Read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molec- ular biology, allowing routine clinical sequencing. NGS data consists of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans, with some strains exhibiting antibiotic resistance. Here we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from other pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

The biology of the glutamatergic system and potential role in migraine

Migraine is a common genetically linked neurovascular disorder. Approximately ~12% of the Caucasian population are affected including 18% of adult women and 6% of adult men (1, 2). A notable female bias is observed in migraine prevalence studies with females affected ~3 times more than males and is credited to differences in hormone levels arising from reproductive achievements. Migraine is extremely debilitating with wide-ranging socioeconomic impact significantly affecting people's health and quality of life. A number of neurotransmitter systems have been implicated in migraine, the most studied include the serotonergic and dopaminergic systems. Extensive genetic research has been carried out to identify genetic variants that may alter the activity of a number of genes involved in synthesis and transport of neurotransmitters of these systems. The biology of the Glutamatergic system in migraine is the least studied however there is mounting evidence that its constituents could contribute to migraine. The discovery of antagonists that selectively block glutamate receptors has enabled studies on the physiologic role of glutamate, on one hand, and opened new perspectives pertaining to the potential therapeutic applications of glutamate receptor antagonists in diverse neurologic diseases. In this brief review, we discuss the biology of the Glutamatergic system in migraine outlining recent findings that support a role for altered Glutamatergic neurotransmission from biochemical and genetic studies in the manifestation of migraine and the implications of this on migraine treatment.

Blog research : the 'computational turn' [Blogforschung: Der 'Computational Turn']

ForscherInnen aus Sozial- und Geisteswissenschaften interessieren sich seit nunmehr einem Jahrzehnt für Blogs, Online-Tagebücher und Online-Journale. Auch wenn die Zuwachsrate der Blogosphäre seit der Blütezeit des Bloggens in den 2000ern stagniert, bleiben Blogs doch eines der bedeutendsten Genres der internetgestützten Kommunikation. Tatsächlich ist nach der Massenabwanderung zu Facebook, Twitter und anderen erst in jüngerer Zeit entstandenen Kommunikationsmitteln eine etwas kleinere, aber umso stärker etablierte Blogosphäre von engagierten und eingeschworenen Teilnehmenden übriggeblieben. Blogs werden mittlerweile als Teil einer institutionellen, persönlichen und Gruppen-Kommunikationstrategie akzeptiert. In Stil und Inhalt liegen sie zwischen den statischeren Informationen auf konventionellen Websites und den ständig aktualisierten Facebook- und Twitter-Newsfeeds. Blogs ermöglichen es ihren AutorInnen (und deren KommentatorInnen), bestimmte Themen im Umfang von einigen hundert bis zu einigen tausend Wörtern zu durchdenken, in kürzeren Posts ins Detail zu gehen und ggf. intensiver durchdachte Texte anderswo zu publizieren. Zudem sind sie auch ein sehr flexibles Medium: Bilder, Audio-, Video- sowie andere Materialien können mühelos eingefügt werden - und natürlich auch das grundlegende Instrument des Bloggens: Hyperlinks.

Computational analysis of laminated glass panels under blast loads: A comparison of two dimensional and three dimensional modelling approaches

This paper illustrates the use of finite element (FE) technique to investigate the behaviour of laminated glass (LG) panels under blast loads. Two and three dimensional (2D and 3D) modelling approaches available in LS-DYNA FE code to model LG panels are presented. Results from the FE analysis for mid-span deflection and principal stresses compared well with those from large deflection plate theory. The FE models are further validated using the results from a free field blast test on a LG panel. It is evident that both 2D and 3D LG models predict the experimental results with reasonable accuracy. The 3D LG models give slightly more accurate results but require considerably more computational time compared to the 2D LG models.

How to increase the accuracy of analysis and reduce the computational time in ANSYS in the case of deformation study of orthopedic bone plates

Currently, finite element analyses are usually done by means of commercial software tools. Accuracy of analysis and computational time are two important factors in efficiency of these tools. This paper studies the effective parameters in computational time and accuracy of finite element analyses performed by ANSYS and provides the guidelines for the users of this software whenever they us this software for study on deformation of orthopedic bone plates or study on similar cases. It is not a fundamental scientific study and only shares the findings of the authors about structural analysis by means of ANSYS workbench. It gives an idea to the readers about improving the performance of the software and avoiding the traps. The solutions provided in this paper are not the only possible solutions of the problems and in similar cases there are other solutions which are not given in this paper. The parameters of solution method, material model, geometric model, mesh configuration, number of the analysis steps, program controlled parameters and computer settings are discussed through thoroughly in this paper.

Bridging the biology of the ovine TRALI model – human inflammatory cell responses to TRALI inducing supernatants

Background Transfusion-related acute lung injury (TRALI) is a serious and potentially fatal consequence of transfusion. A two-event TRALI model demonstrated date-of-expiry - day (D) 5 platelet (PLT) and D42 packed red blood cell (PRBC) supernatants (SN) induced TRALI in LPS-treated sheep. We have adapted a whole blood transfusion culture model as an investigative bridge between the ovine TRALI model human responses to transfusion. Methods A whole blood transfusion model was adapted to replicate the ovine model - specifically +/- 0.23μg/mL LPS as the first event and 10% SN volume (transfusion) as the second event. Four pooled SN from blood products, previously used in the TRALI ovine model, were investigated: D1-PLT, D5-PLT, D1-PRBC, and D42-PRBC. Fresh human whole blood (recipient) was mixed with combinations of LPS and BP-SN stimuli and incubated in vitro for 6 hrs. Addition of golgi plug enabled measurement of monocyte cytokine production (IL-6, IL-8, IL-10, IL-12, TNF-α, IL-1α, CXCL-5, IP-10, MIP-1α, MCP-1) using multi-colour flow cytometry. Responses for 6 recipients were assessed. Results In the presence of LPS, D42-PRBC-SN significantly increased monocyte IL-6 (P=0.031), IL-8 (P=0.016) and IL-1α (P=0.008) production compared to D1-PRBC-SN. This response to D42-PRBC-SN was LPS-dependent, and was not evident in non-LPSstimulated controls. This response was also specific to D42-PRBC-SN, as similar changes were not evident for the D5-PLT-SN, compared to the D1-PLT-SN, regardless of the presence of LPS. D5-PLT-SN significantly increased IL-12 production (P=0.024) compared to D1-PLT-SN. This response was again LPS-dependent. Conclusions These data demonstrate a novel two-event mechanism of monocyte inflammatory response that was dependent upon both the presence of date-of-expiry blood product SN and LPS. Further, these results demonstrate different cytokines responses induced by date-of-expiry PLT-SN and PRBC-SN. These data are consistent with the evidence from the ovine TRALI model, and enhancing its relevance to transfusion related changes in humans.

Training for performance : insights from molecular biology

In this commentary the authors discuss the molecular basis of the training adaptation and review the role of several key signaling proteins important in the adaptation to endurance and resistance training.

Computational fluid dynamic analysis of intracranial aneurysmal bleb formation

Background The management of unruptured aneurysms is controversial with the decision to treat influenced by aneurysm characteristics including size and morphology. Aneurysmal bleb formation is thought to be associated with an increased risk of rupture. Objective To correlate computational fluid dynamic (CFD) indices with bleb formation. Methods Anatomical models were constructed from three-dimensional rotational angiogram (3DRA) data in 27 patients with cerebral aneurysms harbouring single blebs. Additional models representing the aneurysm before bleb formation were constructed by digitally removing the bleb. We characterised haemodynamic features of models both with and without the bleb using CFDs. Flow structure, wall shear stress (WSS), pressure and oscillatory shear index (OSI) were analysed. Results There was a statistically significant association between bleb location at or adjacent to the point of maximal WSS (74.1%, p=0.019), irrespective of rupture status. Aneurysmal blebs were related to the inflow or outflow jet in 88.9% of cases (p<0.001) whilst 11.1% were unrelated. Maximal wall pressure and OSI were not significantly related to bleb location. The bleb region attained a lower WSS following its formation in 96.3% of cases (p<0.001) and was also lower than the average aneurysm WSS in 86% of cases (p<0.001). Conclusion Cerebral aneurysm blebs generally form at or adjacent to the point of maximal WSS and are aligned with major flow structures. Wall pressure and OSI do not contribute to determining bleb location. The measurement of WSS using CFD models may potentially predict bleb formation and thus improve the assessment of rupture risk in unruptured aneurysms.

Computational simulation of the early stage of bone healing under different configurations of locking compression plates

Flexible fixation or the so-called ‘biological fixation’ has been shown to encourage the formation of fracture callus, leading to better healing outcomes. However, the nature of the relationship between the degree of mechanical stability provided by a flexible fixation and the optimal healing outcomes has not been fully understood. In this study, we have developed a validated quantitative model to predict how cells in fracture callus might respond to change in their mechanical microenvironment due to different configurations of locking compression plate (LCP) in clinical practice, particularly in the early stage of healing. The model predicts that increasing flexibility of the LCP by changing the bone–plate distance (BPD) or the plate working length (WL) could enhance interfragmentary strain in the presence of a relatively large gap size (.3 mm). Furthermore, conventional LCP normally results in asymmetric tissue development during early stage of callus formation, and the increase of BPD or WL is insufficient to alleviate this problem.

Porohyperelastic analysis of single chondrocyte using AFM and inverse FEA

The aim of this paper is to determine the creep and relaxation responses of single chondrocytes in vitro. Firstly, Atomic Force Microscopy (AFM) was used to obtain the force-indentation curves of single chondrocytes at the strain-rate of 7.05 s-1. This result was then employed in inverse finite element analysis (FEA) using porohyperelastic (PHE) idealization of the cells to determine their mechanical properties. The PHE model results agreed well with AFM experimental data. This PHE model was then utilized to study chondrocyte’s creep and relaxation behaviors. The results revealed that the effect of fluid was predominant for cell’s mechanical behaviors and that the PHE is a good model for biomechanics studies of chondrocytes.

Rapid match-searching for gene silencing assessment

Motivation: Gene silencing, also called RNA interference, requires reliable assessment of silencer impacts. A critical task is to find matches between silencer oligomers and sites in the genome, in accordance with one-to-many matching rules (G-U matching, with provision for mismatches). Fast search algorithms are required to support silencer impact assessments in procedures for designing effective silencer sequences.Results: The article presents a matching algorithm and data structures specialized for matching searches, including a kernel procedure that addresses a Boolean version of the database task called the skyline search. Besides exact matches, the algorithm is extended to allow for the location-specific mismatches applicable in plants. Computational tests show that the algorithm is significantly faster than suffix-tree alternatives. © The Author 2010. Published by Oxford University Press. All rights reserved.

Correlating flow induced shear stress and chondrocytes activity in micro-porous scaffold using computational fluid dynamics and rapid prototyping

Flow induced shear stress plays an important role in regulating cell growth and distribution in scaffolds. This study sought to correlate wall shear stress and chondrocytes activity for engineering design of micro-porous osteochondral grafts based on the hypothesis that it is possible to capture and discriminate between the transmitted force and cell response at the inner irregularities. Unlike common tissue engineering therapies with perfusion bioreactors in which flow-mediated stress is the controlling parameter, this work assigned the associated stress as a function of porosity to influence in vitro proliferation of chondrocytes. D-optimality criterion was used to accommodate three pore characteristics for appraisal in a mixed level fractional design of experiment (DOE); namely, pore size (4 levels), distribution pattern (2 levels) and density (3 levels). Micro-porous scaffolds (n=12) were fabricated according to the DOE using rapid prototyping of an acrylic-based bio-photopolymer. Computational fluid dynamics (CFD) models were created correspondingly and used on an idealized boundary condition with a Newtonian fluid domain to simulate the dynamic microenvironment inside the pores. In vitro condition was reproduced for the 3D printed constructs seeded by high pellet densities of human chondrocytes and cultured for 72 hours. The results showed that cell proliferation was significantly different in the constructs (p<0.05). Inlet fluid velocity of 3×10-2mms-1 and average shear stress of 5.65×10-2 Pa corresponded with increased cell proliferation for scaffolds with smaller pores in hexagonal pattern and lower densities. Although the analytical solution of a Poiseuille flow inside the pores was found insufficient for the description of the flow profile probably due to the outside flow induced turbulence, it showed that the shear stress would increase with cell growth and decrease with pore size. This correlation demonstrated the basis for determining the relation between the induced stress and chondrocyte activity to optimize microfabrication of engineered cartilaginous constructs.

Electrocatalytically switchable CO2 capture : first principle computational exploration of carbon nanotubes with pyridinic nitrogen

Carbon nanotubes with specific nitrogen doping are proposed for controllable, highly selective, and reversible CO2 capture. Using density functional theory incorporating long-range dispersion corrections, we investigated the adsorption behavior of CO2 on (7,7) single-walled carbon nanotubes (CNTs) with several nitrogen doping configurations and varying charge states. Pyridinic-nitrogen incorporation in CNTs is found to induce an increasing CO2 adsorption strength with electron injecting, leading to a highly selective CO2 adsorption in comparison with N2. This functionality could induce intrinsically reversible CO2 adsorption as capture/release can be controlled by switching the charge carrying state of the system on/off. This phenomenon is verified for a number of different models and theoretical methods, with clear ramifications for the possibility of implementation with a broader class of graphene-based materials. A scheme for the implementation of this remarkable reversible electrocatalytic CO2-capture phenomenon is considered.

Supplementary information : weighted tree kernels for sequence analysis

Genomic sequences are fundamentally text documents, admitting various representations according to need and tokenization. Gene expression depends crucially on binding of enzymes to the DNA sequence at small, poorly conserved binding sites, limiting the utility of standard pattern search. However, one may exploit the regular syntactic structure of the enzyme's component proteins and the corresponding binding sites, framing the problem as one of detecting grammatically correct genomic phrases. In this paper we propose new kernels based on weighted tree structures, traversing the paths within them to capture the features which underpin the task. Experimentally, we and that these kernels provide performance comparable with state of the art approaches for this problem, while offering significant computational advantages over earlier methods. The methods proposed may be applied to a broad range of sequence or tree-structured data in molecular biology and other domains.

A computational study of carbon dioxide adsorption on solid boron

Capturing and sequestering carbon dioxide (CO2) can provide a route to partial mitigation of climate change associated with anthropogenic CO2 emissions. Here we report a comprehensive theoretical study of CO2 adsorption on two phases of boron, α-B12 and γ-B28. The theoretical results demonstrate that the electron deficient boron materials, such as α-B12 and γ-B28, can bond strongly with CO2 due to Lewis acid-base interactions because the electron density is higher on their surfaces. In order to evaluate the capacity of these boron materials for CO2 capture, we also performed calculations with various degrees of CO2 coverage. The computational results indicate CO2 capture on the boron phases is a kinetically and thermodynamically feasible process, and therefore from this perspective these boron materials are predicted to be good candidates for CO2 capture.