Data as an asset : what the upstream oil & gas industry can learn about ‘big data’ from companies like Facebook

The upstream oil & gas industry has been contending with massive data sets and monolithic files for many years, but “Big Data”—that is, the ability to apply more sophisticated types of analytical tools to information in a way that extracts new insights or creates new forms of value—is a relatively new concept that has the potential to significantly re-shape the industry. Despite the impressive amount of value that is being realized by Big Data technologies in other parts of the marketplace, however, much of the data collected within the oil & gas sector tends to be discarded, ignored, or analyzed in a very cursory way. This paper examines existing data management practices in the upstream oil & gas industry, and compares them to practices and philosophies that have emerged in organizations that are leading the Big Data revolution. The comparison shows that, in companies that are leading the Big Data revolution, data is regarded as a valuable asset. The presented evidence also shows, however, that this is usually not true within the oil & gas industry insofar as data is frequently regarded there as descriptive information about a physical asset rather than something that is valuable in and of itself. The paper then discusses how upstream oil & gas companies could potentially extract more value from data, and concludes with a series of specific technical and management-related recommendations to this end.

The elaboration likelihood model : review, critique and research agenda

Purpose: The purpose of this paper is to review, critique and develop a research agenda for the Elaboration Likelihood Model (ELM). The model was introduced by Petty and Cacioppo over three decades ago and has been modified, revised and extended. Given modern communication contexts, it is appropriate to question the model’s validity and relevance. Design/methodology/approach: The authors develop a conceptual approach, based on a fully comprehensive and extensive review and critique of ELM and its development since its inception. Findings: This paper focuses on major issues concerning the ELM. These include model assumptions and its descriptive nature; continuum questions, multi-channel processing and mediating variables before turning to the need to replicate the ELM and to offer recommendations for its future development. Research limitations/implications: This paper offers a series of questions in terms of research implications. These include whether ELM could or should be replicated, its extension, a greater conceptualization of argument quality, an explanation of movement along the continuum and between central and peripheral routes to persuasion, or to use new methodologies and technologies to help better understanding consume thinking and behaviour? All these relate to the current need to explore the relevance of ELM in a more modern context. Practical implications: It is time to question the validity and relevance of the ELM. The diversity of on- and off-line media options and the variants of consumer choice raise significant issues. Originality/value: While the ELM model continues to be widely cited and taught as one of the major cornerstones of persuasion, questions are raised concerning its relevance and validity in 21st century communication contexts.

In silico analyses reveal common cellular pathways affected by loss of heterozygosity (LOH) events in the lymphomagenesis of Non-Hodgkin’s lymphoma (NHL)

Background The analysis of cellular networks and pathways involved in oncogenesis has increased our knowledge about the pathogenic mechanisms that underlie tumour biology and has unmasked new molecular targets that may lead to the design of better anti-cancer therapies. Recently, using a high resolution loss of heterozygosity (LOH) analysis, we identified a number of potential tumour suppressor genes (TSGs) within common LOH regions across cases suffering from two of the most common forms of Non-Hodgkin’s lymphoma (NHL), Follicular Lymphoma (FL) and Diffuse Large B-cell Lymphoma (DLBCL). From these studies LOH of the protein tyrosine phosphatase receptor type J (PTPRJ) gene was identified as a common event in the lymphomagenesis of these B-cell lymphomas. The present study aimed to determine the cellular pathways affected by the inactivation of these TSGs including PTPRJ in FL and DLBCL tumourigenesis. Results Pathway analytical approaches identified that candidate TSGs located within common LOH regions participate within cellular pathways, which may play a crucial role in FL and DLBCL lymphomagenesis (i.e., metabolic pathways). These analyses also identified genes within the interactome of PTPRJ (i.e. PTPN11 and B2M) that when inactivated in NHL may play an important role in tumourigenesis. We also detected genes that are differentially expressed in cases with and without LOH of PTPRJ, such as NFATC3 (nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3). Moreover, upregulation of the VEGF, MAPK and ERBB signalling pathways was also observed in NHL cases with LOH of PTPRJ, indicating that LOH-driving events causing inactivation of PTPRJ, apart from possibly inducing a constitutive activation of these pathways by reduction or abrogation of its dephosphorylation activity, may also induce upregulation of these pathways when inactivated. This finding implicates these pathways in the lymphomagenesis and progression of FL and DLBCL. Conclusions The evidence obtained in this research supports findings suggesting that FL and DLBCL share common pathogenic mechanisms. Also, it indicates that PTPRJ can play a crucial role in the pathogenesis of these B-cell tumours and suggests that activation of PTPRJ might be an interesting novel chemotherapeutic target for the treatment of these B-cell tumours.

Ibuprofen supplementation and its effects on NF-KB activation in skeletal muscle following resistance exercise

Resistance exercise triggers a subclinical inflammatory response that plays a pivotal role in skeletal muscle regeneration. Nuclear factor‐κB (NF‐κB) is a stress signalling transcription factor that regulates acute and chronic states of inflammation. The classical NF‐κB pathway regulates the early activation of post‐exercise inflammation; however there remains scope for this complex transcription factor to play a more detailed role in post‐exercise muscle recovery. Sixteen volunteers completed a bout of lower body resistance exercise with the ingestion of three 400 mg doses of ibuprofen or a placebo control. Muscle biopsy samples were obtained prior to exercise and at 0, 3 and 24 h post‐exercise and analysed for key markers of NF‐κB activity. Phosphorylated p65 protein expression and p65 inflammatory target genes were elevated immediately post‐exercise independent of the two treatments. These changes did not translate to an increase in p65 DNA binding activity. NF‐κB p50 protein expression and NF‐κB p50 binding activity were lower than pre‐exercise at 0 and 3 h post‐exercise, but were elevated at 24 h post‐exercise. These findings provide novel evidence that two distinct NF‐κB pathways are active in skeletal muscle after resistance exercise. The initial wave of activity involving p65 resembles the classical pathway and is associated with the onset of an acute inflammatory response. The second wave of NF‐κB activity comprises the p50 subunit, which has been previously shown to resolve an acute inflammatory program. The current study showed no effect of the ibuprofen treatment on markers of the NF‐κB pathway, however examination of the within group effects of the exercise protocol suggests that this pathway warrants further research.

“Well, hang on, they’re actually much better than that!” : disrupting dominant discourses of deficit about English language learners in senior high school English

This paper explores how four English teachers position their English language learners for critical literacy within senior high school curriculum in Queensland, Australia. Such learners are often positioned, even by their teachers, within a broader “deficit discourse” that claims they are inherently lacking the requisite knowledge and skills to engage with intransigent school curricula. As such, English language learners’ identity formation is often constrained by deficit views that can ultimately see limited kinds of literacy teaching offered to them. Using Fairclough’s (2003) critical discourse analysis method, analysis of 16 interviews with the teachers was conducted as part of a larger, critical instrumental case study in two state high schools during 2010. Five competing discourses were identified: deficit as lack; deficit as need; learner “difference” as a resource; conceptual capacity for critical literacy; and linguistic, cultural and conceptual difficulty with critical literacy. While a deficit view is present, counter-hegemonic discourses also exist in their talk. The combination of discourses challenges monolithic deficit views of English language learners, and opens up generative discursive territory to position English language learners in ways other than “problematic”. This has important implications for how teachers view and teach English language learners and their capacity for critical literacy work in senior high school classrooms.

Retinal anatomy of the New Zealand kiwi: Structural traits consistent with their nocturnal behavior

Kiwi (Apteryx spp.) have a visual system unlike that of other nocturnal birds, and have specializations to their auditory, olfactory and tactile systems. Eye size, binocular visual fields and visual brain centers in kiwi are proportionally the smallest yet recorded among birds. Given the many unique features of the kiwi visual system, we examined the laminar organization of the kiwi retina to determine if they evolved increased light sensitivity with a shift to a nocturnal niche or if they retained features of their diurnal ancestor. The laminar organization of the kiwi retina was consistent with an ability to detect low light levels similar to that of other nocturnal species. In particular, the retina appeared to have a high proportion of rod photoreceptors compared to diurnal species, as evidenced by a thick outer nuclear layer, and also numerous thin photoreceptor segments intercalated among the conical shaped cone photoreceptor inner segments. Therefore, the retinal structure of kiwi was consistent with increased light sensitivity, although other features of the visual system, such as eye size, suggest a reduced reliance on vision. The unique combination of a nocturnal retina and smaller than expected eye size, binocular visual fields and brain regions make the kiwi visual system unlike that of any bird examined to date. Whether these features of their visual system are an evolutionary design that meets their specific visual needs or are a remnant of a kiwi ancestor that relied more heavily on vision is yet to be determined.

A biomechanical investigation of dual growing rods used for fusionless scoliosis correction

Background The use of dual growing rods is a fusionless surgical approach to the treatment of early onset scoliosis (EOS), which aims of harness potential growth in order to correct spinal deformity. The purpose of this study was to compare the in-vitro biomechanical response of two different dual rod designs under axial rotation loading. Methods Six porcine spines were dissected into seven level thoracolumbar multi-segmental units. Each specimen was mounted and tested in a biaxial Instron machine, undergoing nondestructive left/right axial rotation to peak moments of 4Nm at a constant rotation rate of 8deg.s-1. A motion tracking system (Optotrak) measured 3D displacements of individual vertebrae. Each spine was tested in an un-instrumented state first and then with appropriately sized semi-constrained growing rods and ‘rigid’ rods in alternating sequence. Range of motion, neutral zone size and stiffness were calculated from the moment-rotation curves and intervertebral ranges of motion were calculated from Optotrak data. Findings Irrespective of test sequence, rigid rods showed significantly reduction of total rotation across all instrumented levels (with increased stiffness) whilst semi-constrained rods exhibited similar rotation behavior to the un-instrumented (P<0.05). An 11% and 8% increase in stiffness for left and right axial rotation respectively and 15% reduction in total range of motion was recorded with dual rigid rods compared with semi-constrained rods. Interpretation Based on these findings, the semi-constrained growing rods do not increase axial rotation stiffness compared with un-instrumented spines. This is thought to provide a more physiological environment for the growing spine compared to dual rigid rod constructs.

An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss

Background Environmental factors can influence obesity by epigenetic mechanisms. Adipose tissue plays a key role in obesity-related metabolic dysfunction, and gastric bypass provides a model to investigate obesity and weight loss in humans. Results Here, we investigate DNA methylation in adipose tissue from obese women before and after gastric bypass and significant weight loss. In total, 485,577 CpG sites were profiled in matched, before and after weight loss, subcutaneous and omental adipose tissue. A paired analysis revealed significant differential methylation in omental and subcutaneous adipose tissue. A greater proportion of CpGs are hypermethylated before weight loss and increased methylation is observed in the 3′ untranslated region and gene bodies relative to promoter regions. Differential methylation is found within genes associated with obesity, epigenetic regulation and development, such as CETP, FOXP2, HDAC4, DNMT3B, KCNQ1 and HOX clusters. We identify robust correlations between changes in methylation and clinical trait, including associations between fasting glucose and HDAC4, SLC37A3 and DENND1C in subcutaneous adipose. Genes investigated with differential promoter methylation all show significantly different levels of mRNA before and after gastric bypass. Conclusions This is the first study reporting global DNA methylation profiling of adipose tissue before and after gastric bypass and associated weight loss. It provides a strong basis for future work and offers additional evidence for the role of DNA methylation of adipose tissue in obesity.

Breaking the DNA-vaccine bottleneck

Monash University in Australia has developed a new approach towards DNA vaccine development that has the potential to cut the time it takes to produce a vaccine from up to nine months to four weeks or less. The university has designed and filed a patent on a commercially viable, single-stage technology for manufacturing DNA molecules. The technology was used to produce malaria and measles DNA vaccines, which were tested to be homogeneous supercoiled DNA, free from RNA and protein contaminations and meeting FDA regulatory standards for DNA vaccines. The technique is based on customized, smart, polymeric, monolithic adsorbents that can purify DNA very rapidly. The design criteria of solid-phase adsorbent include rapid adsorption and desorption kinetics, physical composition, and adequate selectivity , capacity and recovery. The new show technology significantly improved binding capacities, higher recovery, drastically reduced use of buffers and processing time, less clogging, and higher yields of DNA.

The harnessing of peptide-monolith constructs for single step plasmid DNA purification

The availability of synthetic peptides has paved the way for their use in tailor-made interactions with biomolecules. In this study, a 16mer LacI-based peptide was used as an affinity ligand to examine the scale up feasibility for plasmid DNA purification. First, the peptide was designed and characterized for the affinity purification of lacO containing plasmid DNA, to be employed as a high affinity ligand for the potential capturing of plasmid DNA in a single unit operation. It was found there were no discernible interactions with a control plasmid that did not encode the lacO nucleotide sequence. The dissociation equilibrium constant of the binding between the 16mer peptide and target pUC19 was 5.0 ± 0.5 × 10-8 M as assessed by surface plasmon resonance. This selectivity and moderated affinity indicate that the 16mer is suitable for the adsorption and chromatographic purification of plasmid DNA. The suitability of this peptide was then evaluated using a chromatography system with the 16mer peptide immobilized to a customized monolith to purify plasmid DNA, obtaining preferential purification of supercoiled pUC19. The results demonstrate the applicability of peptide-monolith supports to scale up the purification process for plasmid DNA using designed ligands via a biomimetic approach.

Versatility of polymethacrylate monoliths for chromatographic purification of biomolecules

Polymethacrylate monoliths, specifically poly(glycidyl methacrylate-co-ethylene dimethacrylate) or poly(GMA-co-EDMA) monoliths, are a new generation of chromatographic supports and are significantly different from conventional particle-based adsorbents, membranes, and other monolithic supports for biomolecule purification. Similar to other monoliths, polymethacrylate monoliths possess large pores which allow convective flow of mobile phase and result in high flow rates at reduced pressure drop, unlike particulate supports. The simplicity of the adsorbent synthesis, pH resistance, and the ease and flexibility of tailoring their pore size to that of the target biomolecule are the key properties which differentiate polymethacrylate monoliths from other monoliths. Polymethacrylate monoliths are endowed with reactive epoxy groups for easy functionalization (with anion-exchange, hydrophobic, and affinity ligands) and high ligand retention. In this review, the structure and performance of polymethacrylate monoliths for chromatographic purification of biomolecules are evaluated and compared to those of other supports. The development and use of polymethacrylate monoliths for research applications have grown rapidly in recent times and have enabled the achievement of high through-put biomolecule purification on semi-preparative and preparative scales.

Rapid production of a plasmid DNA encoding a malaria vaccine candidate via amino-functionalized poly(GMA-co-EDMA) monolith

Malaria is a global health problem; an effective vaccine is urgently needed. Due to the relative poverty and lack of infrastructure in malaria endemic areas, DNA-based vaccines that are stable at ambient temperatures and easy to formulate have great potential. While attention has been focused mainly on antigen selection, vector design and efficacy assessment, the development of a rapid and commercially viable process to manufacture DNA is generally overlooked. We report here a continuous purification technique employing an optimized stationary adsorbent to allow high-vaccine recovery, low-processing time, and, hence, high-productivity. A 40.0 mL monolithic stationary phase was synthesized and functionalized with amino groups from 2-Chloro-N,N- diethylethylamine hydrochloride for anion-exchange isolation of a plasmid DNA (pDNA) that encodes a malaria vaccine candidate, VR1020-PyMSP4/5. Physical characterization of the monolithic polymer showed a macroporous material with a modal pore diameter of 750 nm. The final vaccine product isolated after 3 min elution was homogeneous supercoiled plasmid with gDNA, RNA and protein levels in keeping with clinical regulatory standards. Toxicological studies of the pVR1020-PyMSP4/5 showed a minimum endotoxin level of 0.28 EU/m.g pDNA. This cost-effective technique is cGMP compatible and highly scalable for the production of DNA-based vaccines in commercial quantities, when such vaccines prove to be effective against malaria. © 2008 American Institute of Chemical Engineers.

A thermal expulsion approach to homogeneous large-volume methacrylate monolith preparation; enabling large-scale rapid purification of biomolecules

Numerous efforts have been dedicated to the synthesis of large-volume methacrylate monoliths for large-scale biomolecules purification but most were obstructed by the enormous release of exotherms during preparation, thereby introducing structural heterogeneity in the monolith pore system. A significant radial temperature gradient develops along the monolith thickness, reaching a terminal temperature that supersedes the maximum temperature required for structurally homogenous monoliths preparation. The enormous heat build-up is perceived to encompass the heat associated with initiator decomposition and the heat released from free radical-monomer and monomer-monomer interactions. The heat resulting from the initiator decomposition was expelled along with some gaseous fumes before commencing polymerization in a gradual addition fashion. Characteristics of 80 mL monolith prepared using this technique was compared with that of a similar monolith synthesized in a bulk polymerization mode. An extra similarity in the radial temperature profiles was observed for the monolith synthesized via the heat expulsion technique. A maximum radial temperature gradient of only 4.3°C was recorded at the center and 2.1°C at the monolith peripheral for the combined heat expulsion and gradual addition technique. The comparable radial temperature distributions obtained birthed identical pore size distributions at different radial points along the monolith thickness.

Large-volume methacrylate monolith for plasmid purification : process engineering approach to synthesis and application

The extent of exothermicity associated with the construction of large-volume methacrylate monolithic columns has somewhat obstructed the realisation of large-scale rapid biomolecule purification especially for plasmid-based products which have proven to herald future trends in biotechnology. A novel synthesis technique via a heat expulsion mechanism was employed to prepare a 40 mL methacrylate monolith with a homogeneous radial pore structure along its thickness. Radial temperature gradient was recorded to be only 1.8 °C. Maximum radial temperature recorded at the centre of the monolith was 62.3 °C, which was only 2.3 °C higher than the actual polymerisation temperature. Pore characterisation of the monolithic polymer showed unimodal pore size distributions at different radial positions with an identical modal pore size of 400 nm. Chromatographic characterisation of the polymer after functionalisation with amino groups displayed a persistent dynamic binding capacity of 15.5 mg of plasmid DNA/mL. The maximum pressure drop recorded was only 0.12 MPa at a flow rate of 10 mL/min. The polymer demonstrated rapid separation ability by fractionating Escherichia coli DH5α-pUC19 clarified lysate in only 3 min after loading. The plasmid sample collected after the fast purification process was tested to be a homogeneous supercoiled plasmid with DNA electrophoresis and restriction analysis.

The suitability of DEAE-Cl active groups on customized poly(GMA-co-EDMA) continuous stationary phase for fast enzyme-free isolation of plasmid DNA

The creation of a commercially viable and a large-scale purification process for plasmid DNA (pDNA) production requires a whole-systems continuous or semi-continuous purification strategy employing optimised stationary adsorption phase(s) without the use of expensive and toxic chemicals, avian/bovine-derived enzymes and several built-in unit processes, thus affecting overall plasmid recovery, processing time and economics. Continuous stationary phases are known to offer fast separation due to their large pore diameter making large molecule pDNA easily accessible with limited mass transfer resistance even at high flow rates. A monolithic stationary sorbent was synthesised via free radical liquid porogenic polymerisation of ethylene glycol dimethacrylate (EDMA) and glycidyl methacrylate (GMA) with surface and pore characteristics tailored specifically for plasmid binding, retention and elution. The polymer was functionalised with an amine active group for anion-exchange purification of pDNA from cleared lysate obtained from E. coli DH5α-pUC19 pellets in RNase/protease-free process. Characterization of the resin showed a unique porous material with 70% of the pores sizes above 300 nm. The final product isolated from anion-exchange purification in only 5 min was pure and homogenous supercoiled pDNA with no gDNA, RNA and protein contamination as confirmed with DNA electrophoresis, restriction analysis and SDS page. The resin showed a maximum binding capacity of 15.2 mg/mL and this capacity persisted after several applications of the resin. This technique is cGMP compatible and commercially viable for rapid isolation of pDNA.