Search results for: identification partial rbcL

Authors: Bliss Singhal

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Machine learning (ML) is a branch of Artificial Intelligence (AI) where computers analyze data and find patterns in the data. The study focuses on the detection of metastatic cancer using ML. Metastatic cancer is the stage where cancer has spread to other parts of the body and is the cause of approximately 90% of cancer-related deaths. Normally, pathologists spend hours each day to manually classifying whether tumors are benign or malignant. This tedious task contributes to mislabeling metastasis being over 60% of the time and emphasizes the importance of being aware of human error and other inefficiencies. ML is a good candidate to improve the correct identification of metastatic cancer, saving thousands of lives and can also improve the speed and efficiency of the process, thereby taking fewer resources and time. So far, the deep learning methodology of AI has been used in research to detect cancer. This study is a novel approach to determining the potential of using preprocessing algorithms combined with classification algorithms in detecting metastatic cancer. The study used two preprocessing algorithms: principal component analysis (PCA) and the genetic algorithm, to reduce the dimensionality of the dataset and then used three classification algorithms: logistic regression, decision tree classifier, and k-nearest neighbors to detect metastatic cancer in the pathology scans. The highest accuracy of 71.14% was produced by the ML pipeline comprising of PCA, the genetic algorithm, and the k-nearest neighbor algorithm, suggesting that preprocessing and classification algorithms have great potential for detecting metastatic cancer.

Keywords: breast cancer, principal component analysis, genetic algorithm, k-nearest neighbors, decision tree classifier, logistic regression

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Authors: Khawla Askri, Mohamed Haythem Msaddek, AbdelAziz Sebei

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Climate change combined with the increase in anthropogenic activities will affect coastal groundwater systems around the world and, more particularly, the Cap Bon region in the North East of Tunisia. This study aims to study the impact of climate change and human stress on the salinization and quantification of groundwater in the Wadi Chiba watershed. In this regard, a hydro-climatological study and a hydrogeological study were carried out based on the characterization of the aquifer system of the eastern coast at the level of the watershed of Wadi Chiba in order to seek to identify, first of all, the degradation of the state of the aquifer on the quantitative level by the study of the piezometric and its evolution over time. Secondly, we sought to identify the degradation of the state of the aquifer qualitatively by using the geochemical method, in particular the major elements, to assess the mineralization of the aquifer water and understand its hydrogeochemical functioning. The study of the Na + / Cl- and Ca2 + / Mg2 + chemical relationships confirmed the presence of a marine intrusion downstream of the Wadi Chiba watershed northeast of Cap-Bon accompanied by a piezometric depression. For this purpose, we proceeded to: 1) Mapping of both piezometric data and salinity. 2) The interpretation of the mapping results. 3)Identification of the origin of the localized deterioration in the quality of the aquifer water. Finally, the analysis of the results showed that the scarcity of water is already forcing human actions in the Chiba watershed due to the irrigation of agricultural lands and the overexploitation of the water table in the study area.

Keywords: climate change, human activities, water table, Wadi Chiba watershed, piezometric depression, marine intrusion

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Authors: Francesco Pantano, Marta Fogolari, Michele Iuliani, Sonia Simonetti, Silvia Cavaliere, Marco Russano, Fabrizio Citarella, Bruno Vincenzi, Silvia Angeletti, Giuseppe Tonini

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Background: Although immune checkpoint inhibitors (ICIs) have changed the treatment paradigm of non–small cell lung cancer (NSCLC), these drugs fail to elicit durable responses in the majority of NSCLC patients. The gut microbiota, able to regulate immune responsiveness, is emerging as a promising, modifiable target to improve ICIs response rates. Since the oral microbiome has been demonstrated to be the primary source of bacterial microbiota in the lungs, we investigated its composition as a potential predictive biomarker to identify and select patients who could benefit from immunotherapy. Methods: Thirty-five patients with stage IV squamous and non-squamous cell NSCLC eligible for an anti-PD-1/PD-L1 as monotherapy were enrolled. Saliva samples were collected from patients prior to the start of treatment, bacterial DNA was extracted using the QIAamp® DNA Microbiome Kit (QIAGEN) and the 16S rRNA gene was sequenced on a MiSeq sequencing instrument (Illumina). Results: NSCLC patients were dichotomized as “Responders” (partial or complete response) and “Non-Responders” (progressive disease), after 12 weeks of treatment, based on RECIST criteria. A prevalence of the phylum Candidatus Saccharibacteria was found in the 10 responders compared to non-responders (abundance 5% vs 1% respectively; p-value = 1.46 x 10-7; False Discovery Rate (FDR) = 1.02 x 10-6). Moreover, a higher prevalence of Saccharibacteria Genera Incertae Sedis genus (belonging to the Candidatus Saccharibacteria phylum) was observed in "responders" (p-value = 6.01 x 10-7 and FDR = 2.46 x 10-5). Finally, the patients who benefit from immunotherapy showed a significant abundance of TM7 Phylum Sp Oral Clone FR058 strain, member of Saccharibacteria Genera Incertae Sedis genus (p-value = 6.13 x 10-7 and FDR=7.66 x 10-5). Conclusions: These preliminary results showed a significant association between oral microbiota and ICIs response in NSCLC patients. In particular, the higher prevalence of Candidatus Saccharibacteria phylum and TM7 Phylum Sp Oral Clone FR058 strain in responders suggests their potential immunomodulatory role. The study is still ongoing and updated data will be presented at the congress.

Keywords: oral microbiota, immune checkpoint inhibitors, non-small cell lung cancer, predictive biomarker

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Authors: Alisher Ibragimov, Sofya Senotrusova, Aleksandra Beliaeva, Egor Ushakov, Yuri Markin

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Mammography plays a critical role in screening for breast cancer in women, and artificial intelligence has enabled the automatic detection of diseases in medical images. Many of the current techniques used for mammogram analysis focus on a single view (mediolateral or craniocaudal view), while in clinical practice, radiologists consider multiple views of mammograms from both breasts to make a correct decision. Consequently, computer-aided diagnosis (CAD) systems could benefit from incorporating information gathered from multiple views. In this study, the introduce a method based on a Siamese neural network (SNN) model that simultaneously analyzes mammographic images from tri-view: bilateral and ipsilateral. In this way, when a decision is made on a single image of one breast, attention is also paid to two other images – a view of the same breast in a different projection and an image of the other breast as well. Consequently, the algorithm closely mimics the radiologist's practice of paying attention to the entire examination of a patient rather than to a single image. Additionally, to the best of our knowledge, this research represents the first experiments conducted using the recently released Vietnamese dataset of digital mammography (VinDr-Mammo). On an independent test set of images from this dataset, the best model achieved an AUC of 0.87 per image. Therefore, this suggests that there is a valuable automated second opinion in the interpretation of mammograms and breast cancer diagnosis, which in the future may help to alleviate the burden on radiologists and serve as an additional layer of verification.

Keywords: breast cancer, computer-aided diagnosis, deep learning, multi-view mammogram, siamese neural network

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Authors: Cigdem Safak Saglam

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Most thermal power plants use steam as working fluid in their power cycle. Therefore, in addition to fuel, water is the other main input for thermal plants. Water and steam must be highly pure in order to protect the systems from corrosion, scaling and biofouling. Pure process water is produced in water treatment plants having many several treatment methods. Treatment plant design is selected depending on raw water source and required water quality. Although working principle of fossil-fuel fired thermal power plants are same, there is no standard design and equipment arrangement valid for all thermal power plant utility systems. Besides that, there are many other technology evaluation and selection criteria for designing the most optimal water systems meeting the requirements such as local conditions, environmental restrictions, electricity and other consumables availability and transport, process water sources and scarcity, land use constraints etc. Aim of this study is explaining the adopted methodology for technology selection for process water preparation and industrial waste water treatment plant in a thermal power plant project located in Tufanbeyli, Adana Province in Turkey. Thermal power plant is fired with indigenous lignite coal extracted from adjacent lignite reserves. This paper addresses all above-mentioned factors affecting the thermal power plant water treatment facilities (demineralization + waste water treatment) design and describes the ultimate design of Tufanbeyli Thermal Power Plant Water Treatment Plant.

Keywords: thermal power plant, lignite coal, pretreatment, demineralization, electrodialysis, recycling, ash dampening

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Authors: Sujan Tyata, Alison Shilpakar, Nayan Bakhadyo, Kushal K. C., Abhas Maskey

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The Koshi River, acknowledged as the "Sorrow of Bihar," poses intricate challenges characterized by recurrent flooding. Within the Koshi Basin, floods have historically inflicted damage on infrastructure, agriculture, and settlements. The Koshi River exhibits a highly braided pattern across a 48 km stretch to the south of Chatara. The devastating flood from the Koshi River, which began in Nepal's Sunsari District in 2008, led to significant casualties and the destruction of agricultural areas.The catastrophe was exacerbated by a levee breach, underscoring the vulnerability of the region's flood defenses. A comprehensive understanding of environmental changes in the area is unveiled through satellite imagery analysis. This analysis facilitates the identification of high-risk zones and their contributing factors. Employing remote sensing, the analysis specifically pinpoints locations vulnerable to levee breaches. Topographical features of the area along with longitudinal and cross sectional profiles of the river and levee obtained from digital elevation model are used in the hydrological analysis for assessment of flood. To mitigate the impact of floods, the strategy involves the establishment of reservoirs upstream. Leveraging satellite data, optimal locations for water storage are identified. This approach presents a dual opportunity to not only alleviate flood risks but also catalyze the implementation of pumped storage hydropower initiatives. This holistic approach addresses environmental challenges while championing sustainable energy solutions.

Keywords: flood mitigation, levee, remote sensing, satellite imagery analysis, sustainable energy solutions

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Authors: Aroma Elmina Martha

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Environment affects the continuity of life and human well-being and the bodies of other living. Environmental quality is very closely related to the quality of life. Sustainability must be protected from damage due to the use of natural resources, such as tin mining in Bangka island. This research is a descriptive study, which identifies the environmental damage caused by mining land and sea in Bangka district. The approach used is juridical, social and economic. The study uses primary legal materials, secondary, and tertiary, equipped with field research. The analysis technique used is qualitative analysis. The impacts of mining on land among other physical and chemical damage, erosion and widening the depth of the river, a pool of micro-climate, the quality and feasibility, vegetation, wildlife and biodiversity, land values, social and economic. This mining causes damage to the soil structure, and puddles in the former digs which were not backfilled again. The impact of mining on the ocean such as changes in current surge, erosion and abrasion basic coastal waters, shoreline change, marine water quality changes, and changes in marine communities. The findings of the research show that tin mining in the sea also potentially have a significant impact on the life of the reef, populations of marine organisms. However, mining on land needs to consider the impact of the damage, so that the damage can be minimized. In the recovery process needs to be pursued by exploiting the rest of the pile of tin. Thus, mining activities should take into account the distance of beach sediment size, wave height, wave length, wave period, and the acceleration of gravity. The process of the tin washing should be done in a fairly safe area, thus avoiding damage to the coral reefs that will eventually reduce the population of marine life.

Keywords: abration, environmental damage, mining, shoreline

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Authors: Jiří F. Urbánek, Alena Oulehlová, Hana Malachová, Jiří J. Urbánek Jr.

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Crisis situations investigation and modelling are introduced and made within the complex system of energetic critical infrastructure, operating on peril´s environments. Every crisis situations and perils has an origin in the emergency/ crisis event occurrence and they need critical/ crisis interfaces assessment. Here, the emergency events can be expected - then crisis scenarios can be pre-prepared by pertinent organizational crisis management authorities towards their coping; or it may be unexpected - without pre-prepared scenario of event. But the both need operational coping by means of crisis management as well. The operation, forms, characteristics, behaviour and utilization of crisis management have various qualities, depending on real critical infrastructure organization perils, and prevention training processes. An aim is always - better security and continuity of the organization, which successful obtainment needs to find and investigate critical/ crisis zones and functions in critical infrastructure organization models, operating in pertinent perils environment. Our DYVELOP (Dynamic Vector Logistics of Processes) method is disposables for it. Here, it is necessary to derive and create identification algorithm of critical/ crisis interfaces. The locations of critical/ crisis interfaces are the flags of crisis situation in organization of critical infrastructure models. Then, the model of crisis situation will be displayed at real organization of Czech energetic crisis infrastructure subject in real peril environment. These efficient measures are necessary for the infrastructure protection. They will be derived for peril mitigation, crisis situation coping and for environmentally friendly organization survival, continuity and its sustainable development advanced possibilities.

Keywords: algorithms, energetic infrastructure complex system, modelling, peril´s environment

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Authors: Keigo Ide, Toru Maruyama, Michihiro Ito, Hiroyuki Fujimura, Yoshikatu Nakano, Shoichiro Suda, Sachiyo Aburatani, Haruko Takeyama

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Understanding environmental system is one of the important tasks. In recent years, conservation of coral environments has been focused for biodiversity issues. The damage of coral reef under environmental impacts has been observed worldwide. However, the casual relationship between damage of coral and environmental impacts has not been clearly understood. On the other hand, structure/diversity of marine bacterial community may be relatively robust under the certain strength of environmental impact. To evaluate the coral environment conditions, it is necessary to investigate relationship between marine bacterial composition in coral reef and environmental factors. In this study, the Time Scale Network Analysis was developed and applied to analyze the marine environmental data for investigating the relationship among coral, bacterial community compositions and environmental factors. Seawater samples were collected fifteen times from November 2014 to May 2016 at two locations, Ishikawabaru and South of Sesoko in Sesoko Island, Okinawa. The physicochemical factors such as temperature, photosynthetic active radiation, dissolved oxygen, turbidity, pH, salinity, chlorophyll, dissolved organic matter and depth were measured at the coral reef area. Metagenome and metatranscriptome in seawater of coral reef were analyzed as the biological factors. Metagenome data was used to clarify marine bacterial community composition. In addition, functional gene composition was estimated from metatranscriptome. For speculating the relationships between physicochemical and biological factors, cross-correlation analysis was applied to time scale data. Even though cross-correlation coefficients usually include the time precedence information, it also included indirect interactions between the variables. To elucidate the direct regulations between both factors, partial correlation coefficients were combined with cross correlation. This analysis was performed against all parameters such as the bacterial composition, the functional gene composition and the physicochemical factors. As the results, time scale network analysis revealed the direct regulation of seawater temperature by photosynthetic active radiation. In addition, concentration of dissolved oxygen regulated the value of chlorophyll. Some reasonable regulatory relationships between environmental factors indicate some part of mechanisms in coral reef area.

Keywords: coral environment, marine microbiology, network analysis, omics data analysis

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Authors: Sima Shakoorjavan, Mahdieh Eskafi, Dawid Stawski, Somaye Akbari

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In this study, poly (amidoamine) dendritic material (PAMAM) and poly (acrylic acid) (PAA) as polycation and polyanion were deposited on surface charged polylactide (PLA) nonwoven to study the relationship of dye absorption capacity of layered-PLA with the number of deposited layers. To produce negatively charged-PLA, acrylic acid (AA) was grafted on the PLA surface (PLA-g-AA) through a chemical redox reaction with the strong oxidizing agent. Spectroscopy analysis, water contact measurement, and FTIR-ATR analysis confirm the successful grafting of AA on the PLA surface through the chemical redox reaction method. In detail, an increase in dye absorption percentage by 19% and immediate absorption of water droplets ensured hydrophilicity of PLA-g-AA surface; and the presence of new carbonyl bond at 1530 cm-¹ and a wide peak of hydroxyl between 3680-3130 cm-¹ confirm AA grafting. In addition, PLA as linear polyester can undergo aminolysis, which is the cleavage of ester bonds and replacement with amid bonds when exposed to an aminolysis agent. Therefore, to produce positively charged PLA, PAMAM as amine-terminated dendritic material was introduced to PLA molecular chains at different conditions; (1) at 60 C for 0.5, 1, 1.5, 2 hours of aminolysis and (2) at room temperature (RT) for 1, 2, 3, and 4 hours of aminolysis. Weight changes and spectrophotometer measurements showed a maximum in weight gain graph and K/S value curve indicating the highest PAMAM attachment at 60 C for 1 hour and RT for 2 hours which is considered as an optimum condition. Also, the emerging new peak around 1650 cm-1 corresponding to N-H bending vibration and double wide peak at around 3670-3170 cm-1 corresponding to N-H stretching vibration confirm PAMAM attachment in selected optimum condition. In the following, regarding the initial surface charge of grafted-PLA, lbl deposition was performed and started with PAA or PAMAM. FTIR-ATR results confirm chemical changes in samples due to deposition of the first layer (PAA or PAMAM). Generally, spectroscopy analysis indicated that an increase in layer number costed dye absorption capacity. It can be due to the partial deposition of a new layer on the previously deposited layer; therefore, the available PAMAM at the first layer is more than the third layer. In detail, in the case of layer-PLA starting lbl with negatively charged, having PAMAM as the first top layer (PLA-g-AA/PAMAM) showed the highest dye absorption of both cationic and anionic model dye.

Keywords: surface modification, layer-by-layer technique, dendritic materials, PAMAM, dye absorption capacity, PLA nonwoven

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Authors: Sylvain Amailland, Jean-Hugh Thomas, Charles Pézerat, Romuald Boucheron, Jean-Claude Pascal

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The noise requirements for naval and research vessels have seen an increasing demand for quieter ships in order to fulfil current regulations and to reduce the effects on marine life. Hence, new methods dedicated to the characterization of propeller noise, which is the main source of noise in the far-field, are needed. The study of cavitating propellers in closed-section is interesting for analyzing hydrodynamic performance but could involve significant difficulties for hydroacoustic study, especially due to reverberation and boundary layer noise in the tunnel. The aim of this paper is to present a numerical methodology for the identification of hydroacoustic sources on marine propellers using hydrophone arrays in a large hydrodynamic tunnel. The main difficulties are linked to the reverberation of the tunnel and the boundary layer noise that strongly reduce the signal-to-noise ratio. In this paper it is proposed to estimate the reflection coefficients using an inverse method and some reference transfer functions measured in the tunnel. This approach allows to reduce the uncertainties of the propagation model used in the inverse problem. In order to reduce the boundary layer noise, a cleaning algorithm taking advantage of the low rank and sparse structure of the cross-spectrum matrices of the acoustic and the boundary layer noise is presented. This approach allows to recover the acoustic signal even well under the boundary layer noise. The improvement brought by this method is visible on acoustic maps resulting from beamforming and DAMAS algorithms.

Keywords: acoustic imaging, boundary layer noise denoising, inverse problems, model adaptation

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Authors: Nurlaila Effendy

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Companies in Asia face a number of constraints in tight competitiveness in ASEAN Economic Community 2015 and globalization. An economic capitalism system as an integral part of globalization processing brings broad impacts. They need to improve business performance in globalization and ASEAN Economic Community. Organizational development has quite clearly demonstrated that aligning individual’s personal goals with the goals of the organization translates into measurable and sustained performance improvement. Human capital is a key to achieve company performance. Employee Engagement (EE) creates and expresses themselves physically, cognitively and emotionally to achieve company goals and individual goals. One will experience a total involvement when they undertake their jobs and feel a self integration to their job and organization. A leader plays key role in attaining the goals and objectives of a company/organization. Any Manager in a company needs to have leadership competence and global mindset. As one the of positive organizational behavior developments, psychological capital (PsyCap) is assumed to be one of the most important capitals in the global mindset, in addition to intellectual capital and social capital. Textile companies also need to face a number of constraints in tight competitiveness in regional and global. This research involved 42 managers in two textiles and a spinning companies in a group, in Central Java, Indonesia. It is a quantitative research with Partial Least Squares (PLS) studying job resource (Social Support & Organizational Climate) and Personal Resource (4 dimensions of Psychological Capital & Leadership Competence) as prediction of Employee Engagement, also Employee Engagement and leadership competence as prediction of leader’s performance. The performance of a leader is measured by means of achievement on objective strategies in terms of 4 perspectives (financial and non-financial perspectives) in a Balanced Score Card (BSC). It took one year during a business plan of year 2014, from January to December 2014. The result of this research is there is correlation between Job Resource (coefficient value of Social Support is 0.036 & coefficient value of organizational climate is 0.220) and Personal Resource (coefficient value of PsyCap is 0.513 & coefficient value of Leadership Competence is 0.249) with employee engagement. There is correlation between employee engagement (coefficient value is 0.279) and leadership competence (coefficient value is 0.581) with performance.

Keywords: organizational climate, social support, psychological capital leadership competence, employee engagement, performance, integrated textile companies

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Authors: Xuan Dinh Vu, Elmar Csaplovics

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There has been an increasing need for methods to define priority areas for biodiversity conservation since the effectiveness of biodiversity conservation in protected areas largely depends on the availability of material resources. The identification of priority areas requires the integration of biodiversity data together with social data on human pressures and responses. However, the deficit of comprehensive data and reliable methods becomes a key challenge in zoning where the demand for conservation is most urgent and where the outcomes of conservation strategies can be maximized. In order to fill this gap, the study applied an environmental model Condition–Pressure–Response to suggest a set of criteria to identify priority areas for biodiversity conservation. Our empirical data has been compiled from 185 respondents, categorizing into three main groups: governmental administration, research institutions, and protected areas in Vietnam by using a well - designed questionnaire. Then, the Analytic Hierarchy Process (AHP) theory was used to identify the weight of all criteria. Our results have shown that priority level for biodiversity conservation could be identified by three main indicators: condition, pressure, and response with the value of the weight of 26%, 41%, and 33%, respectively. Based on the three indicators, 7 criteria and 15 sub-criteria were developed to support for defining priority areas for biodiversity conservation and zoning protected areas. In addition, our study also revealed that the groups of governmental administration and protected areas put a focus on the 'Pressure' indicator while the group of Research Institutions emphasized the importance of 'Response' indicator in the evaluation process. Our results provided recommendations to apply the developed criteria for identifying priority areas for biodiversity conservation in Vietnam.

Keywords: biodiversity conservation, condition–pressure–response model, criteria, priority areas, protected areas

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Authors: Esubalew Yehualaw Melaku, Tigistu Haile Eritro

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In this study, two basic geophysical methods are applied for mapping the groundwater aquifer system in the Lisana area along the Guder River, northeast of Hosanna town, near the western margin of the Central Main Ethiopian Rift. The main target of the study is to map the potential aquifer zone and investigate the groundwater potential for current and future development of the resource in the Gode area. The geophysical methods employed in this study include, Vertical Electrical Sounding (VES) and magnetic survey techniques. Electrical sounding was used to examine and map the depth to the potential aquifer zone of the groundwater and its distribution over the area. On the other hand, a magnetic survey was used to delineate contact between lithologic units and geological structures. The 2D magnetic modeling and the geoelectric sections are used for the identification of weak zones, which control the groundwater flow and storage system. The geophysical survey comprises of twelve VES readings collected by using a Schlumberger array along six profile lines and more than four hundred (400) magnetic readings at about 10m station intervals along four profiles and 20m along three random profiles. The study result revealed that the potential aquifer in the area is obtained at a depth range from 45m to 92m. This is the response of the highly weathered/ fractured ignimbrite and pumice layer with sandy soil, which is the main water-bearing horizon. Overall, in the neighborhood of four VES points, VES- 2, VES- 3, VES-10, and VES-11, shows good water-bearing zones in the study area.

Keywords: vertical electrical sounding, magnetic survey, aquifer, groundwater potential

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Authors: Dalal Sadeqi

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Groundwater is an important component of Kuwait’s water resources. Although limited in quantity and often poor in quality, the significance of this natural source of water cannot be overemphasized. Recharge of groundwater in Kuwait occurs during periodical storm events, especially in open desert areas. Runoff water dissolves accumulated surficial meteoric salts and subsequently leaches them into the groundwater following a period of evaporative enrichment at or near the soil surface. Geochemical processes governing groundwater recharge vary in time and space. Stable isotope (18O and 2H) and geochemical signatures are commonly used to gain some insight into recharge processes and groundwater salinization mechanisms, particularly in arid and semiarid regions. This article addresses the mechanism used in identifying and characterizing the main water shed areas in Kuwait using stable isotopes in an attempt to determine favorable groundwater recharge sites in the country. Stable isotopes of both rainwater and groundwater were targeted in different hydrogeological settings. Additionally, data and information obtained from subsurface logs in the study area were collected and analyzed to develop a better understanding of the lateral and vertical extent of the groundwater aquifers. Geographic Information System (GIS) and RockWorks 3D modelling software were used to map out the hydrogeomorphology of the study area and the subsurface lithology of the investigated aquifers. The collected data and information, including major ion chemistry, isotopes, subsurface characteristics, and hydrogeomorphology, were integrated in a GIS platform to identify and map out suitable natural recharge areas as part of an integrated water resources management scheme that addresses the challenges of the sustainability of the groundwater reserves in the country.

Keywords: scarcity, integrated, recharge, isotope

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Authors: W. Mohammedsaeed, A. J. Mcbain, S. M. Cruickshank, C. A. O’Neill

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Many studies have demonstrated the importance of probiotics and their potential therapeutic effects within the gut. Recently, the possible therapeutic effects of probiotics in other tissues have also begun to be investigated. Comparatively few studies have evaluated the use of topical probiotics in relation to the skin. In this study, we have conducted preliminary investigations into whether a well-known probiotic, Lactobacillus rhamnosus GG (LGG), can increase the rate of re-epithelialization in a model wound. Full-thickness skin was obtained from individuals undergoing elective cosmetic surgery. This skin was wounded using excisional punch and cultured using a serum-free medium, either in the presence or absence of L. rhamnosus GG lysate. Histological staining of the sections was performed with Haematoxylin& Eosin E to quantify “epithelial tongue length”. This is the length of the new epithelial ‘tongue’ that grows and covers the exposed dermis at the inner wound edges. The length of the new epithelial ‘tongue’ was compared in untreated section and section treated with and L. rhamnosus GG made using108CFU/ml bacterial cells. L. rhamnosus GG lysate enhanced significantly the re-epithelialisation of treated wounds compared with that of untreated wounds (P=0.005, n=3). Tongue length, at day 1 was 7.55μm 0.15, at day 3 it was 18.5μm 0.25 and at day 7 was 22.9μm 0.35. These results can be compared with untreated cultures in which tongue length was 3.25μm 0.35, day 3 was 9.65μm 0.25 and day 7 was 13.5μm 0.15 post-wounding. In ex-vivo proliferation and migration cells were measured by determining the expression of nuclear proliferation marker Ki-67 and the expression of Phosphorylated cortactin respectively demonstrated that L. rhamnosus GG significantly increased NHEK proliferation and migration rates relative to controls. However, the dominant mechanism was migration because in ex-vivo skin treated with the L. rhamnosus GG up-regulated the gene expression of the chemokine receptor and ligands CXCR2 and CXCL2 comparing with controls (P=0.02, P=0.03 respectively, n=3). High levels of CXCL2/CXCL2 have already been implicated in multiple aspects of stimulation of wound healing through activation of keratinocyte migration. These data demonstrate that lysates from Lactobacillus rhamnosus GG increase re-epithelialization by stimulation of keratinocyte migration. The current study identifies the partial mechanism that contribute to stimulating the wound-healing process ex vivo in response to L. rhamnosus GG lysate is an increase in the production of CXCL2/ CXCR2 in ex vivo models. The use of probiotic lysates potentially offers new options to develop treatments that could improve wound healing.

Keywords: Lactobacillus rhamnosus GG, wounds, migration, lysate

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Authors: Masoud Sheidai

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Biologists with a special field of population genetics and phylogeny have different research tasks such as populations’ genetic variability and divergence, species relatedness, the evolution of genetic and morphological characters, and identification of DNA SNPs with adaptive potential. To tackle these problems and reach a concise conclusion, they must use the proper and efficient statistical and bioinformatic methods as well as suitable genetic and morphological characteristics. In recent years application of different bioinformatic and statistical methods, which are based on various well-documented assumptions, are the proper analytical tools in the hands of researchers. The species delineation is usually carried out with the use of different clustering methods like K-means clustering based on proper distance measures according to the studied features of organisms. A well-defined species are assumed to be separated from the other taxa by molecular barcodes. The species relationships are studied by using molecular markers, which are analyzed by different analytical methods like multidimensional scaling (MDS) and principal coordinate analysis (PCoA). The species population structuring and genetic divergence are usually investigated by PCoA and PCA methods and a network diagram. These are based on bootstrapping of data. The Association of different genes and DNA sequences to ecological and geographical variables is determined by LFMM (Latent factor mixed model) and redundancy analysis (RDA), which are based on Bayesian and distance methods. Molecular and morphological differentiating characters in the studied species may be identified by linear discriminant analysis (DA) and discriminant analysis of principal components (DAPC). We shall illustrate these methods and related conclusions by giving examples from different edible and medicinal plant species.

Keywords: GWAS analysis, K-Means clustering, LFMM, multidimensional scaling, redundancy analysis

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Authors: Noppadol Poomvises, Prateep Pakdeerod, Anchalee Kongsuk

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In the middle of September 2017, a tropical storm named ‘DOKSURI’ swept through Udon Thani, Northeastern Thailand. The storm dumped heavy rain for many hours and caused large amount of water flowing into Huai Phueng reservoir. Level of impounding water increased rapidly, and the extra water flowed over a service spillway, morning-glory type constructed by concrete material for about 50 years ago. Subsequently, a sinkhole was formed on the dam crest and five points of water piping were found on downstream slope closely to spillway. Three techniques of geophysical investigation were carried out to inspect cause of failures; Electrical Resistivity Imaging (ERI), Multichannel Analysis of Surface Wave (MASW), and Ground Penetrating Radar (GPR), respectively. Result of ERI clearly shows evidence of overtop event and heterogeneity around spillway that implied possibility of previous shape of sinkhole around the pipe. The shear wave velocity of subsurface soil measured by MASW can numerically convert to undrained shear strength of impervious clay core. Result of GPR clearly reveals partial settlements of freeboard zone at top part of the dam and also shaping new refilled material to plug the sinkhole back to the condition it should be. In addition, the GPR image is a main answer to confirm that there are not any sinkholes in the survey lines, only that found on top of the spillway. Integrity interpretation of the three results together with several evidences observed during a field walk-through and data from drilled holes can be interpreted that there are four main causes in this account. The first cause is too much water flowing over the spillway. Second, the water attacking morning glory spillway creates cracks upon concrete contact where the spillway is cross-cut to the center of the dam. Third, high velocity of water inside the concrete pipe sucking fine particle of embankment material down via those cracks and flushing out to the river channel. Lastly, loss of clay material of the dam into the concrete pipe creates the sinkhole at the crest. However, in case of failure by piping, it is possible that they can be formed both by backward erosion (internal erosion along or into embedded structure of spillway walls) and also by excess saturated water of downstream material.

Keywords: dam inspection, GPR, MASW, resistivity

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Authors: Narjes Ebrahimi, Soheila Alyasin, Navid Nezafat, Hossein Esmailzadeh, Younes Ghasemi, Seyed Hesamodin Nabavizadeh

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Immunotherapy with allergy vaccines is of great importance in allergen-specific immunotherapy. In recent years, B-cell epitope-based vaccines have attracted considerable attention and the prediction of epitopes is crucial to design these types of allergy vaccines. B-cell epitopes might be linear or conformational. The prerequisite for the identification of conformational epitopes is the information about allergens' tertiary structures. Bioinformatics approaches have paved the way towards the design of epitope-based allergy vaccines through the prediction of tertiary structures and epitopes. Mite allergens are one of the major allergy contributors. Several mite allergens can elicit allergic reactions; however, their structures and epitopes are not well established. So, B-cell epitopes of various groups of mite allergens (24 allergens in 6 allergen groups) were predicted in the present work. Tertiary structures of 17 allergens with unknown structure were predicted and refined with RaptorX and GalaxyRefine servers, respectively. The predicted structures were further evaluated by Rampage, ProSA-web, ERRAT and Verify 3D servers. Linear and conformational B-cell epitopes were identified with Ellipro, Bcepred, and DiscoTope 2 servers. To improve the accuracy level, consensus epitopes were selected. Fifty-four conformational and 133 linear consensus epitopes were predicted. Furthermore, overlapping epitopes in each allergen group were defined, following the sequence alignment of the allergens in each group. The predicted epitopes were also compared with the experimentally identified epitopes. The presented results provide valuable information for further studies about allergy vaccine design.

Keywords: B-cell epitope, Immunotherapy, In silico prediction, Mite allergens, Tertiary structure

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Authors: Hsiao-Chuan Huang, King-Lung Kuo, Mei-Hsin Lo, Hsiao-Yun Chou, Yusen Lin

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The most robust and economical method for laboratory diagnosis of TB is to identify mycobacterial bacilli (AFB) under acid-fast staining despite its disadvantages of low sensitivity and labor-intensive. Though digital pathology becomes popular in medicine, an automated microscopic system for microbiology is still not available. A new AI-assisted automated microscopic system, consisting of a microscopic scanner and recognition program powered by big data and deep learning, may significantly increase the sensitivity of TB smear microscopy. Thus, the objective is to evaluate such an automatic system for the identification of AFB. A total of 5,930 smears was enrolled for this study. An intelligent microscope system (TB-Scan, Wellgen Medical, Taiwan) was used for microscopic image scanning and AFB detection. 272 AFB smears were used for transfer learning to increase the accuracy. Referee medical technicians were used as Gold Standard for result discrepancy. Results showed that, under a total of 1726 AFB smears, the automated system's accuracy, sensitivity and specificity were 95.6% (1,650/1,726), 87.7% (57/65), and 95.9% (1,593/1,661), respectively. Compared to culture, the sensitivity for human technicians was only 33.8% (38/142); however, the automated system can achieve 74.6% (106/142), which is significantly higher than human technicians, and this is the first of such an automated microscope system for TB smear testing in a controlled trial. This automated system could achieve higher TB smear sensitivity and laboratory efficiency and may complement molecular methods (eg. GeneXpert) to reduce the total cost for TB control. Furthermore, such an automated system is capable of remote access by the internet and can be deployed in the area with limited medical resources.

Keywords: TB smears, automated microscope, artificial intelligence, medical imaging

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Authors: Noor Us Saher

Abstract:

Oceans and Marine areas have a great importance, mainly regarding food resources, fishery products and reliance of livelihood. Aquatic pollution is common due to the incorporation of various chemicals mainly entering from urbanization, industrial and commercial facilities, such as oil and chemical spills. Many hazardous wastes and industrial effluents contaminate the nearby areas and initiate to affect the marine environment. These contaminated conditions may become worse in those aquatic environments situated besides the world’s largest cities, which are hubs of various commercial activities. Heavy metal contamination is one of the most important predicaments for marine environments and during past decades this problem has intensified due to an increase in urbanization and industrialization. Coastal regions of Pakistan are facing severe threats from various organic and inorganic pollutants, especially the estuarine and coastal areas of Karachi city, the most populated and industrialized city situated along the coastline. Metal contamination causes severe toxicity in biota resulting the degradation of Marine environments and depletion of fishery resources and sustainability. There are several abiotic (air, water and sediment) and biotic (fauna and flora) indicators that indicate metal contamination. However, all these indicators have certain limitations and complexities, which delay their implementation for rehabilitation and conservation in the marine environment. The inadequate evidences have presented on this significant topic till the time and this study discussed metal pollution and its consequences along the marine environment of Pakistan. This study further helps in identification of possible hazards for the ecological system and allied resources for management strategies and decision making for sustainable approaches.

Keywords: coastal and estuarine environment, heavy metals pollution, pollution indicators, Pakistan

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: Hela Gargouri, Nizar Moalla, Hassen Hadj Kacem

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Meat adulteration affecting the safety and quality of food is becoming one of the main concerns of public interest across the world. The drastic consequences on the meat industry highlighted the urgent necessity to control the products' quality and to point out the complexity of both supply and processing circuits. Due to the expansion of this problem, the authentic testing of foods, particularly meat and its products, is deemed crucial to avoid unfair market competition and to protect consumers from fraudulent practices of meat adulteration. The adoption of authentication methods by the food quality-control laboratories is becoming a priority issue. However, in some developing countries, the number of food tests is still insignificant, although a variety of processed and traditional meat products are widely consumed. Little attention has been paid to provide an easy, fast, reproducible, and low-cost molecular test, which could be conducted in a basic laboratory. In the current study, the 359 bp fragment of the cytochrome-b gene was mapped by PCR-RFLP using firstly fresh biological supports (DNA and meat) and then turkey salami as an example of commercial processed meat. This technique has been established through several optimizations, namely: the selection of restriction enzymes. The digestion with BsmAI, SspI, and TaaI succeed to identify the seven included animal species when meat is formed by individual species and when the meat is a mixture of different origin. In this study, the PCR-RFLP technique using universal primer succeed to meet our needs by providing an indirect sequencing method identifying by restriction enzymes the specificities characterizing different species on the same amplicon reducing the number of potential tests.

Keywords: adulteration, animal species, authentication, meat, mtDNA, PCR-RFLP

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Authors: Krishna Pal Singh, Shailendra Kumar Gupta, Olaf Wolkenhauer

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Background: Our study aimed to identify common genes and potential targets across the four diseases, which include rheumatoid arthritis, melanoma metastasis, ulcerative colitis, and Crohn’s disease. We used a network and systems biology approach to identify the hub gene, which can act as a potential target for all four disease conditions. The regulatory network was extracted from the PPI using the MCODE module present in Cytoscape. Our objective was to investigate the significance of hub genes in these diseases using gene ontology and KEGG pathway enrichment analysis. Methods: Our methodology involved collecting disease gene-related information from DisGeNET databases and performing protein-protein interaction (PPI) network and core genes screening. We then conducted gene ontology and KEGG pathway enrichment analysis. Results: We found that IL6 plays a critical role in all disease conditions and in different pathways that can be associated with the development of all four diseases. Conclusions: The theoretical importance of our research is that we employed various systems and structural biology techniques to identify a crucial protein that could serve as a promising target for treating multiple diseases. Our data collection and analysis procedures involved rigorous scrutiny, ensuring high-quality results. Our conclusion is that IL6 plays a significant role in all four diseases, and it can act as a potential target for treating them. Our findings may have important implications for the development of novel therapeutic interventions for these diseases.

Keywords: melanoma metastasis, rheumatoid arthritis, inflammatory bowel diseases, integrated bioinformatics analysis

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Authors: Yonwaba Atyosi, Moses Cho, Abel Ramoelo, Nobuhle Majozi, Cecilia Masemola, Yoliswa Mkhize

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Spectroscopy has been widely used to understand the hyperspectral remote sensing of soils. Accurate and efficient measurement of soil moisture is essential for precision agriculture. The aim of this study was to understand the spectral behavior of soil at different soil water content levels and identify the significant spectral bands for soil moisture content retrieval at field-scale. The study consisted of 60 soil samples from a maize farm, divided into four different treatments representing different moisture levels. Spectral signatures were measured for each sample in laboratory under artificial light using an Analytical Spectral Device (ASD) spectrometer, covering a wavelength range from 350 nm to 2500 nm, with a spectral resolution of 1 nm. The results showed that the absorption features at 1450 nm, 1900 nm, and 2200 nm were particularly sensitive to soil moisture content and exhibited strong correlations with the water content levels. Continuum removal was developed in the R programming language to enhance the absorption features of soil moisture and to precisely understand its spectral behavior at different water content levels. Statistical analysis using partial least squares regression (PLSR) models were performed to quantify the correlation between the spectral bands and soil moisture content. This study provides insights into the spectral behavior of soil at different water content levels and identifies the significant spectral bands for soil moisture content retrieval. The findings highlight the potential of spectroscopy for non-destructive and rapid soil moisture measurement, which can be applied to various fields such as precision agriculture, hydrology, and environmental monitoring. However, it is important to note that the spectral behavior of soil can be influenced by various factors such as soil type, texture, and organic matter content, and caution should be taken when applying the results to other soil systems. The results of this study showed a good agreement between measured and predicted values of Soil Moisture Content with high R2 and low root mean square error (RMSE) values. Model validation using independent data was satisfactory for all the studied soil samples. The results has significant implications for developing high-resolution and precise field-scale soil moisture retrieval models. These models can be used to understand the spatial and temporal variation of soil moisture content in agricultural fields, which is essential for managing irrigation and optimizing crop yield.

Keywords: soil moisture content retrieval, precision agriculture, continuum removal, remote sensing, machine learning, spectroscopy

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Authors: Yo Fukutani, Shuji Moriguchi, Takuma Kotani, Terada Kenjiro

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If risk management of the assets owned by companies, risk assessment of real estate portfolio, and risk identification of the entire region are to be implemented, it is necessary to consider simultaneous damage to multiple buildings. In this research, the Sagami Trough earthquake tsunami that could have a significant effect on the Japanese capital region is focused on, and a method is proposed for simultaneous damage assessment using copulas that can take into consideration the correlation of tsunami depths and building damage between two sites. First, the tsunami inundation depths at two sites were simulated by using a nonlinear long-wave equation. The tsunamis were simulated by varying the slip amount (five cases) and the depths (five cases) for each of 10 sources of the Sagami Trough. For each source, the frequency distributions of the tsunami inundation depth were evaluated by using the response surface method. Then, Monte-Carlo simulation was conducted, and frequency distributions of tsunami inundation depth were evaluated at the target sites for all sources of the Sagami Trough. These are marginal distributions. Kendall’s tau for the tsunami inundation simulation at two sites was 0.83. Based on this value, the Gaussian copula, t-copula, Clayton copula, and Gumbel copula (n = 10,000) were generated. Then, the simultaneous distributions of the damage rate were evaluated using the marginal distributions and the copulas. For the correlation of the tsunami inundation depth at the two sites, the expected value hardly changed compared with the case of no correlation, but the damage rate of the ninety-ninth percentile value was approximately 2%, and the maximum value was approximately 6% when using the Gumbel copula.

Keywords: copulas, Monte-Carlo simulation, probabilistic risk assessment, tsunamis

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Authors: Kate Crinion, Martin Haran, Stanley McGreal, David McIlhatton

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Past research has demonstrated that disasters are continuing to escalate in frequency and magnitude worldwide, representing a key concern for the global community. Understanding and responding to the increasing risk posed by disaster events has become a key concern for disaster managers. An emerging trend within literature, acknowledges the need to move beyond a state of coping and reinstatement of the status quo, towards incremental adaptive change and transformational actions for long-term sustainable development. As such, a growing interest in research concerns the understanding of the change required to address ever increasing and unpredictable disaster events. Capturing transformational capacity and resilience, however is not without its difficulties and explains the dearth in attempts to capture this capacity. Adopting a case study approach, this research seeks to enhance an awareness of transformational resilience by identifying key components and indicators that determine the resilience of flood-affected communities within Cumbria. Grounding and testing a theoretical resilience framework within the case studies, permits the identification of how perceptions of risk influence community resilience actions. Further, it assesses how levels of social capital and connectedness impacts upon the extent of interplay between resources and capacities that drive transformational resilience. Thus, this research seeks to expand the existing body of knowledge by enhancing the awareness of resilience in post-disaster affected communities, by investigating indicators of community capacity building and resilience actions that facilitate transformational resilience during the recovery and reconstruction phase of a flood disaster.

Keywords: capacity building, community, flooding, transformational resilience

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Authors: Hagos Abraham, Solomon Gizaw, Mengistu Urge

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A sound breeding objective is the basis for genetic improvement in overall economic merit of farm animals. Begait goat is one of the identified breeds in Ethiopia, which is a multipurpose breed as it serves as source of cash income and source of food (meat and milk). Despite its importance, no formal breeding objectives exist for Begait goat. The objective of the present study was to identify breeding objectives for the breed through two approaches: using own-flock ranking experiment and developing deterministic bio-economic models as a preliminary step towards designing sustainable breeding programs for the breed. In the own-flock ranking experiment, a total of forty five households were visited at their homesteads and were asked to select, with reasons, the first best, second best, third best and the most inferior does from their own flock. Age, previous reproduction and production information of the identified animals were inquired; live body weight and some linear body measurements were taken. The bio-economic model included performance traits (weights, daily weight gain, kidding interval, litter size, milk yield, kid mortality, pregnancy and replacement rates) and economic (revenue and costs) parameters. It was observed that there was close agreement between the farmers’ ranking and bio-economic model results. In general, the results of the present study indicated that Begait goat owners could improve performance of their goats and profitability of their farms by selecting for litter size, six month weight, pre-weaning kid survival rate and milk yield.

Keywords: bio-economic model, economic parameters, own-flock ranking, performance traits

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Authors: José Eduardo García-Mendiola

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In this work, a phenomenological approach to computational modeling of analogy processing is carried out. The paper goes through the consideration of the structure of the analogy, based on the possibility of sustaining the genesis of its elements regarding Husserl's genetic theory of association. Among particular processes which take place in order to get analogical inferences, there is one which arises crucial for enabling efficient base cases retrieval through long-term memory, namely analogical transference grounded on familiarity. In general, it has been argued that analogical reasoning is a way by which a conscious agent tries to determine or define a certain scope of objects and relationships between them using previous knowledge of other familiar domain of objects and relations. However, looking for a complete description of analogy process, a deeper consideration of phenomenological nature is required in so far, its simulation by computational programs is aimed. Also, one would get an idea of how complex it would be to have a fully computational account of the analogy elements. In fact, familiarity is not a result of a mere chain of repetitions of objects or events but generated insofar as the object/attribute or event in question is integrable inside a certain context that is taking shape as functionalities and functional approaches or perspectives of the object are being defined. Its familiarity is generated not by the identification of its parts or objective determinations as if they were isolated from those functionalities and approaches. Rather, at the core of such a familiarity between entities of different kinds lays the way they are functionally encoded. So, and hoping to make deeper inroads towards these topics, this essay allows us to consider that cognitive-computational perspectives can visualize, from the phenomenological projection of the analogy process reviewing achievements already obtained as well as exploration of new theoretical-experimental configurations towards implementation of analogy models in specific as well as in general purpose machines.

Keywords: analogy, association, encoding, retrieval

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Authors: Rakesh Kumar Meena, Tanushree Chatterjee

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Okra (Abelmoschus esculentas L. Moench) or lady’s finger is an important vegetable crop belonging to the Malvaceae family. Unfortunately, production and productivity of Okra are majorly affected by Yellow Vein mosaic virus (YVMV). The AO: 189 (resistant parent) X AO: 191(susceptible parent) used for the development of mapping population. The mapping population has 143 individuals (F₂:F₃). Population was characterized by physiological and pathological observations. Screening of 360 DNA markers was performed to survey for parental polymorphism between the contrasting parents’, i.e., AO: 189 and AO: 191. Out of 360; 84 polymorphic markers were used for genotyping of the mapping population. Total markers were distributed into four linkage groups (LG1, LG2, LG3, and LG4). LG3 covered the longest span (106.8cM) with maximum number of markers (27) while LG1 represented the smallest linkage group in terms of length (71.2cM). QTL identification using the composite interval mapping approach detected two prominent QTLs, QTL1 and QTL2 for resistance against YVMV disease. These QTLs were placed between the marker intervals of NBS-LRR72-Path02 and NBS-LRR06- NBS-LRR65 on linkage group 02 and linkage group 04 respectively. The LOD values of QTL1 and QTL2 were 5.7 and 6.8 which accounted for 19% and 27% of the total phenotypic variation, respectively. The findings of this study provide two linked markers which can be used as efficient diagnostic tools to distinguish between YVMV resistant and susceptible Okra cultivars/genotypes. Lines identified as highly resistant against YVMV infection can be used as donor lines for this trait. This will be instrumental in accelerating the trait improvement program in Okra and will substantially reduce the yield losses due to this viral disease.

Keywords: Okra, yellow vein mosaic virus, resistant, linkage map, QTLs

Procedia PDF Downloads 215