The use of continuum models for conducting both linear and nonlinear analyses of lattice structures

Large structural projects, such as lattices for framing tall buildings or space purpose can result in huge finite element models. The use of continuum methodology for conducting both linear and nonlinear analyses of lattice structures in finite-element models results in significantly fewer degrees of freedom than discrete finite-element models, which individually model each structural element. Hence, the use of continuum models can result in a considerable reduction in computational effort with a corresponding savings in cost, at least during early 1990s when Pentium computer was not available. Now, it can still be a good design method especially for tall buildings in the preliminary stages of structural design because through the displacements under the axial, shear and moments stresses on the continuum model, the sizes and shapes of members can be determined for the structural system. Besides, it is also useful to check the results obtained from a commercially available computer structural program

Alveolar macrophage heterogeneity in idiopathic pulmonary fibrosis

Idiopathic Pulmonary Fibrosis (IPF) involves excess extracellular matrix (ECM) deposition within the lung interstitium, caused by non-resolving chronic inflammation and dysregulated repair. Alveolar macrophage (AMφ) may contribute to IPF through releasing various mediators by different subsets, investigated here in vitro, and ex vivo using a mouse model of bleomycin (BLM)-induced pulmonary fibrosis. The role of foamy AMφ in the reported increased susceptibility of Hermansky Pudlak Syndrome (HPS) 1 mice to BLM-induced pulmonary fibrosis was also assessed. Novel characterisation studies revealed that terminally differentiated AMφ are inducible into M1-like [nitric oxide synthase 2 (NOS2)hi interleukin (IL)-1βhi IL-12 p40 (total)hi major histocompatibility protein (MHC)-IIhi mannose receptor C, type 1 (MRC1)-] or M2-like [Arginase 1 (Arg1)hi Fibronectinhi IGF-1hi MHC-IIlo MRC1-/+] phenotypes following IFN-Υ or IL-13 priming respectively. Lipopolysccharide (LPS) altered these AMφ subset phenotypes. AMφ heterogeneity in a novel multiple oropharyngeal dose, BLM-induced pulmonary fibrosis was evaluated from days 7 to 21. Accumulation of M1-like AMφ at day 7, and M1/M2-hybrid AMφ [Arg1hi IL-12 p40 (total)hi fibronectinhi MHC-IIlo MRC1-/+] from days 7 to 21, may promote inflammation and fibrosis respectively. Toll-like Receptor (TLR) 9 messenger ribonucleic acid (mRNA) and TLR2 surface protein, and both TLRs2 and 9 ex vivo activities were increased in BLM-challenged mice from days 7 to 21, suggesting their roles in inflammation and fibrosis. Foamy AMφ accumulated in BLM-induced pulmonary fibrosis, and their potential role in the reported increased susceptibility to BLM-induced pulmonary fibrosis of HPS1 mice was evaluated. BLM-challenged HPS1 mice (days 7-21) had increased weight loss indicating reduced BLM tolerance from days 7 to 11, but little/no difference in collagen accumulation, suggesting that reduced BLM tolerance is not correlated with increased pulmonary fibrosis. In conclusion AMφ alter their phenotype in response to their environment that contributes to different stages of BLM-induced pulmonary fibrosis. Reduced BLM tolerance in HPS1 mice is not correlated with increased pulmonary fibrosis.Open Acces

Integrated reporting and financial performance (evidence from Malaysia) / Luk Pui Wen, Angeline Yap Kiew Heong and Simon Lim Chee Hooi.

Although the consciousness of Integrated Reporting (IR) is increasing within Malaysian companies, how IR creates value for their business is not completely understood. This paper attempts to investigate the potential contribution of IR implementation to the financial performance of the top 50 Malaysian public listed companies during the period of 2012 to 2015. The eight (8) IR content elements from the International Integrated Reporting Council (IIRC) framework are examined to predict the adoption rate of IR in relation to financial performance. This includes disclosure on organizational overview and external environment, governance, business model, risks and opportunities, strategy and resource allocation, performance, outlook, and basis of preparation and presentation. The data indicates that Malaysian PLCs reported more than 50% for every content element, except Basis of Preparation and Presentation (CE8).  Data analysis indicates that among the eight (8) content elements, four (4) of them, namely governance, business model, risks and opportunities, and performance disclosure, have significant positive impact on financial performances.  The finding of this paper provides insight into the contribution of IR in effecting the maintenance of business resilience and competitiveness in a fluctuating market. Therefore, this paper provides a significant impetus for implementation of IR among the Malaysian companies

Safe-Error Analysis of Post-Quantum Cryptography Mechanisms

International audienceThe NIST selection process for standardizing Post-Quantum Cryptography Mechanisms is currently running. Many papers already studied their theoretical security, but the resistance in deployed device has not been much investigated so far. In particular, fault attack is a serious threat for algorithms implemented in embedded devices. One particularly powerful technique is to used safe-error attacks. Such attacks exploit the fact that a specific fault may or may not lead to a faulty output depending on a secret value. In this paper, we investigate the resistance of various Post-Quantum candidates algorithms against such attacks

Towards controlling activity of a peptide asparaginyl ligase (PAL) by lumazine synthetase compartmentalization

Peptide asparaginyl ligases (PALs) hold significant potential in protein bioconjugation due to their excellent kinetic properties and broad substrate compatibility. However, realizing their full potential in biocatalytic applications requires precise control of their activity. Inspired by nature, we aimed to compartmentalize a representative PAL, OaAEP1-C247A, within protein containers to create artificial organelles with substrate sorting capability. Two encapsulation approaches were explored using engineered lumazine synthases (AaLS). The initial strategy involved tagging the PAL with a super-positively charged GFP(+36) for encapsulation into the super-negatively charged AaLS-13 variant, but it resulted in undesired truncation of the enzyme. The second approach involved genetic fusion of the OaAEP1-C247A with a circularly permutated AaLS variant (cpAaLS) and its co-production with AaLS-13, which successfully enabled compartmentalization of the PAL within a patch-work protein cage. Although the caged PAL retained its activity, it was significantly reduced compared to the free enzyme (~30-40-fold), likely caused by issues related to OaAEP1-C247A stability and folding. Nevertheless, these findings demonstrated feasibility of the AaLS encapsulation approach and encourages further optimization in the design of peptide-ligating artificial organelle in E. coli, aiming for a more effective and stable system for protein modifications

Asparaginyl endopeptidases: enzymology, applications and limitations

Asparaginyl endopeptidases (AEP) are cysteine proteases found in mammalian and plant cells. Several AEP isoforms from plant species were found to exhibit transpeptidase activity which is integral for the key head-to-tail cyclisation reaction during the biosynthesis of cyclotides. Since many plant AEPs exhibit excellent enzyme kinetics for peptide ligation via a relatively short substrate recognition sequence, they have become appealing tools for peptide and protein modification. In this review, research focused on the enzymology of AEPs and their applications in polypeptide cyclisation and labelling will be presented. Importantly, the limitations of using AEPs and opportunities for future research and innovation will also be discussed

Use of an asparaginyl endopeptidase for chemo-enzymatic peptide and protein labeling

Asparaginyl endopeptidases (AEPs) are ideal for peptide and protein labeling. However, because of the reaction reversibility, a large excess of labels or backbone modified substrates are needed. In turn, simple and cheap reagents can be used to label N-terminal cysteine, but its availability inherently limits the potential applications. Aiming to address these issues, we have created a chemo-enzymatic labeling system that exploits the substrate promiscuity of AEP with the facile chemical reaction between N-terminal cysteine and 2-formyl phenylboronic acid (FPBA). In this approach, AEP is used to ligate polypeptides with a Asn–Cys–Leu recognition sequence with counterparts possessing an N-terminal Gly–Leu. Instead of being a labeling reagent, the commercially available FPBA serves as a scavenger converting the byproduct Cys–Leu into an inert thiazolidine derivative. This consequently drives the AEP labeling reaction forward to product formation with a lower ratio of label to protein substrate. By carefully screening the reaction conditions for optimal compatibility and minimal hydrolysis, conversion to the ligated product in the model reaction resulted in excellent yields. The versatility of this AEP-ligation/FPBA-coupling system was further demonstrated by site-specifically labeling the N- or C-termini of various proteins

Cytoplasmic Forkhead Box M1 (FoxM1) in Esophageal Squamous Cell Carcinoma Significantly Correlates with Pathological Disease Stage

Abstract: Esophageal cancer is a deadly cancer with esophageal squamous cell carcinoma (ESCC) as the major type. Until now there has been a lack of reliable prognostic markers for this malignancy. This study aims to investigate the clinical correlation between Forkhead box M1 (FoxM1) and patients' parameters in ESCC. Methods: Immunohistochemistry was performed to investigate the expression and localization of FoxM1 in 64 ESCC tissues and 10 nontumor esophageal tissues randomly selected from 64 patients before these data were used for clinical correlations. Results: Cytoplasmic and nuclear expressions of FoxM1 were found in 63 and 16 of the 64 ESCC tissues, respectively. Low cytoplasmic expression of FoxM1 was correlated with early pathological stage in ESCC (P = 0.018), while patients with nuclear FoxM1 were younger in age than those without nuclear expression (P < 0.001). Upregulation of FoxM1 mRNA was found in five ESCC cell lines (HKESC-1, HKESC-2, HKESC-3, HKESC-4, and SLMT-1) when compared to non-neoplastic esophageal squamous cell line NE-1 using quantitative polymerase chain reaction (qPCR). Except for HKESC-3, all studied ESCC cell lines demonstrated a high expression of FoxM1 protein using immunoblot. A high mRNA level of FoxM1 was observed in all of the ESCC tissues examined when compared to their adjacent nontumor tissues using qPCR. Conclusion: Cytoplasmic FoxM1 was correlated with pathological stage and might be a biomarker for advanced ESCC. © 2011 The Author(s).published_or_final_versionSpringer Open Choice, 21 Feb 201

Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics

The past decade has seen the development of a new class of rare event methods in which molecular configuration space is divided into a set of boundaries/interfaces, and then short trajectories are run between boundaries. For all these methods, an important concern is how to generate boundaries. In this paper, we outline an algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm. BXD is a simple technique for accelerating the simulation of rare events and free energy sampling which has proven useful for calculating kinetics and free energy profiles in reactive and non-reactive molecular dynamics (MD) simulations across a range of systems, in both NVT and NVE ensembles. Two key developments outlined in this paper make it possible to automate BXD, and to adaptively map free energy and kinetics in complex systems. First, we have generalized BXD to multidimensional CV space. Using strategies from rigid-body dynamics, we have derived a simple and general velocity-reflection procedure that conserves energy for arbitrary collective variable definitions in multiple dimensions, and show that it is straightforward to apply BXD to sampling in multidimensional CV space so long as the Cartesian gradients ∇CV are available. Second, we have modified BXD to undertake on-the-fly statistical analysis during a trajectory, harnessing the information content latent in the dynamics to automatically determine boundary locations. Such automation not only makes BXD considerably easier to use; it also guarantees optimal boundaries, speeding up convergence. We have tested the multidimensional adaptive BXD procedure by calculating the potential of mean force for a chemical reaction recently investigated using both experimental and computational approaches - i.e., F + CD3CN → DF + D2CN in both the gas phase and a strongly coupled explicit CD3CN solvent. The results obtained using multidimensional adaptive BXD agree well with previously published experimental and computational results, providing good evidence for its reliability

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO