inflated first fixations to NV-homographs when only syntactic cues are available for disambiguation (i.e., in syntactic prose). This effect is eliminated with the addition of disambiguating semantic information. Older adults (60+) as a group fail to show the first fixation effect in syntactic prose; they instead reread NV homographs longer. This pattern mirrors that in prior event-related potential work (Lee & Federmeier, 2009, 2011), which reported a sustained frontal negativity to NV-homographs in syntactic prose for young adults, which was eliminated by semantic constraints. The frontal negativity was not observed in older adults as a group, although older adults with high verbal fluency showed the young-like pattern. Analyses of individual differences in eye-tracking patterns revealed a similar effect of verbal fluency in both young and older adults: high verbal fluency groups of both ages show larger first fixation effects, while low verbal fluency groups show larger downstream costs (rereading and/or refixating NV homographs). Jointly, the eye-tracking and ERP data suggest that effortful meaning selection recruits frontal brain areas important for suppressing contextually inappropriate meanings, which also slows eye movements. Efficacy of fronto-temporal circuitry, as captured by verbal fluency, predicts the success of engaging these mechanisms in both young and older adults. Failure to recruit these processes requires compensatory rereading or leads to comprehension failures (Lee & Federmeier, in press).

Green's function retrieval through cross-correlations in a two -dimensional complex reverberating medium

International audience

Cross-talk and regulatory interactions between the essential response regulator RpaB and cyanobacterial circadian clock output

The response regulator RpaB (regulator of phycobilisome associated B), part of an essential two-component system conserved in cyanobacteria that responds to multiple environmental signals, has recently been implicated in the control of cell dimensions and of circadian rhythms of gene expression in the model cyanobacterium Synechococcus elongatus PCC 7942. However, little is known of the molecular mechanisms that underlie RpaB functions. In this study we show that the regulation of phenotypes by RpaB is intimately connected with the activity of RpaA (regulator of phycobilisome associated A), the master regulator of circadian transcription patterns. RpaB affects RpaA activity both through control of gene expression, a function requiring an intact effector domain, and via altering RpaA phosphorylation, a function mediated through the N-terminal receiver domain of RpaB. Thus, both phosphorylation cross-talk and coregulation of target genes play a role in the genetic interactions between the RpaA and RpaB pathways. In addition, RpaB∼P levels appear critical for survival under light:dark cycles, conditions in which RpaB phosphorylation is environmentally driven independent of the circadian clock. We propose that the complex regulatory interactions between the essential and environmentally sensitive NblS-RpaB system and the SasA-RpaA clock output system integrate relevant extra- and intracellular signals to the circadian clock.

Cross-strand disulfides in the non-hydrogen bonding site of antiparallel β-sheet (aCSDns): poised for biological switching

Forbidden disulfides are stressed disulfides found in recognisable protein contexts previously defined as structurally forbidden. The torsional strain of forbidden disulfides is typically higher than for structural disulfides, but not so high as to render them immediately susceptible to reduction under physionormal conditions. The meta-stability of forbidden disulfides makes them likely candidates as redox switches. Here we mined the Protein Data Bank for examples of the most common forbidden disulfide, the aCSDn. This is a canonical motif in which disulfide-bonded cysteine residues are positioned directly opposite each other on adjacent anti-parallel β-strands such that the backbone hydrogen bonded moieties are directed away from each other. We grouped these aCSDns into homologous clusters and performed an extensive physicochemical and informatic analysis of the examples found. We estimated their torsional energies using quantum chemical calculations and studied differences between the preferred conformations of the computational model and disulfides found in solved protein structures to understand the interaction between the forces imposed by the disulfide linkage and typical constraints of the surrounding β-sheet. In particular, we assessed the twisting, shearing and buckling of aCSDn-containing β-sheets, as well as the structural and energetic relaxation when hydrogen bonds in the motif are broken. We show the strong preference of aCSDns for the right-handed staple conformation likely arises from its compatibility with the twist, shear and Cα separation of canonical β-sheet. The disulfide can be accommodated with minimal distortion of the sheet, with almost all the strain present as torsional strain within the disulfide itself. For each aCSDn cluster, we summarise the structural and strain data, taxonomic conservation and any evidence of redox activity. aCSDns are known substrates of thioredoxin-like enzymes. This, together with their meta-stability, means they are ideally suited to biological switching roles and are likely to play important roles in the molecular pathways of oxidative stress.

Covalent/crystallite cross-linked co-network hydrogels : an efficient and simple strategy for mechanically strong and tough hydrogels

Covalent/crystallite cross-linked co-network hydrogels have been prepared using epoxy and PVA through a cyclic freezing-thawing process. The PVA/epoxy hydrogels show enhanced mechanical strength and toughness. PVA/epoxy hydrogels with 4 wt% epoxy loading display maximum tensile strength and toughness of 1.1 MPa and 2838 kJ/m3 respectively. The fracture toughness of PVA/epoxy hydrogels ranges from 160 to 450 J/m2. Radius of gyration and fractal information of the hydrogels were obtained by fitting the SAXS data to the Guinier and power law models. The enhanced mechanical properties are attributed to the increase in covalent bonding and decrease in crystallite distribution with an increase in epoxy content. However a larger hysteresis is shown for PVA/epoxy hydrogels due to irreversible destruction of covalent bonds between epoxy and PVA.