Search results for: spatial gene

Authors: Hadi Allafta, Christian Opp

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Soil erosion is a major concern in the Shatt Al-Arab basin owing to the steepness of its topography as well as the remarkable altitudinal deference between the upstream and downstream parts of the basin. Such conditions resulted in soil vulnerability to erosion; huge amounts of soil are annually transported, creating enormous implications such as land degradation, structure damage, biodiversity loss, productivity decline, etc. Thus, evaluation of soil erosion risk and its spatial distribution is crucial to build adatabase for efficient control measures. The present study used revised universal soil loss equation (RUSLE) model integrated with Geographic Information System (GIS) for depicting soil erosion hazard zones in the Shatt Al-Arab basin. The RUSLE model incorporated several parameters such as rainfall-runoff erosivity, soil erodibility, slope length and steepness, land cover and management, and conservation support practice for soil erosion zonation. High to medium soil loss of 100 to 20 ton perhectare per year represents around 25% of the basin area, while the areas of low soil loss of less than 20 ton per hectare per year occupied the rest of the total area. The high soil loss rates are linked to areas of high rainfall levels, loamy soil domination, elevated terrains/plateau margins with steep side slope, and high cultivation activities. The findings of the current study can be useful for managers and policy makers in the implementation of a suitable conservation program to reduce soil erosion or to recommend soil conservation acts if development projects are to be continued at regions of high soil erosion risk.

Keywords: geographic information system, revised universal soil loss equation, shatt Al-Arab basin, soil erosion

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Authors: Zongyao Sha

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Green vegetation plays a vital role in energy flows and matter cycles in terrestrial ecosystems, and vegetation phenology may not only be influenced by but also impose active feedback on climate changes. The phenological events of vegetation, such as the start of the season (SOS), end of the season (EOS), and length of the season (LOS), can respond to climate changes and affect gross primary productivity (GPP). Here we coupled satellite remote sensing imagery with FLUXNET observations to systematically map the shift of SOS, EOS, and LOS in global vegetated areas and explored their response to climate fluctuations and feedback on GPP during the last two decades. Results indicated that SOS advanced significantly, at an average rate of 0.19 days/year at a global scale, particularly in the northern hemisphere above the middle latitude (≥30°N) and that EOS was slightly delayed during the past two decades, resulting in prolonged LOS in 72.5% of the vegetated area. The climate factors, including seasonal temperature and precipitation, are attributed to the shifts in vegetation phenology but with a high spatial and temporal difference. The study revealed interactions between vegetation phenology and climate changes. Both temperature and precipitation affect vegetation phenology. Higher temperature as a direct consequence of global warming advanced vegetation green-up date. On the other hand, 75.9% and 20.2% of the vegetated area showed a positive correlation and significant positive correlation between annual GPP and length of vegetation growing season (LOS), likely indicating an enhancing effect on vegetation productivity and thus increased carbon uptake from the shifted vegetation phenology. Our study highlights a comprehensive view of the vegetation phenology changes of the global terrestrial ecosystems during the last two decades. The interactions between the shifted vegetation phenology and climate changes may provide useful information for better understanding the future trajectory of global climate changes. The feedback on GPP from the shifted vegetation phenology may serve as an adaptation mechanism for terrestrial ecosystems to mitigate global warming through improved carbon uptake from the atmosphere.

Keywords: vegetation phenology, growing season, NPP, correlation analysis

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Authors: Rosa Tsegaye Aga, Xuan Jiang, Pavel Vazquez Faci, Siqing Liu, Simon Rayner, Endalkachew Alemu, Markos Abebe

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Tuberculosis (TB) is a major cause of disease globally. In most cases, TB is treatable and curable, but only with the proper treatment. There is a time when drug-resistant TB occurs when bacteria become resistant to the drugs that are used to treat TB. Current strategies to identify drug-resistant TB bacteria are laboratory-based, and it takes a longer time to identify the drug-resistant bacteria and treat the patient accordingly. But machine learning (ML) and data science approaches can offer new approaches to the problem. In this study, we propose to develop an ML-based model to predict the antibiotic resistance phenotypes of TB isolates in minutes and give the right treatment to the patient immediately. The study has been using the whole genome sequence (WGS) of TB isolates as training data that have been extracted from the NCBI repository and contain different countries’ samples to build the ML models. The reason that different countries’ samples have been included is to generalize the large group of TB isolates from different regions in the world. This supports the model to train different behaviors of the TB bacteria and makes the model robust. The model training has been considering three pieces of information that have been extracted from the WGS data to train the model. These are all variants that have been found within the candidate genes (F1), predetermined resistance-associated variants (F2), and only resistance-associated gene information for the particular drug. Two major datasets have been constructed using these three information. F1 and F2 information have been considered as two independent datasets, and the third information is used as a class to label the two datasets. Five machine learning algorithms have been considered to train the model. These are Support Vector Machine (SVM), Random forest (RF), Logistic regression (LR), Gradient Boosting, and Ada boost algorithms. The models have been trained on the datasets F1, F2, and F1F2 that is the F1 and the F2 dataset merged. Additionally, an ensemble approach has been used to train the model. The ensemble approach has been considered to run F1 and F2 datasets on gradient boosting algorithm and use the output as one dataset that is called F1F2 ensemble dataset and train a model using this dataset on the five algorithms. As the experiment shows, the ensemble approach model that has been trained on the Gradient Boosting algorithm outperformed the rest of the models. In conclusion, this study suggests the ensemble approach, that is, the RF + Gradient boosting model, to predict the antibiotic resistance phenotypes of TB isolates by outperforming the rest of the models.

Keywords: machine learning, MTB, WGS, drug resistant TB

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Authors: Hamidullah Binol, Abdullah Bal

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Nowadays, food safety is a great public concern; therefore, robust and effective techniques are required for detecting the safety situation of goods. Hyperspectral Imaging (HSI) is an attractive material for researchers to inspect food quality and safety estimation such as meat quality assessment, automated poultry carcass inspection, quality evaluation of fish, bruise detection of apples, quality analysis and grading of citrus fruits, bruise detection of strawberry, visualization of sugar distribution of melons, measuring ripening of tomatoes, defect detection of pickling cucumber, and classification of wheat kernels. HSI can be used to concurrently collect large amounts of spatial and spectral data on the objects being observed. This technique yields with exceptional detection skills, which otherwise cannot be achieved with either imaging or spectroscopy alone. This paper presents a nonlinear technique based on kernel Fukunaga-Koontz transform (KFKT) for detection of fat content in ground meat using HSI. The KFKT which is the nonlinear version of FKT is one of the most effective techniques for solving problems involving two-pattern nature. The conventional FKT method has been improved with kernel machines for increasing the nonlinear discrimination ability and capturing higher order of statistics of data. The proposed approach in this paper aims to segment the fat content of the ground meat by regarding the fat as target class which is tried to be separated from the remaining classes (as clutter). We have applied the KFKT on visible and nearinfrared (VNIR) hyperspectral images of ground meat to determine fat percentage. The experimental studies indicate that the proposed technique produces high detection performance for fat ratio in ground meat.

Keywords: food (ground meat) inspection, Fukunaga-Koontz transform, hyperspectral imaging, kernel methods

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Authors: Paul Longley Arthur

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This paper reports on an Australian Research Council-funded project utilising the Australian digital research infrastructure the ‘Time-Layered Cultural Map of Australia’ (TLCMap) (https://www.tlcmap.org/) [1]. This resource has been developed to help researchers create digital maps from cultural, textual, and historical data, layered with datasets registered on the platform. TLCMap is a set of online tools that allows humanities researchers to compile humanities data using spatio-temporal coordinates – to upload, gather, analyse and visualise data. It is the only purpose-designed, Australian-developed research tool for humanities and social science researchers to identify geographical clusters and parallel journeys by sight. This presentation discusses a series of Aboriginal mapping and visualisation experiments using TLCMap to show how Indigenous knowledge can reconfigure contemporary understandings of space including the urbanised landscape [2, 3]. The research data being generated – investigating the historical movements of Aboriginal people, the distribution of networks, and their relation to land – lends itself to mapping and geo-spatial visualisation and analysis. TLCMap allows researchers to create layers on a 3D map which pinpoint locations with accompanying information, and this has enabled our research team to plot out traditional historical journeys undertaken by Aboriginal people as well as to compile a gazetteer of Aboriginal place names, many of which have largely been undocumented until now [4]. The documented journeys intersect with and overlay many of today’s urban formations including main roads, municipal boundaries, and state borders. The paper questions how such data can be incorporated into a more culturally and ethically responsive understanding of contemporary urban spaces and as well as natural environments [5].

Keywords: spatio-temporal mapping, visualisation, Indigenous knowledge, mobility and migration, research infrastructure

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Authors: Y. Landkocz, P. Gosset, A. Héliot, C. Corbière, C. Vendeville, V. Keravec, S. Billet, A. Verdin, C. Monteil, D. Préterre, J-P. Morin, F. Sichel, T. Douki, P. J. Martin

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Air Pollution produced by automobile traffic is one of the main sources of pollutants in urban atmosphere and is largely due to exhausts of the diesel engine powered vehicles. The International Agency for Research on Cancer, which is part of the World Health Organization, classified in 2012 diesel engine exhaust as carcinogenic to humans (Group 1), based on sufficient evidence that exposure is associated with an increased risk for lung cancer. Amongst the strategies aimed at limiting exhausts in order to take into consideration the health impact of automobile pollution, filtration of the emissions and use of biofuels are developed, but their toxicological impact is largely unknown. Diesel exhausts are indeed complex mixtures of toxic substances difficult to study from a toxicological point of view, due to both the necessary characterization of the pollutants, sampling difficulties, potential synergy between the compounds and the wide variety of biological effects. Here, we studied the potential indirect genotoxicity of emission of Diesel engines through on-line exposure of rats in inhalation chambers to a subchronic high but realistic dose. Following exposure to standard gasoil +/- rapeseed methyl ester either upstream or downstream of a particle filter or control treatment, rats have been sacrificed and their lungs collected. The following indirect genotoxic parameters have been measured: (i) telomerase activity and telomeres length associated with rTERT and rTERC gene expression by RT-qPCR on frozen lungs, (ii) γH2AX quantification, representing double-strand DNA breaks, by immunohistochemistry on formalin fixed-paraffin embedded (FFPE) lung samples. These preliminary results will be then associated with global cellular response analyzed by pan-genomic microarrays, monitoring of oxidative stress and the quantification of primary DNA lesions in order to identify biological markers associated with a potential pro-carcinogenic response of diesel or biodiesel, with or without filters, in a relevant system of in vivo exposition.

Keywords: diesel exhaust exposed rats, γH2AX, indirect genotoxicity, lung carcinogenicity, telomerase activity, telomeres length

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Authors: Vipin Kumar Verma, Neeta Sehgal, Om Prakash

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Cyprinus carpio has a wide spread occurrence in the lakes and rivers of Europe and Asia. Heavy losses in natural environment due to anthropogenic activities, including pollution as well as pathogenic diseases have landed this fish in IUCN red list of vulnerable species. The significance of a suitable diet in preserving the health status of fish is widely recognized. In present study, artificial feed supplemented with leaves of two weed plants, Eichhornia crassipes and Ricinus communis were evaluated for their role on the fish immune system. To achieve this objective fish were acclimatized to laboratory conditions (25 ± 1 °C; 12 L: 12D) for 10 days prior to start of experiment and divided into 4 groups: non-challenged (negative control= A), challenged [positive control (B) and experimental (C & D)]. Group A, B were fed with non-supplemented feed while group C & D were fed with feed supplemented with 5% Eichhornia crassipes and 5% Ricinus communis respectively. Supplemented feeds were evaluated for their effect on growth, health, immune system and disease resistance in fish when challenged with Vibrio harveyi. Fingerlings of C. carpio (weight, 2.0±0.5 g) were exposed with fresh overnight culture of V. harveyi through bath immunization (concentration 2 Χ 105) for 2 hours on 10 days interval for 40 days. The growth was monitored through increase in their relative weight. The rate of mortality due to bacterial infection as well as due to effect of feed was recorded accordingly. Immune response of fish was analyzed through differential leucocyte count, percentage phagocytosis and phagocytic index. The effect of V. harveyi on fish organs were examined through histo-pathological examination of internal organs like spleen, liver and kidney. The change in the immune response was also observed through gene expression analysis. The antioxidant potential of plant extracts was measured through DPPH and FRAP assay and amount of total phenols and flavonoids were calculates through biochemical analysis. The chemical composition of plant’s methanol extracts was determined by GC-MS analysis, which showed presence of various secondary metabolites and other compounds. Investigation revealed immuno-modulatory effect of plants, when supplemented with the artificial feed of fish.

Keywords: immuno-modulation, gc-ms, Cyprinus carpio, Eichhornia crassipes, Ricinus communis

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

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Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

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Authors: Mohan Li

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Nowadays, intelligent research technology is more and more important than traditional research methods in urban research work, and this proportion will greatly increase in the next few decades. Frequently such analyzing work cannot be carried without some software engineering knowledge. And here, domain models of urban research will be necessary when applying software engineering knowledge to urban work. In many urban plan practice projects, making rational models, feeding reliable data, and providing enough computation all make indispensable assistance in producing good urban planning. During the whole work process, domain models can optimize workflow design. At present, human beings have entered the era of big data. The amount of digital data generated by cities every day will increase at an exponential rate, and new data forms are constantly emerging. How to select a suitable data set from the massive amount of data, manage and process it has become an ability that more and more planners and urban researchers need to possess. This paper summarizes and makes predictions of the emergence of technologies and technological iterations that may affect urban research in the future, discover urban problems, and implement targeted sustainable urban strategies. They are summarized into seven major domain models. They are urban and rural regional domain model, urban ecological domain model, urban industry domain model, development dynamic domain model, urban social and cultural domain model, urban traffic domain model, and urban space domain model. These seven domain models can be used to guide the construction of systematic urban research topics and help researchers organize a series of intelligent analytical tools, such as Python, R, GIS, etc. These seven models make full use of quantitative spatial analysis, machine learning, and other technologies to achieve higher efficiency and accuracy in urban research, assisting people in making reasonable decisions.

Keywords: big data, domain model, urban planning, urban quantitative analysis, machine learning, workflow design

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Authors: Samuel Abraham Berhane, Lingbing Bu

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This paper presents the spatiotemporal variability of aerosols, clouds, and precipitation within the major cities in Eritrea and it investigates the relationship between aerosols, clouds, and precipitation concerning the presence of aerosols over the study region. In Eritrea, inadequate water supplies will have both direct and indirect adverse impacts on sustainable development in areas such as health, agriculture, energy, communication, and transport. Besides, there exists a gap in the knowledge on suitable and potential areas for cloud seeding. Further, the inadequate understanding of aerosol-cloud-precipitation (ACP) interactions limits the success of weather modification aimed at improving freshwater sources, storage, and recycling. Spatiotemporal variability of aerosols, clouds, and precipitation involve spatial and time series analysis based on trend and anomaly analysis. To find the relationship between aerosols and clouds, a correlation coefficient is used. The spatiotemporal analysis showed larger variations of aerosols within the last two decades, especially in Assab, indicating that aerosol optical depth (AOD) has increased over the surrounding Red Sea region. Rainfall was significantly low but AOD was significantly high during the 2011 monsoon season. Precipitation was high during 2007 over most parts of Eritrea. The correlation coefficient between AOD and rainfall was negative over Asmara and Nakfa. Cloud effective radius (CER) and cloud optical thickness (COT) exhibited a negative correlation with AOD over Nakfa within the June–July–August (JJA) season. The hybrid single-particle Lagrangian integrated trajectory (HYSPLIT) model that is used to find the path and origin of the air mass of the study region showed that the majority of aerosols made their way to the study region via the westerly and the southwesterly winds.

Keywords: aerosol-cloud-precipitation, aerosol optical depth, cloud effective radius, cloud optical thickness, HYSPLIT

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Authors: Fatema-Tuz-Zohra Khanam, Ali Al-Naji, Asanka G. Perera, Kim Gibson, Javaan Chahl

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Conventional contact-based vital signs monitoring sensors such as pulse oximeters or electrocardiogram (ECG) may cause discomfort, skin damage, and infections, particularly in neonates with fragile, sensitive skin. Therefore, remote monitoring of the vital sign is desired in both clinical and non-clinical settings to overcome these issues. Camera-based vital signs monitoring is a recent technology for these applications with many positive attributes. However, there are still limited camera-based studies on neonates in a clinical setting. In this study, the heart rate (HR) and respiratory rate (RR) of eight infants at the Neonatal Intensive Care Unit (NICU) in Flinders Medical Centre were remotely monitored using a digital camera applying color and motion-based computational methods. The region-of-interest (ROI) was efficiently selected by incorporating an image decomposition method. Furthermore, spatial averaging, spectral analysis, band-pass filtering, and peak detection were also used to extract both HR and RR. The experimental results were validated with the ground truth data obtained from an ECG monitor and showed a strong correlation using the Pearson correlation coefficient (PCC) 0.9794 and 0.9412 for HR and RR, respectively. The RMSE between camera-based data and ECG data for HR and RR were 2.84 beats/min and 2.91 breaths/min, respectively. A Bland Altman analysis of the data also showed a close correlation between both data sets with a mean bias of 0.60 beats/min and 1 breath/min, and the lower and upper limit of agreement -4.9 to + 6.1 beats/min and -4.4 to +6.4 breaths/min for both HR and RR, respectively. Therefore, video camera imaging may replace conventional contact-based monitoring in NICU and has potential applications in other contexts such as home health monitoring.

Keywords: neonates, NICU, digital camera, heart rate, respiratory rate, image decomposition

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Authors: Eriko Ochiai, Fumiko Satoh, Keiko Miyashita, Yu Kakimoto, Motoki Osawa

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Sudden and unexpected deaths from unknown causes occur in infants and youths. Recently, molecular links between a part of these deaths and several genetic diseases are examined in the postmortem. For instance, hereditary long QT syndrome and Burgada syndrome are occasionally fatal through critical ventricular tachyarrhythmia. There are a large number of target genes responsible for such diseases, the conventional analysis using the Sanger’s method has been laborious. In this report, we attempted to analyze sudden deaths comprehensively using the next generation sequencing (NGS) technique. Multiplex PCR to subject’s DNA was performed using Ion AmpliSeq Library Kits 2.0 and Ion AmpliSeq Inherited Disease Panel (Life Technologies). After the library was constructed by emulsion PCR, the amplicons were sequenced 500 flows on Ion Personal Genome Machine System (Life Technologies) according to the manufacture instruction. SNPs and indels were analyzed to the sequence reads that were mapped on hg19 of reference sequences. This project has been approved by the ethical committee of Tokai University School of Medicine. As a representative case, the molecular analysis to a 40 years old male who received a diagnosis of Brugada syndrome demonstrated a total of 584 SNPs or indels. Non-synonymous and frameshift nucleotide substitutions were selected in the coding region of heart disease related genes of ANK2, AKAP9, CACNA1C, DSC2, KCNQ1, MYLK, SCN1B, and STARD3. In particular, c.629T-C transition in exon 3 of the SCN1B gene, resulting in a leu210-to-pro (L210P) substitution is predicted “damaging” by the SIFT program. Because the mutation has not been reported, it was unclear if the substitution was pathogenic. Sudden death that failed in determining the cause of death constitutes one of the most important unsolved subjects in forensic pathology. The Ion AmpliSeq Inherited Disease Panel can amplify the exons of 328 genes at one time. We realized the difficulty in selection of the true source from a number of candidates, but postmortem genetic testing using NGS analysis deserves of a diagnostic to date. We now extend this analysis to SIDS suspected subjects and young sudden death victims.

Keywords: postmortem genetic testing, sudden death, SIDS, next generation sequencing

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Authors: Wenyang Wan

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The study of urban land use and landscape pattern is the current hotspot in the fields of planning and design, ecology, etc., which is of great significance for the construction of the overall humanistic ecosystem of the city and optimization of the urban spatial structure. Banan District, as the main part of the eastern eco-city planning of Chongqing Municipality, is a new high ground for highlighting the ecological characteristics of Chongqing, realizing effective transformation of ecological value, and promoting the integrated development of urban and rural areas. The analytical methods of land use transfer matrix (GIS) and landscape pattern index (Fragstats) were used to study the characteristics and laws of the evolution of land use landscape pattern in Banan District from 2000 to 2020, which provide some reference value for Banan District to alleviate the ecological contradiction of landscape. The results of the study show that: ① Banan District is rich in land use types, of which the area of cultivated land will still account for 57.15% of the total area of the landscape until 2020, accounting for an absolute advantage in the land use structure of Banan District; ② From 2000 to 2020, land use conversion in Banan District is characterized as: Cropland > woodland > grassland > shrubland > built-up land > water bodies > wetlands, with cropland converted to built-up land being the largest; ③ From 2000 to 2020, the landscape elements of Banan District were distributed in a balanced way, and the landscape types were rich and diversified, but due to the influence of human interference, it also presented the characteristics that the shape of the landscape elements tended to be irregular, and the dominant patches were distributed in a scattered manner, and the patches had poor connectivity. It is recommended that in future regional ecological construction, the layout should be rationally optimized, the relationship between landscape components should be coordinated, and the connectivity between landscape patches should be strengthened, and the degree of landscape fragmentation should be reduced.

Keywords: land use transfer, landscape pattern evolution, GIS and FRAGSTATS, Banan District

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Authors: Philippa Saunders, Claire Fletcher

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INTRODUCTION: Prostate cancer is the most prevalent malignancy affecting Western males. It is initially an androgen-dependent disease: androgens bind to the androgen receptor and drive the expression of genes that promote proliferation and evasion of apoptosis. Despite reduced androgen dependence in advanced prostate cancer, androgen receptor signaling remains a key driver of growth. Androgen deprivation therapy (ADT) is, therefore, a first-line treatment approach and works well initially, but resistance inevitably develops. Abiraterone and Enzalutamide are drugs widely used in ADT and are androgen synthesis and androgen receptor signaling inhibitors, respectively. The shortage of other treatment options means acquired resistance to these drugs is a major clinical problem. MicroRNAs (miRs) are important mediators of post-transcriptional gene regulation and show altered expression in cancer. Several have been linked to the development of resistance to ADT. Manipulation of such miRs may be a pathway to breakthrough treatments for advanced prostate cancer. This study aimed to validate ADT resistance-implicated miRs and their clinically relevant targets. MATERIAL AND METHOD: Small RNA-sequencing of Abiraterone- and Enzalutamide-resistant C42 prostate cancer cells identified subsets of miRs dysregulated as compared to parental cells. Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) was used to validate altered expression of candidate ADT resistance-implicated miRs 195-5p, 497-5p and 29a-5p in ADT-resistant and -responsive prostate cancer cell lines, patient-derived xenografts (PDXs) and primary prostate cancer explants. RESULTS AND DISCUSSION: This study suggests a possible role for miR-497-5p in the development of ADT resistance in prostate cancer. MiR-497-5p expression was increased in ADT-resistant versus ADT-responsive prostate cancer cells. Importantly, miR-497-5p expression was also increased in Enzalutamide-treated, castrated (ADT-mimicking) PDXs versus intact PDXs. MiR-195-5p was also elevated in ADT-resistant versus -responsive prostate cancer cells, while there was a drop in miR-29a-5p expression. Candidate clinically relevant targets of miR-497-5p in prostate cancer were identified by mining AGO-PAR-CLIP-seq data sets and may include AVL9 and FZD6. CONCLUSION: In summary, this study identified microRNAs that are implicated in prostate cancer resistance to androgen deprivation therapy and could represent novel therapeutic targets for advanced disease.

Keywords: microRNA, androgen deprivation therapy, Enzalutamide, abiraterone, patient-derived xenograft

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Authors: Shalini TV, Gangadharan GG, Sriranjini S Jaideep, ASN Seshasayee, Awadhesh Pandit

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Introduction: Prakriti (body-mind constitution of an individual) is a conventional, customized and unique understanding of which is essential for the personalized medicine described in Ayurveda, Indian System of Medicine. Based on the Doshas( functional, bio humoral unit in the body), individuals are categorized into three major Prakriti- Vata, Pitta, and Kapha. The human gut microbiome hosts plenty of highly diverse and metabolically active microorganisms, mainly dominated by the bacteria, which are known to influence the physiology of an individual. Few researches have shown the correlation between the Prakriti and the biochemical parameters. In this study, an attempt was made to explore any correlation between the Prakriti (phenotype of an individual) with the Genetic makeup of the gut microbiome in healthy individuals. Materials and methods: 270 multi-ethnic, healthy volunteers of both sex with the age group between 18 to 40 years, with no history of antibiotics in the last 6 months were recruited into three groups of Vata, Pitta, and Kapha. The Prakriti of the individual was determined using Ayusoft, a software designed by CDAC, Pune, India. The volunteers were subjected to initial screening for the assessment of their height, weight, Body Mass Index, Vital signs and Blood investigations to ensure they are healthy. The stool and saliva samples of the recruited volunteers were collected as per the standard operating procedure developed, and the bacterial DNA was isolated using Qiagen kits. The extracted DNA was subjected to 16s rRNA sequencing using the Illumina kits. The sequencing libraries are targeting the variable V3 and V4 regions of the 16s rRNA gene. Paired sequencing was done on the MiSeq system and data were analyzed using the CLC Genomics workbench 11. Results: The 16s rRNA sequencing of the V3 and V4 regions showed a diverse pattern in both the oral and stool microbial DNA. The study did not reveal any specific pattern of bacterial flora amongst the Prakriti. All the p-values were more than the effective alpha values for all OTUs in both the buccal cavity and stool samples. Therefore, there was no observed significant enrichment of an OTU in the patient samples from either the buccal cavity or stool samples. Conclusion: In healthy volunteers of multi-ethnicity, due to the influence of the various factors, the correlation between the Prakriti and the gut microbiome was not seen.

Keywords: gut microbiome, ayurveda Prakriti, sequencing, multi-ethnic urban population

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Authors: Rajkumar Ghosh

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Urban flooding is a common occurrence throughout Asia. Almost every city is vulnerable to urban floods in some fashion, and city people are particularly vulnerable. Pluvial and fluvial flooding are the most prominent causes of urban flooding in the Gomti Nagar region of Lucknow, Uttar Pradesh, India. The pluvial flooding is regarded to be less damaging because it is caused by heavy rainfall, Seasonal rainfall fluctuations, water flows off concrete infrastructures, blockages of the drainage system, and insufficient drainage capacity or low infiltration capacity. However, this study considers pluvial flooding in Lucknow to be a significant source of cumulative damage over time, and the risks of such events are increasing as a result of changes in ageing infrastructure, hazard exposure, rapid urbanization, massive water logging and global warming. As a result, urban flooding has emerged as a critical field of study. The popularity of analytical approaches to project the spatial extent of flood dangers has skyrocketed. To address future urban flood resilience, more effort is needed to enhance both hydrodynamic models and analytical tools to simulate risks under present and forecast conditions. Proper urban planning with drainage system and ample space for high infiltration capacity are required to reduce urban flooding. A better India with no urban flooding is a pipe dream that can be realized by putting household rooftop rainwater collection systems in every structure. According to the current study, domestic RTRWHs are strongly recommended as an alternative source of water, as well as to prevent surface runoff and urban floods in this region of Lucknow, urban areas of India.

Keywords: rooftop rainwater harvesting, urban flood, pluvial flooding, fluvial flooding

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Authors: Lawrence Babatunde Ogunsanya

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The university has been in existence, in one form or another, for over a thousand years and has contributed in multiple ways to modern society. It is considered a center of culture, aesthetic direction, and moral forces shaping the civilized society. Universities also contribute in important ways to the economic health and physical landscape of neighborhoods and cities, serving as permanent fixtures of the urban economy and the built environment. Due to the size and location of university campuses, they put demands on the urban character, systems, and infrastructure of the neighboring communities. These demands or impacts have substantial implications for the built environment. It is important to understand the impacts university campuses have on their surrounding communities and urban environments because the destiny of the university is inextricably linked to the destiny of the adjacent neighborhoods. This paper identifies the diverse factors generated by universities in shaping the built environments of their local communities within different spatial contexts such as urban, rural, and township regions situated in South Africa.By applying a mixed methods approach in four university campuses within the province of KwaZulu-Natal in South Africa. Several data collection instruments were used, such as in-depth interviews, a survey, remote sensing, and onsite observations. The thematic findings revealed numerous factors which influence the morphology of neighbourhood built environments and the myriad of relationships the university has with its local community. This paper also reveals that the university campus is more than a precinct which accommodates buildings and academic endeavours, the role of the university in this century has changed dramatically from its traditional roots of being an elite enclave of academics to a more inclusive and engaged entity that is concerned about providing relevant holistic solutions to society’s current challenges in the built environment.

Keywords: university campus, built environment, architecture, neighborhood planning

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Authors: Miriam Sosa-Díaz, Faustino Sánchez-Garduño

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In population dynamics the study of both, the abundance and the spatial distribution of the populations in a given habitat, is a fundamental issue a From ecological point of view, the determination of the factors influencing such changes involves important problems. In this paper a mathematical model to describe the temporal dynamic and the spatiotemporal dynamic of the interaction of three populations (pollinators, plants and herbivores) is presented. The study we present is carried out by stages: 1. The temporal dynamics and 2. The spatio-temporal dynamics. In turn, each of these stages is developed by considering three cases which correspond to the dynamics of each type of interaction. For instance, for stage 1, we consider three ODE nonlinear systems describing the pollinator-plant, plant-herbivore and plant-pollinator-herbivore, interactions, respectively. In each of these systems different types of dynamical behaviors are reported. Namely, transcritical and pitchfork bifurcations, existence of a limit cycle, existence of a heteroclinic orbit, etc. For the spatiotemporal dynamics of the two mathematical models a novel factor are introduced. This consists in considering that both, the pollinators and the herbivores, move towards those places of the habitat where the plant population density is high. In mathematical terms, this means that the diffusive part of the pollinators and herbivores equations depend on the plant population density. The analysis of this part is presented by considering pairs of populations, i. e., the pollinator-plant and plant-herbivore interactions and at the end the two mathematical model is presented, these models consist of two coupled nonlinear partial differential equations of reaction-diffusion type. These are defined on a rectangular domain with the homogeneous Neumann boundary conditions. We focused in the role played by the density dependent diffusion term into the coexistence of the populations. For both, the temporal and spatio-temporal dynamics, a several of numerical simulations are included.

Keywords: bifurcation, heteroclinic orbits, steady state, traveling wave

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Authors: Oshma Chakoory, Sophie Comtet-Marre, Pierre Peyret

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Metagenomic classifiers are widely used for the taxonomic profiling of metagenomic data and estimation of taxa relative abundance. Small subunit rRNA genes are nowadays a gold standard for the phylogenetic resolution of complex microbial communities, although the power of this marker comes down to its use as full-length. We benchmarked the performance and accuracy of rRNA-specialized versus general-purpose read mappers, reference-targeted assemblers and taxonomic classifiers. We then built a pipeline called RiboTaxa to generate a highly sensitive and specific metataxonomic approach. Using metagenomics data, RiboTaxa gave the best results compared to other tools (Kraken2, Centrifuge (1), METAXA2 (2), PhyloFlash (3)) with precise taxonomic identification and relative abundance description, giving no false positive detection. Using real datasets from various environments (ocean, soil, human gut) and from different approaches (metagenomics and gene capture by hybridization), RiboTaxa revealed microbial novelties not seen by current bioinformatics analysis opening new biological perspectives in human and environmental health. In a study focused on corals’ health involving 20 metagenomic samples (4), an affiliation of prokaryotes was limited to the family level with Endozoicomonadaceae characterising healthy octocoral tissue. RiboTaxa highlighted 2 species of uncultured Endozoicomonas which were dominant in the healthy tissue. Both species belonged to a genus not yet described, opening new research perspectives on corals’ health. Applied to metagenomics data from a study on human gut and extreme longevity (5), RiboTaxa detected the presence of an uncultured archaeon in semi-supercentenarians (aged 105 to 109 years) highlighting an archaeal genus, not yet described, and 3 uncultured species belonging to the Enorma genus that could be species of interest participating in the longevity process. RiboTaxa is user-friendly, rapid, allowing microbiota structure description from any environment and the results can be easily interpreted. This software is freely available at https://github.com/oschakoory/RiboTaxa under the GNU Affero General Public License 3.0.

Keywords: metagenomics profiling, microbial diversity, SSU rRNA genes, full-length phylogenetic marker

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Authors: Sandisiwe Mangali, Graeme Bradley

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Genome is complete set of the organism's hereditary information encoded as either deoxyribonucleic acid or ribonucleic acid in most viruses. The three different types of genomes are nuclear, mitochondrial and the plastid genome and their sequences which are uncovered by genome sequencing are known as an archive for all genetic information and enable researchers to understand the composition of a genome, regulation of gene expression and also provide information on how the whole genome works. These sequences enable researchers to explore the population structure, genetic variations, and recent demographic events in threatened species. Particularly, genome sequencing refers to a process of figuring out the exact arrangement of the basic nucleotide bases of a genome and the process through which all the afore-mentioned genomes are sequenced is referred to as whole or complete genome sequencing. Gelidium pristoides is South African endemic Rhodophyta species which has been harvested in the Eastern Cape since the 1950s for its high economic value which is one motivation for its sequencing. Its endemism further motivates its sequencing for conservation biology as endemic species are more vulnerable to anthropogenic activities endangering a species. As sequencing, mapping and annotating the Gelidium pristoides genome is the aim of this study. To accomplish this aim, the genomic DNA was extracted and quantified using the Nucleospin Plank Kit, Qubit 2.0 and Nanodrop. Thereafter, the Ion Plus Fragment Library was used for preparation of a 600bp library which was then sequenced through the Ion S5 sequencing platform for two runs. The produced reads were then quality-controlled and assembled through the SPAdes assembler with default parameters and the genome assembly was quality assessed through the QUAST software. From this assembly, the plastid and the mitochondrial genomes were then sampled out using Gelidiales organellar genomes as search queries and ordered according to them using the Geneious software. The Qubit and the Nanodrop instruments revealed an A260/A280 and A230/A260 values of 1.81 and 1.52 respectively. A total of 30792074 reads were obtained and produced a total of 94140 contigs with resulted into a sequence length of 217.06 Mbp with N50 value of 3072 bp and GC content of 41.72%. A total length of 179281bp and 25734 bp was obtained for plastid and mitochondrial respectively. Genomic data allows a clear understanding of the genomic constituent of an organism and is valuable as foundation information for studies of individual genes and resolving the evolutionary relationships between organisms including Rhodophytes and other seaweeds.

Keywords: Gelidium pristoides, genome, genome sequencing and assembly, Ion S5 sequencing platform

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Authors: Hamed Ahari, Behrouz Akbari Adreghani, Vadood Razavilar, Amirali Anvar, Sima Moradi, Hourieh Shalchi

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Considering the ever increasing population and industrialization of the developmental trend of humankind's life, we are no longer able to detect the toxins produced in food products using the traditional techniques. This is due to the fact that the isolation time for food products is not cost-effective and even in most of the cases, the precision in the practical techniques like the bacterial cultivation and other techniques suffer from operator errors or the errors of the mixtures used. Hence with the advent of nanotechnology, the design of selective and smart sensors is one of the greatest industrial revelations of the quality control of food products that in few minutes time, and with a very high precision can identify the volume and toxicity of the bacteria. Methods and Materials: In this technique, based on the bacterial antibody connection to nanoparticle, a sensor was used. In this part of the research, as the basis for absorption for the recognition of bacterial toxin, medium sized silica nanoparticles of 10 nanometer in form of solid powder were utilized with Notrino brand. Then the suspension produced from agent-linked nanosilica which was connected to bacterial antibody was positioned near the samples of distilled water, which were contaminated with Staphylococcus aureus bacterial toxin with the density of 10-3, so that in case any toxin exists in the sample, a connection between toxin antigen and antibody would be formed. Finally, the light absorption related to the connection of antigen to the particle attached antibody was measured using spectrophotometry. The gene of 23S rRNA that is conserved in all Staphylococcus spp., also used as control. The accuracy of the test was monitored by using serial dilution (l0-6) of overnight cell culture of Staphylococcus spp., bacteria (OD600: 0.02 = 107 cell). It showed that the sensitivity of PCR is 10 bacteria per ml of cells within few hours. Result: The results indicate that the sensor detects up to 10-4 density. Additionally, the sensitivity of the sensors was examined after 60 days, the sensor by the 56 days had confirmatory results and started to decrease after those time periods. Conclusions: Comparing practical nano biosensory to conventional methods like that culture and biotechnology methods(such as polymerase chain reaction) is accuracy, sensitiveness and being unique. In the other way, they reduce the time from the hours to the 30 minutes.

Keywords: exotoxin, nanobiosensor, recognition, Staphylococcus aureus

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Authors: Alokananda Ghosh, Shraban Sarkar

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The study aims to identify suitable sites for new hospitals with critical obstetric care facilities in Birbhum, one of the vulnerable and underserved districts of Eastern India, considering six main and 14 sub-criteria, using GIS-based Analytic Hierarchy Process (AHP) and Multi-Attribute Utility Theory (MAUT) approach. The criteria were identified through field surveys and previous literature. After collecting expert decisions, a pairwise comparison matrix was prepared using the Saaty scale to calculate the weights through AHP. On the contrary, objective weighting methods, i.e., Entropy and Criteria Importance through Interaction Correlation (CRITIC), were used to perform the MAUT. Finally, suitability maps were prepared by weighted sum analysis. Sensitivity analyses of AHP were performed to explore the effect of dominant criteria. Results from AHP reveal that ‘maternal death in transit’ followed by ‘accessibility and connectivity’, ‘maternal health care service (MHCS) coverage gap’ were three important criteria with comparatively higher weighted values. Whereas ‘accessibility and connectivity’ and ‘maternal death in transit’ were observed to have more imprint in entropy and CRITIC, respectively. While comparing the predictive suitable classes of these three models with the layer of existing hospitals, except Entropy-MAUT, the other two are pointing towards the left-over underserved areas of existing facilities. Only 43%-67% of existing hospitals were in the moderate to lower suitable class. Therefore, the results of the predictive models might bring valuable input in future planning.

Keywords: hospital site suitability, analytic hierarchy process, multi-attribute utility theory, entropy, criteria importance through interaction correlation, multi-criteria decision analysis

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Authors: Rahul Jain, Pradhir Parmar, Dhruvesh Patel

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Planning and drawing are the important aspects of civil engineering. For testing theories about spatial location and interaction between land uses and related activities the computer based solution of urban models are used. The planner’s primary interest is in creation of 3D models of building and to obtain the terrain surface so that he can do urban morphological mappings, virtual reality, disaster management, fly through generation, visualization etc. 3D city models have a variety of applications in urban studies. Gujarat International Finance Tec-City (GIFT) is an ongoing construction site between Ahmedabad and Gandhinagar, Gujarat, India. It will be built on 3590000 m2 having a geographical coordinates of North Latitude 23°9’5’’N to 23°10’55’’ and East Longitude 72°42’2’’E to 72°42’16’’E. Therefore to develop 3D city models of GIFT city, the base map of the city is collected from GIFT office. Differential Geographical Positioning System (DGPS) is used to collect the Ground Control Points (GCP) from the field. The GCP points are used for the registration of base map in QGIS. The registered map is projected in WGS 84/UTM zone 43N grid and digitized with the help of various shapefile tools in QGIS. The approximate height of the buildings that are going to build is collected from the GIFT office and placed on the attribute table of each layer created using shapefile tools. The Shuttle Radar Topography Mission (SRTM) 1 Arc-Second Global (30 m X 30 m) grid data is used to generate the terrain of GIFT city. The Google Satellite Map is used to place on the background to get the exact location of the GIFT city. Various plugins and tools in QGIS are used to convert the raster layer of the base map of GIFT city into 3D model. The fly through tool is used for capturing and viewing the entire area in 3D of the city. This paper discusses all techniques and their usefulness in 3D city model creation from the GCP, base map, SRTM and QGIS.

Keywords: 3D model, DGPS, GIFT City, QGIS, SRTM

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Authors: Kamran Jawed, Anu Jose Mattam, Zia Fatma, Saima Wajid, Malik Z. Abdin, Syed Shams Yazdani

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Worldwide demand of natural and sustainable fuels and chemicals have encouraged researchers to develop microbial platform for synthesis of short chain fatty acids as they are useful precursors to replace petroleum-based fuels and chemicals. In this study, we evaluated the role of fatty acid synthesis and β-oxidation cycle of Escherichia coli to produce butyric acid, a 4-carbon short chain fatty acid, with the help of three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron. We found that E. coli strain transformed with gene for TesBT and grown in presence of 8 g/L glucose produced maximum butyric acid titer at 1.46 g/L, followed by that of TesBF at 0.85 g/L and TesAT at 0.12 g/L, indicating that these thioesterases were efficiently converting short chain fatty acyl-ACP intermediate of fatty acid synthesis pathway into the corresponding acid. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. Deletion of genes for fatty acyl-CoA synthetase and acyl-CoA dehydrogenase, which are involved in initiating the fatty acid degradation cycle, and overexpression of FadR, which is a dual transcriptional regulator and exerts negative control over fatty acid degradation pathway, reduced up to 30% of butyric acid titer. This observation suggested that β-oxidation pathway is working synergistically with fatty acid synthesis pathway in production of butyric acid. Moreover, accelerating the fatty acid elongation cycle by overexpressing acetyl-CoA carboxyltransferase (Acc) and 3-hydroxy-acyl-ACP dehydratase (FabZ) or by deleting FabR, the transcription suppressor of elongation, did not improve the butyric acid titer, rather favored the long chain fatty acid production. Finally, a balance between cell growth and butyric acid production was achieved with the use of phosphorous limited growth medium and 14.3 g/L butyric acid, and 17.5 g/L total free fatty acids (FFAs) titer was achieved during fed-batch cultivation. We have engineered an E. coli strain which utilizes the intermediate of both fatty acid synthesis and degradation pathway, i.e. butyryl-ACP and -CoA, to produce butyric acid from glucose. The strategy used in this study resulted in highest reported titers of butyric acid and FFAs in engineered E. coli.

Keywords: butenoic acid, butyric acid, Escherichia coli, fed-batch fermentation, short chain fatty acids, thioesterase

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Authors: David Taillis, Oussama Becissa, Julien Gabaston, Jean-Michel Merillon, Tristan Richard, Stephanie Cluzet

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Nowadays, there is a strong pressure to reduce the phytosanitary inputs of synthetic chemistry in vineyards. It is, therefore, necessary to find viable alternatives in order to protect the vine against its major diseases. For this purpose, we suggest the use of a plant extract enriched in antimicrobial compounds. Being produced from vine trunks and roots, which are co-products of wine production, the extract produced is part of a circular economy. The antimicrobial molecules present in this plant material are polyphenols and, more particularly, stilbenes, which are derived from a common base, the resveratrol unit, and that are well known vine phytoalexins. The stilbenoids were extracted from trunks and roots (30/70, w/w) by a double extraction with ethyl acetate followed by enrichment by liquid-liquid extraction. The produced extract was characterized by UHPLC-MS, then its antimicrobial activities were tested on Plasmopara viticola and Botrytis cinerea in the laboratory and/or in greenhouse and in vineyard. The major compounds were purified, and their antimicrobial activity was evaluated on B. cinerea. Moreover, after its spraying, the effect of the stilbene extract on the plant defence status was evaluated by analysis of defence gene expression. UHPLC-MS analysis revealed that the extract contains 50% stilbenes with resveratrol, ε-viniferin and r-viniferin as major compounds. The extract showed antimicrobial activities on P. viticola with IC₅₀ and IC₁₀₀ respectively of 90 and 300 mg/L in the laboratory. In addition, it inhibited 40% of downy mildew development in greenhouse. However, probably because of the sensitivity of stilbenes to the environment, such as UV degradation, no activity has been observed in vineyard towards P. viticola development. For B. cinerea, the extract IC50 was 123 mg/L, with resveratrol and ε-viniferin being the most active stilbenes (IC₅₀ of 88 and 142 mg/L, respectively). The analysis of the expression of defence genes revealed that the extract can induce the expression of some defence genes 24, 48, and 72 hours after treatment, meaning that the extract has a defence-stimulating effect at least for the first three days after treatment. In conclusion, we produced a plant extract enriched in stilbenes with antimicrobial properties against two major grapevine pathogenic agents P. viticola and B. cinerea. In addition, we showed that this extract displayed eliciting activity of plant defences. This extract can therefore represent, after formulation development, a viable eco-friendly alternative for vineyard protection. Subsequently, the effect of the stilbenoid extract on primary metabolism will be evaluated by quantitative NMR.

Keywords: antimicrobial, bioprotection, grapevine, Plasmopara viticola, stilbene

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Authors: B. L. Gadiga

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This study assesses the major ecological zones in Nigeria with the view to understanding the spatial pattern of vegetation zones and the implications on conservation within the period of sixteen (16) years. Satellite images used for this study were acquired from the SPOT-VEGETATION between 1998 and 2013. The annual NDVI images selected for this study were derived from SPOT-4 sensor and were acquired within the same season (November) in order to reduce differences in spectral reflectance due to seasonal variations. The images were sliced into five classes based on literatures and knowledge of the area (i.e. <0.16 Non-Vegetated areas; 0.16-0.22 Sahel Savannah; 0.22-0.40 Sudan Savannah, 0.40-0.47 Guinea Savannah and >0.47 Forest Zone). Classification of the 1998 and 2013 images into forested and non forested areas showed that forested area decrease from 511,691 km² in 1998 to 478,360 km² in 2013. Differencing change detection method was performed on 1998 and 2013 NDVI images to identify areas of ecological concern. The result shows that areas undergoing vegetation degradation covers an area of 73,062 km² while areas witnessing some form restoration cover an area of 86,315 km². The result also shows that there is a weak correlation between rainfall and the vegetation zones. The non-vegetated areas have a correlation coefficient (r) of 0.0088, Sahel Savannah belt 0.1988, Sudan Savannah belt -0.3343, Guinea Savannah belt 0.0328 and Forest belt 0.2635. The low correlation can be associated with the encroachment of the Sudan Savannah belt into the forest belt of South-eastern part of the country as revealed by the image analysis. The degradation of the forest vegetation is therefore responsible for the serious erosion problems witnessed in the South-east. The study recommends constant monitoring of vegetation and strict enforcement of environmental laws in the country.

Keywords: vegetation, NDVI, SPOT-vegetation, ecology, degradation

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Authors: Zeynep Yazgan, Gökhan Aygün, Reyhan Çalışkan

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Objective: Invasive fungal infections are a serious threat in terms of morbidity and mortality, especially in immunocompromised patients. The most frequently isolated agents are Aspergillus genus fungi, and sensitivity to azoles, which are the first choice in treatment, decreases. In our study, we aimed to investigate the use of the agar plate screening method as a fast, easy, and practical method in determining azole resistance in Aspergillus spp. species. Methods: Our study was conducted with 125 Aspergillus spp. isolates produced from various clinical samples. Aspergillus spp. isolates were identified by conventional methods and azole resistance was determined by gradient test and agar plate screening method. Broth microdilution method was applied to resistant isolates, and CypA-L98H and CypA-M220 mutations in the cyp51A gene were investigated. Results: In our study, 55 A. fumigatus complex (44%), 42 A. flavus (33.6%), 6 A. terreus (5%), 4 A. niger (3%) and 18 Aspergillus spp. (14%) were identified. With the gradient test method, resistance to VOR and POS was detected in 1 (1.8%) of A.fumigatus isolates, and resistance to ITR was detected in 3 (5.45%). With the agar plate method, 1 of the A.fumigatus isolates (1.8%) had VOR, ITR, POS, 1 of the A.terreus isolates (16.7%) had VOR, 1 of the A.niger isolates (25%) had ITR. Resistance to VOR and POS was detected in 2 Aspergillus spp. isolates (11%), and resistance to ITR was detected in 1 (5.6%). Sensitivity and specificity were determined as 100% for VOR and POS in A. fumigatus species, 33.3% and 100% for ITR, respectively, 100% for ITR in A. flavus species, and 100% for ITR and POS in A. terreus species. By broth microdilution method in 7 isolates in which resistance was detected by gradient test and/or agar plate screening method; 1 A.fumigatus resistant to ITR, VOR, POS, 2 A.fumigatus resistant to ITR, 2 Aspergillus spp. ITR, VOR, POS MICs were determined as 2µg/ml and 8µg/ml, 8µg/ml and >32µg/ml, 0.5µg/ml and 4µg/ml, respectively. CypA-L98H mutations were detected in 5 of these isolates, CypA-M220 mutations were detected in 6, and no mutation was detected in 1. CypA-L98H and CypA-M220 mutations were detected in 1 isolate for which resistance was not detected. Conclusion: The need for rapid antifungal susceptibility screening tests is increasing in the treatment of aspergillosis. Although the sensitivity of the agar plate method was determined to be 33.3% for A.fumigatus ITR in our study, its sensitivity and specificity were determined to be 100% for ITR, VOR, and POS in other species. The low sensitivity value detected for A.fumigatus showed that agar plate drug concentrations should be updated in accordance with the latest regulations of EUCAST guidelines. The CypA-L98H and CypA-M220 mutations detected in our study suggested that the distribution of azole resistance-related mutations in different regions in our country should be investigated. In conclusion, it is thought that the agar plate method, which can be easily applied to detect azole resistance, is a fast and practical method in routine use and can contribute to both the determination of effective treatment strategies and the generation of epidemiological data.

Keywords: Aspergillus, agar plate, azole resistance, cyp51A, cypA-L98H, cypA-M220

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Authors: Suleyman Karabal, Timothy L. Burnett, Egemen Avcu, Andrew H. Sherry, Philip J. Withers

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SA508 Grade 3 steel is widely used in the construction of nuclear pressure vessels, where its fracture toughness plays a critical role in ensuring operational safety and reliability. Understanding the ductile failure mechanisms in this steel grade is crucial for designing robust pressure vessels that can withstand severe nuclear environment conditions. In the present study, round bar specimens of SA508 Grade 3 steel with four distinct notch geometries were subjected to tensile loading while capturing continuous 2D images at 5-second intervals in order to monitor any alterations in their geometries to construct true stress-strain curves of the specimens. 3D reconstructions of X-ray computed tomography (CT) images at high-resolution (a spatial resolution of 0.82 μm) allowed for a comprehensive assessment of the influences of second-phase particles (i.e., manganese sulfide inclusions and cementite particles) on ductile failure initiation as a function of applied plastic strain. Additionally, based on 2D and 3D images, plasticity modeling was executed, and the results were compared to experimental data. A specific ‘two-parameter criterion’ was established and calibrated based on the correlation between stress triaxiality and equivalent plastic strain at failure initiation. The proposed criterion demonstrated substantial agreement with the experimental results, thus enhancing our knowledge of ductile fracture behavior in this steel grade. The implementation of X-ray CT and fractography analysis provided new insights into the diverse roles played by different populations of second-phase particles in fracture initiation under varying stress triaxiality conditions.

Keywords: ductile fracture, two-parameter criterion, x-ray computed tomography, stress triaxiality

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Authors: Andrew Kanzunguze, Sopani Sichinga, Paston Simkoko, George Nxumayo, Cosmas, V. B. Dambo

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Early detection of plant invasions is a necessary prerequisite for effective invasive plant management in protected areas. This study was conducted to determine the distribution and abundance of alien invasive trees in Nyika National Park (NNP). Data on species' presence and abundance were collected from belt transects (n=31) in a 100 square kilometer area on the central plateau. The data were tested for normality using the Shapiro-Wilk test; Mann-Whitney test was carried out to compare frequencies and abundances between the species, and geographical information systems were used for spatial analyses. Results revealed that Black Wattle (Acacia mearnsii), Mexican Pine (Pinus patula) and Himalayan Raspberry (Rubus ellipticus) were the main alien invasive trees on the plateau. A. mearnsii was localized in the areas where it was first introduced, whereas P. patula and R. ellipticus were spread out beyond original points of introduction. R. ellipticus occurred as dense, extensive (up to 50 meters) thickets on the margins of forest patches and pine stands, whilst P. patula trees were frequent in the valleys, occurring most densely (up to 39 stems per 100 square meters) south-west of Chelinda camp on the central plateau with high variation in tree heights. Additionally, there were no significant differences in abundance between R. ellipticus (48) and P. patula (48) in the study area (p > 0.05) It was concluded that R. ellipticus and P. patula require more attention as compared to A. mearnsii. Howbeit, further studies into the invasion ecology of both P. patula and R. ellipticus on the Nyika plateau are highly recommended so as to assess the threat posed by the species on biodiversity, and recommend appropriate conservation measures in the national park.

Keywords: alien-invasive trees, Himalayan raspberry, Nyika National Park, Mexican pine

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