Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays

Android application collusion demystified

Application collusion is an emerging threat to Android based devices. In app collusion, two or more apps collude in some manner to perform a malicious action that they are unable to do independently. Detection of colluding apps is a challenging task. Existing commercial malware detection systems analyse each app separately, hence fail to detect any joint malicious action performed by multiple apps through collusion. In this paper, we discuss the current state of research on app collusion and open challenges to the detection of colluding apps. We compare existing approaches and present an integrated approach to effectively detect app collusion

Primary cilia elongation in response to interleukin-1 mediates the inflammatory response

Primary cilia are singular, cytoskeletal organelles present in the majority of mammalian cell types where they function as coordinating centres for mechanotransduction, Wnt and hedgehog signalling. The length of the primary cilium is proposed to modulate cilia function, governed in part by the activity of intraflagellar transport (IFT). In articular cartilage, primary cilia length is increased and hedgehog signaling activated in osteoarthritis (OA). Here, we examine primary cilia length with exposure to the quintessential inflammatory cytokine interleukin-1 (IL-1), which is up-regulated in OA. We then test the hypothesis that the cilium is involved in mediating the downstream inflammatory response. Primary chondrocytes treated with IL-1 exhibited a 50 % increase in cilia length after 3 h exposure. IL-1-induced cilia elongation was also observed in human fibroblasts. In chondrocytes, this elongation occurred via a protein kinase A (PKA)-dependent mechanism. G-protein coupled adenylate cyclase also regulated the length of chondrocyte primary cilia but not downstream of IL-1. Chondrocytes treated with IL-1 exhibit a characteristic increase in the release of the inflammatory chemokines, nitric oxide and prostaglandin E2. However, in cells with a mutation in IFT88 whereby the cilia structure is lost, this response to IL-1 was significantly attenuated and, in the case of nitric oxide, completely abolished. Inhibition of IL-1-induced cilia elongation by PKA inhibition also attenuated the chemokine response. These results suggest that cilia assembly regulates the response to inflammatory cytokines. Therefore, the cilia proteome may provide a novel therapeutic target for the treatment of inflammatory pathologies, including OA

Drawing to Remember: External Support of Older Adults’ Eyewitness Performance

Although healthy aging is accompanied by a general decline in memory functioning, environmental support at retrieval can improve older adults’ (+65 years) episodic remembering. Despite those over the age of 65years representing a growing proportion of the population, few environmental retrieval support methods have been empirically evaluated for use with older witnesses and victims of crime. Here, the efficacy of a novel retrieval technique, the Sketch Mental Reinstatement of Context, is compared with a standard Mental Reinstatement of Context and a no support control (Control). Fifty-one participants witnessed an unexpected live event, and 48 hours later were interviewed using one of three aforementioned techniques. In line with predictions emanating from cognitive theories of aging and the environmental support hypothesis, participants in the Sketch Mental Reinstatement of Context condition recalled significantly more correct information and fewer inaccurate items. The Sketch Mental Reinstatement of Context technique appears to scaffold memory retrieval in an age-appropriate manner during a post-event interview, possibly by encouraging more effortful retrieval and reducing dual-task load. As such, this procedure offers an effective alternative to current approaches, adding to the toolbox of techniques available to forensic and other interviewers

Protecting eyewitness evidence: Examining the efficacy of a self-administered interview tool

Given the crucial role of eyewitness evidence, statements should be obtained as soon as possible after an incident. This is not always achieved due to demands on police resources. Two studies trace the development of a new tool, the Self-Administered Interview (SAI), designed to elicit a comprehensive initial statement. In Study 1, SAI participants reported more correct details than participants who provided a free recall account, and performed at the same level as participants given a Cognitive Interview. In Study 2, participants viewed a simulated crime and half recorded their statement using the SAI. After a delay of 1 week, all participants completed a free recall test. SAI participants recalled more correct details in the delayed recall task than control participants

Benign thyroid disease and dietary factors in thyroid cancer: a case-control study in Kuwait

We conducted a population-based study of 313 case–control pairs in Kuwait to examine the aetiology of thyroid cancer, the second most common neoplasm among women in this and several other countries in the Gulf region. Among the demographic variables, individuals with 12+ years of education had a significantly reduced risk of thyroid cancer (OR=0.6; 95% CI: 0.3–0.9). The average age at diagnosis (s.d.) of thyroid cancer was 34.711 years in women and 3913.4 years in men. History of thyroid nodule was reported only by cases (n=34; 10.9%; lower 95% CI: 12.0); and goitre by 21 cases and four controls (OR=5.3; 95% CI: 1.8–15.3). There was no significant increase in risk with history of hypothyroidism (OR=1.8) or hyperthyroidism (OR=1.7). For any benign thyroid disease, the OR was 6.4 (95% CI: 3.4–12.0); and the population attributable risk was about 26% (95% CI: 21.1–30.9). Stepwise regression analysis showed that high consumption of processed fish products (OR=2.2; 95% CI: 1.6–3.0) fresh fish (OR=0.5; 95% CI: 0.4–0.7) and chicken (OR=1.7; 95% CI: 1.2–2.3) were independently associated with thyroid cancer with significant dose-response relationships. Among the thyroid cancer patients who reported high consumption of fish products, a large majority also reported high consumption of fresh fish (98%) and shellfish (68%). No clear association emerged with consumption of cruciferous vegetables. These data support the hypothesis that hyperplastic thyroid disease is strongly related to thyroid cancer; and that habitual high consumption of various seafoods may be relevant to the aetiology of thyroid cancer. The association with chicken consumption requires further study

Treated residential greywater and its effect on shoot dry matter and nutrient uptake in maize (Zea mays)

This is the final version. Available from the publisher via the DOI in this record.Shortage of freshwater resources and limited fertilizer usage due to cost related issues in agriculture are the basic limiting factors in food production. This study evaluated the effect of greywater application on shoot dry mater and uptake of maize crop. The experiment included five treatments canal water, untreated greywater and treated greywater through reed bed technology using Cyperus iria, Phragmites karka and Typha elephantina, arranged in a randomized complete block design. All the treatments received a basal doze of NPK fertilizer. The soil used in the experiment was silty clay in texture with 55% clay, pH - 7.70, EC - 1.07 dS m-1 , CaCO3 - 12.50% organic matter - 0.17%, NO3-N – 4.60 mg kg-1 , NH4-N – 1.68 mg kg-1 , ammonium bicarbonate diethylene triamine penta acetic acid (AB-DTPA) extractable P and K as 0.18 and 270 mg kg-1 , respectively. The treated greywater had a highly significant effect on shoot dry matter and N, P and K uptake in maize. The highest contents were found in treatments applied with greywater, treated under reed bed technology using Cyperus iria and the lowest in canal water applied treatments. Part of applied fertilizer was supplemented through greywater application

Characteristics of micro-propagated banana (Musa spp.) cultures stressed with NaCl and polyethylene glycol

The effect of NaCl and PEG was assessed on plant micro-propagation rate in banana (Musa spp.) cv., Basrai. Well micro-propagated plantlets were cultured on four different stresses of NaCl and PEG-4000 including control level: MS2b (MS0 + 3.0 mg l-1 BAP), MS2c (MS0 + 100 mol m-3 NaCl), MS2d (MS0 + 5% PEG) and MS2e (MS0 + 100 mol m-3 NaCl + 5 % PEG) for 6-weeks. Efficiency of plant micro-propagation was reduced significantly among the stressed cultures. Similarly, photosynthetic pigments like chl a was decreased non-significantly but chl b, chl ab were decreased significantly. Total carotenoids were increased in the saline as well as PEG stressed cultures. Cell size of epidermis and aerenchyma was increased (p < 0.05), while parenchyma decreased. Proline and glycinebetain contents were increased (p < 0.05) in each stressed culture but were high in MS2 than in MS3 and MS4 cultures. Meanwhile, proteins, sugars, phenolics and nitrates were observed to be in the reversed (p < 0.05) phenomena. In conclusion, NaCl treatment was observed to be most toxic than the PEG or PEG with NaCl on the banana micro-propagation.Key words: Musa spp., micro-propagation, NaCl (sodium chloride), PEG (polyethylene glycol), chlorophyll contents, proline, reducing sugars

Developing GUI Applications in a Verified Setting

Although there have been major achievements in verified software, work on verifying graphical user interfaces (GUI) applications is underdeveloped relative to their ubiquity and societal importance.In this paper, we present a library for the development of verified, state-dependent GUI applications in the dependently typed programming language Agda. The library uses Agda's expressive type system to ensure that the GUI, its controller, and the underlying model are all consistent, significantly reducing the scope for GUI-related bugs.We provide a way to specify and prove correctness properties of GUI applications in terms of user interactions and state transitions. Critically, GUI applications and correctness properties are not restricted to finite state machines and may involve the execution of arbitrary interactive programs. Additionally, the library connects to a standard, imperative GUI framework, enabling the development of native GUI applications with expected features, such as concurrency.We present applications of our library to building GUI applications to manage healthcare processes. The correctness properties we consider are the following: (1) That a state can only be reached by passing through a particular intermediate state, for example, that a particular treatment can only be reached after having conducted an X-Ray. (2) That one eventually reaches a particular state, for example, that one eventually decides on a treatment. The specification of such properties is defined in terms of a GUI application simulator, which simulates all possible sequences of interactions carried out by the user