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

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

Performance evaluation of conventional and water saving taps

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record The rapid pace of urbanisation comes with considerable environmental implications including pressures on already stressed limited water resources. In urban areas, most of the water use is associated with water consumption in buildings. The second largest use of water is via taps. It is often assumed that water taps with low flow rates can contribute to reduced per capita water consumption. However, this is based on very little evidence. This paper presents the synthesis of a 13,000 high resolution observations made to investigate the actual water consumption of innovative (water saving) electronic taps and conventional mixer taps. High resolution flow-meters and data loggers were fitted into two washrooms in two different buildings of a higher education institution to record the water use through the basin taps. The recorded data provided information on duration, frequency of use and volume of water consumption per use. The data was helpful in identifying trends in hot and cold water use and therefore can be useful in estimating energy for producing hot water and associated greenhouse gas emissions. Analysis of the observed data suggests that the low flow taps have greater mean water consumption per event than the conventional taps and water consumption is more influenced by user behaviour rather than the technology.Engineering and Physical Sciences Research Council (EPSRC

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

The application of proximal visible and near-infrared spectroscopy to estimate soil organic matter on the Triffa Plain of Morocco

© 2020 Soil organic matter (SOM) is a fundamental soil constituent. The estimation of this parameter in the laboratory using the classical method is complex time-consuming and requires the use of chemical reagents. The objectives of this study were to assess the accuracy of two laboratory measurement setups of the VIS-NIR spectroscopy in estimating SOM content and determine the important spectral bands in the SOM estimation model. A total of 115 soil samples were collected from the non-root zone (0–20 cm) of soil in the study area of the Triffa Plain and then analysed for SOM in the laboratory by the Walkley–Black method. The reflectance spectra of soil samples were measured by two protocols, Contact Probe (CP) and Pistol Grip (PG)) of the ASD spectroradiometer (350–2500 nm) in the laboratory. Partial least squares regression (PLSR) was used to develop the prediction models. The results of coefficient of determination (R2) and the root mean square error (RMSE) showed that the pistol grip offers reasonable accuracy with an R2 = 0.93 and RMSE = 0.13 compared to the contact probe protocol with an R2 = 0.85 and RMSE = 0.19. The near-Infrared range were more accurate than those in the visible range for predicting SOM using the both setups (CP and PG). The significant wavelengths contributing to the prediction of SOM for (PG) setup were at: 424, 597, 1432, 1484, 1830,1920, 2200, 2357 and 2430 nm, while were at 433, 587, 1380, 1431, 1929, 2200 and 2345 nm for (CP) setup

The application of proximal visible and near-infrared spectroscopy to estimate soil organic matter on the Triffa Plain of Morocco

© 2020 The Authors. Published by Elsevier. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1016/j.iswcr.2020.04.005Soil organic matter (SOM) is a fundamental soil constituent. The estimation of this parameter in the laboratory using the classical method is complex time-consuming and requires the use of chemical reagents. The objectives of this study were to assess the accuracy of two laboratory measurement setups of the VIS-NIR spectroscopy in estimating SOM content and determine the important spectral bands in the SOM estimation model. A total of 115 soil samples were collected from the non-root zone (0–20 cm) of soil in the study area of the Triffa Plain and then analysed for SOM in the laboratory by the Walkley–Black method. The reflectance spectra of soil samples were measured by two protocols, Contact Probe (CP) and Pistol Grip (PG)) of the ASD spectroradiometer (350–2500 nm) in the laboratory. Partial least squares regression (PLSR) was used to develop the prediction models. The results of coefficient of determination (R2) and the root mean square error (RMSE) showed that the pistol grip offers reasonable accuracy with an R2 = 0.93 and RMSE = 0.13 compared to the contact probe protocol with an R2 = 0.85 and RMSE = 0.19. The near-Infrared range were more accurate than those in the visible range for predicting SOM using the both setups (CP and PG). The significant wavelengths contributing to the prediction of SOM for (PG) setup were at: 424, 597, 1432, 1484, 1830,1920, 2200, 2357 and 2430 nm, while were at 433, 587, 1380, 1431, 1929, 2200 and 2345 nm for (CP) setup.The authors acknowledge the facilities and financial supports provided by the Mohammed First University and the National Institute of Agronomic Research (INRA) of Oujda.Published versio

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

Antimicrobial Resistance in Typhoidal Salmonella: Surveillance for Enteric Fever in Asia Project, 2016-2019

Background: Clinicians have limited therapeutic options for enteric as a result of increasing antimicrobial resistance, and therefore typhoid vaccination is recommended as a preventive measure. As a part of the Surveillance for Enteric Fever in Asia Project (SEAP), we investigated the extent measured the burden of antimicrobial resistance (AMR) among confirmed enteric fever cases in Bangladesh, Nepal, and Pakistan. Methods: From September 2016-September 2019, SEAP recruited study participants of all age groups from its outpatient, inpatient, hospital laboratory, laboratory network, and surgical sites who had a diagnosis of febrile illness that was either suspected or blood culture confirmed for enteric fever. Antimicrobial resistance of isolates was determined by disc diffusion using Clinical and Laboratory Standard Institute cut-off points. We reported the frequency of multidrug resistance (MDR)(resistance to ampicillin, cotrimoxazole, and chloramphenicol), extensive drug resistance (XDR) (MDR plus non-susceptible to fluoroquinolone and any 3rd generation cephalosporins), and fluoroquinolone (FQ) and azithromycin non-susceptibility. Results: We enrolled 8,705 blood culture confirmed enteric fever cases: 4,873 (56%) from Bangladesh, 1,602 (18%) from Nepal and 2,230 (26%) from Pakistan. Of these, 7,591 (87%) were Salmonella Typhi and 1114 (13%) were S. Paratyphi. MDR S. Typhi was identified in 17% (701/4065) of isolates in Bangladesh, and 1% (19/1342) in Nepal. In Pakistan, 16 % (331/2084) of S. Typhi isolates were MDR, and 64% (1319/2074) were XDR. FQ nonsusceptibility among S. Typhi isolates was 98% in Bangladesh, 87% in Nepal, and 95% in Pakistan. Azithromycin non-susceptibility was detected in 77 (2%) in Bangladesh, 9 (.67%) in Nepal and 9 (.59%) isolates in Pakistan. In Pakistan, three (2%) S. Paratyphi isolates were MDR; no MDR S. Paratyphi was reported from Bangladesh or Nepal. Conclusions: Although AMR against S. Paratyphi was low across the three countries, there was widespread drug resistance among S. Typhi, including FQ non-susceptibility and the emergence of XDR S. Typhi in Pakistan, limiting treatment options. As typhoid conjugate vaccine (TCV) is rolled out, surveillance should continue to monitor changes in AMR to inform policies and to monitor drug resistance in S. Paratyphi, for which there is no vaccine