Search results for: spatial gene

Authors: Kyoung Lee

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Numerous aerobic bacteria have the ability to form multicellular communities on the surface layer of the air-liquid (A-L) interface as a biofilm called a pellicle. Pellicles occupied at the A-L interface will benefit from the utilization of oxygen from air and nutrient from liquid. Buoyancy of cells can be obtained by high surface tension at the A-L interface. Thus, formation of pellicles is an adaptive advantage in utilization of excess nutrients in the standing culture where oxygen depletion is easily set up due to rapid cell growth. In natural environments, pellicles are commonly observed on the surface of lake or pond contaminated with pollutants. Previously, we have shown that when cultured in standing LB media an alkylphenol-degrading bacteria Pseudomonas alkylphenolia KL28 forms pellicles in a diameter of 0.3-0.5 mm with a thickness of ca 40 µm. The pellicles have unique features for possessing flatness and unusual rigidity. In this study, the biogenesis of the circular pellicles has been investigated by observing the cell organization at early stages of pellicle formation and cell arrangements in pellicle, providing a clue for highly organized cellular arrangement to be adapted to the air-liquid niche. Here, we first monitored developmental patterns of pellicle from monolayer to multicellular organization. Pellicles were shaped by controlled growth of constituent cells which accumulate extracellular polymeric substance. The initial two-dimensional growth was transited to multilayers by a constraint force of accumulated self-produced extracellular polymeric substance. Experiments showed that pellicles are formed by clonal growth and even with knock-out of genes for flagella and pilus formation. In contrast, the mutants in the epm gene cluster for alginate-like polymer biosynthesis were incompetent in cell alignment for initial two-dimensional growth of pellicles. Electron microscopic and confocal laser scanning microscopic studies showed that the fully matured structures are highly packed by matrix-encased cells which have special arrangements. The cells on the surface of the pellicle lie relatively flat and inside longitudinally cross packed. HPLC analysis of the extrapolysaccharide (EPS) hydrolysate from the colonies from LB agar showed a composition with L-fucose, L-rhamnose, D-galactosamine, D-glucosamine, D-galactose, D-glucose, D-mannose. However, that from pellicles showed similar neutral and amino sugar profile but missing galactose. Furthermore, uronic acid analysis of EPS hydrolysates by HPLC showed that mannuronic acid was detected from pellicles not from colonies, indicating the epm-derived polymer is critical for pellicle formation as proved by the epm mutants. This study verified that for the circular pellicle architecture P. alkylphenolica KL28 cells utilized EPS building blocks different from that used for colony construction. These results indicate that P. alkylphenolica KL28 is a clever architect that dictates unique cell arrangements with selected EPS matrix material to construct sophisticated building, circular biofilm pellicles.

Keywords: biofilm, matrix, pellicle, pseudomonas

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Authors: Yinsheng Zhang

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Changes in the extent and amount of snow cover in Eurasia are of great interest because of their vital impacts on the global climate system and regional water resource management. This study investigated the spatial and temporal variability of the snow cover extent (SCE) and snow water equivalent (SWE) of continental Eurasia using the Northern Hemisphere Equal-Area Scalable Earth Grid (EASE-Grid) Weekly SCE data for 1972–2006 and the Global Monthly EASE-Grid SWE data for 1979–2004. The results indicated that, in general, the spatial extent of snow cover significantly decreased during spring and summer, but varied little during autumn and winter over Eurasia in the study period. The date at which snow cover began to disappear in spring has significantly advanced, whereas the timing of snow cover onset in autumn did not vary significantly during 1972–2006. The snow cover persistence period declined significantly in the western Tibetan Plateau as well as the partial area of Central Asia and northwestern Russia but varied little in other parts of Eurasia. ‘Snow-free breaks’ (SFBs) with intermittent snow cover in the cold season were mainly observed in the Tibetan Plateau and Central Asia, causing a low sensitivity of snow cover persistence period to the timings of snow cover onset and disappearance over the areas with shallow snow. The averaged SFBs were 1–14 weeks in the Tibetan Plateau during 1972–2006 and the maximum intermittence could reach 25 weeks in some extreme years. At a seasonal scale, the SWE usually peaked in February or March but fell gradually since April across Eurasia. Both annual mean and annual maximum SWE decreased significantly during 1979–2004 in most parts of Eurasia except for eastern Siberia as well as northwestern and northeastern China.

Keywords: Eurasia, snow cover extent, snow cover persistence period, snow-free breaks, onset and disappearance timings, snow water equivalent

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Authors: Elizabeth M. Annoni, Elena G. Tolkacheva

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Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia that is a known prognostic marker for stroke, heart failure and death. Reentrant mechanisms of rotor formation, which are stable electrical sources of cardiac excitation, are believed to cause AF. No existing commercial mapping systems have been demonstrated to consistently and accurately predict rotor locations outside of the pulmonary veins in patients with persistent AF. There is a clear need for robust spatio-temporal techniques that can consistently identify rotors using unique characteristics of the electrical recordings at the pivot point that can be applied to clinical intracardiac mapping. Recently, we have developed four new signal analysis approaches – Shannon entropy (SE), Kurtosis (Kt), multi-scale frequency (MSF), and multi-scale entropy (MSE) – to identify the pivot points of rotors. These proposed techniques utilize different cardiac signal characteristics (other than local activation) to uncover the intrinsic complexity of the electrical activity in the rotors, which are not taken into account in current mapping methods. We validated these techniques using high-resolution optical mapping experiments in which direct visualization and identification of rotors in ex-vivo Langendorff-perfused hearts were possible. Episodes of ventricular tachycardia (VT) were induced using burst pacing, and two examples of rotors were used showing 3-sec episodes of a single stationary rotor and figure-8 reentry with one rotor being stationary and one meandering. Movies were captured at a rate of 600 frames per second for 3 sec. with 64x64 pixel resolution. These optical mapping movies were used to evaluate the performance and robustness of SE, Kt, MSF and MSE techniques with respect to the following clinical limitations: different time of recordings, different spatial resolution, and the presence of meandering rotors. To quantitatively compare the results, SE, Kt, MSF and MSE techniques were compared to the “true” rotor(s) identified using the phase map. Accuracy was calculated for each approach as the duration of the time series and spatial resolution were reduced. The time series duration was decreased from its original length of 3 sec, down to 2, 1, and 0.5 sec. The spatial resolution of the original VT episodes was decreased from 64x64 pixels to 32x32, 16x16, and 8x8 pixels by uniformly removing pixels from the optical mapping video.. Our results demonstrate that Kt, MSF and MSE were able to accurately identify the pivot point of the rotor under all three clinical limitations. The MSE approach demonstrated the best overall performance, but Kt was the best in identifying the pivot point of the meandering rotor. Artifacts mildly affect the performance of Kt, MSF and MSE techniques, but had a strong negative impact of the performance of SE. The results of our study motivate further validation of SE, Kt, MSF and MSE techniques using intra-atrial electrograms from paroxysmal and persistent AF patients to see if these approaches can identify pivot points in a clinical setting. More accurate rotor localization could significantly increase the efficacy of catheter ablation to treat AF, resulting in a higher success rate for single procedures.

Keywords: Atrial Fibrillation, Optical Mapping, Signal Processing, Rotors

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Authors: Sanchari Mukhopadhyay

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Today, almost the entire realm of human activities are becoming increasingly dependent on the power of information, where through ICTs it is now possible to cater distances and avail various services at a few clicks. In principle, ICTs are thus expected to blur location-specific differences and affiliations of development and bring in an inclusive society at the wake of globalization. However, eventually researchers and policy analysts realized that ICTs are also generating inequality in spite of the hope for an integrated world and widespread social well-being. Regarding this unevenness, location plays a major role as often ICT development is seen to be concentrated into pockets, leaving behind large tracks as underprivileged. Thus, understanding the spatial pattern of ICT development and distribution is significant in relation to exploring the extent to which ICTs are fulfilling the promises or reassuring the existing divisions. In addition, it is also profoundly crucial to investigate how regions are connecting and competing both locally and globally. The focus of the research paper is to evaluate the spatial structure of ICT led development in India. Thereby, it attempts to understand the state level (four selected states) pattern of ICT penetration, the pattern of diffusion across districts with respect to large urban centres and the rural-urban disparity of technology adoption. It also tries to assess the changes in access dynamisms of ICTs as one move away from a large metropolitan city towards the periphery. In brief, the analysis investigates into the tendency towards the uneven growth of development through the identification of the core areas of ICT advancement within the country and its diffusion from the core to the periphery. In order to assess the level of ICT development and rural-urban disparity across the districts of selected states, two indices named ICT Development Index and Rural-Urban Digital Divide Index have been constructed. The study mostly encompasses the latest Census (2011) of the country and TRAI (Telecom Regulatory Authority of India) in some cases.

Keywords: ICT development, diffusion, core-periphery, digital divide

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Authors: Elene Zhuravliova, Tamar Barbakadze, Irina Kalandadze, Elnari Zaalishvili, Lali Shanshiashvili, David Mikeladze

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Background: Multiple sclerosis (MS) is an inflammatory, neurodegenerative disease, which is accompanied by demyelination and autoimmune response to myelin proteins. Among post-translational modifications, which mediate the modulation of inflammatory pathways during MS, methylation is the main one. The methylation of DNA, also amino acids lysine and arginine, occurs in the cell. It was found that decreased trans-methylation is associated with neuroinflammatory diseases. Therefore, abnormal regulation of the methyl cycle could induce demyelination through the action on PAD (peptidyl-arginine-deiminase) gene promoter. PAD takes part in protein citrullination and targets myelin basic protein (MBP), which is affected during demyelination. To determine whether MBP charge isomers are changing the methyl cycle, we have estimated the concentrations of methyl cycle metabolites in MBP-activated primary astrocytes and oligodendrocytes. For this purpose, the action of the citrullinated MBP- C8 and the most cationic MBP-C1 isomers on the primary cells were investigated. Methods: Primary oligodendrocyte and astrocyte cell cultures were prepared from whole brains of 2-day-old Wistar rats. The methyl cycle metabolites, including homocysteine, S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH), were estimated by HPLC analysis using fluorescence detection and prior derivatization. Results: We found that the action of MBP-C8 and MBP-C1 induces a decrease in the concentration of both methyl cycle metabolites, S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), in astrocytes compared to the control cells. As for oligodendrocytes, the concentration of SAM was increased by the addition of MBP-C1, while MBP-C8 has no significant effect. As for SAH, its concentration was increased compared to the control cells by the action of both MBP-C1 and MBP-C8. A significant increase in homocysteine concentration was observed by the action of the MBP-C8 isomer in both oligodendrocytes and astrocytes. Conclusion: These data suggest that MBP charge isomers change the concentration of methyl cycle metabolites. MBP-C8 citrullinated isomer causes elevation of homocysteine in astrocytes and oligodendrocytes, which may be the reason for decreased astrocyte proliferation and increased oligodendrocyte cell death which takes place in neurodegenerative processes. Elevated homocysteine levels and subsequent abnormal regulation of methyl cycles in oligodendrocytes possibly change the methylation of DNA that activates PAD gene promoter and induces the synthesis of PAD, which in turn provokes the process of citrullination, which is the accompanying process of demyelination. Acknowledgment: This research was supported by the SRNSF Georgia RF17_534 grant.

Keywords: myelin basic protein, astrocytes, methyl cycle metabolites, homocysteine, oligodendrocytes

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Authors: Jie Su, Zhenghua Zhou, Yushi Wang, Yongyi Li

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The ground motion characteristics, which are given by the analysis of acceleration records, underlie the formulation and revision of the seismic design code of structural engineering. China Digital Strong Motion Network had recorded a lot of accelerograms of main shock from 478 permanent seismic stations, during the Ms8.0 Wenchuan earthquake on 12th May, 2008. These accelerograms provided a large number of essential data for the analysis of ground motion characteristics of the event. The spatial distribution characteristics, rupture directivity effect, hanging-wall and footwall effect had been studied based on these acceleration records. The results showed that the contours of horizontal peak ground acceleration and peak velocity were approximately parallel to the seismogenic fault which demonstrated that the distribution of the ground motion intensity was obviously controlled by the spatial extension direction of the seismogenic fault. Compared with the peak ground acceleration (PGA) recorded on the sites away from which the front of the fault rupture propagates, the PGA recorded on the sites toward which the front of the fault rupture propagates had larger amplitude and shorter duration, which indicated a significant rupture directivity effect. With the similar fault distance, the PGA of the hanging-wall is apparently greater than that of the foot-wall, while the peak velocity fails to observe this rule. Taking account of the seismic intensity distribution of Wenchuan Ms8.0 earthquake, the shape of strong ground motion contours was significantly affected by the directional effect in the regions with Chinese seismic intensity level VI ~ VIII. However, in the regions whose Chinese seismic intensity level are equal or greater than VIII, the mutual positional relationship between the strong ground motion contours and the surface outcrop trace of the fault was evidently influenced by the hanging-wall and foot-wall effect.

Keywords: hanging-wall and foot-wall effect, peak ground acceleration, rupture directivity effect, strong ground motion

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Authors: Anastasia Tsakiridi

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Geographic information systems (GIS) have been utilized in numerous spatial problems, such as site research, land suitability, and demographic analysis. Besides, GIS has been applied in scientific fields like geography, health, and economics. In business studies, GIS has been used to provide insights and spatial perspectives in demographic trends, spending indicators, and network analysis. To date, the information regarding the available usages of GIS in supply chain management (SCM) and how these analyses can benefit businesses is limited. A systematic literature review (SLR) of the last 5-year peer-reviewed academic literature was conducted, aiming to explore the existing usages of GIS in SCM. The searches were performed in 3 databases (Web of Science, ProQuest, and Business Source Premier) and reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology. The analysis resulted in 79 papers. The results indicate that the existing GIS applications used in SCM were in the following domains: a) network/ transportation analysis (in 53 of the papers), b) location – allocation site search/ selection (multiple-criteria decision analysis) (in 45 papers), c) spatial analysis (demographic or physical) (in 34 papers), d) combination of GIS and supply chain/network optimization tools (in 32 papers), and e) visualization/ monitoring or building information modeling applications (in 8 papers). An additional categorization of the literature was conducted by examining the usage of GIS in the supply chain (SC) by the business sectors, as indicated by the volume of the papers. The results showed that GIS is mainly being applied in the SC of the biomass biofuel/wood industry (33 papers). Other industries that are currently utilizing GIS in their SC were the logistics industry (22 papers), the humanitarian/emergency/health care sector (10 papers), the food/agro-industry sector (5 papers), the petroleum/ coal/ shale gas sector (3 papers), the faecal sludge sector (2 papers), the recycle and product footprint industry (2 papers), and the construction sector (2 papers). The results were also presented by the geography of the included studies and the GIS software used to provide critical business insights and suggestions for future research. The results showed that research case studies of GIS in SCM were conducted in 26 countries (mainly in the USA) and that the most prominent GIS software provider was the Environmental Systems Research Institute’s ArcGIS (in 51 of the papers). This study is a systematic literature review of the usage of GIS in SCM. The results showed that the GIS capabilities could offer substantial benefits in SCM decision-making by providing key insights to cost minimization, supplier selection, facility location, SC network configuration, and asset management. However, as presented in the results, only eight industries/sectors are currently using GIS in their SCM activities. These findings may offer essential tools to SC managers who seek to optimize the SC activities and/or minimize logistic costs and to consultants and business owners that want to make strategic SC decisions. Furthermore, the findings may be of interest to researchers aiming to investigate unexplored research areas where GIS may improve SCM.

Keywords: supply chain management, logistics, systematic literature review, GIS

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Authors: Lakmini Wijesooriya, Vicki Chalker, Jessica Day, Priyantha Perera, N. P. Sunil-Chandra

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M. pneumoniae has been identified as an etiology for exacerbation of asthma (EQA), although viruses play a major role in EOA. M. pneumoniae infection is treated empirically with macrolides, and its antibiotic sensitivity is not detected routinely. Characterization of the organism by genotyping and determination of macrolide resistance is important epidemiologically as it guides the empiric antibiotic treatment. To date, there is no such characterization of M. pneumoniae performed in Sri Lanka. The present study describes the characterization of M. pneumoniae detected from a child with EOA following a screening of 100 children with EOA. Of the hundred children with EOA, M. pneumoniae was identified only in one child by Real-Time polymerase chain reaction (PCR) test for identifying the community-acquired respiratory distress syndrome (CARDS) toxin nucleotide sequences. The M. pneumoniae identified from this patient underwent detection of macrolide resistance via conventional PCR, amplifying and sequencing the region of the 23S rDNA gene that contains single nucleotide polymorphisms that confer resistance. Genotyping of the isolate was performed via nested Multilocus Sequence Typing (MLST) in which eight (8) housekeeping genes (ppa, pgm, gyrB, gmk, glyA, atpA, arcC, and adk) were amplified via nested PCR followed by gene sequencing and analysis. As per MLST analysis, the M. pneumoniae was identified as sequence type 14 (ST14), and no mutations that confer resistance were detected. Resistance to macrolides in M. pneumoniae is an increasing problem globally. Establishing surveillance systems is the key to informing local prescriptions. In the absence of local surveillance data, antibiotics are started empirically. If the relevant microbiological samples are not obtained before antibiotic therapy, as in most occasions in children, the course of antibiotic is completed without a microbiological diagnosis. This happens more frequently in therapy for M. pneumoniae which is treated with a macrolide in most patients. Hence, it is important to understand the macrolide sensitivity of M. pneumoniae in the setting. The M. pneumoniae detected in the present study was macrolide sensitive. Further studies are needed to examine a larger dataset in Sri Lanka to determine macrolide resistance levels to inform the use of macrolides in children with EOA. The MLST type varies in different geographical settings, and it also provides a clue to the existence of macrolide resistance. The present study enhances the database of the global distribution of different genotypes of M. pneumoniae as this is the first such characterization performed with the increased number of samples to determine macrolide resistance level in Sri Lanka. M. pneumoniae detected from a child with exacerbation of asthma in Sri Lanka was characterized as ST14 by MLST and no mutations that confer resistance were detected.

Keywords: mycoplasma pneumoniae, Sri Lanka, characterization, macrolide resistance

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Authors: Gail Louw, Helena Boshoff, Taeksun Song, Clifton Barry

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Drug resistance in Mycobacterium tuberculosis is primarily attributed to mutations in target genes. These mutations incur a fitness cost and result in bacterial generations that are less fit, which subsequently acquire compensatory mutations to restore fitness. We hypothesize that mutations in specific drug target genes influence bacterial metabolism and cellular function, which affects its ability to develop subsequent resistance to additional agents. We aim to determine whether the sequential acquisition of drug resistance and specific mutations in a well-defined clinical M. tuberculosis strain promotes or limits the development of additional resistance. In vitro mutants resistant to pretomanid, linezolid, moxifloxacin, rifampicin and kanamycin were generated from a pan-susceptible clinical strain from the Beijing lineage. The resistant phenotypes to the anti-TB agents were confirmed by the broth microdilution assay and genetic mutations were identified by targeted gene sequencing. Growth of mono-resistant mutants was done in enriched medium for 14 days to assess in vitro fitness. Double resistant mutants were generated against anti-TB drug combinations at concentrations 5x and 10x the minimum inhibitory concentration. Subsequently, mutation frequencies for these anti-TB drugs in the different mono-resistant backgrounds were determined. The initial level of resistance and the mutation frequencies observed for the mono-resistant mutants were comparable to those previously reported. Targeted gene sequencing revealed the presence of known and clinically relevant mutations in the mutants resistant to linezolid, rifampicin, kanamycin and moxifloxacin. Significant growth defects were observed for mutants grown under in vitro conditions compared to the sensitive progenitor. Mutation frequencies determination in the mono-resistant mutants revealed a significant increase in mutation frequency against rifampicin and kanamycin, but a significant decrease in mutation frequency against linezolid and sutezolid. This suggests that these mono-resistant mutants are more prone to develop resistance to rifampicin and kanamycin, but less prone to develop resistance against linezolid and sutezolid. Even though kanamycin and linezolid both inhibit protein synthesis, these compounds target different subunits of the ribosome, thereby leading to different outcomes in terms of fitness in the mutants with impaired cellular function. These observations showed that oxazolidinone treatment is instrumental in limiting the development of multi-drug resistance in M. tuberculosis in vitro.

Keywords: oxazolidinones, mutations, resistance, tuberculosis

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Authors: Dayron Camilo Bermudez Mendoza

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Road transportation is a significant source of externalities, notably in terms of environmental degradation and the emission of pollutants. These emissions adversely affect public health, attributable to criteria pollutants like particulate matter (PM2.5 and PM10) and carbon monoxide (CO), and also contribute to climate change through the release of greenhouse gases, such as carbon dioxide (CO2). It is, therefore, crucial to quantify the emissions from mobile sources and develop a methodological framework for their economic valuation, aiding in the assessment of associated costs and informing policy decisions. The forthcoming congress will shed light on the externalities of transportation in Bogotá, showcasing methodologies and findings from the construction of emission inventories and their spatial analysis within the city. This research focuses on the economic valuation of emissions from mobile sources in Bogotá, employing methods like hedonic pricing and contingent valuation. Conducted within the urban confines of Bogotá, the study leverages demographic, transportation, and emission data sourced from the Mobility Survey, official emission inventories, and tailored estimates and measurements. The use of hedonic pricing and contingent valuation methodologies facilitates the estimation of the influence of transportation emissions on real estate values and gauges the willingness of Bogotá's residents to invest in reducing these emissions. The findings are anticipated to be instrumental in the formulation and execution of public policies aimed at emission reduction and air quality enhancement. In compiling the emission inventory, innovative data sources were identified to determine activity factors, including information from automotive diagnostic centers and used vehicle sales websites. The COPERT model was utilized to ascertain emission factors, requiring diverse inputs such as data from the national transit registry (RUNT), OpenStreetMap road network details, climatological data from the IDEAM portal, and Google API for speed analysis. Spatial disaggregation employed GIS tools and publicly available official spatial data. The development of the valuation methodology involved an exhaustive systematic review, utilizing platforms like the EVRI (Environmental Valuation Reference Inventory) portal and other relevant sources. The contingent valuation method was implemented via surveys in various public settings across the city, using a referendum-style approach for a sample of 400 residents. For the hedonic price valuation, an extensive database was developed, integrating data from several official sources and basing analyses on the per-square meter property values in each city block. The upcoming conference anticipates the presentation and publication of these results, embodying a multidisciplinary knowledge integration and culminating in a master's thesis.

Keywords: economic valuation, transport economics, pollutant emissions, urban transportation, sustainable mobility

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Authors: Boutheina Ben Abdelmoumen Mardassi, Salim Chibani, Safa Boujemaa, Amaury Vaysse, Julien Guglielmini, Elhem Yacoub

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Background and aim: Mycoplasma hominis (MH) is a pathogenic bacterium belonging to the Mollicutes class. It causes a wide range of gynecological infections and infertility among adults. Recently, we have explored for the first time the phylodistribution of Tunisian M. hominis clinical strains using an expanded MLST. We have demonstrated their distinction into two pure lineages, which each corresponding to a specific pathotype: genital infections and infertility. The aim of this project is to gain further insight into the evolutionary dynamics and the specific genetic factors that distinguish MH pathotypes Methods: Whole genome sequencing of Mycoplasma hominis clinical strains was performed using illumina Miseq. Denovo assembly was performed using a publicly available in-house pipeline. We used prokka to annotate the genomes, panaroo to generate the gene presence matrix and Jolytree to establish the phylogenetic tree. We used treeWAS to identify genetic loci associated with the pathothype of interest from the presence matrix and phylogenetic tree. Results: Our results revealed a clear categorization of the 62 MH clinical strains into two distinct genetic lineages, with each corresponding to a specific pathotype.; gynecological infections and infertility[AV1] . Genome annotation showed that GC content is ranging between 26 and 27%, which is a known characteristic of Mycoplasma genome. Housekeeping genes belonging to the core genome are highly conserved among our strains. TreeWas identified 4 virulence genes associated with the pathotype gynecological infection. encoding for asparagine--tRNA ligase, restriction endonuclease subunit S, Eco47II restriction endonuclease, and transcription regulator XRE (involved in tolerance to oxidative stress). Five genes have been identified that have a statistical association with infertility, tow lipoprotein, one hypothetical protein, a glycosyl transferase involved in capsule synthesis, and pyruvate kinase involved in biofilm formation. All strains harbored an efflux pomp that belongs to the family of multidrug resistance ABC transporter, which confers resistance to a wide range of antibiotics. Indeed many adhesion factors and lipoproteins (p120, p120', p60, p80, Vaa) have been checked and confirmed in our strains with a relatively 99 % to 96 % conserved domain and hypervariable domain that represent 1 to 4 % of the reference sequence extracted from gene bank. Conclusion: In summary, this study led to the identification of specific genetic loci associated with distinct pathotypes in M hominis.

Keywords: mycoplasma hominis, infertility, gynecological infections, virulence genes, antibiotic resistance

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Authors: Liyun Chang, Cheng-Hsiang Tsai

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To ensure the radiation precisely delivering to the target of cancer patients, the linear accelerator equipped with the pretreatment on-board imaging system is introduced and through it the patient setup is verified before the daily treatment. New generation radiotherapy using beam-intensity modulation, usually associated the treatment with steep dose gradients, claimed to have achieved both a higher degree of dose conformation in the targets and a further reduction of toxicity in normal tissues. However, this benefit is counterproductive if the beam is delivered imprecisely. To avoid shooting critical organs or normal tissues rather than the target, it is very important to carry out the quality assurance (QA) of this on-board imaging system. The QA of the On-Board Imager® (OBI) system of one Varian Clinac-iX linear accelerator was performed through our procedures modified from a relevant report and AAPM TG142. Two image modalities, 2D radiography and 3D cone-beam computed tomography (CBCT), of the OBI system were examined. The daily and monthly QA was executed for five months in the categories of safety, geometrical accuracy and image quality. A marker phantom and a blade calibration plate were used for the QA of geometrical accuracy, while the Leeds phantom and Catphan 504 phantom were used in the QA of radiographic and CBCT image quality, respectively. The reference images were generated through a GE LightSpeed CT simulator with an ADAC Pinnacle treatment planning system. Finally, the image quality was analyzed via an OsiriX medical imaging system. For the geometrical accuracy test, the average deviations of the OBI isocenter in each direction are less than 0.6 mm with uncertainties less than 0.2 mm, while all the other items have the displacements less than 1 mm. For radiographic image quality, the spatial resolution is 1.6 lp/cm with contrasts less than 2.2%. The spatial resolution, low contrast, and HU homogenous of CBCT are larger than 6 lp/cm, less than 1% and within 20 HU, respectively. All tests are within the criteria, except the HU value of Teflon measured with the full fan mode exceeding the suggested value that could be due to itself high HU value and needed to be rechecked. The OBI system in our facility was then demonstrated to be reliable with stable image quality. The QA of OBI system is really necessary to achieve the best treatment for a patient.

Keywords: CBCT, image quality, quality assurance, OBI

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Authors: S. J. Kim, Y. J. Yoo

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Slack-tide sampling was carried out at seven stations at high and low tides for a tidal cycle, in summer (7, 8, 9) and fall (10), 2016 to determine the differences of water quality according to tides in Masan Bay. The data were analyzed by Pearson correlation and factor analysis. The mixing state of all the water quality components investigated is well explained by the correlation with salinity (SAL). Turbidity (TURB), dissolved silica (DSi), nitrite and nitrate nitrogen (NNN) and total nitrogen (TN), which find their way into the bay from the streams and have no internal source and sink reaction, showed a strong negative correlation with SAL at low tide, indicating the property of conservative mixing. On the contrary, in summer and fall, dissolved oxygen (DO), hydrogen sulfide (H2S) and chemical oxygen demand with KMnO4 (CODMn) of the surface and bottom water, which were sensitive to an internal source and sink reaction, showed no significant correlation with SAL at high and low tides. The remaining water quality parameters showed a conservative or a non-conservative mixing pattern depending on the mixing characteristics at high and low tides, determined by the functional relationship between the changes of the flushing time and the changes of the characteristics of water quality components of the end-members in the bay. Factor analysis performed on the concentration difference data sets between high and low tides helped in identifying the principal latent variables for them. The concentration differences varied spatially and temporally. Principal factors (PFs) scores plots for each monitoring situation showed high associations of the variations to the monitoring sites. At sampling station 1 (ST1), temperature (TEMP), SAL, DSi, TURB, NNN and TN of the surface water in summer, TEMP, SAL, DSi, DO, TURB, NNN, TN, reactive soluble phosphorus (RSP) and total phosphorus (TP) of the bottom water in summer, TEMP, pH, SAL, DSi, DO, TURB, CODMn, particulate organic carbon (POC), ammonia nitrogen (AMN), NNN, TN and fecal coliform (FC) of the surface water in fall, TEMP, pH, SAL, DSi, H2S, TURB, CODMn, AMN, NNN and TN of the bottom water in fall commonly showed up as the most significant parameters and the large concentration differences between high and low tides. At other stations, the significant parameters showed differently according to the spatial and temporal variations of mixing pattern in the bay. In fact, there is no estuary that always maintains steady-state flow conditions. The mixing regime of an estuary might be changed at any time from linear to non-linear, due to the change of flushing time according to the combination of hydrogeometric properties, inflow of freshwater and tidal action, And furthermore the change of end-member conditions due to the internal sinks and sources makes the occurrence of concentration difference inevitable. Therefore, when investigating the water quality of the estuary, it is necessary to take a sampling method considering the tide to obtain average water quality data.

Keywords: conservative mixing, end-member, factor analysis, flushing time, high and low tide, latent variables, non-conservative mixing, slack-tide sampling, spatial and temporal variations, surface and bottom water

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Authors: Jevonte Abioye, Dylan Savary

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The aim of this research is to present a disaggregated geostatistical analysis of the subnational provincial trends of child mortality variation in Zimbabwe from a child health policy perspective. Soon after gaining independence in 1980, the government embarked on efforts towards promoting equitable health care, namely through the provision of primary health care. Government intervention programmes brought hope and promise, but achieving equity in primary health care coverage was hindered by previous existing disparities in maternal health care disproportionately concentrated in urban settings to the detriment of rural communities. The article highlights policies and programs adopted by the government during the millennium development goals period between 1990-2015 as a response to the inequities that characterised the country’s maternal health care. A longitudinal comparative method for a spatial variation on child mortality rates across provinces is developed based on geostatistical analysis. Cross-sectional and time-series data was extracted from the World Health Organisation (WHO) global health observatory data repository, demographic health survey reports, and previous academic and technical publications. Results suggest that although health care policy was uniform across provinces, not all provinces received the same antenatal and perinatal services. Accordingly, provincial rates of child mortality growth between 1994 and 2015 varied significantly. Evidence on the trends of child mortality rates and maternal health policies in Zimbabwe can be valuable for public child health policy planning and public service delivery design both in Zimbabwe and across developing countries pursuing the sustainable development agenda.

Keywords: antenatal care, perinatal care, infant mortality rate, neonatal mortality rate, under-five mortality rate, millennium development goals, sustainable development agenda

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Authors: Sibel Ecemiş Kılıç, Muhammed Aydoğan

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The rapid development of culture tourism has drawn attention to conserving cultural values especially by developing countries that would like to benefit from the economic contribution this type of tourism attracts. Tourism can have both positive and negative outcomes for historical settlements and their residents. The accommodation-purposed rehabilitation and revitalization project in “Sigacik Old City Zone” are to be discussed with spatial, economic, social and organizational dimensions. It is aimed to evaluate the relationship between the development of tourism and sustainable heritage conservation.

Keywords: Sığacık, urban conservation, sustainable tourism, Seferihisar

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Authors: Cristian Cazacu, Bela Kobulniczky

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Even though nowadays the median area of the Bucharest’s Sector 1 owns one of the best reputations in terms of quality of life level, the problems in urban planning from the last twenty years, as well as those related to the urban environment, became more and more obvious and shrill. And all this happened as long as non-compliance with urban and spatial planning laws, corroborated with uncontrolled territorial expansion on certain areas and faulty management of public and private spaces were more acute. The action of all these factors has been felt more and more strongly in the territory in the last twenty years, generating the degradation of the quality of the urban environment and affecting in parallel the general level of the inhabitants¬’ quality of life. Our methodology is based on analyzing a wide range of environmental parameters and it is also based on using advanced resources and skills for mapping planning and environmental dysfunctions as well as the possibility of integrating information into GIS programs, all data sets corroborated with problems related to spatial planning management and inaccuracies of the urbanistic sector. In the end, we managed to obtain a calculated and realistic image of the dysfunctions and a quantitative view of their magnitude in the territory. We also succeeded to create a full general map of the degree of degradation of the urban environment by typologies of urban tissues. Moreover, the methods applied by us can also be used globally to calculate and create realistic images and intelligent maps over the quality of the environment in areas larger than this one. Our study shows that environmental degradation occurred differently in the urban tissues from our study area, depending on several factors, reviewing the faulty way in which the processes of recovery / urban regeneration of the gap in recent years have led to the creation of new territorial dysfunctions. The general, centralized results show that the analyzed space has a much wider range of problems than initially thought, although notoriety and social etiquette place them far above other spaces from the same city of study.

Keywords: environment, GIS, planning, urban tissues

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Authors: Likith Reddy Pinninti, Fredrik Ribsskog Staven, Leslie Robert Noble, Jorge Manuel de Oliveira Fernandes, Deepti Manjari Patel, Torstein Kristensen

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Understanding fish behavior is essential to improve animal welfare in aquaculture research. Behavioral traits can have a strong influence on fish health and habituation. To identify the genes and biological pathways responsible for lumpfish behavior, we performed an experiment to understand the interspecies relationship (mutualism) between the lumpfish and salmon. Also, we tested the correlation between the gene expression data vs. observational/physiological data to know the essential genes that trigger stress and swimming behavior in lumpfish. After the de novo assembly of the brain transcriptome, all the samples were individually mapped to the available lumpfish (Cyclopterus lumpus L.) primary genome assembly (fCycLum1.pri, GCF_009769545.1). Out of ~16749 genes expressed in brain samples, we found 267 genes to be statistically significant (P > 0.05) found only in odor and control (1), model and control (41) and salmon and control (225) groups. However, genes with |LogFC| ≥0.5 were found to be only eight; these are considered as differentially expressed genes (DEG’s). Though, we are unable to find the differential genes related to the behavioral traits from RNA-Seq data analysis. From the correlation analysis, between the gene expression data vs. observational/physiological data (serotonin (5HT), dopamine (DA), 3,4-Dihydroxyphenylacetic acid (DOPAC), 5-hydroxy indole acetic acid (5-HIAA), Noradrenaline (NORAD)). We found 2495 genes found to be significant (P > 0.05) and among these, 1587 genes are positively correlated with the Noradrenaline (NORAD) hormone group. This suggests that Noradrenaline is triggering the change in pigmentation and skin color in lumpfish. Genes related to behavioral traits like rhythmic, locomotory, feeding, visual, pigmentation, stress, response to other organisms, taxis, dopamine synthesis and other neurotransmitter synthesis-related genes were obtained from the correlation analysis. In KEGG pathway enrichment analysis, we find important pathways, like the calcium signaling pathway and adrenergic signaling in cardiomyocytes, both involved in cell signaling, behavior, emotion, and stress. Calcium is an essential signaling molecule in the brain cells; it could affect the behavior of fish. Our results suggest that changes in calcium homeostasis and adrenergic receptor binding activity lead to changes in fish behavior during stress.

Keywords: behavior, De novo, lumpfish, salmon

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Authors: Jamileh Ahmed, Helena Hernandez, Gabriel De Erausquin

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H1N1 virus susceptibility of iPSC-derived DA neurons from schizophrenia patients and controls will compared. C57/BL-6 fibroblasts were reprogrammed into iPSCs using a lenti-viral vector containing SOKM genes. Pluripotency verification with the AP assay and immunocytochemistry ensured iPSC presence. The experimental outcome of ISPCs from DA neuron differentiation will be discussed in the Results section. Fibroblasts from patients and controls will be reprogrammed into iPSCs using a sendai-virus vector containing SOKM. IPSCs will be characterized using the AP assay, immunocytochemistry and RT-PCR. IPSCs will then be differentiated into DA neurons. Gene methylation will be compared for both groups with custom-designed microarrays.

Keywords: schizophrenia, iPSCs, stem cells, neuroscience

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Authors: Mona Mihailescu, Rebeca Tudor, Irina A. Paun, Cristian Kusko, Eugen I. Scarlat, Mihai Kusko

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Specific intensity distributions in the laser beams are required in many fields: optical communications, material processing, microscopy, optical tweezers. In optical communications, the information embedded in specific beams and the superposition of multiple beams can be used to increase the capacity of the communication channels, employing spatial modulation as an additional degree of freedom, besides already available polarization and wavelength multiplexing. In this regard, optical vortices present interest due to their potential to carry independent data which can be multiplexed at the transmitter and demultiplexed at the receiver. Also, in the literature were studied their combinations: 1) axial or perpendicular superposition of multiple optical vortices or 2) with other laser beam types: Bessel, Airy. Optical vortices, characterized by stationary ring-shape intensity and rotating phase, are achieved using computer generated holograms (CGH) obtained by simulating the interference between a tilted plane wave and a wave passing through a helical phase object. Here, we propose a method to combine information through the reunion of two CGHs. One is obtained using the helical phase distribution, characterized by its topological charge, m. The other is obtained using conical phase distribution, characterized by its radial factor, r0. Each CGH is obtained using plane wave with different tilts: km and kr for CGH generated from helical phase object and from conical phase object, respectively. These reunions of two CGHs are calculated to be phase optical elements, addressed on the liquid crystal display of a spatial light modulator, to optically process the incident beam for investigations of the diffracted intensity pattern in far field. For parallel reunion of two CGHs and high values of the ratio between km and kr, the bright ring from the first diffraction order, specific for optical vortices, is changed in an asymmetric intensity pattern: a number of circle arcs. Both diffraction orders (+1 and -1) are asymmetrical relative to each other. In different planes along the optical axis, it is observed that this asymmetric intensity pattern rotates around its centre: in the +1 diffraction order the rotation is anticlockwise and in the -1 diffraction order, the rotation is clockwise. The relation between m and r0 controls the diameter of the circle arcs and the ratio between km and kr controls the number of arcs. For perpendicular reunion of the two CGHs and low values of the ratio between km and kr, the optical vortices are multiplied and focalized in different planes, depending on the radial parameter. The first diffraction order contains information about both phase objects. It is incident on the phase masks placed at the receiver, computed using the opposite values for topological charge or for the radial parameter and displayed successively. In all, the proposed method is exploited in terms of constructive parameters, for the possibility offered by the combination of different types of beams which can be used in robust optical communications.

Keywords: asymmetrical diffraction orders, computer generated holograms, conical phase distribution, optical vortices, spatial light modulator

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Authors: Asif Zaman, Moinul Islam Zaber, Amin Ahsan Ali

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In recent years of industrialization, the South Asian countries are being affected by air pollution due to a severe increase in fine particulate matter 2.5 (PM₂.₅). Among them, Bangladesh is one of the most polluting countries. In this paper, statistical analyses were conducted on the time series of PM₂.₅ from various districts in Bangladesh, mostly around Dhaka city. Research has been conducted on the dynamic interactions and relationships between PM₂.₅ concentrations in different zones. The study is conducted toward understanding the characteristics of PM₂.₅, such as spatial-temporal characterization, correlation of other contributors behind air pollution such as human activities, driving factors and environmental casualties. Clustering on the data gave an insight on the districts groups based on their AQI frequency as representative districts. Seasonality analysis on hourly and monthly frequency found higher concentration of fine particles in nighttime and winter season, respectively. Cross correlation analysis discovered a phenomenon of correlations among cities based on time-lagged series of air particle readings and visualization framework is developed for observing interaction in PM₂.₅ concentrations between cities. Significant time-lagged correlations were discovered between the PM₂.₅ time series in different city groups throughout the country by cross correlation analysis. Additionally, seasonal heatmaps depict that the pooled series correlations are less significant in warmer months, and among cities of greater geographic distance as well as time lag magnitude and direction of the best shifted correlated particulate matter time series among districts change seasonally. The geographic map visualization demonstrates spatial behaviour of air pollution among districts around Dhaka city and the significant effect of wind direction as the vital actor on correlated shifted time series. The visualization framework has multipurpose usage from gathering insight of general and seasonal air quality of Bangladesh to determining the pathway of regional transportation of air pollution.

Keywords: air quality, particles, cross correlation, seasonality

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Authors: Fereydoon Bondarian, Samira Shaygan

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Today, many nutritionists recommend the consumption of plants, fruits, and vegetables to provide the antioxidants needed by the body because the use of plant antioxidants usually causes fewer side effects and better treatment. Natural antioxidants increase the power of plasma antioxidants and reduce the incidence of some diseases, such as cancer. Bad lifestyles and environmental factors play an important role in increasing the incidence of cancer. In this study, different extracts of white teas taken from two types of tea available in Iran (clone 100 and Chinese hybrid) due to the presence of a hydroxyl functional group in their structure to inhibit free radicals and anticancer properties, using 3 aqueous, methanolic and aqueous-methanolic methods were used. The total polyphenolic content was calculated using the Folin-Ciocalcu method, and the percentage of inhibition and trapping of free radicals in each of the extracts was calculated using the DPPH method. With the help of high-performance liquid chromatography, a small amount of each catechin in the tea samples was obtained. Clone 100 white tea was found to be the best sample of tea in terms of all the examined attributes (total polyphenol content, antioxidant properties, and individual amount of each catechin). The results showed that aqueous and aqueous-methanolic extracts of Clone 100 white tea have the highest total polyphenol content with 27.59±0.08 and 36.67±0.54 (equivalent gallic acid per gram dry weight of leaves), respectively. Due to having the highest level of different groups of catechin compounds, these extracts have the highest property of inhibiting and trapping free radicals with 66.61±0.27 and 71.74±0.27% (mg/l) of the extracted sample against ascorbic acid). Using the MTT test, the inhibitory effect of clone 100 white tea extract in inhibiting the growth of HCT-116 colon cancer cells was investigated and the best time and concentration treatments were 500, 150 and 1000 micrograms in 8, 16 and 24 hours, respectively. To investigate gene expression changes, selected genes, including tumorigenic genes, proto-oncogenes, tumor suppressors, and genes involved in apoptosis, were selected and analyzed using the real-time PCR method and in the presence of concentrations obtained for white tea. White tea extract at a concentration of 1000 μg/ml 3 times 16, 8, and 24 hours showed the highest growth inhibition in cancer cells with 53.27, 55.8, and 86.06%. The concentration of 1000 μg/ml aqueous extract of white tea under 24-hour treatment increased the expression of tumor suppressor genes compared to the normal sample.

Keywords: catechin, gene expression, suppressor genes, colon cell line

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Authors: Seok Woo Chang, Kee Yeon Kum, Kwang Shik Bae, WooCheol Lee

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Aim: The objective of this study was to compare the biocompatibilities and mineralization potential of ProRoot MTA and newly developed calcium phosphate based cement, Capseal. Materials and Methods: The biocompatibilities and mineralization-related gene expressions (Bone sialoprotein (BSP) and osteocalcin (OCN)) of ProRoot MTA and Capseal were also compared by a methylthiazol tetrazolium (MTT) assay and reverse transcription-polymerization chain reaction (RT-PCR) analysis on 1, 3, and 7 days, respectively. Empty rings were used as control group. The results were statistically analyzed by Kruskal-Wallis test with a Bonferroni correction. P-value of < 0.05 was considered significant. Results: The biocompatibilities of ProRoot MTA and Capseal were equally favorable. ProRoot MTA and Capseal affected the messenger RNA expression of osteocalcin and osteonectin. Conclusions: Based on the results, both ProRoot MTA and Capseal could be a useful biomaterial in clinical endodontics.

Keywords: biocompatibility, calcium silicate cement, MTT, RT-PCR

Procedia PDF Downloads 385

Authors: Valeria Velasco, Ana M. Bonilla, José L. Vergara, Alcides Lofa, Jorge Campos, Pedro Rojas-García

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Staphylococcus aureus is both commensal bacterium and opportunistic pathogen that can cause different diseases in humans and can rapidly develop antimicrobial resistance. Since this bacterium has the ability to colonize the nares and skin of humans and animals, there is a risk of contamination of food in different steps of the food chain supply. Emerging strains have been detected in food-producing animals and meat, such as methicillin-resistant S. aureus (MRSA). The aim of this study was to determine the prevalence and oxacillin susceptibility of S. aureus in the pork chain supply in Chile and to suggest some natural antimicrobials for control. A total of 487 samples were collected from pigs (n=332), carcasses (n=85), and retail pork meat (n=70). Presumptive S. aureus colonies were isolated by selective enrichment and culture media. The confirmation was carried out by biochemical testing (Api® Staph) and molecular technique PCR (detection of nuc and mecA genes, associated with S. aureus and methicillin resistance, respectively). The oxacillin (β-lactam antibiotic that replaced methicillin) susceptibility was assessed by minimum inhibitory concentration (MIC) using the Epsilometer test (Etest). A preliminary assay was carried out to test thymol, carvacrol, oregano essential oil (Origanum vulgare L.), Maqui or Chilean wineberry extract (Aristotelia chilensis (Mol.) Stuntz) as anti-staphylococcal agents using the disc diffusion method at different concentrations. The overall prevalence of S. aureus in the pork chain supply reached 33.9%. A higher prevalence of S. aureus was determined in carcasses (56.5%) than in pigs (28.3%) and pork meat (32.9%) (P ≤ 0.05). The prevalence of S. aureus in pigs sampled at farms (40.6%) was higher than in pigs sampled at slaughterhouses (23.3%) (P ≤ 0.05). The contamination of no packaged meat with S. aureus (43.1%) was higher than in packaged meat (5.3%) (P ≤ 0.05). The mecA gene was not detected in S. aureus strains isolated in this study. Two S. aureus strains exhibited oxacillin resistance (MIC ≥ 4µg/mL). Anti-staphylococcal activity was detected in solutions of thymol, carvacrol, and oregano essential oil at all concentrations tested. No anti-staphylococcal activity was detected in Maqui extract. Finally, S. aureus is present in the pork chain supply in Chile. Although the mecA gene was not detected, oxacillin resistance was found in S. aureus and could be attributed to another resistance mechanism. Thymol, carvacrol, and oregano essential oil could be used as anti-staphylococcal agents at low concentrations. Research project Fondecyt No. 11140379.

Keywords: antimicrobials, mecA gen, nuc gen, oxacillin susceptibility, pork meat

Procedia PDF Downloads 218

Authors: Senol Dogan, Gunay Karli

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Identification of relevant publications based on a Medline query is time-consuming and error-prone. An all based process has the potential to solve this problem without any manual work. To the best of our knowledge, our study is the first to investigate the ability of machine learning to identify relevant articles accurately. 5 different machine learning algorithms were tested using 23 predictors based on several metadata fields attached to publications. We find that the Boosted model is the best-performing algorithm and its overall accuracy is 96%. In addition, specificity and sensitivity of the algorithm is 97 and 93%, respectively. As a result of the work, we understood that we can apply the same procedure to understand cancer gene expression big data.

Keywords: prediction of publications, machine learning, algorithms, bariatric surgery, comparison of algorithms, boosted, tree, logistic regression, ANN model

Procedia PDF Downloads 199

Authors: Thomas Louis, Irina Primac, Florent Morfoisse, Tania Durre, Silvia Blacher, Agnes Noel

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In vitro and in vivo lymphangiogenesis assays are essential for the identification of potential lymphangiogenic agents and the screening of pharmacological inhibitors. In the present study, we analyse three biological models: in vitro lymphatic endothelial cell spheroids, in vivo ear sponge assay, and in vivo lymph node colonisation by tumour cells. These assays provide suitable 3D models to test pro- and anti-lymphangiogenic factors or drugs. 3D images were acquired by confocal laser scanning and light sheet fluorescence microscopy. Virtual scan microscopy followed by 3D reconstruction by image aligning methods was also used to obtain 3D images of whole large sponge and ganglion samples. 3D reconstruction, image segmentation, skeletonisation, and other image processing algorithms are described. Fixed and time-lapse imaging techniques are used to analyse lymphatic endothelial cell spheroids behaviour. The study of cell spatial distribution in spheroid models enables to detect interactions between cells and to identify invasion hierarchy and guidance patterns. Global measurements such as volume, length, and density of lymphatic vessels are measured in both in vivo models. Branching density and tortuosity evaluation are also proposed to determine structure complexity. Those properties combined with vessel spatial distribution are evaluated in order to determine lymphangiogenesis extent. Lymphatic endothelial cell invasion and lymphangiogenesis were evaluated under various experimental conditions. The comparison of these conditions enables to identify lymphangiogenic agents and to better comprehend their roles in the lymphangiogenesis process. The proposed methodology is validated by its application on the three presented models.

Keywords: 3D image segmentation, 3D image skeletonisation, cell invasion, confocal microscopy, ear sponges, light sheet microscopy, lymph nodes, lymphangiogenesis, spheroids

Procedia PDF Downloads 363

Authors: Yanqun Li, Hong Geng

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The rapid urbanization process taking big cities as the main body leads to the unequal configuration of urban and rural areas in the aspects of land supply, industrial division of labor, service supply and space allocation, and induces the shrinking characterization of service energy, industrial system and population vitality in small towns. As an important spatial unit in the spectrum of urbanization that serves, connects and couples urban and rural areas, the shrinking phenomenon faced by small towns has an important influence on the healthy development of urbanization. Based on the census of small towns in Wuhan metropolitan area, we have found that the shrinking of small towns is a passive contraction of elastic tension under the squeeze in cities. Once affected by the external forces such as policy regulation, planning guidance, and population return, small towns will achieve expansion and growth. Based on the theory of complex adaptive systems, this paper comprehensively constructs the development index evaluation system of small towns from five aspects of population, economy, space, society and ecology, measures the shrinking level of small towns, further analyzes the shrinking characteristics of small towns, and identifies whether the shrinking is elastic or not. And then this paper measures the resilience ability index of small town contract from the above-mentioned five aspects. Finally, this paper proposes an adaptive mechanism of urban-rural interaction evolution under fine division of labor to response the passive shrinking in small towns of Wuhan. Based on the above, the paper creatively puts forward the planning response measures of the small towns on the aspects of spatial layout, function orientation and service support, which can provide reference for other regions.

Keywords: complex adaptive systems, resiliency shrinking, adaptation mechanism, planning response

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Authors: Christelle E. Chua, Alicia L. Ho

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The development of a panel of differential gene expression signatures has been of interest in the field of biomarker discovery for radiation exposure. In the absence of the availability of exposed human subjects, lymphocyte cell lines have often been used as a surrogate to human whole blood, when performing ex vivo irradiation studies. The extent of variation between different lymphocyte cell lines is currently unclear, especially with regard to the expression of extracellular miRNA. This study compares the expression profile of extracellular miRNA isolated from different lymphocyte cell lines. It also compares the profile of miRNA obtained when different exosome isolation kits are used. Lymphocyte cell lines were created using lymphocytes isolated from healthy adult males of similar racial descent (Chinese American and Chinese Singaporean) and immortalised with Epstein-Barr virus. The cell lines were cultured in exosome-free cell culture media for 72h and the cell culture supernatant was removed for exosome isolation. Two exosome isolation kits were used. Total exosome isolation reagent (TEIR, ThermoFisher) is a polyethylene glycol (PEG)-based exosome precipitation kit, while ExoSpin (ES, Cell Guidance Systems) is a PEG-based exosome precipitation kit that includes an additional size exclusion chromatography step. miRNA from the isolated exosomes were isolated using miRNEASY minikit (Qiagen) and analysed using nCounter miRNA assay (Nanostring). Principal component analysis (PCA) results suggested that the overall extracellular miRNA expression profile differed between the lymphocyte cell line originating from the Chinese American donor and the cell line originating from the Chinese Singaporean donor. As the gender, age and racial origins of both donors are similar, this may suggest that there are other genetic or epigenetic differences that account for the variation in extracellular miRNA gene expression in lymphocyte cell lines. However, statistical analysis showed that only 3 miRNA genes had a fold difference > 2 at p < 0.05, suggesting that the differences may not be of that great a significance as to impact overall conclusions drawn from different cell lines. Subsequent analysis using cell lines from other donors will give further insight into the reproducibility of results when difference cell lines are used. PCA results also suggested that the method of exosome isolation impacted the expression profile. 107 miRNA had a fold difference > 2 at p < 0.05. This suggests that the inclusion of an additional size exclusion chromatography step altered the subset of the extracellular vesicles that were isolated. In conclusion, these results suggest that extracellular miRNA can be isolated and analysed from exosomes derived from lymphocyte cell lines. However, care must be taken in the choice of cell line and method of exosome isolation used.

Keywords: biomarker, extracellular miRNA, isolation methods, lymphocyte cell line

Procedia PDF Downloads 189

Authors: Alexander Norbach

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The script in this paper describes the use of advanced simulation environment using electronic systems (Microcontroller, Operational Amplifiers, and FPGA). The simulation may be used for all dynamic systems with the diffusion and the ionisation behaviour also. By additionally required observer structure, the system works with parallel real-time simulation based on diffusion model and the state-space representation for other dynamics. The proposed deposited model may be used for electrodynamic effects, including ionising effects and eddy current distribution also. With the script and proposed method, it is possible to calculate the spatial distribution of the electromagnetic fields in real-time. For further purpose, the spatial temperature distribution may be used also. With upon system, the uncertainties, unknown initial states and disturbances may be determined. This provides the estimation of the more precise system states for the required system, and additionally, the estimation of the ionising disturbances that occur due to radiation effects. The results have shown that a system can be also developed and adopted specifically for space systems with the real-time calculation of the radiation effects only. Electronic systems can take damage caused by impacts with charged particle flux in space or radiation environment. In order to be able to react to these processes, it must be calculated within a shorter time that ionising radiation and dose is present. All available sensors shall be used to observe the spatial distributions. By measured value of size and known location of the sensors, the entire distribution can be calculated retroactively or more accurately. With the formation, the type of ionisation and the direct effect to the systems and thus possible prevent processes can be activated up to the shutdown. The results show possibilities to perform more qualitative and faster simulations independent of kind of systems space-systems and radiation environment also. The paper gives additionally an overview of the diffusion effects and their mechanisms. For the modelling and derivation of equations, the extended current equation is used. The size K represents the proposed charge density drifting vector. The extended diffusion equation was derived and shows the quantising character and has similar law like the Klein-Gordon equation. These kinds of PDE's (Partial Differential Equations) are analytically solvable by giving initial distribution conditions (Cauchy problem) and boundary conditions (Dirichlet boundary condition). For a simpler structure, a transfer function for B- and E- fields was analytically calculated. With known discretised responses g₁(k·Ts) and g₂(k·Ts), the electric current or voltage may be calculated using a convolution; g₁ is the direct function and g₂ is a recursive function. The analytical results are good enough for calculation of fields with diffusion effects. Within the scope of this work, a proposed model of the consideration of the electromagnetic diffusion effects of arbitrary current 'waveforms' has been developed. The advantage of the proposed calculation of diffusion is the real-time capability, which is not really possible with the FEM programs available today. It makes sense in the further course of research to use these methods and to investigate them thoroughly.

Keywords: advanced observer, electrodynamics, systems, diffusion, partial differential equations, solver

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Authors: Fakhrosadat Sajjadian

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The majority of deaths in cancer patients are caused by distant metastasis. Breast cancer shows a unique spread pattern, often affecting bone, liver, lung, and brain. Breast cancer can be categorized into various subtypes according to gene expression patterns, and these subtypes exhibit specific preferences for organs where metastasis occurs. Breast tumors with luminal characteristics have a preference for spreading to the bone, whereas basal-like breast cancer (BLBC) shows a tendency to metastasize to the lungs. Still, the mechanisms behind this particular pattern of metastasis in organs have yet to be fully understood. In this evaluation, we will outline the latest progress in molecular signaling pathways and treatment methods for breast cancer lung metastasis.

Keywords: lung cancer, liver cancer, diagnosis, BLBC, metastasis

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Authors: Tiberiu Boros, Angela Ionita, Maria Visan

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Wildfires are one of the frequent and uncontrollable phenomena that currently affect large areas of the world where the climate, geographic and social conditions make it impossible to prevent and control such events. In this paper we introduce the ground concepts that lie behind the SIAFIM (Satellite Image Analysis for Fire Monitoring) project in order to create a context and we introduce a set of newly created tools that are external to the project but inherently in interventions and complex decision making based on geospatial information and spatial data infrastructures.

Keywords: wildfire, forest fire, natural language processing, mobile applications, communication, GPS

Procedia PDF Downloads 570