Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct genetic transformation of Hibiscus sabdariffa L.

Transgenic Hibiscus sabdariffa plants have been produced by a tissue culture independent method using Agrobacterium tumefasciens transformation procedure. Embryo axes of mature seeds with one cotyledon excised were infected by immersion in a suspension of Agrobacterium LBA 4404 strain culture that carries pBal plasmid with β-glucuronidase p35SGUSINT and plant selectable marker Neomycin Phospho-Transferase gene ( npt II). Following a 24 h co-cultivation with Agrobacterium strain and decontamination with cefotaxime, embryos were grown on soil rite containing MS medium added with a killer concentration of kanamycin (100 μg/ml) during 4 weeks at room conditions and thereafter transferred to greenhouse. 54.3% of the seedlings grew well on the selective medium; 68% of the explants excised from putative transformed plants were found to be GUS positive. After 60 days evaluation point, the assessment of the transformation by PCR revealed that H. sabdariffa line tested, carried the npt II gene. Key Words: Hibiscus sabdariffa; genetic transformation. African Journal of Biotechnology Vol. 3 (4), 2004: 226-228
Rhythmic ammonium regeneration and flushing in intertidal sediments of the Sado estuary

The effects of exposure to the atmosphere on ammonium cycling in intertidal sediments were examined at a single site in the Sado estuary (Portugal) during a tidal cycle in November 1994. During a 9‐h period, covering pre‐ebb to postflood, 11 high‐resolution vertical profiles of dissolved and sorbed ammonia and water content were collected. In addition, the vertical distribution of temperature was measured, primarily at the beginning and the end of the exposure period. The most dramatic changes occurred at the end of the exposed period when water flooded the sediment; ~75% of the dissolved and sorbed NH4+ pool (44.2 mmol m‐2) was flushed into the water column by buoyancy‐driven Porewater exchange. Some 64% of the flushed inventory (28.2 mmol m‐2) was produced during the exposure period, at an average rate of 4.9 mmol NH4+ m‐2 h‐1. The build‐up of ammonium in the sediment was faster in the sorbed pool than in the dissolved pool. An average first‐order carbon mineralization rate of 85.2 mmol C m‐2 h‐l during exposure was estimated from the ammonification rate. Residence times for the organic carbon and nitrogen pools were also calculated (37.5 and 43.4 d, respectively), giving indication of the rapidity of the turnover of organic matter possible in estuary intertidal sediments.
Mobile augmented reality learning objects in higher education

Teachers and learners in all sectors of education continue to have access to a growing number of mobile augmented reality (AR) applications for the creation and implementation of mobile AR experiences and learning objects (LOs). In this study, affordances of mobile AR and LOs for higher education are investigated through the mobile AR platform HP Reveal. Digital trace data from publicly shared and published AR users’ LOs were examined to investigate affordances of AR technology in educational organisations and institutions and their potential implications in areas of higher education. For this purpose, a quantitative comparative analysis of system data and content from 632 AR LOs was conducted at two instances over a 2-year interval period. Each LO was thematically coded to determine multimodal functionalities and characteristics. Further thematic coding and categorisation revealed four emergent categories for affordances in higher education: learner interaction, collaboration, cultural exploration and digital storytelling. Results also revealed increases over time in the use of recorded and online video content and the use of three-dimensional (3D) characters for educational purposes. An examination of the affordances offered by the AR platform revealed opportunities for educators to explore further interactive and collaborative uses of AR with their learners for pedagogical purposes in higher education. This paper is part of the special collection Mobile Mixed Reality Enhanced Learning, edited by ThomCochrane, Fiona Smart, Helen Farley and Vickel Narayan. More papers from this collection can befound here.
Prediction model for estimating optimum harvesting time of oil palm fresh fruit bunches

This study introduced the image based measurement for modelling the oil palm fresh fruit bunches (FFB) maturity prediction which enables the determination of the correct time for harvesting. The experimental procedure starts from collection of the fruitlets of FFB during unripe (black colour surface) until overripe (orange colour surface) stages of Tenera (Elaeis guineensis) oil palm planting material. The calculations to determine the mesocarp oil content was developed based on ratio of oil to dry mesocarp. The images were analysed for optical properties of colour, namely hue, using the analysis software that was developed at our research laboratory. Regression analysis of polynomial 2 nd order equation method showed that the optical property of oil palm fruit was significant in determining the oil from the fruit mesocarp, with respect to the degree of maturity. A high correlation was found for relationship of mesocarp oil content versus day of harvesting with equation of Y=-1.1405X+73.719 and R 2 of 0.81 was acceptable. The model will then can be used to develop an equation for the software to enable the oil palm planters to determine the time of harvesting the matured oil palm fruit bunches.
Erratum

In recent years, the number of publications dealing with the mathematical and physical 3-D aspects of the magnetotelluric method has increased drastically. However, field experiments on a grid are often impractical and surveys are frequently restricted to single or widely separated profiles. So, in many cases we find ourselves with the following question: is the applicability of the 2-D hypothesis valid to extract geoelectric and geological information from real 3-D environments? The aim of this paper is to explore a few instructive but general situations to understand the basics of a 2-D interpretation of 3-D magnetotelluric data and to determine which data subset (TE-mode or TM-mode) is best for obtaining the electrical conductivity distribution of the subsurface using 2-D techniques. A review of the mathematical and physical fundamentals of the electromagnetic fields generated by a simple 3-D structure allows us to prioritise the choice of modes in a 2-D interpretation of responses influenced by 3-D structures. This analysis is corroborated by numerical results from synthetic models and by real data acquired by other authors. One important result of this analysis is that the mode most unaffected by 3-D effects depends on the position of the 3-D structure with respect to the regional 2-D strike direction. When the 3-D body is normal to the regional strike, the TE-mode is affected mainly by galvanic effects, while the TM-mode is affected by galvanic and inductive effects. In this case, a 2-D interpretation of the TM-mode is prone to error. When the 3-D body is parallel to the regional 2-D strike the TE-mode is affected by galvanic and inductive effects and the TM-mode is affected mainly by galvanic effects, making it more suitable for 2-D interpretation. In general, a wise 2-D interpretation of 3-D magnetotelluric data can be a guide to a reasonable geological interpretation.
The use of transgenic and naturally occurring mutants to understand and manipulate tomato fruit ripening

In the years since we last reviewed the use of mutants to study tomato fruit ripening (Grierson et al. 1987), considerable information has been gained by the cloning, sequencing and identification of many mRNAs implicated in this developmental process. Genes involved in cell wall degradation, colour change and ethylene synthesis have been cloned, and antisense techniques have been developed and used to produce genetically engineered mutant fruit deficient in these aspects of ripening (see Gray et al. 1992). Recently, a previously cloned ripening gene has been used to complement a naturally occurring fruit colour mutant, yellow flesh (Fray & Grierson 1993a), and a ripening impaired mutant, ripening inhibitor, has been used to identify several new ripening-related mRNAs (Picton et al. 1993b). The chromosomal region bearing the ripening inhibitor mutation has been subjected to high-resolution mapping (Churchill, Giovannoni & Tanksley 1993) and chromosome walking experiments are in progress to identify this gene.
Preliminary analysis of expressed sequence tags for sugarcane.

Sugarcane (Saccharum spp. hybrids), with its complex polyploid genome, is not well understood at the genetic level. Partial sequencing of anonymous cDNA clones is a widely used technique for gene identification. These partial cDNA sequences, or Expressed Sequence Tags (ESTs) have potential application for the identification of important genes for genetic manipulation. This study aimed to initiate the preliminary development of an EST database for sugarcane and thereby gain some potentially useful information on sugarcane gene sequences. A nondirectional cDNA library has been constructed from sugarcane leaf roll (meristematic region) tissue. Two hundred fifty clones have been randomly selected, subjected to single-pass sequencing from the 5' end of the vector, and identified by sequence similarity searches against gene sequences in international databases. Of the 250 leaf roll clones, 26% exhibit similarity to known plant genes, 50% to non-plant genes, while 24% represent new gene sequences. Analysis of the identified clones indicated sequence similarity to a broad diversity of genes encoding proteins such as enzymes, structural proteins, and regulatory factors. A significant proportion of genes identified in the leaf roll were involved in processes related to protein synthesis and protein modification, as would be expected in meristematic tissues. These results present a successful application of EST analysis in sugarcane and provide a preliminary indication of gene expression in leaf roll tissue.
Land-Use Change Detection with Convolutional Neural Network Methods

Convolutional neural networks (CNN) have been used increasingly in several land-use classification tasks, but there is a need to further investigate its potential. This study aims to evaluate the performance of CNN methods for land classification and to identify land-use (LU) change. Eight transferred CNN-based models were fully evaluated on remote sensing data for LU scene classification using three pre-trained CNN models AlexNet, GoogLeNet, and VGGNet. The classification accuracy of all the models ranges from 95% to 98% with the best-performed method the transferred CNN model combined with support vector machine (SVM) as feature classifier (CNN-SVM). The transferred CNN-SVM model was then applied to orthophotos of the northeastern Cloverdale as part of the City of Surrey, Canada from 2004 to 2017 to perform LU classification and LU change analysis. Two sources of datasets were used to train the CNN–SVM model to solve a practical issue with the limited data. The obtained results indicated that residential areas were expanding by creating higher density, while green areas and low-density residential areas were decreasing over the years, which accurately indicates the trend of LU change in the community of Cloverdale study area.
Severity gradation of psoriatic plaques using ensemble of deep convolutional neural networks

Severity gradation of psoriatic plaque is important for the estimation of Psoriasis Area Severity Index (abbreviated as PASI) that facilitates the diagnosis as well as the treatment of the disease. Severity assessment by manual examination of the plaques of the diseased person or by observation of images of the affected skin area suffers from inter and intra-observer variability.Therefore, automated techniques can not only lead to reduced effort but also can reduce inaccuracy, provided a sufficient amount of correctly annotated data is available. Recent advancements of deep learning in computer vision and medical imaging domain has led to a substantial improvement of performance over traditional image processing techniques.This work has proposed five new methods for severity scoring in order to bring about improvement in accuracy from the baseline. The first method uses a small-sized CNN with very less number of parameters for classification; the second method uses a two-stage classification approach based on CNN; the third method is a pair wise CNN based classification method; the fourth one is a majority voting based CNN ensemble and fifth one is a stacking or super-learning based CNN ensemble. Other approaches like Texture CNN based classification have also been tried and depicted in the thesis as well.
OXA β-lactamases in Acinetobacter: the story so far

The emergence of carbapenem resistance in Acinetobacter baumannii has become a global concern since these beta-lactams are often the only effective treatment left against many multiresistant strains. A recent development has been the discovery of a novel group of narrow-spectrum OXA beta-lactamases in carbapenem-resistant strains, some of which have acquired the ability to hydrolyse the carbapenems. The first of these was found in a strain isolated in Edinburgh before imipenem was in use in the hospital. Whether these carbapenemases have been acquired or are part of the genetic make-up of this species has yet to be determined. More importantly, however, they represent an important stage in the evolution of antibiotic resistance in Acinetobacter. This paper discusses the emergence of these unusual enzymes over the past decade.
On Using Hardware Assertion Checkers for Bit-flip Detection in Post-Silicon Validation

With the rising demand for integrating more features in a single product, modern designs feature more and more functionality on a single die. The complexity resulted from this growth makes it more difficult to guarantee that all errors are detected and fixed before the product is manufactured. Efforts carried out before the design is manufactured, known as pre-silicon verification, are unable to detect all the errors. Electrical errors, such as those caused by cross-talk or power droops, are particularly difficult to catch during the pre-silicon phase because of the insufficient accuracy of device models, which is often traded-off against simulation time. This challenge is further aggravated by the rising number of voltage domains, especially if subtle errors are excited in unique electrical states. These electrically-induced subtle errors most commonly manifest in the logic domain as bit-flips in flip-flops. Therefore, once the design prototypes are available, the verification tasks continue on them to identify and eliminate errors that have escaped pre-silicon verification phase and have the potential to cause catastrophic problems if they remain undetected. This task is commonly referred to as post-silicon validation and has become an important step in the design flow of system-on-chip devices. Limited internal node observability is one of the main challenges of post-silicon validation because it causes long error detection latencies. The existing approaches
Predators, parasitoids and pathogens: species richness, trophic generality and body sizes in a natural food web

Summary 1. A food web is presented which describes trophic interactions among the herbivores, parasitoids, predators and pathogens associated with broom, Cytisus scoparius (L.) Link. The data come from published work on the community at a single site. The web comprises a total of 154 taxa: one plant, 19 herbivores, 66 parasitoids, 60 predators, five omnivores and three pathogens. There are 370 trophic links between these taxa in the web. The taxa form 82 functionally distinct groups, called trophic species. 2. Predators consumed significantly more species than did parasitoids: a median of two prey species per species of predator (range = 1–9), compared to a median of one host species per species of parasitoid (range = 1–4). Significant differences in the number of species consumed were also found among the five predator groups: birds (median = 4), spiders (median = 5), Coleoptera (median = 1), Diptera (median = 2) and Hemiptera (median = 7). 3. Vulnerability, measured by numbers of consumer species, was significantly affected by the herbivores’ feeding styles: externally feeding herbivores were most vulnerable and the concealed herbivores were least vulnerable. Miners were vulnerable to the most parasitoid species and externally feeding herbivores were the most vulnerable to predators. 4. Resource species had a median vulnerability of 13 consumer species, a figure far higher than that in most published food webs. No significant relationship was found between species’ vulnerability to predators and vulnerability to parasitoids. However, there was a strong negative relationship between the percentage mortality due to predation and percentage mortality due to parasitism. 5. The broom food web contains nine orders of insects, a figure higher than previously recorded. The web also contains vertebrates, arachnids, bacteria and fungi. Most of the interactions between the orders were weak. Connectance was calculated for the complete web, the parasitoid sub-web and the predator sub-web. The connectance of the predator sub-web, a value of 0·0364, was more than an order of magnitude larger than the connectance of the entire web (0·0156) or the parasitoid sub-web (0·018). 6. The body lengths of 52 species in the food web were estimated from field guides or museum specimens. Larger predators consumed smaller prey in 93% of predator–prey interactions. Smaller parasitoids consumed larger hosts in 79% of parasitoid–host interactions. Parasitoids were significantly smaller than predators. 7. The 52 species were arranged in order of increasing body length along the columns and down the rows of a food web matrix. The predator sub-web was predominantly upper triangular with 8% of non-zero elements falling below the leading diagonal. The parasitoid sub-web was predominantly lower triangular with 21% non-zero elements falling above the leading diagonal. The entire web contains entries both above and below the main diagonal and thus violates a central assumption of the cascade model.
Experiences and Practices of Nurses Caring for Terminally Ill Cancer Patients: A Qualitative Study

The aim of this study was to explore the experiences and practices of nurses caring for terminally ill cancer patients at the Pietersburg Hospital, in the Limpopo Province, South Africa. Data was collected using semi-structured interviews. Data were analysed using Tesch’s open coding data analysis method. Some of the nurses feel that caring for terminally ill cancer patients was emotionally demanding, strenuous and stressful because of the extensive pain that patients experience. The nurses bond with the patients to such an extent that they feel as if they are family. However, most of the oncology nurses blame themselves, feeling as if they do not do enough to help patients survive, when caring for the terminally ill cancer patients. Family members have expectations of nurses when their patient is in hospital; and when their expectations fail, they sometimes become aggressive and fault-finding. Most oncology nurses consider caring for terminally ill patient a stressful job; yet others expressed love for it. The findings of this study indicate that oncology patients need nurses to support and care for them at all times. Nurses who care for cancer patients have different experiences, some of which cause stress which is painful because they become close to patients and understand the pain they are suffering. Nurses, who care for cancer patients need care and support from hospital management in order to cope with their work.
Morphometric Variation in the Tunisian Green Frog, Rana saharica (Anura: Ranidae)

Rana saharica is the most widely distributed anuran in Tunisia. We examined morphological variation in 124 specimens as a function of their geographical origin, using univariate and multivariate statistics with traditional morphometrics. Our results supported the existence of three morphotypes of this species, correctly classified 84.7% of specimens, and indicated significant degrees of variation in morphometric characteristics between regions. No significant differences were found between sexes among populations. We observed an increase in body size and a decrease in body mass as a function of latitude. Specimens from the southernmost region had the smallest body size and the greatest morphometric divergence. The pattern of morphometric variation probably results from phenotypic plasticity correlated with local environmental factors.
Service Function Chaining

This document describes a Hybrid Hierarchical Multi-Domain Service Function Chaining (hhSFC) architecture that extends Service Function Chaining (SFC) to multiple domains with different technology, administration or ownership. The goals of Hybrid Hierarchical SFC are to reduce the complexity of the control plane in a single domain and make the negotiation between different domains possible. Table of
Mutation-based genetic improvement of software

Genetic Improvement (GI) of software is a recent field that has drawn much attention from Software Engineering researchers. It aims to use search techniques to automatically modify and improve existing software. The drawback in previous GI approaches is scalability of these approaches, due to the large search space formed by the code base in real-world systems. To overcome the scalability challenge, more recent studies have confined the granularity of code modification at the statement level and applied a prior sensitivity analysis to further reduce the search space. However, some software improvements may require code changes at a finer level of granularity. This thesis demonstrates that, by combining with Mutation Testing techniques, GI can operate at this finer granularity while preserving scalability. The thesis applies Mutation Operators to automatically modify the source code of the target software. After a prior sensitivity analysis on First Order Mutants, "deep" (previously unavailable) parameters are exposed from the most sensitive locations, followed by a bi-objective optimisation process to fine tune them together with existing ("shallow") parameters. The objective is to improve both time and memory resources required by the computation. Since this approach relies on the selection of Mutation Operators and traditional Mutation Operators are not concerned with memory performance, the thesis proposes and evaluates Memory Mutation Operators in the Mutation Testing context. Using both traditional and Memory Mutation Operators, the thesis further seeks to improve the target software by searching for Higher Order Mutants (HOMs). The thesis presents the result of a code analysis study, which reveals that, among all the code modifications that contribute to the improvement, more than half of them require a finer control of the code, which our approach is better at than previous GI approaches.