Search results for: as-recorded seismic sequences

Authors: N. Benkaci, E. Oubaiche, J.-L. Chatelain, R. Bensalem, K. Abbes

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The ambient vibration H/V technique is widely used nowadays in microzonation studies, because of its easy field handling and its low cost, compared to other geophysical methods. However, in presence of complex geology or lateral heterogeneity evidenced by more than one peak frequency in the H/V curve, it is difficult to interpret the results, especially when soil information is lacking. In this work, we focus on the construction site of the Baraki 40000=place stadium, located in the north-east side of the Mitidja basin (Algeria), to identify the seismic wave amplification zones. H/V curve analysis leads to the observation of spatial and time variability of the H/V frequency peaks. The spatial variability allows dividing the studied area into three main zones: (1) one with a predominant frequency around 1,5 Hz showing an important amplification level, (2) the second exhibits two peaks at 1,5 Hz and in the 4 Hz – 10 Hz range, and (3) the third zone is characterized by a plateau between 2 Hz and 3 Hz. These H/V curve categories reveal a consequent lateral heterogeneity dividing the stadium site roughly in the middle. Furthermore, a continuous ambient vibration recording during several weeks allows showing that the first peak at 1,5 Hz in the second zone, completely disappears between 2 am and 4 am, and reaching its maximum amplitude around 12 am. Consequently, the anthropogenic noise source generating these important variations could be the Algiers Rocade Sud highway, located in the maximum amplification azimuth direction of the H/V curves. This work points out that the H/V method is an important tool to perform nano-zonation studies prior to geotechnical and geophysical investigations, and that, in some cases, the H/V technique fails to reveal the resonance frequency in the absence of strong anthropogenic source.

Keywords: ambient vibrations, amplification, fundamental frequency, lateral heterogeneity, site effect

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Authors: Tarek M. Alguhane, Ayman H. Khalil, M. N. Fayed, Ayman M. Ismail

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This paper deals with different modeling aspects of masonry infill: no infill model, Layered shell infill model, and strut infill model. These models consider the complicated behavior of the in-filled plane frames under lateral load similar to an earthquake load. Three strut infill models are used: NBCC (2005) strut infill model, ASCE/SEI 41-06 strut infill model and proposed strut infill model based on modification to Canadian, NBCC (2005) strut infill model. Pushover and modal analyses of a masonry infill concrete frame with a single storey and an existing 5-storey RC building have been carried out by using different models for masonry infill. The corresponding hinge status, the value of base shear at target displacement as well as their dynamic characteristics have been determined and compared. A validation of the structural numerical models for the existing 5-storey RC building has been achieved by comparing the experimentally measured and the analytically estimated natural frequencies and their mode shapes. This study shows that ASCE/SEI 41-06 equation underestimates the values for the equivalent properties of the diagonal strut while Canadian, NBCC (2005) equation gives realistic values for the equivalent properties. The results indicate that both ASCE/SEI 41-06 and Canadian, NBCC (2005) equations for strut infill model give over estimated values for dynamic characteristic of the building. Proposed modification to Canadian, NBCC (2005) equation shows that the fundamental dynamic characteristic values of the building are nearly similar to the corresponding values using layered shell elements as well as measured field results.

Keywords: masonry infill, framed structures, RC buildings, non-structural elements

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Authors: Fumihiro Imai, Shinichi Watanabe, Shingo Maeda, Haruna Imai, Hiroki Niimi

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It is important to know the growth rate of brain tumors before surgery because it influences treatment planning, including not only surgical resection strategy but also adjuvant therapy after surgery. Amide proton transfer (APT) imaging is an emerging molecular magnetic resonance imaging (MRI) technique based on chemical exchange saturation transfer without the administration of a contrast medium. The underlying assumption in APT imaging of tumors is that there is a close relationship between the proliferative activity of the tumor and mobile protein synthesis. We aimed to evaluate the diagnostic performance of APT imaging of pre-and post-treatment brain tumors. Ten patients with brain tumor underwent conventional and APT-weighted sequences on a 3.0 Tesla MRI before clinical intervention. The maximum and the minimum APT-weighted signals (APTWmax and APTWmin) in each solid tumor region were obtained and compared before and after a clinical intervention. All surgical specimens were examined for histopathological diagnosis. Eight of ten patients underwent adjuvant therapy after surgery. Histopathological diagnosis was glioma in 7 patients (WHO grade 2 in 2 patients, WHO grade 3 in 3 patients, and WHO grade 4 in 2 patients), meningioma WHO grade 1 in 2 patients, and primary lymphoma of the brain in 1 patient. High-grade gliomas showed significantly higher APTW signals than that low-grade gliomas. APTWmax in one huge parasagittal meningioma infiltrating into the skull bone was higher than that in glioma WHO grade 4. On the other hand, APTWmax in another convexity meningioma was the same as that in glioma WHO grade 3. Diagnosis of primary lymphoma of the brain was possible with APT imaging before pathological confirmation. APTW signals in residual tumors decreased dramatically within one year after adjuvant therapy in all patients. APT imaging demonstrated excellent diagnostic performance for the planning of surgery and adjuvant therapy of brain tumors.

Keywords: amides, magnetic resonance imaging, brain tumors, cell proliferation

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Authors: D. Manai, J. Alvarez-Marron, M. Inoubli

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The southern Tunisian Atlas is a part of the wide Cenozoic intracontinental deformation that affected North Africa as a result of convergence between African and Eurasian plates. The Southern Tunisian Atlas Front (STAF) corresponds to the chotts area that covers several hundreds of Km² and represents a 60 km wide transition between the deformed Tunisian Atlas to the North and the undeformed Saharan platform to the South. It includes three morphostructural alignments, a fold and thrust range in the North, a wide depression in the middle and a monocline to horizontal zone to the south. Four cross-sections have been constructed across the chotts area to illustrate the structure of the Southern Tunisian Atlas Front based on integrated geological and geophysical data including geological maps, petroleum wells, and seismic data. The fold and thrust zone of the northern chotts is interpreted as related to a detachment level near the Triassic-Jurassic contact. The displacement of the basal thrust seems to die out progressively under the Fejej antiform and it is responsible to the south dipping of the southern chotts range. The restoration of the cross-sections indicates that the Southern Tunisian Atlas front is a weakly deformed wide zone developed during the Cenozoic inversion with a maximum calculated shortening in the order of 1000 m. The wide structure of this STAF has been influenced by a pre-existing large thickness of upper Jurassic-Aptian sediments related to the rifting episodes associated to the evolution of Tethys in the Maghreb. During Jurassic to Aptian period, the chotts area corresponded to a highly subsiding basin.

Keywords: Southern Tunisian Atlas Front, subsident sub- basin, wide deformation, balanced cross-sections.

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Authors: Mohammad Nazri Abdul Bahari, Nurshafika Mohd Sakeh, Siti Nor Akmar Abdullah

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Basal stem rot (BSR) is the most devastating disease in oil palm. Among the oil palm pathogenic fungi, the most prevalent and virulent species associated with BSR is Ganoderma boninense. Early detection of G. boninense attack in oil palm wherein physical symptoms has not yet appeared can offer opportunities to prevent the spread of the necrotrophic fungus. However, poor understanding of molecular defense responses and roles of antifungal metabolites in oil palm against G. boninense has complicated the resolving measures. Hence, characterization of defense-related molecular responses and production of antifungal compounds during early interaction with G. boninense is of utmost important. Four month-old oil palm (Elaeis guineensis) seedlings were artificially infected with G. boninense-inoculated rubber wood block via sitting technique. RNA of samples were extracted from roots and leaves tissues at 0, 3, 7 and 11 days post inoculation (d.p.i) followed with sequencing using RNA-Seq method. Differentially-expressed genes (DEGs) of oil palm-G. boninense interaction were identified, while changes in metabolite profile will be scrutinized related to the DEGs. The RNA-Seq data generated a total of 113,829,376 and 313,293,229 paired-end clean reads from untreated (0 d.p.i) and treated (3, 7, 11 d.p.i) samples respectively, each with two biological replicates. The paired-end reads were mapped to Elaeis guineensis reference genome to screen out non-oil palm genes and subsequently generated 74,794 coding sequences. DEG analysis of phytohormone biosynthetic genes in oil palm roots revealed that at p-value ≤ 0.01, ethylene and jasmonic acid may act in antagonistic manner with salicylic acid to coordinate defense response at early interaction with G. boninense. Findings on metabolite profiling of G. boninense-infected oil palm roots and leaves are hoped to explain the defense-related compounds elicited by Elaeis guineensis in response to G. boninense colonization. The study aims to shed light on molecular defense response of oil palm at early interaction with G. boninense and promote prevention measures against Ganoderma infection.

Keywords: Ganoderma boninense, metabolites, phytohormones, RNA-Seq

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Authors: Wen Zhen

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Compared to content words, function words have been relatively overlooked by English learners especially articles. The article system, to a certain extent, becomes a resistance to know English better, driven by different elements. Three principal factors can be summarized in term of the nature of the articles when referring to the difficulty of the English article system. However, making the article system more complex are difficulties in the second acquisition process, for [-ART] learners have to create another category, causing even most non-native speakers at proficiency level to make errors. According to the sequences of acquisition of the English article, it is showed that the zero article is first acquired and in high inaccuracy. The zero article is often overused in the early stages of L2 acquisition. Although learners at the intermediate level move to underuse the zero article for they realize that the zero article does not cover any case, overproduction of the zero article even occurs among advanced L2 learners. The aim of the study is to investigate noun-phrase factors which give rise to incorrect usage or overuse of the zero article, thus providing suggestions for L2 English acquisition. Moreover, it enables teachers to carry out effective instruction that activate conscious learning of students. The research question will be answered through a corpus-based, data- driven approach to analyze the noun-phrase elements from the semantic context and countability of noun-phrases. Based on the analysis of the International Thurber Thesis corpus, the results show that: (1) Although context of [-definite,-specific] favored the zero article, both[-definite,+specific] and [+definite,-specific] showed less influence. When we reflect on the frequency order of the zero article , prototypicality plays a vital role in it .(2)EFL learners in this study have trouble classifying abstract nouns as countable. We can find that it will bring about overuse of the zero article when learners can not make clear judgements on countability altered from (+definite ) to (-definite).Once a noun is perceived as uncountable by learners, the choice would fall back on the zero article. These findings suggest that learners should be engaged in recognition of the countability of new vocabulary by explaining nouns in lexical phrases and explore more complex aspects such as analysis dependent on discourse.

Keywords: noun phrase, zero article, corpus, second language acquisition

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Authors: Hossein Motaghedi, Siavash Salamatpoor, Abbas Mokhtari

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Noor costal city which is located in Mazandaran province, Iran, regularly visited by many tourists. Accordingly, many tall building and heavy structures are going to be constructed over this coastal area. This region is overlaid by poorly graded clean sand and because of high water level, is susceptible to liquefaction. In this study, undrained triaxial tests under isotropic consolidation were conducted on the reconstituted samples of Noor sand, which underlies a densely populated, seismic region of southern bank of Caspian Sea. When the strain level is large enough, soil samples under shearing tend to be in a state of continuous deformation under constant shear and normal stresses. There exists a correlation between the void ratio and mean effective principal stress, which is referred to as the ultimate steady state line (USSL). Soil behavior can be achieved by expressing the state of effective confining stress and defining the location of this point relative to the steady state line. Therefore, one can say that sand behavior not only is dependent to relative density but also a description of stress state has to be defined. The current study tries to investigate behavior of this sand under different conditions such as confining effective stress and relative density using undrained monotonic triaxial compression tests. As expected, the analyzed results show that the sand behavior varies from dilative to contractive state while initial isotropic effective stress increases. Therefore, confining effective stress level will directly affect the overall behavior of sand. The observed behavior obtained from the conducted tests is then compared with some previously tested sands including Yamuna, Ganga, and Toyoura.

Keywords: noor sand, liquefaction, undrained test, steady state

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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

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Authors: Isabel Lopez-Oliva, Akshay Paropkari, Shweta Saraswat, Stefan Serban, Paola de Pablo, Karim Raza, Andrew Filer, Iain Chapple, Thomas Dietrich, Melissa Grant, Purnima Kumar

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Objective: We aimed to explicate the role of the subgingival microbiome in the causal link between rheumatoid arthritis (RA) and periodontitis (PD). Methods: Subjects with/without RA and with/without PD were randomized for treatment with scaling and root planing (SRP) or oral hygiene instructions. Subgingival biofilm, gingival crevicular fluid, and serum were collected at baseline and at 3- and 6-months post-operatively. Correlations were generated between 72 million 16S rDNA sequences, immuno-inflammatory mediators, circulating antibodies to oral microbial antigens, serum inflammatory molecules, and clinical metrics of RA. The dynamics of inter-microbial and host-microbial interactions were modeled using differential network analysis. Results: RA superseded periodontitis as a determinant of microbial composition, and DAS28 score superseded the severity of periodontitis as a driver of microbial assemblages (p=0.001, ANOSIM). RA subjects evidenced higher serum anti-PPAD (p=0.0013), anti-Pg-enolase (p=0.0031), anti-RPP3, anti- Pg-OMP and anti- Pi-OMP (p=0.001) antibodies than non-RA controls (with and without periodontitis). Following SRP, bacterial networks anchored by IL-1b, IL-4, IL-6, IL-10, IL-13, MIP-1b, and PDGF-b underwent ≥5-fold higher rewiring; and serum antibodies to microbial antigens decreased significantly. Conclusions: Our data suggest a circular relationship between RA and PD, beginning with an RA-influenced dysbiosis within the healthy subgingival microbiome that leads to exaggerated local inflammation in periodontitis and circulating antibodies to periodontal pathogens and positive correlation between severity of periodontitis and RA activity. Periodontal therapy restores host-microbial homeostasis, reduces local inflammation, and decreases circulating microbial antigens. Our data highlights the importance of integrating periodontal care into the management of RA patients.

Keywords: rheumatoid arthritis, periodontal, subgingival, DNA sequence analysis, oral microbiome

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Authors: Hsin Lee, Hsuan Lee

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Legal artificial intelligence (LegalAI) has been increasing applications within legal systems, propelled by advancements in natural language processing (NLP). Compared with general documents, legal case documents are typically long text sequences with intrinsic logical structures. Most existing language models have difficulty understanding the long-distance dependencies between different structures. Another unique challenge is that while the Judiciary of Taiwan has released legal judgments from various levels of courts over the years, there remains a significant obstacle in the lack of labeled datasets. This deficiency makes it difficult to train models with strong generalization capabilities, as well as accurately evaluate model performance. To date, models in Taiwan have yet to be specifically trained on judgment data. Given these challenges, this research proposes a Longformer-based pre-trained language model explicitly devised for retrieving similar judgments in Taiwanese legal documents. This model is trained on a self-constructed dataset, which this research has independently labeled to measure judgment similarities, thereby addressing a void left by the lack of an existing labeled dataset for Taiwanese judgments. This research adopts strategies such as early stopping and gradient clipping to prevent overfitting and manage gradient explosion, respectively, thereby enhancing the model's performance. The model in this research is evaluated using both the dataset and the Average Entropy of Offense-charged Clustering (AEOC) metric, which utilizes the notion of similar case scenarios within the same type of legal cases. Our experimental results illustrate our model's significant advancements in handling similarity comparisons within extensive legal judgments. By enabling more efficient retrieval and analysis of legal case documents, our model holds the potential to facilitate legal research, aid legal decision-making, and contribute to the further development of LegalAI in Taiwan.

Keywords: legal artificial intelligence, computation and language, language model, Taiwanese legal cases

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Authors: Marco Jan Rafael C. Sicam, Maria Daniella C. Yambao

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The Philippines is a tectonically active archipelagic country situated near the Circum-Pacific Belt. Hence, seismic hazard assessments are important in the nation-building. In 2014, the Philippines Institute of Volcanology and Seismology (PHIVOLCS) mapped a 12-km NW-trending unnamed active fault near Boso-Boso River, Rizal. Given the limited nature of their technical report, they would like to further consolidate relevant data about this fault. As such, this study aims to characterize the surface and subsurface expression of the fault along Boso-Boso River using rangefront morphology, structural criteria, and ground penetrating radar. This fault is subdivided into two segments: the first segment located in the city of Antipolo is mainly manifested in the upper Kinabuan Formation and terminating near Mt. Qutago, and the second segment in Baras, Pinugay, Rizal cuts through recent fluvial deposits and to the Guadalupe Formation. IfSAR-derived DTM data reveals the morphological expression of the fault defined by offset streams and ridges, linear sidehill valleys, and linear valleys. Fault gouges, fault breccia, transtentional flower structures, slickensides, and other shear sense markers observed in the units of the upper Cretaceous Kinabuan Formation indicate a sinistral sense of displacement. GPR radargram profiles revealed the presence of displacement in reflectors at 3-5 meters below the surface which may be suggestive of the fault within the area. Finally, the fault in Boso-Boso river may be a segment of the larger sinistral Montalban Fault in the north or largely affected by the movement from the Marikina Valley Fault System.

Keywords: NW unnamed fault, range-front morphology, shear sense markers, ground penetrating radar, boso-boso river, antipolo

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Authors: Luis Lara-Valencia, Mateo Ramirez-Acevedo, Daniel Caicedo, Jose Brito, Yosef Farbiarz

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Controlling wind-induced vibrations as well as aerodynamic forces, is an essential part of the structural design of tall buildings in order to guarantee the serviceability limit state of the structure. This paper presents a numerical investigation on the optimal design parameters of a Tuned Inerter Damper (TID) based system for the control of wind-induced vibration in tall buildings. The control system is based on the conventional TID, with the main difference that its location is changed from the ground level to the last two story-levels of the structural system. The TID tuning procedure is based on an evolutionary cultural algorithm in which the optimum design variables defined as the frequency and damping ratios were searched according to the optimization criteria of minimizing the root mean square (RMS) response of displacements at the nth story of the structure. A Monte Carlo simulation was used to represent the dynamic action of the wind in the time domain in which a time-series derived from the Davenport spectrum using eleven harmonic functions with randomly chosen phase angles was reproduced. The above-mentioned methodology was applied on a case-study derived from a 37-story prestressed concrete building with 144 m height, in which the wind action overcomes the seismic action. The results showed that the optimally tuned TID is effective to reduce the RMS response of displacements up to 25%, which demonstrates the feasibility of the system for the control of wind-induced vibrations in tall buildings.

Keywords: evolutionary cultural algorithm, Monte Carlo simulation, tuned inerter damper, wind-induced vibrations

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Authors: Caspar S. Carson, Gabriel W. Prather, Nicholas E. Wong, Jeffery R. Anton, William H. McCoy

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Cutibacterium acnes is a commensal bacterium found on human skin that has been linked to acne. C. acnes can also be an opportunistic pathogen when it infiltrates the body during surgery. This pathogen can cause dangerous infections of medical implants, such as shoulder replacements, leading to life-threatening blood infections. Compounding this issue, C. acnes resistance to many antibiotics has become an increasing problem worldwide, creating a need for special forms of treatment. C. acnes expresses the protein RoxP, and it requires this protein to colonize human skin. Though this protein is required for C. acnes skin colonization, its function is not yet understood. Inhibition of RoxP function might be an effective treatment for C. acnes infections. To develop such reagents, the McCoy Laboratory generated four unique anti-RoxP antibodies. Preliminary studies in the McCoy Lab have established that each antibody binds a distinct site on RoxP. To assess the potential of these antibodies as therapeutics, it is necessary to specifically characterize these antibody epitopes and evaluate them in assays that assess their ability to inhibit RoxP-dependent C. acnes growth. To provide material for these studies, an antibody expression construct, Fv-clasp(v2), was adapted to encode anti-RoxP antibody sequences. The author hypothesizes that this expression strategy can produce sufficient amounts of >95% pure antibody fragments for further characterization of these antibodies. Four anti-RoxP Fv-clasp(v2) expression constructs (pET vector-based) were transformed into E. coli BL21-Gold(DE3) cells and a small-scale expression and purification trial was performed for each construct to evaluate anti-RoxP Fv-clasp(v2) yield and purity. Successful expression and purification of these antibody constructs will allow for their use in structural studies, such as protein crystallography and cryogenic electron microscopy. Such studies would help to define the antibody binding sites on RoxP, which could then be leveraged in the development of certain methods to treat C. acnes infection through RoxP inhibition.

Keywords: structural biology, protein expression, infectious disease, antibody, therapeutics, E. coli

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Authors: Laxmi Versain, R. S. Banshtu

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Landslides are found to be the most commonly occurring geological hazards in the mountainous regions of the Himalaya. This mountainous zone is facing large number of seismic turbulences, climatic changes, and topography changes due to increasing urbanization. That eventually has lead several researchers working for best suitable methodologies to infer the ultimate results. Landslide Hazard Zonation has widely come as suitable method to know the appropriate factors that trigger the lansdslide phenomenon on higher reaches. Most vulnerable zones or zones of weaknesses are indentified and safe mitigation measures are to be suggested to mitigate and channelize the study of an effected area. Use of Landslide Hazard Zonation methodology in relative zones of weaknesses depend upon the data available for the particular site. The causative factors are identified and data is made available to infer the results. Factors like seismicity in mountainous region have closely associated to make the zones of thrust and faults or lineaments more vulnerable. Data related to soil, terrain, rainfall, geology, slope, nature of terrain, are found to be varied for various landforms and areas. Thus, the relative causes are to be identified and classified by giving specific weightage to each parameter. Factors which cause the instability of slopes are several and can be grouped to infer the potential modes of failure. The triggering factors of the landslides on the mountains are not uniform. The urbanization has crawled like ladder and emergence of concrete jungles are in a very fast pace on hilly region of Himalayas. The local terrains has largely been modified and hence instability of several zones are triggering at very fast pace. More strategic and pronounced methods are required to reduce the effect of landslide.

Keywords: zonation, LHZ, susceptible, weightages, methodology

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Authors: Hadach Fatiha, Algouti Ahmed, Algouti Abdellah, Jdaba Naji, Es-Sarrar Othman, Mourabit Zahra

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This paper investigates the structure and evolution of diapirism in the Ait Ourir basin, located in the High Atlas of Marrakesh, using structural and sedimentological fieldwork integrated with field mapping. A tectonic-sedimentological study of the Mesozoic cover of the Ait Ourir basin area revealed that these units were subjected to important saccadic halokinetic activity, reflected by anticline structures associated with regional faults that created several synclinal mini-basins. However, the lack of seismic coverage in the study area makes the proposed interpretation based on extrapolations of information observed on the surface. In this work, we suggest that faults and salt activity led to the formation of different structures within the studied area. The growth of the Triassic evaporites at different stages during the Mesozoic is reflected by progressive and local unconformities, recorded as having different ages. These structures created high diapiric zones with reduced sedimentation, showing abrupt lateral thickness variations in several places where this activity was occurring; this is clearly defined within the Wanina and Jbel Sour’s mini-basins, where the Senonian was observed to rest at an angular unconformity over the entire sedimentary cover encompassing the time period from the Liassic to the Turonian. The diapirism associated with the major faults, especially encountered between the basins, is often accompanied by late Triassic volcanic material. This diapir-fault relationship resulted in shallow and often depocentric zones in a pull-apart system within a distensive context.

Keywords: diapir, evaporites, faults, pull-apart, Mesozoic cover, Ait Ourir, western High Atlas, Morocco

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Authors: Maryam Jaberi, Siavosh Shayan, Mojtaba Yamani

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Habble-Rud River basin (HR), up to 100 km length, one of the largest watersheds which drain into deserts to the north of Central Iran (Dasht-e Kavir). This stream is oblique with the NE-SW trending, flow in the southern range of central Alborz Mountains and the northern border of Central Iran. The end of the ~17 km suddenly change direction and with the southern trending to have a morphology which meanders passes through the Alborz Mountain ridge and flows into the Garmsar plain where it forms one of the largest alluvial fans in Iran, i.e. the vast Garmsar alluvial fan with an area of 476 km2. This study was carried out through morphometric analyses, longitudinal river profiles, and study of geomorpholic evidence such as fluvial terraces, gypsum-salt domes, seismic data, and satellite images. This study aimed to investigate the changes in the pattern of rivers in the southern part of the HR river basin. The southern part of HR river basin located at the southern foothills of the Central Alborz is characterized the thrust faults (Sorkheh-Kalut and Garmsar faults), folds,diapirs and arid climate. The activity of more than 10 salt domes that belong to the Oligocene-Miocene period has considerably influenced the pattern of streams in this region. Dissolution of these domes has not only reduced the quality of water and soil resources, but also has led to the formation of badlands and gullies.Our results indicated that the pattern of rivers in the southern part of HR river basin was influenced by discharge of the HR river in Quaternary, geological structure, subsidence of Central Iran and vertical uplift of Alborz mountain. These agents caused the formation meanders in the southern part of the HR River and evaluation of the seasonal rivers like Shoor-Darre and Garmabsar.

Keywords: geomorphologic evaluation, rivers pattern, Habble-Rud River basin, seasonal rivers

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Authors: Reza E. Sedgh, Rajesh P. Dhakal

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Shear walls have been used extensively as the main lateral force resisting systems in multi-storey buildings. The recent development in performance based design urges practicing engineers to conduct nonlinear static or dynamic analysis to evaluate seismic performance of multi-storey shear wall buildings by employing distinct analytical models suggested in the literature. For practical purpose, application of macroscopic models to simulate the global and local nonlinear behavior of structural walls outweighs the microscopic models. The skill level, computational time and limited access to RC specialized finite element packages prevents the general application of this method in performance based design or assessment of multi-storey shear wall buildings in design offices. Hence, this paper organized to verify capability of nonlinear shell element in commercially available package (Sap2000) in simulating results of some specimens under monotonic and cyclic loads with very oversimplified available cyclic material laws in the analytical tool. The selection of constitutive models, the determination of related parameters of the constituent material and appropriate nonlinear shear model are presented in detail. Adoption of proposed simple model demonstrated that the predicted results follow the overall trend of experimental force-displacement curve. Although, prediction of ultimate strength and the overall shape of hysteresis model agreed to some extent with experiment, the ultimate displacement(significant strength degradation point) prediction remains challenging in some cases.

Keywords: analytical model, nonlinear shell element, structural wall, shear behavior

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Authors: Suharni Mohamad Suharni Mohamad, Nurul Izzati Hamzan Nurul Izzati Hamzan, Norhayu Abdul Rahman Norhayu Abdul Rahman, Siti Suraiya Md Noor Siti Suraiya Md Noor

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Human papillomavirus (HPV) is an important risk factor for development of oral cancer. HPV16 is the most common type found in HPV-positive squamous cell carcinoma. In the present study, we established a real-time loop-mediated isothermal amplification (real-time LAMP) for detection of HPV16. A set of six primers was specially designed to recognize eight distinct sequences of HPV16-E6. Detection and quantification was achieved by real-time monitoring using a real-time turbidimeter based on threshold time required for turbidity in the LAMP reaction. LAMP reagents (MgSO4, dNTPs, Bst polymerase concentrations) and various incubation times and temperatures were optimized. The sensitivity was determined using 10-fold serial dilutions of HPV16 standard strain. The specificity of was evaluated using other HPV genotypes. The optimized method was established with specifically designed primers by real-time detection in approximately 30 min at 65°C. The limit of detection of HPV16 using the LAMP assay was 10 pg/ml that could be detected in 30 min. The LAMP assay was 10 times more sensitive than the conventional PCR in detecting HPV16. No cross-reactivity with other HPV genotypes was observed. This quantitative real-time LAMP assay may improve diagnostic potential for the detection and quantification of HPV16 in clinical samples and epidemiological studies due to its rapidity, simplicity, high sensitivity and specificity. This assay will be further evaluated with HPV DNAs of saliva from patients with oral squamous cell carcinoma. Acknowledgement: This study was financially supported by the ScienceFund Grant, Ministry of Science, Technology and Innovation (305/PPSG/6113219).

Keywords: Oral Squamous Cell Carcinoma (OSCC), Human Papillomavirus 16 (HPV16), Loop-Mediated Isothermal Amplification (LAMP), rapid detection

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Authors: Irena Maus, Katharina Gabriella Cibis, Andreas Bremges, Yvonne Stolze, Geizecler Tomazetto, Daniel Wibberg, Helmut König, Alfred Pühler, Andreas Schlüter

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Within the agricultural sector, the production of biogas from organic substrates represents an economically attractive technology to generate bioenergy. Complex consortia of microorganisms are responsible for biomass decomposition and biogas production. Recently, species belonging to the phylum Thermotogae were detected in thermophilic biogas-production plants utilizing renewable primary products for biomethanation. To analyze adaptive genome features of representative Thermotogae strains, Defluviitoga tunisiensis L3 was isolated from a rural thermophilic biogas plant (54°C) and completely sequenced on an Illumina MiSeq system. Sequencing and assembly of the D. tunisiensis L3 genome yielded a circular chromosome with a size of 2,053,097 bp and a mean GC content of 31.38%. Functional annotation of the complete genome sequence revealed that the thermophilic strain L3 encodes several genes predicted to facilitate growth of this microorganism on arabinose, galactose, maltose, mannose, fructose, raffinose, ribose, cellobiose, lactose, xylose, xylan, lactate and mannitol. Acetate, hydrogen (H2) and carbon dioxide (CO2) are supposed to be end products of the fermentation process. The latter gene products are metabolites for methanogenic archaea, the key players in the final step of the anaerobic digestion process. To determine the degree of relatedness of dominant biogas community members within selected digester systems to D. tunisiensis L3, metagenome sequences from corresponding communities were mapped on the L3 genome. These fragment recruitments revealed that metagenome reads originating from a thermophilic biogas plant covered 95% of D. tunisiensis L3 genome sequence. In conclusion, availability of the D. tunisiensis L3 genome sequence and insights into its metabolic capabilities provide the basis for biotechnological exploitation of genome features involved in thermophilic fermentation processes utilizing renewable primary products.

Keywords: genome sequence, thermophilic biogas plant, Thermotogae, Defluviitoga tunisiensis

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Authors: Ahilya Singh, Brad Carte, Ramesh Subramani, William Aalbersberg

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A total of 37 actinomycete strains were purified from 25 Solomon Islands marine sediments using four different types of isolation media. Among them, 54% of the strains had obligate requirement of seawater for growth. The ethyl acetate extract of 100 ml fermentation product of each strain was screened for antimicrobial activity against multidrug resistant human pathogens and cytotoxic activity against brine shrimps. A total of 67% of the ethyl acetate extracts showed antimicrobial and/or cytotoxic activities. A strain F-1915 was selected for isolation and evaluation of bioactive compound(s) based on its bioactive properties and chemical profile analysis using the LC-MS. The strain F-1915 was identified to have 96% sequence similarity to Streptomyces violaceusniger on the basis of 16S rDNA sequences using BLAST analysis. The 16S rDNA revealed that the strain F-1915 is a new member of MAR4 clade of actinomycetes. The MAR4 clade is an interesting clade of actinomycetes known for the production of pharmaceutically important hybrid isoprenoid compounds. The ethyl acetate extract of the fermentation product of this strain was purified by silica gel column chromatography and afforded the isolation of one bioactive pure compound. Based on the 1D and 2D NMR spectral data of compound 1 it was identified as a new mono-brominated phenazinone, Marinophenazimycin A, a structure which has already been studied by external collaborators at Scripps Institution of Oceanography but is yet to be published. Compound 1 displayed significant antimicrobial activity against drug resistant human pathogens. The minimum inhibitory concentration (MIC) of compound 1 was against Methicillin Resistant Staphylococcus aureus (MRSA) was about 1.9 μg/ml and MIC recorded against Amphotericin Resistant Candida albicans (ARCA) was about 0.24 μg/ml. The bioactivity of compound 1 against ARCA was found to be better than the standard antifungal agent amphotericin B. Compound 1 however did not show any cytotoxic activity against brine shrimps.

Keywords: actinomycetes, antimicrobial activity, brominated phenazine, MAR4 clade, marine natural products, multidrug resistent, 1D and 2D NMR

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Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: Suchithra V., Shreedhanya, Kavya Menon, Vidya Niranjan

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Skin metagenomics has a wide range of applications with direct relevance to the health of the organism. It gives us insight to the diverse community of microorganisms (the microbiome) harbored on the skin. In the recent years, it has become increasingly apparent that the interaction between skin microbiome and the human body plays a prominent role in immune system development, cancer development, disease pathology, and many other biological implications. Next Generation Sequencing has led to faster and better understanding of environmental organisms and their mutual interactions. This project is studying the human skin microbiome of different individuals having varied skin conditions. Bacterial 16S rRNA data of skin microbiome is downloaded from SRA toolkit provided by NCBI to perform metagenomics analysis. Twelve samples are selected with two controls, and 3 different categories, i.e., sex (male/female), skin type (moist/intermittently moist/sebaceous) and occlusion (occluded/intermittently occluded/exposed). Quality of the data is increased using Cutadapt, and its analysis is done using FastQC. USearch, a tool used to analyze an NGS data, provides a suitable platform to obtain taxonomy classification and abundance of bacteria from the metagenome data. The statistical tool used for analyzing the USearch result is METAGENassist. The results revealed that the top three abundant organisms found were: Prevotella, Corynebacterium, and Anaerococcus. Prevotella is known to be an infectious bacterium found on wound, tooth cavity, etc. Corynebacterium and Anaerococcus are opportunist bacteria responsible for skin odor. This result infers that Prevotella thrives easily in sebaceous skin conditions. Therefore it is better to undergo intermittently occluded treatment such as applying ointments, creams, etc. to treat wound for sebaceous skin type. Exposing the wound should be avoided as it leads to an increase in Prevotella abundance. Moist skin type individuals can opt for occluded or intermittently occluded treatment as they have shown to decrease the abundance of bacteria during treatment.

Keywords: bacterial 16S rRNA , next generation sequencing, skin metagenomics, skin microbiome, taxonomy

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Authors: Saima Saleem, Zubair Abbasi, Abdul Hameed, Mansoor Ahmed Khan, Navid Rashid Qureshi, Abid Azhar

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Oral Squamous Cell Carcinoma (OSCC) is the leading cause of death in the developing countries like Pakistan. This problem aggravates because of the excessive use of available chewing products. In spite of widespread information on their use and purported legislations against their use the Pakistani markets are classical examples of selling chewable carcinogenic mutagens. Reported studies indicated that these products are rich in reactive oxygen species (ROS) and polyphenols. TP53 gene is involved in the suppression of tumor. It has been reported that somatic mutations caused by TP53 gene are the foundation of the cancer. This study aims to find the loss of TP53 functions due to mutation/polymorphism caused by genomic alteration and interaction with tobacco and its related ingredients. Total 260 tissues and blood specimens were collected from OSCC patients and compared with age and sex matched controls. Mutations in exons 2-11 of TP53 were examined by PCR-SSCP. Samples showing mobility shift were directly sequenced. Two mutations were found in exon 4 at nucleotide position 108 and 215 and one in exon 7 at nucleotide position 719 of the coding sequences in patient’s tumor samples. These results show that substitution of proline with arginine at codon 72 and serine with threonine at codon 240 of p53 protein. These polymorphic changes, found in tumor samples of OSCC, could be involved in loss of heterozygocity and apoptotic activity in the binding domain of TP53. The model of the mutated TP53 gene elaborated a nonfunctional unfolded p53 protein, suggesting an important role of these mutations in p53 protein inactivation and malfunction. This nonfunctional 3D model also indicates that exogenous tobacco related carcinogens may act as DNA-damaging agents affecting the structure of DNA. The interpretations could be helpful in establishing the pathways responsible for tumor formation in OSCC patients.

Keywords: TP53 mutation/polymorphism, OSCC, PCR-SSCP, direct DNA sequencing, 3D structure

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Authors: Y. B. Sharma, K. B. Biswas

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This research project examines a 5000 cal yr BP sediment core record to reveal the consequences of human impact and climate variability on the tropical dry forests of the Mahi river basin, western India. To date there has been little research to assess the impact of climate variability and human impact on the vegetation dynamics of this region. There has also been little work to link changes in vegetation cover to documented changes in the basin hydrology over the past 100 years – although it is assumed that the two are closely linked. The key objective of this research project therefore is to understand the driving mechanisms responsible for the abrupt changes in the Mahi river basin as detailed in historical documentation and its impact on water resource management. The Mahi river basin is located in western India (22° 11’-24° 35’ N 72° 46’-74° 52’ E). Mahi river arises in the Malwa Plateau, Madhya Pradesh near Moripara and flows through the uplands and alluvial plain of Rajasthan and Gujarat provinces before draining into the Gulf of Cambay. Palaeoecological procedures (sedimentology, geochemical analysis, C&N isotopes and fossil pollen evidences) have been applied on sedimentary sequences collected from lakes in the Mahi basin. These techniques then facilitate to reconstruct the soil erosion, nutrient cycling, vegetation changes and climatic variability over the last 5000 years. Historical documentation detailing changes in demography, climate and landscape use over the past 100 years in this region will also be collated to compare with the most recent palaeoecological records. The results of the research work provide a detailed record of vegetation change, soil erosion, changes in aridity, and rainfall patterns in the region over the past 5000 years. This research therefore aims to determine the drivers of change and natural variability in the basin. Such information is essential for its current and future management including restoration.

Keywords: human impact, climate variability, vegetation cover, hydrology, water resource management, Mahi river basin, sedimentology, geochemistry, fossil pollen, nutrient cycling, vegetation changes, palaeoecology, aridity, rainfall, drivers of change

Procedia PDF Downloads 346

Authors: A. Akbarpour, M. R. Adib Ramezani, M. Zhian, N. Ghorbani Amirabad

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One way to improve the performance of structures against of earthquake is passive control which requires no external power source. In this research, tuned liquid column dampers which are among of systems with the capability to transfer energy between various modes of vibration, are used. For the first time, a liquid column damper for vibration control structure is presented. After modeling this structure in design building software and performing the static and dynamic analysis and obtaining the necessary parameters for the design of tuned liquid column damper, the whole structure will be analyzed in finite elements software. The tuned liquid column dampers are installed on the structure and nonlinear time-history analysis is done in two cases of structures; with and without dampers. Finally the seismic behavior of building in the two cases will be examined. In this study the nonlinear time-history analysis on a twelve-story steel structure equipped with damper subject to records of earthquake including Loma Prieta, Northridge, Imperiall Valley, Pertrolia and Landers was performed. The results of comparing between two cases show that these dampers have reduced lateral displacement and acceleration of levels on average of 10%. Roof displacement and acceleration also reduced respectively 5% and 12%. Due to structural asymmetric in the plan, the maximum displacements of surrounding structures as well as twisting were studied. The results show that the dampers lead to a 10% reduction in the maximum response of structure stories surrounding points. At the same time, placing the dampers, caused to reduce twisting on the floor plan of the structure, Base shear of structure in the different earthquakes also has been reduced on the average of 6%.

Keywords: retrofitting, passive control, tuned liquid column damper, finite element analysis

Procedia PDF Downloads 387

Authors: Guna Raj Dhungana, Roshan Nepal, Apshara Parajuli, , Archana Maharjan, Shyam K. Mishra, Pramod Aryal, Rajani Malla

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Introduction: Klebsiella pneumoniae is a well-known opportunistic human pathogen, primarily causing healthcare-associated infections. The global emergence of carbapenemase-producing K. pneumoniaeis a major public health burden, which is often extensively multidrug resistant.Thus, because of the difficulty to treat these ‘superbug’ and menace and some term as ‘apocalypse’ of post antibiotics era, an alternative approach to controlling this pathogen is prudent and one of the approaches is phage mediated control and/or treatment. Objective: In this study, we aimed to isolate novel bacteriophage against carbapenemase-producing K. pneumoniaeand characterize for potential use inphage therapy. Material and Methods: Twenty lytic phages were isolated from river water using double layer agar assay and purified. Biological features, physiochemical characters, burst size, host specificity and activity spectrum of phages were determined. One most potent phage: Phage TU_Kle10O was selected and characterized by electron microscopy. Whole genome sequences of the phage were analyzed for presence/absence of virulent factors, and other lysin genes. Results: Novel phage TU_Kle10O showed multiple host range within own genus and did not induce any BIM up to 5th generation of host’s life cycle. Electron microscopy confirmed that the phage was tailed and belonged to Caudovirales family. Next generation sequencing revealed its genome to be 166.2 Kb. bioinformatical analysis further confirmed that the phage genome ‘did not’ contain any ‘bacterial genes’ within phage genome, which ruled out the concern for transfer of virulent genes. Specific 'lysin’ enzyme was identified phages which could be used as 'antibiotics'. Conclusion: Extensively multidrug resistant bacteria like carbapenemase-producing K. pneumoniaecould be treated efficiently by phages.Absence of ‘virulent’ genes of bacterial origin and presence of lysin proteins within phage genome makes phages an excellent candidate for therapeutics.

Keywords: bacteriophage, Klebsiella pneumoniae, MDR, phage therapy, carbapenemase,

Procedia PDF Downloads 156

Authors: M. Gogniashvili, I. Maisaia, A. Kotorashvili, N. Kotaria, T. Beridze

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Three types of plasmon (A, B and G) is typical for genus Triticum. In polyploid species - Triticum turgidum L. and Triticum aestivum L. plasmon B is detected. In the forthcoming paper, complete nucleotide sequence of chloroplast DNA of 11 representatives of Georgian wheat polyploid species, carrying plasmon B was determined. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. All contigs were aligned to the reference chloroplast genome sequence using BLASTN. For detection of SNPs and Indels and phylogeny tree construction computer programs Mafft and Blast were used. Using Triticum aestivum L. subsp. macha (Dekapr. & Menabde) Mackey var. paleocolchicum Dekapr. et Menabde as a reference, 5 SNPs can be identified in chloroplast DNA of Georgian endemic polyploid wheat. The number of noncoding substitutions is 2, coding substitutions - 3. In comparison with reference DNA two - 38 bp and 56 bp inversions were observed in paleocolchicum subspecies. There were six 1 bp indels detected in Georgian polyploid wheats, all of them at microsatellite stretches. The phylogeny tree shows that subspecies macha, carthlicum and paleocolchicum occupy different positions. According to the simplified scheme based on SNP and indel data, the ancestral, female parent of the all studied polyploid wheat is unknown X predecesor, from which four lines were formed. 1 SNP and two inversions (38 bp and 56 bp) caused the formation of subsp. paleocolchicum. Three other lines are macha, durum and carthlicum lines. Macha line is further divided into two sublines (M_1 and M_4). Carthlicum line includes subsp.carthlicum and T.aestivum - C_1 - C_2 - A_1. One of the central question of wheat domestication is which people(s) participated in wheat domestication? It is proposed that the predecessors of Georgian peoples (Proto-Kartvelians) must be placed, on the evidence of archaic lexical and toponymic data, in the mountainous regions of the western and central part of the Little Caucasus (the Transcaucasian foothills) at least 4,000 years ago. One of the possibility to explain the ‘wheat puzzle’ is that Kartvelian speakers brought domesticated wheat species and subspecis from Fertile Crescent further north to South Caucasus.

Keywords: chloroplast DNA, sequencing, SNP, triticum

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Authors: Narayan Moger, Divya B., Preethi Jambagi, Krishnaveni C. K., Apsana M. R., B. R. Patil, Basvaraj Bagewadi

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Salinity is one of the major threats to world food security. Considering the requirement for salt tolerant crop plants in the present study was undertaken to clone and transferred the salt tolerant ectA gene from marine ecosystem into agriculture crop system to impart salinity tolerance. Ectoine is the compatible solute which accumulates in the cell membrane, is known to be involved in salt tolerance activity in most of the Halophiles. The present situation is insisting to development of salt tolerant transgenic lines to combat abiotic stress. In this background, the investigation was conducted to develop transgenic tomato lines by cloning and transferring of ectA gene is an ectoine derivative capable of enzymatic action for the production of acetyl-diaminobutyric acid. The gene ectA is involved in maintaining the osmotic balance of plants. The PCR amplified ectA gene (579bp) was cloned into T/A cloning vector (pTZ57R/T). The construct pDBJ26 containing ectA gene was sequenced by using gene specific forward and reverse primers. Sequence was analyzed using BLAST algorithm to check similarity of ectA gene with other isolates. Highest homology of 99.66 per cent was found with ectA gene sequences of isolates Halomonas elongata with the available sequence information in NCBI database. The ectA gene was further sub cloned into pRI101-AN plant expression vector and transferred into E. coli DH5α for its maintenance. Further pDNM27 was mobilized into A. tumefaciens LBA4404 through tri-parental mating system. The recombinant Agrobacterium containing pDNM27 was transferred into tomato plants through In planta plant transformation method. Out of 300 seedlings, co-cultivated only twenty-seven plants were able to well establish under the greenhouse condition. Among twenty-seven transformants only twelve plants showed amplification with gene specific primers. Further work must be extended to evaluate the transformants at T1 and T2 generations for ectoine accumulation, salinity tolerance, plant growth and development and yield.

Keywords: salinity, computable solutes, ectA, transgenic, in planta transformation

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Authors: S. Behnia, S. Fathizadeh, A. Akhshani

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In the recent decades, DNA has increasingly interested in the potential technological applications that not directly related to the coding for functional proteins that is the expressed in form of genetic information. One of the most interesting applications of DNA is related to the construction of nanostructures of high complexity, design of functional nanostructures in nanoelectronical devices, nanosensors and nanocercuits. In this field, DNA is of fundamental interest to the development of DNA-based molecular technologies, as it possesses ideal structural and molecular recognition properties for use in self-assembling nanodevices with a definite molecular architecture. Also, the robust, one-dimensional flexible structure of DNA can be used to design electronic devices, serving as a wire, transistor switch, or rectifier depending on its electronic properties. In order to understand the mechanism of the charge transport along DNA sequences, numerous studies have been carried out. In this regard, conductivity properties of DNA molecule could be investigated in a simple, but chemically specific approach that is intimately related to the Su-Schrieffer-Heeger (SSH) model. In SSH model, the non-diagonal matrix element dependence on intersite displacements is considered. In this approach, the coupling between the charge and lattice deformation is along the helix. This model is a tight-binding linear nanoscale chain established to describe conductivity phenomena in doped polyethylene. It is based on the assumption of a classical harmonic interaction between sites, which is linearly coupled to a tight-binding Hamiltonian. In this work, the Hamiltonian and corresponding motion equations are nonlinear and have high sensitivity to initial conditions. Then, we have tried to move toward the nonlinear dynamics and phase space analysis. Nonlinear dynamics and chaos theory, regardless of any approximation, could open new horizons to understand the conductivity mechanism in DNA. For a detailed study, we have tried to study the current flowing in DNA and investigated the characteristic I-V diagram. As a result, It is shown that there are the (quasi-) ohmic areas in I-V diagram. On the other hand, the regions with a negative differential resistance (NDR) are detectable in diagram.

Keywords: DNA conductivity, Landauer resistance, negative dierential resistance, Chaos theory, mean Lyapunov exponent

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Authors: Amar F. Siddique

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The Guwahati city is one of the fastest growing cities of the north-eastern region of India, situated on the South Bank of the Brahmaputra River falls in the highest seismic zone level V. The city has witnessed many high magnitude earthquakes in the past decades. The Assam earthquake occurred on August 15, 1950, of moment magnitude 8.7 epicentered near Rima, Tibet was one of the major earthquakes which caused a serious structural damage and widespread soil liquefaction in and around the region. Hence the study of ground motion characteristics of Guwahati city is very essential. In this present work 1D equivalent linear ground response analysis (GRA) has been adopted using Deep soil software. The analysis has been done for two typical sites namely, Panbazar and Azara comprising total four boreholes location in Guwahati city of India. GRA of the sites is carried out by using an input motion recorded at Nongpoh station (recorded PGA 0.048g) and Nongstoin station (recorded PGA 0.047g) of 1997 Indo-Burma earthquake. In comparison to motion recorded at Nongpoh, different amplifications of bedrock peak ground acceleration (PGA) are obtained for all the boreholes by the motion recorded at Nongstoin station; although, the Fourier amplitude ratios (FAR) and fundamental frequencies remain almost same. The difference in recorded duration and frequency content of the two motions mainly influence the amplification of motions thus getting different surface PGA and amplification factor keeping a constant bedrock PGA. From the results of response spectra, it is found that at the period of less than 0.2 sec the ground motion recorded at Nongpoh station will give a high spectral acceleration (SA) on the structures than at Nongstoin station. Again for a period greater than 0.2 sec the ground motion recorded at Nongstoin station will give a high SA on the structures than at Nongpoh station.

Keywords: fourier amplitude ratio, ground response analysis, peak ground acceleration, spectral acceleration

Procedia PDF Downloads 155