Search results for: spatial gene

Authors: Sanjay Kumar Behera, Kanhu Charan Patra

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A GIS-based method has been applied for the determination of soil erosion and sediment yield in a small watershed in Ong River basin, Odisha, India. The method involves spatial disintegration of the catchment into homogenous grid cells to capture the catchment heterogeneity. The gross soil erosion in each cell was calculated using Universal Soil Loss Equation (USLE) by carefully determining its various parameters. The concept of sediment delivery ratio is used to route surface erosion from each of the discretized cells to the catchment outlet. The process of sediment delivery from grid cells to the catchment outlet is represented by the topographical characteristics of the cells. The effect of DEM resolution on sediment yield is analyzed using two different resolutions of DEM. The spatial discretization of the catchment and derivation of the physical parameters related to erosion in the cell are performed through GIS techniques.

Keywords: DEM, GIS, sediment delivery ratio, sediment yield, soil erosion

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Authors: Tingke Wu, Man Yuan

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“National Territorial Planning (2016-2030)” was issued by the State Council of China in 2017. As an important initiative of putting it into effect, territorial planning at provincial level makes overall arrangement of territorial development, resources and environment protection, comprehensive renovation and security system construction. Hubei province, as the pivot of the “Rise of Central China” national strategy, is now confronted with great opportunities and challenges in territorial development, protection, and renovation. Territorial spatial pattern experiences long time evolution, influenced by multiple internal and external driving forces. It is not clear what are the main causes of its formation and what are effective ways of optimizing it. By analyzing land use data in 2016, this paper reveals present status of territory in Hubei. Combined with economic and social data and construction information, driving forces of territorial spatial pattern are then analyzed. Research demonstrates that the three types of territorial space aggregate distinctively. The four aspects of driving forces include natural background which sets the stage for main functions, population and economic factors which generate agglomeration effect, transportation infrastructure construction which leads to axial expansion and significant provincial strategies which encourage the established path. On this basis, targeted strategies for optimizing territory spatial pattern are then put forward. Hierarchical protection pattern should be established based on development intensity control as respect for nature. By optimizing the layout of population and industry and improving the transportation network, polycentric network-based development pattern could be established. These findings provide basis for Hubei Territorial Planning, and reference for future territorial planning in other provinces.

Keywords: driving forces, Hubei, optimizing strategies, spatial pattern, territory

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Authors: K. Ali, M. F. Qamar, M. A. Zaman, M. Younus, I. Khan, S. Ehtisham-ul-Haque, R. Tamkeen, M. I. Rashid, Q. Ali

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This study centers on molecular identification of Haemonchus contortus and isolation of Benz-imidazoles (BZ) resistant strains. Different abattoirs’ of two geographic regions of Punjab (Pakistan) were frequently visited for the collection of worms. Out of 1500 (n=1500) samples that were morphologically confirmed as H. contortus, 30 worms were subjected to molecular procedures for isolation of resistant strains. Resistant worms (n=8) were further subjected to DNA gene sequencing. Bio edit sequence alignment editor software was used to detect the possible mutation, deletion, replacement of nucleotides. Genetic diversity was noticed and genetic variation existing in β-tubulin isotype 1 of the H. contortus population of small ruminants of different regions considered in this study. H. contortus showed three different type of genetic sequences. 75%, 37.5%, 25% and 12.5% of the studied samples showed 100% query cover and identity with isolates and clones of China, UK, Australia and other countries, respectively. Interestingly the neighbor countries such as India and Iran haven’t many similarities with the Pakistani isolates. Thus, it suggests that population density of same genetic makeup H. contortus is scattered worldwide rather than clustering in a single region.

Keywords: Haemonchus contortus, Benzimidazole resistant, β-tubulin-1 gene, abattoirs

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Authors: Ali A. Aldosari

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Change detection of Earth surface features is extremely important for better understanding of our environment in order to promote better decision making. Al-Jawf is remarkable for its abundant agricultural water where there is fertile agricultural land due largely to underground water. As result, this region has large areas of cultivation of dates, olives and fruits trees as well as other agricultural products such as Alfa Alfa and wheat. However this agricultural area was declined due to the reduction of government supports in the last decade. This reduction was not officially recorded or measured in this region at large scale or governorate level. Remote sensing data are primary sources extensively used for change detection in agriculture applications. This study is applied the technology of GIS and used the Normalized Difference Vegetation Index (NDVI) which can be used to measure and analyze the spatial and temporal changes in the agriculture areas in the Aljouf region.

Keywords: spatial analysis, geographical information system, change detection

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Authors: Alime Cengiz, Talip Kahyaoglu

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Roasting process has the major importance to obtain desired aromatic taste of nuts. In this study, two kinds of roasting process were applied to hulled sesame seeds - vacuum oven and hot air roasting. Efficiency of Gene Expression Programming (GEP), a new soft computing technique of evolutionary algorithm that describes the cause and effect relationships in the data modelling system, and response surface methodology (RSM) were examined in the modelling of roasting processes over a range of temperature (120-180°C) for various times (30-60 min). Color attributes (L*, a*, b*, Browning Index (BI)), textural properties (hardness and fracturability) and moisture content were evaluated and modelled by RSM and GEP. The GEP-based formulations and RSM approach were compared with experimental results and evaluated according to correlation coefficients. The results showed that both GEP and RSM were found to be able to adequately learn the relation between roasting conditions and physical and textural parameters of roasted seeds. However, GEP had better prediction performance than the RSM with the high correlation coefficients (R2 >0.92) for the all quality parameters. This result indicates that the soft computing techniques have better capability for describing the physical changes occuring in sesame seeds during roasting process.

Keywords: genetic expression programming, response surface methodology, roasting, sesame seed

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Authors: Xuan Linh Nguyen, Tien Yin Chou, Yao Min Fang, Feng Cheng Lin, Thanh Van Hoang, Yin Min Huang

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In Vietnam, land use planning is the most important and powerful tool of the government for sustainable land use and land management. Nevertheless, many of land use planning locations are facing protests from surrounding households due to environmental impacts. In addition, locations are planned completely based on the subjective decisions of planners who are unsupported by tools or scientific methods. Hence, this research aims to assist the decision-makers in evaluating the rationality of planning locations by developing a Spatial Decision Support System (SDSS) using approaches of Geographic Information System (GIS)-based technology, Analytic Hierarchy Process (AHP) multi-criteria-based technique and Fuzzy set theory. An ArcGIS Desktop add-ins named SDSS-LUPA was developed to support users analyzing data and presenting results in friendly format. The Fuzzy-AHP method has been utilized as analytic model for this SDSS. There are 18 planned locations in Hung Ha district (Thai Binh province, Vietnam) as a case study. The experimental results indicated that the assessment threshold higher than 0.65 while the 18 planned locations were irrational because of close to residential areas or close to water sources. Some potential sites were also proposed to the authorities for consideration of land use planning changes.

Keywords: analytic hierarchy process, fuzzy set theory, land use planning, spatial decision support system

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Authors: Amr A. El Hanafy, Yasser M. Saad, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan

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Camels are substantial providers of transport, milk, sport, meat, shelter, fuel, security and capital in many countries, particularly Saudi Arabia. Identification of animal breeds has progressed rapidly during the last decade. Advanced molecular techniques are playing a significant role in breeding or strain protection laws. On the other hand, fingerprinting of some molecular markers related to some productive traits in farm animals represents most important studies to our knowledge, which aim to conserve these local genetic resources, and to the genetic improvement of such local breeds by selective programs depending on gene markers. Milk records were taken two days in each week from female camels of Majahem, Safara, Wathaha, and Hamara breeds, respectively from different private farms in northern Jeddah, Riyadh and Alwagh governorates and average weekly yields were calculated. DNA sequencing for CSN2 gene was used for evaluating the genetic variations and calculating the genetic distance values among four Saudi camel populations which are Hamra(R), Safra(Y), Wadha(W) and Majaheim(M). In addition, this marker was analyzed for reconstructing the Neighbor joining tree among evaluating camel breeds. In respect to milk yield during winter season, result indicated that average weekly milk yield of Safara camel breed (30.05 Kg/week) is significantly (p < 0.05) lower than the other 3 breeds which ranged from 39.68 for Hamara to 42.42 Kg/week for Majahem, while there are not significant differences between these three breeds. The Neighbor Joining analysis that re-constructed based on DNA variations showed that samples are clustered into two unique clades. The first clade includes Y (from Y4 to Y18) and M (from M1, to M9). On the other hand, the second cluster is including all R (from R1 to R6) and W (from W1 to W6). The genetic distance values were equal 0.0068 (between the groups M&Y and R&W) and equal 0 (within each group).

Keywords: milk yield, beta-casein precursor (CSN2), Saudi camel, molecular markers

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Authors: A. Kavya Sri, K. Sai Vineela, R. Vanitha, S. Rohith

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Large pieces of ice that break from the glaciers are known as icebergs. The threat that icebergs pose to navigation, production of offshore oil and gas services, and underwater pipelines makes their detection crucial. In this project, an automated iceberg tracking method using deep learning techniques and satellite images of icebergs is to be developed. With a temporal resolution of 12 days and a spatial resolution of 20 m, Sentinel-1 (SAR) images can be used to track iceberg drift over the Southern Ocean. In contrast to multispectral images, SAR images are used for analysis in meteorological conditions. This project develops a web-based graphical user interface to detect and track icebergs using sentinel-1 images. To track the movement of the icebergs by using temporal images based on their latitude and longitude values and by comparing the center and area of all detected icebergs. Testing the accuracy is done by precision and recall measures.

Keywords: synthetic aperture radar (SAR), icebergs, deep learning, spatial resolution, temporal resolution

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Authors: Kuo-Cheng Liu

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In the perceptual image coding, the objective is to shape the coding distortion such that the amplitude of distortion does not exceed the error visibility threshold, or to remove perceptually redundant signals from the image. While most researches focus on color image coding, the perceptual-based quantizer developed for luminance signals are always directly applied to chrominance signals such that the color image compression methods are inefficient. In this paper, the internal generative mechanism is integrated into the design of a color image compression method. The internal generative mechanism working model based on the structure-based spatial masking is used to assess the subjective distortion visibility thresholds that are visually consistent to human eyes better. The estimation method of structure-based distortion visibility thresholds for color components is further presented in a locally adaptive way to design quantization process in the wavelet color image compression scheme. Since the lowest subband coefficient matrix of images in the wavelet domain preserves the local property of images in the spatial domain, the error visibility threshold inherent in each coefficient of the lowest subband for each color component is estimated by using the proposed spatial error visibility threshold assessment. The threshold inherent in each coefficient of other subbands for each color component is then estimated in a local adaptive fashion based on the distortion energy allocation. By considering that the error visibility thresholds are estimated using predicting and reconstructed signals of the color image, the coding scheme incorporated with locally adaptive perceptual color quantizer does not require side information. Experimental results show that the entropies of three color components obtained by using proposed IGM-based color image compression scheme are lower than that obtained by using the existing color image compression method at perceptually lossless visual quality.

Keywords: internal generative mechanism, structure-based spatial masking, visibility threshold, wavelet domain

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Authors: Zi-Han Li, Zi-Jun Sun, Dong-Yuan Chang, Li Zhu, Min Chen, Ming-Hui Zhao

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Aims: A genome-wide association study (GWAS) reported that patients with the rs55703767 minor allele in collagen type IV α3 chain encoding gene COL4A3 showed protection against diabetic kidney disease (DKD) in type 1 diabetes mellitus (T1DM). However, the role of rs55703767 in type 2 DKD has not been elucidated. The aim of the current study was to investigate the association between COL4A3 variant rs55703767 and DKD risk in Chinese patients with type 2 diabetes mellitus (T2DM). Methods: This nested case-control study was performed on 1311 patients who had T2DM for at least 10 years, including 580 with DKD and 731 without DKD. We detected the genotypes of all patients by TaqMan SNP Genotyping Assay and analyzed the association between COL4A3 variant rs55703767 and DKD risk. Results: Genetic analysis revealed that there was no significant difference between T2DM patients with DKD and those without DKD regarding allele or genotype frequencies of rs55703767, and the effect of this variant was not hyperglycemia specific. Conclusion: Our findings suggested that there was no detectable association between the COL4A3 variant rs55703767 and the susceptibility to DKD in the Chinese T2DM population.

Keywords: collagen type IV α3 chain, gene polymorphism, type 2 diabetes, diabetic kidney disease

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Authors: Akbar Nawaz Khan, Abdul Ghaffar, Muhammad Naeem Riaz

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The study was conducted to investigate the phenotypic features, morphometry and production potentialities of indigenous naked neck chicken (NN) of Pakistan under intensive management condition. A total of 35 NN chicks were randomly selected, and the experiment was performed at Poultry and wildlife research section NARC Islamabad for a period of 22 weeks. The predominant plumage color was black and golden while skin color was observed white. The average shank length, leg length, thigh length, keel length, chest breadth, head width, wing space, wing length, body length, body girth, body height and pubic bone width in adult males and females were 69.19 ± 3.34mm, 117.93 ± 4.42mm, 117.93 ± 4.42mm, 90.87 ± 6.53mm, 95.03 ± 4.56mm, 49.77 ± 2.53mm, 30.63 ± 1.50cm, 27.24 ± 2.71cm, 18.88 ± 0.65cm, 17.77 ± 1.01cm, 25.96 ± 0.56cm, 47.81 ± 1.41cm and 35.69 ± 4.09mm respectively. The average age and live body weight of NN chicken at sexual maturity were recorded as 165.85 days and 1269.38 g. While hen-day egg production of NN was recorded as 45%. The present study was aimed to investigate the existence of polymorphism at IGF-I gene in indigenous naked neck chicken through PCR based Restriction Fragment Length Polymorphism. Based on restriction analysis using Hinf I restriction enzyme, three genotypes were detected designated as AA, AC, and CC. Restriction analysis of PCR amplified product showed the presence of DNA fragments of 622, 378, 244 and 191, (genotypes). The PCR-RFLP analysis is easy, cost effective method which permits the easy characterization of IGF-I gene. This showed the investigated IGF-I genes can serve as good molecular markers for marker assisted selection (MAS) concerning growth related traits in chicken.

Keywords: Desi chicken, naked neck, morphology, morphometry, production potential, egg traits, egg geometry, IGF-I, growth, PCR- RFLP, chicken

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Authors: Ali Bagherpour

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The aim of this study was to determinate the variety of Anaplasma species among cattle of Khuzestan province, Iran. From April 2013 to June 2013, a total of 200 blood samples were collected via the jugular vein from healthy cattle (100), randomly. The extracted DNA from blood cells were amplified by Anaplasma-all primers, which amplify an approximately 1468bp DNA fragment from region of 16S rRNA gene from various members of the genus Anaplasma. For raising the test sensivity, the PCR products were amplified with the primers, which were designed from the region flanked by the first primers. The amplified nested PCR product had an expected PCR product with 345 nucleotides in length. 44 out of 100 cattle blood samples were Anaplasma spp. positive by first PCR and nested PCR. All cattle positive samples were further analyzed for the presence of A. centrale, A. bovis and A. phagocytophilum by specific nested PCR. A.phagocytophilum was identified by specific nested PCR in 3% of cattle blood samples. The extracted DNA from positive Anaplasma spp. samples were amplified by Anaplasma marginale/ovis specific primers, which amplify an approximately 866bp DNA fragment from region of msp4 gene. 41 out of 100 cattle blood samples (41%) were positive for Anaplasma marginale and Anaplasma ovis, respectively.

Keywords: Iran, Khuzestan, Anaplasma species, Cattle, A. marginale, A. ovis, A. phagocytophilum, PCR

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Authors: Jianhong Xiang, Rui Sun, Linyu Wang

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In recent years, due to the continuous improvement of deep learning theory, Convolutional Neural Network (CNN) has played a great superior performance in the research of Hyperspectral Image (HSI) classification. Since HSI has rich spatial-spectral information, only utilizing a single dimensional or single size convolutional kernel will limit the detailed feature information received by CNN, which limits the classification accuracy of HSI. In this paper, we design a multi-scale CNN with MLP based on residual and attention modules (INRAM-3DCNN) for the HSI classification task. We propose to use multiple 3D convolutional kernels to extract the packet feature information and fully learn the spatial-spectral features of HSI while designing residual 3D convolutional branches to avoid the decline of classification accuracy due to network degradation. Secondly, we also design the 2D Inception module with a joint channel attention mechanism to quickly extract key spatial feature information at different scales of HSI and reduce the complexity of the 3D model. Due to the high parallel processing capability and nonlinear global action of the Multilayer Perceptron (MLP), we use it in combination with the previous CNN structure for the final classification process. The experimental results on two HSI datasets show that the proposed INRAM-3DCNN method has superior classification performance and can perform the classification task excellently.

Keywords: INRAM-3DCNN, residual, channel attention, hyperspectral image classification

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Authors: Yueying Chen

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A city can be developed through memory, and memory is one of the most important elements for urban contexts. Collective memory is a collection of personal memories that can be preserved with objects, places, and events of heritage, expressing culture through spatial changes. These preserved forms can evoke a sense of community and certain emotions. Collective memory in cities reflects urban spatial alterations and historical developments. It can be preserved and reflected by revitalisation projects. A major current focus in collective memory research is how to identify and preserve memory in an intangible way. The influential elements within the preservation of collective memory mainly include institutions and objects. However, current research lacks the assessment of the collective memory after alterations of urban heritage. The assessment of urban heritage lacks visualization and qualitative methods. The emergence of the application of space syntax can fill in this gap. Hengshan Mansions was a new project in 2015. The original residential area has been replaced with a comprehensive commercial area integrating boutique shopping, upscale restaurants, and creative offices. Hengshan Mansions is located in the largest historic area in Shanghai, and its development is the epitome of the traditional culture in Shanghai. Its alteration is the newest project in this area and presents the new concept of revitalisation of urban heritage. For its physical parts, modern vitality is created, and historical information is preserved at the same time. However, most of the local people are moved away, and its functions are altered a lot. The preservation of its collective memory needs to discuss furtherly. Thus, the article builds a framework to assess the collective memory of urban heritage, including spatial configuration, spatial interaction, and cultural cognition. Then, it selects Hengshan Mansions in Shanghai as a case to analyse the assessed framework. Space syntax can be applied to visualize the assessment. Based on the analysis, the article will explore the influential reasons for the collective memory after alterations and proposes relevant advice for the preservation of the collective memory of urban heritage.

Keywords: collective memory, alternation of urban heritage, space syntax, Hengshan Mansions

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Authors: Hae Jeong Park, Joo-Ho Chung

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In this study, the effect of essential oil from Chamaecyparis obtuse (EOCO) on early life stress using maternal separation (MS) rats was investigated. Anxiety-related behaviors were examined in MS rats using the elevated plus-maze (EPM) test. The changes of gene expressions by EOCO in the hippocampus of MS rats were analyzed using a microarray method. Rats in the MS groups were separated from their respective mothers from postnatal day (pnd) 14 to 28. Rats in the EOCO-treated groups were exposed to EOCO for 1 h or 2 h by inhalation from pnd 21 to 28. The EOCO-treated MS rats showed decreased anxiety-related behaviors compared to the MS rats in the EPM test. In the microarray analysis, EOCO downregulated the expressions of cytokine genes such as Ccl2, Il6, Cxcl10, Ccl19, and Il1rl in the hippocampus of MS rats, and it was also confirmed through RT-PCR. In particular, the expressions of Ccl2 and Il6 were predominantly decreased by EOCO in the hippocampus of MS rats. Interestingly, their protein expressions were also reduced by EOCO in MS rats. These results indicate that EOCO decreases MS-induced anxiety-related behaviors, and modulate cytokines, particularly Ccl2 and Il6, in the hippocampus of MS rats.

Keywords: anxiety-related behavior, Chamaecyparis obtuse, cytokine gene, early-life stress, maternal separation

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Authors: Chevonne Reynolds, Robert J. Fletcher, Jr, Celine M. Carneiro, Nicole Jennings, Alison Ke, Michael C. LaScaleia, Mbhekeni B. Lukhele, Mnqobi L. Mamba, Muzi D. Sibiya, James D. Austin, Cebisile N. Magagula, Themba’alilahlwa Mahlaba, Ara Monadjem, Samantha M. Wisely, Robert A. McCleery

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A key challenge for the developing world is reconciling biodiversity conservation with the growing demand for food. In these regions, agriculture is typically interspersed among other land-uses creating heterogeneous landscapes. A primary hypothesis for promoting biodiversity in agricultural landscapes is the habitat heterogeneity hypothesis. While there is evidence that landscape heterogeneity positively influences biodiversity, the application of this hypothesis is hindered by a need to determine which components of landscape heterogeneity drive these effects and at what spatial scale(s). Additionally, whether diverse taxonomic groups are similarly affected is central for determining the applicability of this hypothesis as a general conservation strategy in agricultural mosaics. Two major components of landscape heterogeneity are compositional and configurational heterogeneity. Disentangling the roles of each component is important for biodiversity conservation because each represents different mechanisms underpinning variation in biodiversity. We identified a priori independent gradients of compositional and configurational landscape heterogeneity within an extensive agricultural mosaic in north-eastern Swaziland. We then tested how bird, dung beetle, ant and meso-carnivore diversity responded to compositional and configurational heterogeneity across six different spatial scales. To determine if a general trend could be observed across multiple taxa, we also tested which component and spatial scale was most influential across all taxonomic groups combined, Compositional, not configurational, heterogeneity explained diversity in each taxonomic group, with the exception of meso-carnivores. Bird and ant diversity was positively correlated with compositional heterogeneity at fine spatial scales < 1000 m, whilst dung beetle diversity was negatively correlated to compositional heterogeneity at broader spatial scales > 1500 m. Importantly, because of these contrasting effects across taxa, there was no effect of either component of heterogeneity on the combined taxonomic diversity at any spatial scale. The contrasting responses across taxonomic groups exemplify the difficulty in implementing effective conservation strategies that meet the requirements of diverse taxa. To promote diverse communities across a range of taxa, conservation strategies must be multi-scaled and may involve different strategies at varying scales to offset the contrasting influences of compositional heterogeneity. A diversity of strategies are likely key to conserving biodiversity in agricultural mosaics, and we have demonstrated that a landscape management strategy that only manages for heterogeneity at one particular scale will likely fall short of management objectives.

Keywords: agriculture, biodiversity, composition, configuration, heterogeneity

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Authors: Sinem Tas

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This research paper attempts to study the perspective of personal experience in relation to spatial dynamics and artistic outcomes within the realm of cultural identity. This article serves as a partial analysis within a broader PhD investigation that focuses on the cultural dynamics and political structures behind cultural identity through an autoethnography of narrative while presenting its correlation with artistic creation in the context of space and people. Focusing on the artistic/creative practice project AUTRUI, the primary goal is to analyse and understand the influence of personal experiences and culturally constructed identity as an artist in resulting in the compositional modality of the last image considering self-reflective experience. Referencing the works of Joyce Davidson and Christine Milligan - the scholars who emphasise the importance of emotion and spatial experience in geographical studies contribute to this work as they highlight the significance of emotion across various spatial scales in their work Embodying Emotion Sensing Space: Introducing Emotional Geographies (2004). Their perspective suggests that understanding emotions within different spatial contexts is crucial for comprehending human experiences and interactions with space. Incorporating the insights of scholars like Yi-Fu Tuan, particularly his seminal work Space and Place: The Perspective of Experience (1979), is important for creating an in-depth frame of geographical experience. Tuan's humanistic perspective on space and place provides a valuable theoretical framework for understanding the interplay between personal experiences and spatial contexts. A substantial contextualisation of the geopolitics of Turkey - the implications for national identity and cohesion - will be addressed by drawing an outline of the political and geographical frame as a methodological strategy to understand the dynamics behind this research. Besides the bibliographical reading, the methods used to study this relation are participatory observation, memory work along with memoir analysis, personal interviews, and discussion of photographs and news. The utilisation of the self as data requires the analysis of the written sources with personal engagement. By delving into written sources such as written communications or diaries as well as memoirs, the research gains a firsthand perspective, enriching the analytical depth of the study. Furthermore, the examination of photography and news articles serves as a valuable means of contextualising experiences from a journalist's background within specific geographical settings. The inclusion of interviews with close family members access provides firsthand perspectives and intimate insights rooted in shared experiences within similar geographical contexts, offering complementary insights and diversified viewpoints, enhancing the comprehensiveness of the investigation.

Keywords: art, autoethnography, place and space, Turkey

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Authors: Yahia I. Mohamed, Ahmed I. Marzouk, Mohamed A. Yacout

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Aim of this work was to study the genetic basis for oil accumulation in olive fruit via tracking DGAT2 (Diacylglycerol acyltransferase type-2) gene in three Egyptian Origen Olive cultivars namely Toffahi, Hamed and Maraki using molecular marker techniques and bioinformatics tools. Results illustrate that, firstly: specific genomic band of Maraki cultivars was identified as DGAT2 (Diacylglycerol acyltransferase type-2) and identical for this gene in Olea europaea with 100 % of similarity. Secondly, differential genomic band of Maraki cultivars which produced from RAPD fingerprinting technique reflected predicted distinguished sequence which identified as DGAT2 (Diacylglycerol acyltransferase type-2) in Fragaria vesca subsp. Vesca with 76% of sequential similarity. Third and finally, specific genomic specific band of Hamed cultivars was indentified as two fragments, 1-Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA, complete cds with two matches regions with 99% or 2-PREDICTED: Fragaria vesca subsp. vesca diacylglycerol O-acyltransferase 2-like (LOC101313050), mRNA with 86% of similarity.

Keywords: Olea europaea, fingerprinting, diacylglycerol acyltransferase type-2 (DGAT2), Egypt

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Authors: Tayaba Dastgeer, Farhan Rasheed, Muhammad Saeed, Maqsood Ahmad, Zia Ashraf, Abdul Waheed, Muhammad Kamran, Mohsin Khurshid

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Objectives: The study aimed to determine the efficacy of linezolid against clinical isolates of methicillin-resistant staphylococcus aureus (MRSA). Methodology: This cross-sectional study was conducted in the microbiology department of Allama Iqbal Medical College Lahore from August 2017 to September 2019. Isolates were confirmed as MRSA via the presence of the mec-A gene. Confirmed MRSA isolates were processed for susceptibility testing against different antimicrobials, especially linezolid, via the disc diffusion method. Zone sizes were interpreted according to CLSI guidelines. Results: Various types of clinical samples were included in the study; however, the highest frequency of MRSA isolates was found in pus samples, followed by other clinical samples. Among hospitalized patients, most MRSA isolates were obtained from patients in the surgical ward. Of 243 mec-A gene detected isolates, Vancomycin and linezolid showed 100% susceptibility, chloramphenicol showed declining resistance 78 (32.09%), and emerging sensitivity 165 (67.90%) against MRSA. Conclusion: Linezolid is a very efficient drug against MRSA, but the use of this novel drug must be conserved for vancomycin-resistant Staphylococcus aureus or when more resistant pathogens are suspected.

Keywords: MRSA, chloramphenicol, linezolid, nosocomial infections

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Authors: Sahabeh Safarpour, Khiruddin Abdullah, Hwee San Lim, Mohsen Dadras

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Air pollution is a growing problem arising from domestic heating, high density of vehicle traffic, electricity production, and expanding commercial and industrial activities, all increasing in parallel with urban population. Monitoring and forecasting of air quality parameters are important due to health impact. One widely available metric of aerosol abundance is the aerosol optical depth (AOD). The AOD is the integrated light extinction coefficient over a vertical atmospheric column of unit cross section, which represents the extent to which the aerosols in that vertical profile prevent the transmission of light by absorption or scattering. Seasonal aerosol optical depth (AOD) values at 550 nm derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor onboard NASA’s Terra satellites, for the 10 years period of 2000-2010 were used to test 7 different spatial interpolation methods in the present study. The accuracy of estimations was assessed through visual analysis as well as independent validation based on basic statistics, such as root mean square error (RMSE) and correlation coefficient. Based on the RMSE and R values of predictions made using measured values from 2000 to 2010, Radial Basis Functions (RBFs) yielded the best results for spring, summer, and winter and ordinary kriging yielded the best results for fall.

Keywords: aerosol optical depth, MODIS, spatial interpolation techniques, Radial Basis Functions

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Authors: Thomas E. Portegys

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An animal behavior problem is presented in the form of a nest-building task that involves two cooperating virtual birds, a male and female. The female builds a nest into which she lays an egg. The male's job is to forage in a forest for food for both himself and the female. In addition, the male must fetch stones from a nearby desert for the female to use as nesting material. The task is completed when the nest is built, and an egg is laid in it. A goal-seeking neural network and a recurrent neural network were trained and tested with little success. The goal-seeking network was then enhanced with “place cells”, allowing the birds to spatially navigate the world, building the nest while keeping themselves fed. Place cells are neurons in the hippocampus that map space.

Keywords: artificial animal intelligence, artificial life, goal-seeking neural network, nest-building, place cells, spatial navigation

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Authors: Xiaoxing Ye

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To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

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Authors: Jingyuan Hu, Zhandong Liu

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CRISPR genome editing technology has transformed molecular biology by accurately targeting and altering an organism’s DNA. Despite the state-of-art precision of CRISPR genome editing, the imprecise mutation outcome and off-target effects present considerable risk, potentially leading to unintended genetic changes. Targeted deep sequencing, combined with bioinformatics sequence alignment, can detect such unwanted mutations. Nevertheless, the classical method, Needleman-Wunsch (NW) algorithm may produce false alignment outcomes, resulting in inaccurate mutation identification. The key to precisely identifying CRISPR-induced mutations lies in determining optimal parameters for the sequence alignment algorithm. Hidden Markov models (HMM) are ideally suited for this task, offering flexibility across CRISPR systems by leveraging forward-backward algorithms for parameter estimation. In this study, we introduce CRISPR-HMM, a statistical software to precisely call CRISPR-induced mutations. We demonstrate that the software significantly improves precision in identifying CRISPR-induced mutations compared to NW-based alignment, thereby enhancing the overall understanding of the CRISPR gene-editing process.

Keywords: CRISPR, HMM, sequence alignment, gene editing

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Authors: Mahsa Jalili, Essa Ehsan Khan, Signe Dille Lovmo, Augustine Akruwe, Egil Lien, Rolf Erik Olsen, Trygve Sigholt, Atle Magnus Bones

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Data from the Norwegian Directorate of Fisheries reported that >1.2 million tons of Atlantic salmon were produced in Norway aquaculture industry in 2016. Peroxisome proliferator-activated receptors (PPARs) are one of the key transcription factor families that respond to nutritional ligands. Recent studies have shown the connection between PPARs with lipid and carbohydrate metabolism in aquaculture. To our knowledge, there is no published data about the effects of krill meal, soybean meal, Bactocell ® and butyrate feedings compared to control group on PPARs gene and protein expressions in Atlantic salmon. Fish, 1year +postsmolt, average weight 250 gram were cultured for 12 weeks after acclimatization by control commercial feeding in 2 weeks after hatchery. Water oxygen rate, salinity, and temperature were monitored every second day. At the end of the trial, fish were taken from tanks randomly, and four replicates per group were collected and stored in -80 freezers until analysis. Total RNA extracted from posterior part of dorsal fin muscle tissues and Nanodrop and Bioanalyzer was used to check the quality of RNA. Gene expression of PPAR α, β and γ were determined by RT-PCR. The expression of genes of interest was measured relative to control group after normalization to three reference genes. Total protein concentration was calculated by Bradford method, and protein expression was determined with primary PPARγ antibody by western blot. All data were analyzed by ANOVA followed by Benjamini-Hochberg and Bonferroni tests. Probability values <0.05 considered significant. Bactocell® and butyrate groups showed significantly lower PPARα expression. PPARβ and γ were not significantly different among groups. PPARγ mRNA expression was approximately consistent with protein expression pattern, except than butyrate group showed lower mRNA level. The order of PPARγ expression was Bactocell® > soy meal > butyrate > krill meal > control respectively. PPARβ gene expression decreased more in soy meal > butyrate > krill meal > Bactocell® > control groups respectively. In conclusion, the increased expression of PPARγ and α is proposed to represent a reduction tendency of lipid storage in fish fed by Bactocell®, butyrate, soy and krill meal.

Keywords: aquaculture, blotting western, gene expression, krill protein extract, prebiotics, probiotics, Salmo salar

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Authors: Pattanapon Kayansamruaj, Ha Thanh Dong, Nopadon Pirarat, Channarong Rodkhum

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Streptococcus iniae (SI) is a devastating pathogenic bacteria causing heavy mortality in farmed fish. The application of commercialized bacterin vaccine has been reported failures as the outbreaks of the new serotype of SI were emerged in farms after vaccination and subsequently caused severe losses. In the present study, we attempted to develop effective DNA vaccines against SI infection using Nile tilapia (Oreochromis niloticus) as an animal model. Two monovalent DNA vaccines were constructed by the insertion of coding sequences of cell wall-associated virulence factors-encoding genes, comprised of eno (α-enolase) and mtsB (hydrophobic membrane protein), into cytomegalovirus expression vector (pCI-neo). In the animal trial, 30-g Nile tilapia were injected intramuscularly with 15 µg of each vaccine (mock vaccine group was injected by naked pCI-neo) and maintained for 35 days prior challenging with pathogenic SI at the dosage of 107 CFU/fish. At 13 days post-challenge, the relative percent survival of pEno, pMtsB and mock vaccine were 57%, 45% and 27%, respectively. The expression levels of immune responses-associated genes, namely, IL1β, TNF-α, TGF-β, COX2, IL-6, IL-12 and IL-13, were investigated from the spleen of experimental animal at 7 days post-vaccination (PV) and 7 days post-challenge (PC) using quantitative RT-PCR technique. Generally, at 7 days PV, the pEno vaccinated group exhibited highest level of up-regulation (1.7 to 2.9 folds) of every gene, but TGF-β, comparing to pMtsB and mock vaccine groups. However, at 7 days PC, pEno group showed significant up-regulation (1.4 to 8.5 folds) of immune-related genes as similar as mock vaccine group, while pMtsB group had lowest level of up-regulation (0.7 to 3.3 folds). Summarily, this study indicated that the pEno and pMtsB vaccines could elicit the immune responses of the fish and the magnitude of gene expression at 7 days PV was also consistent with the protection level conferred by the vaccine.

Keywords: gene expression, DNA vaccine, Nile tilapia, Streptococcus iniae

Procedia PDF Downloads 322

Authors: Naveed Mazhar

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Our cities are known to have significant modifying effects on the local climate. The nature of the modifications depends on a range of physical variables, usually assessed at a wide range of spatial scales. Physical spatial dimensions, such as measured parameters of microclimates and their significant influence on human sensations, are known to have far-reaching effects on human thermal comfort and by corollary a force that influences human perception. Less scholarship has thrown light on the subjective dimension and insufficiently demonstrates a relational approach between human behavior and how it is affected by the phenomenon of urban microclimates. Other than identifying gaps in the most recent scholarship and providing future research opportunities, the scope of this study will help improve urban design guidelines and raise framework standards of socially responsive urban design. This study will help equip future professionals to ameliorate the effects of urban microclimates on participant’s perceptions enabling more frequent usage of the outdoor urban spaces. However, it is informed that the physical parameters of an outdoor open space determine psychological human adaptations and is a measure of the degree to which people are willing to adapt to their surroundings. A large amount of research is available related to urban microclimates. However, very few studies are focused on the elucidation of the critical factors influencing human perceptions of the microclimates in urban spatial configurations. Based on the most recent scholarship, this study has evaluated the role urban microclimatic conditions have in the formation of human perceptions and, by extension, behavioral patterns formulating in outdoor open spaces. Furthermore, this study also defines, in the backdrop of the current scholarly literature, the socio-spatial interdependence of behavioral patterns with relationship to the built urban fabric and its resultant correlation with human perception. A comprehensive review and analysis of the recent research conducted within the scope of the study will help frame gaps, issues, current research methods and future research opportunities.

Keywords: urban design, urban microcliamate, human perception, human behavioral patterns

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Authors: Abdulwahab Kammon, Tan Sheau Wei, Abdul Rahman Omar, Abdunaser Dayhum, Ibrahim Eldghayes, Monier Sharif

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Infectious bronchitis virus (IBV) is a very dynamic and evolving virus which causing major economic losses to the global poultry industry. Recently, the Libyan poultry industry faced severe outbreak of respiratory distress associated with high mortality and dramatic drop in egg production. Tracheal and cloacal swabs were analyzed for several poultry viruses. IBV was detected using SYBR Green I real-time PCR detection based on the nucleocapsid (N) gene. Sequence analysis of the partial N gene indicated high similarity (~ 94%) to IBV strain 3382/06 that was isolated from Taiwan. Even though the IBV strain 3382/06 is more similar to that of the Mass type H120, the isolate has been implicated associated with intertypic recombinant of 3 putative parental IBV strains namely H120, Taiwan strain 1171/92 and China strain CK/CH/LDL/97I. Complete sequencing and antigenicity studies of the Libya IBV strains are currently underway to determine the evolution of the virus and its importance in vaccine induced immunity. In this paper, we documented for the first time the presence of possibly variant IBV strain from Libya which required a dramatic change in the vaccination program.

Keywords: Libya, infectious bronchitis, molecular characterization, viruses, vaccine

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Authors: Subham Kharel, Sudha Ravindranath, A. Vidya, B. Chandrasekaran, K. Ganesha Raj, T. Shesadri

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Digitization of urban features is a tedious and time-consuming process when done manually. In addition to this problem, Indian cities have complex habitat patterns and convoluted clustering patterns, which make it even more difficult to map features. This paper makes an attempt to classify urban objects in the satellite image using object-oriented classification techniques in which various classes such as vegetation, water bodies, buildings, and shadows adjacent to the buildings were mapped semi-automatically. Building layer obtained as a result of object-oriented classification along with already available building layers was used. The main focus, however, lay in the extraction of high-rise buildings using spatial technology, digital image processing, and modeling, which would otherwise be a very difficult task to carry out manually. Results indicated a considerable rise in the total number of buildings in the city. High-rise buildings were successfully mapped using satellite imagery, spatial technology along with logical reasoning and mathematical considerations. The results clearly depict the ability of Remote Sensing and GIS to solve complex problems in urban scenarios like studying urban sprawl and identification of more complex features in an urban area like high-rise buildings and multi-dwelling units. Object-Oriented Technique has been proven to be effective and has yielded an overall efficiency of 80 percent in the classification of high-rise buildings.

Keywords: object oriented classification, shadow extraction, high-rise buildings, satellite imagery, spatial technology

Procedia PDF Downloads 141

Authors: Srijata Mitra, Mobina Parveen, Pranab Roy, Narayan Chandra Chattopadhyay

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Chlorinated hydrocarbon can be a major pollution problem in groundwater as well as soil. Many people interact with these chemicals on daily accidentally or by professionally in the laboratory. One of the most common sources for Chlorinated hydrocarbon contamination of soil and groundwater are industrial effluents. The wide use and discharge of Trichloroethylene (TCE), a volatile chlorohydrocarbon from chemical industry, led to major water pollution in rural areas. TCE is an mainly used as an industrial metal degreaser in industries. Biotransformation of TCE to the potent carcinogen vinyl chloride (VC) by consortia of anaerobic bacteria might have role for the above purpose. For these reasons, the aim of current study was to isolate and characterized the genes involved in TCE metabolism and also to investigate the in silico study of those genes. To our knowledge, only one aromatic dioxygenase system, the toluene dioxygenase in Pseudomonas putida F1 has been shown to be involved in TCE degradation. This is first instance where Bacillus cereus group being used in biodegradation of trichloroethylene. A novel bacterial strain 2479 was isolated from oil depot site at Rajbandh, Durgapur (West Bengal, India) by enrichment culture technique. It was identified based on polyphasic approach and ribotyping. The bacterium was gram positive, rod shaped, endospore forming and capable of degrading trichloroethylene as the sole carbon source. On the basis of phylogenetic data and Fatty Acid Methyl Ester Analysis, strain 2479 should be placed within the genus Bacillus and species cereus. However, the present isolate (strain 2479) is unique and sharply different from the usual Bacillus strains in its biodegrading nature. Fujiwara test was done to estimate that the strain 2479 could degrade TCE efficiently. The gene for TCE biodegradation was PCR amplified from genomic DNA of Bacillus cereus 2479 by using todC1 gene specific primers. The 600bp amplicon was cloned into expression vector pUC I8 in the E. coli host XL1-Blue and expressed under the control of lac promoter and nucleotide sequence was determined. The gene sequence was deposited at NCBI under the Accession no. GU183105. In Silico approach involved predicting the physico-chemical properties of deduced Tce1 protein by using ProtParam tool. The tce1 gene contained 342 bp long ORF encoding 114 amino acids with a predicted molecular weight 12.6 kDa and the theoretical pI value of the polypeptide was 5.17, molecular formula: C559H886N152O165S8, total number of atoms: 1770, aliphatic index: 101.93, instability index: 28.60, Grand Average of Hydropathicity (GRAVY): 0.152. Three differentially expressed proteins (97.1, 40 and 30 kDa) were directly involved in TCE biodegradation, found to react immunologically to the antibodies raised against TCE inducible proteins in Western blot analysis. The present study suggested that cloned gene product (TCE1) was capable of degrading TCE as verified chemically.

Keywords: cloning, Bacillus cereus, in silico analysis, TCE

Procedia PDF Downloads 388

Authors: Chen Zhang, Nan Chen

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High-dimensional process monitoring becomes increasingly important in many application domains, where usually the process distribution is unknown and much more complicated than the normal distribution, and the between-stream correlation can not be neglected. However, since the process dimension is generally much bigger than the reference sample size, most traditional nonparametric multivariate control charts fail in high-dimensional cases due to the curse of dimensionality. Furthermore, when the process goes out of control, the influenced variables are quite sparse compared with the whole dimension, which increases the detection difficulty. Targeting at these issues, this paper proposes a new nonparametric monitoring scheme for high-dimensional processes. This scheme first projects the high-dimensional process into several subprocesses using random projections for dimension reduction. Then, for every subprocess with the dimension much smaller than the reference sample size, a local nonparametric control chart is constructed based on the spatial rank test to detect changes in this subprocess. Finally, the results of all the local charts are fused together for decision. Furthermore, after an out-of-control (OC) alarm is triggered, a diagnostic framework is proposed. using the square-root LASSO. Numerical studies demonstrate that the chart has satisfactory detection power for sparse OC changes and robust performance for non-normally distributed data, The diagnostic framework is also effective to identify truly changed variables. Finally, a real-data example is presented to demonstrate the application of the proposed method.

Keywords: random projection, high-dimensional process control, spatial rank, sequential change detection

Procedia PDF Downloads 289