Characterization and Comparison of the Tissue-Related Modules in Human and Mouse

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity,'' a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

Two Immunoregulatory Peptides with Antioxidant Activity from Tick Salivary Glands

Ticks are blood-feeding arthropods that may secrete immunosuppressant molecules, which inhibit host inflammatory and immune responses and provide survival advantages to pathogens at tick bleeding sites in hosts. In the current work, two families of immunoregulatory peptides, hyalomin-A and -B, were first identified from salivary glands of hard tick Hyalomma asiaticum asiaticum. Three copies of hyalomin-A are encoded by an identical gene and released from the same protein precursor. Both hyalomin-A and -B can exert significant anti-inflammatory functions, either by directly inhibiting host secretion of inflammatory factors such as tumor necrosis factor-alpha, monocyte chemotectic protein-1, and interferon-gamma or by indirectly increasing the secretion of immunosuppressant cytokine of interleukin-10. Hyalomin-A and -B were both found to potently scavenge free radical in vitro in a rapid manner and inhibited adjuvant-induced inflammation in mouse models in vivo. The JNK/SAPK subgroup of the MAPK signaling pathway was involved in such immunoregulatory functions of hyalomin-A and -B. These results showed that immunoregulatory peptides of tick salivary glands suppress host inflammatory response by modulating cytokine secretion and detoxifying reactive oxygen species.

Effect of building integrated photovoltaics on microclimate of urban canopy layer

Building integrated photovoltaics (BIPV) has potential of becoming the mainstream of renewable energy in the urban environment. BIPV has significant influence on the thermal performance of building envelope and changes radiation energy balance by adding or replacing conventional building elements in urban areas. PTEBU model was developed to evaluate the effect of photovoltaic (PV) system on the microclimate of urban canopy layer. PTEBU model consists of four sub-models: PV thermal model, PV electrical performance model, building energy consumption model, and urban canyon energy budget model. PTEBU model is forced with temperature, wind speed, and solar radiation above the roof level and incorporates detailed data of PV system and urban canyon in Tianjin, China. The simulation results show that PV roof and PV façade with ventilated air gap significantly change the building surface temperature and sensible heat flux density, but the air temperature of urban canyon with PV module varies little compared with the urban canyon of no PV. The PV module also changes the magnitude and pattern of diurnal variation of the storage heat flux and the net radiation for the urban canyon with PV increase slightly. The increase in the PV conversion efficiency not only improves the PV power output, but also reduces the urban canyon air temperature. © 2006.

Effect of urban climate on building integrated photovoltaics performance

It is generally recognized that BIPV (building integrated photovoltaics) has the potential to become a major source of renewable energy in the urban environment. The actual output of a PV module in the field is a function of orientation, total irradiance, spectral irradiance, wind speed, air temperature, soiling and various system-related losses. In urban areas, the attenuation of solar radiation due to air pollution is obvious, and the solar spectral content subsequently changes. The urban air temperature is higher than that in the surrounding countryside, and the wind speed in urban areas is usually less than that in rural areas. Three different models of PV power are used to investigate the effect of urban climate on PV performance. The results show that the dimming of solar radiation in the urban environment is the main reason for the decrease of PV module output using the climatic data of urban and rural sites in Mexico City for year 2003. The urban PV conversion efficiency is higher than that of the rural PV system because the PV module temperature in the urban areas is slightly lower than that in the rural areas in the case. The DC power output of PV seems to be underestimated if the spectral response of PV in the urban environment is not taken into account based on the urban hourly meteorological data of Sao Paulo for year 2004. © 2006 Elsevier Ltd. All rights reserved.

Explosion pressure prediction via polynomial mathematical correlation based on advanced CFD Modelling

Computational Fluid Dynamics CFD can be used as a powerful tool supporting engineers throughout the steps of the design. The combination of CFD with response surface methodology can play an important role in such cases. During the conceptual engineering design phase, a quick response is always a matter of urgency. During this phase even a sketch of the geometrical model is rare. Therefore, the utilisation of typical response surface developed for congested and confined environment rather than CFD can be an important tool to help the decision making process, when the geometrical model is not available, provided that similarities can be considered when taking into account the characteristic of the geometry in which the response surface was developed. The present work investigates how three different types of response surfaces behave when predicting overpressure in accidental scenarios based on CFD input. First order, partial second order and complete second order polynomial expressions are investigated. The predicted results are compared with CFD findings for a classical offshore experiment conducted by British Gas on behalf of Mobil and good agreement is observed for higher order response surfaces. The higher order response surface calculations are also compared with CFD calculations for a typical offshore module and good agreement is also observed. © 2011 Elsevier Ltd.

Lyapunov's stability and operational margin of grid-connected photovoltaic modules

Analyses of photovoltaic power generation based on Lyapunov's theorems are presented. The characteristics of the photovoltaic module and the power conditioning unit are analyzed in order to establish energy functions that assess the stability of solutions and define safe regions of operation. Furthermore, it is shown that grid-connected photovoltaic modules driven at maximum power may become unstable under normal grid transients. In such cases, stability can be maintained by allowing an operational margin defined as the energy difference between the stable and the unstable solutions of the system. Simulations show that modules cope well with grid transients when a sufficiently large margin is used.

Interaction between human interleukin-16 and CD4 receptor of HIV-1

AIM: To study the interaction between human interleukin-16 (IL-16) and the receptor CD4 (T-lymphocyte differentiation antigen) of human immunodeficiency virus type 1 (HIV-1). METHODS: Two structurally con served regions (SCRs) of human IL-16 were built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of human interleukin-1 (HIL-4) and HIL-2 as the templates. The coordinates for amino-terminal residue sequence, carboxyl-terminal residue sequences, and cytoplasm loops were generated using Biopolymer's LOOP SEARCH algorithm. RESULTS: HIL-16 first formed a homodimer, then contacted with CD4 dimer further forming a dimeric complex. Subsequently, the dimeric complex constructed the tetrameric complex by two disulfide bridges between the cysteines of HIL-16 (Cys31-Cys31). CONCLUSION: The interaction model is useful to propose the action mechanism of HIL-16 and is beneficial for rational designing of novel anti-HIV drugs.

Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

Regenerative polymeric bus architecture for board-level optical interconnects

A scalable multi-channel optical regenerative bus architecture based on the use of polymer waveguides is presented for the first time. The architecture offers high-speed interconnection between electrical cards allowing regenerative bus extension with multiple segments and therefore connection of an arbitrary number of cards onto the bus. In a proof-ofprinciple demonstration, a 4-channel 3-card polymeric bus module is designed and fabricated on standard FR4 substrates. Low insertion losses (≤ -15 dB) and low crosstalk values (< -30 dB) are achieved for the fabricated samples while better than ± 6 μm -1 dB alignment tolerances are obtained. 10 Gb/s data communication with a bit-error-rate (BER) lower than 10-12 is demonstrated for the first time between card interfaces on two different bus modules using a prototype 3R regenerator. © 2012 Optical Society of America.

Extracellular-matrix tethering regulates stem-cell fate.

To investigate how substrate properties influence stem-cell fate, we cultured single human epidermal stem cells on polydimethylsiloxane (PDMS) and polyacrylamide (PAAm) hydrogel surfaces, 0.1 kPa-2.3 MPa in stiffness, with a covalently attached collagen coating. Cell spreading and differentiation were unaffected by polydimethylsiloxane stiffness. However, cells on polyacrylamide of low elastic modulus (0.5 kPa) could not form stable focal adhesions and differentiated as a result of decreased activation of the extracellular-signal-related kinase (ERK)/mitogen-activated protein kinase (MAPK) signalling pathway. The differentiation of human mesenchymal stem cells was also unaffected by PDMS stiffness but regulated by the elastic modulus of PAAm. Dextran penetration measurements indicated that polyacrylamide substrates of low elastic modulus were more porous than stiff substrates, suggesting that the collagen anchoring points would be further apart. We then changed collagen crosslink concentration and used hydrogel-nanoparticle substrates to vary anchoring distance at constant substrate stiffness. Lower collagen anchoring density resulted in increased differentiation. We conclude that stem cells exert a mechanical force on collagen fibres and gauge the feedback to make cell-fate decisions.

Polymer waveguide-based backplanes for board-level optical interconnects

Optical interconnects are increasingly considered for use in high-performance electronic systems. Multimode polymer waveguides are a promising technology for the formation of optical backplane as they enable cost-effective integration of optical links onto standard printed circuit boards. In this paper, two different types of polymer waveguide-based optical backplanes are presented. The first one implements a passive shuffle architecture enabling non-blocking on-board optical interconnection between different cards/modules, while the second one deploys a regenerative bus architecture allowing the interconnection of an arbitrary number of electrical cards over a common optical bus. The polymer materials and the multimode waveguide components used to form the optical backplanes are presented, while details of the interconnection architectures and design of the backplanes are described. Proof-of-principle demonstrators fabricated onto low-cost FR4 substrates, including a 10-card 1 Tb/s-capacity passive shuffle router and 4-channel 3-card polymeric bus modules, are reported and their optical performance characteristics are presented. Low-loss, low-crosstalk on-board interconnection is achieved and error-free (BER10 12) 10 Gb/s communication between different card/module interfaces is demonstrated in both polymeric backplane systems. © 2012 IEEE.

秀丽隐杆线虫抗性基因研究进展

从3个方面总结了秀丽隐杆线虫在抗性基因方面的研究进展。秀丽隐杆线虫的先天性免疫系统在抗病原菌、抗氧化应激等方面至关重要,它主要是通过MAPK、DAF-2、TGF-β三条信号途径发挥作用;另外,含TIR区蛋白和抗菌多肽也是秀丽隐杆线虫抗微生物感染机制的重要组成部分。在秀丽隐杆线虫的抗药性基因研究方面,发现了许多抗药性相关蛋白,如P-糖蛋白和多药耐药性相关蛋白MRP在抵抗多种药物的过程中发挥重要作用;而抗驱虫剂相关蛋白也在专门针对各种驱虫剂作用机制的研究中被发现;转录因子SKN-1、信息沉默调节蛋白SIR2、

Graduate education for leadership and organisational change in sustainable development

This paper reflects on the motivation, method and effectiveness of teaching leadership and organisational change to graduate engineers. Delivering progress towards sustainable development requires engineers who are aware of pressing global issues (such as resource depletion, climate change, social inequity and an interdependent economy) since it is they who deliver the goods and services that underpin society within these constraints. They also must understand how to implement change in the organisations within which they will work. In recognition of this fact the Cambridge University MPhil in Engineering for Sustainable Development has focussed on educating engineers to become effective change agents in their professional field with the confidence to challenge orthodoxy in adopting traditional engineering solutions. This paper reflects on ten years of delivering a special module to review how teaching change management and leadership aspects of the programme have evolved and progressed over that time. As the students who embark on this professional practice have often extensive experience as practising engineers and scientists, many have already learned the limitations of their technical background when solving complex problems. Students often join the course recognising their need to broaden their knowledge of relevant cross-disciplinary skills. The programme offers an opportunity for these early to mid-career engineers to explore an ethical and value-based approach to bringing about effective change in their particular sectors and organisations. This is achieved through action learning assignments in combination with reflections on the theory of change to enable students to equip themselves with tools that help them to be effective in making their professional and personal life choices. This paper draws on feedback gathered from students during their participation on the programme and augments this with alumni reflections gathered some years after their graduation. These professionals are able to look back on their experience of the taught components and reflect on how they have been able to apply this key learning in their subsequent careers. Copyright © 2012 September.

Antiwindup design for induction motor control in the field weakening domain

Operation of induction machines in the high-speed and/or high-torque range requires field-weakening to comply with voltage and current physical limitations. This paper presents an anti-windup approach to this problem: rather than developing an ad-hoc field weakening strategy in the high-speed region, we equip an unconstrained vector-control design with an anti-windup module that automatically adjusts the current and flux set-points so that voltage and current constraints are satisfied at every operating point. The anti-windup module includes a feedforward modification of the set point aimed at maximizing the available torque in steady-state and a feedback modification of the controller based on an internal model-based antiwindup scheme. This paper includes a complete stability analysis of the proposed solution and presents encouraging experimental results on an industrial drive. © 2012 IEEE.

Coupled neutronic thermo-hydraulic analysis of full PWR core with Monte-Carlo based BGCore system

BGCore reactor analysis system was recently developed at Ben-Gurion University for calculating in-core fuel composition and spent fuel emissions following discharge. It couples the Monte Carlo transport code MCNP with an independently developed burnup and decay module SARAF. Most of the existing MCNP based depletion codes (e.g. MOCUP, Monteburns, MCODE) tally directly the one-group fluxes and reaction rates in order to prepare one-group cross sections necessary for the fuel depletion analysis. BGCore, on the other hand, uses a multi-group (MG) approach for generation of one group cross-sections. This coupling approach significantly reduces the code execution time without compromising the accuracy of the results. Substantial reduction in the BGCore code execution time allows consideration of problems with much higher degree of complexity, such as introduction of thermal hydraulic (TH) feedback into the calculation scheme. Recently, a simplified TH feedback module, THERMO, was developed and integrated into the BGCore system. To demonstrate the capabilities of the upgraded BGCore system, a coupled neutronic TH analysis of a full PWR core was performed. The BGCore results were compared with those of the state of the art 3D deterministic nodal diffusion code DYN3D (Grundmann et al.; 2000). Very good agreement in major core operational parameters including k-eff eigenvalue, axial and radial power profiles, and temperature distributions between the BGCore and DYN3D results was observed. This agreement confirms the consistency of the implementation of the TH feedback module. Although the upgraded BGCore system is capable of performing both, depletion and TH analyses, the calculations in this study were performed for the beginning of cycle state with pre-generated fuel compositions. © 2011 Published by Elsevier B.V.