Faculty of engineering, Design and Technology
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- ItemBiologically directed environmental monitoring, fate, and transport of estrogenic endocrine disrupting compounds in water: A review(Elsevier Publications, 2006) Campbell, Chris G.; Borglin, Sharon E.; Green, F. Bailey; Grayson, Allen; Wozei, Eleanor; Stringfellow, William T.Endocrine disrupting compounds (EDCs) are contaminants that may be hormonally active at low concentrations and are emerging as a major concern for water quality. Estrogenic EDCs (e-EDCs) are a subclass of EDCs that, when organisms are exposed to them, function as estrogens. Given that there are numerous e-EDCs that can negatively affect humans and wildlife, general screening techniques like biologically based assays (BBAs) may provide major advantages by estimating the total estrogenic effects of many e-EDCs in the environment. These techniques may potentially be adapted for field portable biologically directed sampling and analyses. This article summarizes available BBAs used to measure estrogenic e-EDCs in the environmental samples and also presents results relating to fate and transport of e-EDCs. Estrogenic EDCs appear to be almost ubiquitous in the environment, despite low solubility and high affinity of organic matter. Potential transport mechanisms may include: (1) transport of more soluble precursors, (2) colloid facilitated transport, (3) enhanced solubility through elevated pH, and (4) the formation of micelles by longer-chain ethoxylates. Due to their persistent and ubiquitous nature, source control strategies for e-EDCs may reduce influent concentration to wastewater treatment plants so that the post treatment effluent will decrease concentrations to estrogenically inactive levels. Alternatively if source reduction is not possible, then more testing is needed on tertiary treatment technologies and treatment efficiencies for e-EDCs. There is still a need for research on remediation and restoration approaches for habitats disturbed by elevated e-EDC concentrations.
- ItemDetecting estrogenic activity in water samples with estrogen-sensitive yeast cells using spectrophotometry and fluorescence microscopy(2006-03) Wozei, Eleanor; Holman, H-Y.N.; Hermanowicz, S.W.; Borglin, S.Environmental estrogens are environmental contaminants that can mimic the biological activities of the female hormone estrogen in the endocrine system, i.e. they act as endocrine disrupters. Several substances are reported to have estrogen-like activity or estrogenic activity. These include steroid hormones, synthetic estrogens (xenoestrogens), environmental pollutants and phytoestrogens (plant estrogens). Using the chromogenic substrate ortho-nitrophenyl-β-D-galactopyranoside (ONPG) we show that an estrogen-sensitive yeast strain RMY/ER-ERE, with human estrogen receptor (hERα) gene and the lacZ gene which encodes the enzyme β-galactosidase, is able to detect estrogenic activity in water samples over a wide range of spiked concentrations of the hormonal estrogen 17β-estradiol (E2). Ortho-nitrophenol (ONP), the yellow product of this assay can be detected using spectrophotometry but requires cell lysis to release the enzyme and allow product formation. We improved this aspect in a fluorogenic assay by using fluorescein di-β-D galactopyranoside (FDG) as a substrate. The product was visualized using fluorescence microscopy without the need to kill, fix or lyse the cells. We show that in live yeast cells, the uptake of E2 and the subsequent production of β-galactosidase enzyme occur quite rapidly, with maximum enzyme-catalyzed fluorescent product formation evident after about 30 minutes of exposure to E2. The fluorogenic assay was applied to a selection of estrogenic compounds and the Synchrotron-based Fourier transform infrared (SR-FTIR) spectra of the cells obtained to better understand the yeast whole cell response to the compounds. The fluorogenic assay is most sensitive to E2, but the SR-FTIR spectra suggest that the cells respond to all the estrogenic compounds tested even when no fluorescent response was detected. These findings are promising and may shorten the duration of environmental water screening and monitoring regimes using yeast-based estrogen assays, and the development of biosensors for environmental estrogens designed to complement quantification methods.
- ItemApplication of a yeast-based assay protocol developed to monitor total oestrogenic activity induced by 17β-oestradiol in activated sludge supernatants from batch experiments(Lawrence Berkeley National Laboratory, 2006-04-11) Wozei, Eleanor; Hermanowicz, SWBatch experiments were carried out with activated sludge from laboratory reactors and a full-scale treatment plant spiked with 17β-oestradiol (E2). An oestrogen-sensitive yeast-based assay protocol, described in detail in a related publication, was used to measure reduction of E2-induced total oestrogenic activity from the sludge supernatant over a 15 d period after which the sludge was re-spiked to check for possible enhancement of reduction by pre-exposed sludge during an additional 15 d period. The reduction was generally improved by increasing sludge solids concentrations and by continuous mixing. For a 100 ngE2/ℓ spike there was >40% reduction of oestrogenic activity within 15 d, which improved to >70% by pre-exposing the sludge. The oestrogenic activity produced by a dose of 100 μgE2/ℓ was readily removed by most sludges within 15 d. How¬ever, re-spiking the activated sludge with the same E2 concentration caused some sludges to lose reduction capacity.
- ItemDeveloping a yeast-based assay protocol to monitor total oestrogenic activity induced by 17β-oestradiol in activated sludge supernatants from batch experiments(Lawrence Berkeley National Laboratory, 2006-04-11) Wozei, Eleanor; Hermanowicz, SWA yeast-based assay protocol developed for detecting oestrogenic activity in activated sludge (AS) supernatant is described. The protocol used Saccharomyces cerevisiae construct RMY/ER-ERE with human oestrogen receptor (ERα) and lacZ reporter genes, and was developed by modifying existing assays for use with AS samples from batch experiments. The method was able to detect total oestrogenic activity (without prior extraction) in supernatants of AS spiked with 17β-oestra¬diol (E2) with a detection limit of 0.03 ngE2-equivalent/ℓ and an overall quantification limit of 100 ngE2-equivalent/ℓ. Mean E2-induced oestrogenic activity recoveries of >56% were obtained from the spiked samples.
- ItemComputational identification of transposable elements in the mouse genome(2007) Jjingo, Daudi; Makalowski, WojciechRepeat sequences cover about 39 percent of the mouse genome and completion of sequencing of the mouse genome  has enabled extensive research on the role of repeat sequences in mammalian genomics. This research covers the identification of Transposable elements (TEs) within the mouse transcriptome, based on available sequence information on mouse cDNAs (complementary DNAs) from GenBank . The transcripts are screened for repeats using RepeatMasker , whose results are sieved to retain only Interspersed repeats (IRS). Using various bioinformatics software tools as well as tailor made programming, the research establishes: (i) the absolute location coordinates of the TEs on the transcript. (ii) The location of the IRs with respect to the 5’UTR, CDS and 3’UTR sequence features. (iii) The quality of alignment of the TE’s consensus sequence on the transcripts where they exist, (iv) the frequencies and distributions of the TEs on the cDNAs, (v) descriptions of the types and roles of transcripts containing TEs. This information has been collated and stored in a relational database (MTEDB) at http://warta.bio.psu.edu/htt_doc/M TEDB/homepage.htm).
- ItemRapid water sample screening for estrogenic activity using live yeast cells(2007) Wozei, Eleanor; Borglin, S. E.; Holman, H-Y.N.Endocrine disrupting compounds (EDCs) are substances that influence the endocrine system in living organisms. They include natural hormones, medicinal drugs, chemical compounds in industry, and pesticides in agriculture. The substances may be present in water and wastewater, soil and sediments, or airborne. Our research is focused on the estrogenic EDCs, i.e. substances which mimic the natural hormone estrogen produced by the body, and their occurrence and fate in the context of wastewater management. The primary contributors to estrogenic activity wastewater are 17_-estradiol, estrone, and 17_-ethinylestradiol. We are interested in readily detecting and quantifying this estrogenic activity as a first step in the daily management and reduction of estrogenic EDCs in wastewater before discharge into the environment with effluent and biosolids. We report progress on a fluorescence assay for the presence of estrogenic activity in water samples using a living estrogen-sensitive yeast cell strain, and on a study of responses of living yeast cells to estrogen and alkylphenol exposure using synchrotron radiation-based Fourier Transform infrared spectromicroscopy (SRFTIR). The fluorescent response of the yeast allows for rapid sample screening, and the SR-FTIR infrared spectrum is a measure of the overall in vivo yeast biochemical response to the sample.
- ItemReal-Time Molecular Monitoring of Chemical Environment in Obligate Anaerobes during Oxygen Adaptive Response(California Digital Library, University of California, 2009-08-26) Holman, Hoi-Ying N.; Wozei, Eleanor; Lin, Zhang; Comolli, Luis R.; Ball, David. A.; Borglin, Sharon; Fields, Matthew W.; Hazen, Terry C.; Downing, Kenneth H.Determining the transient chemical properties of the intracellular environment can elucidate the paths through which a biological system adapts to changes in its environment, for example, the mechanisms which enable some obligate anaerobic bacteria to survive a sudden exposure to oxygen. Here we used high-resolution Fourier Transform Infrared (FTIR) spectromicroscopy to continuously follow cellular chemistry within living obligate anaerobes by monitoring hydrogen bonding in their cellular water. We observed a sequence of well-orchestrated molecular events that correspond to changes in cellular processes in those cells that survive, but only accumulation of radicals in those that do not. We thereby can interpret the adaptive response in terms of transient intracellular chemistry and link it to oxygen stress and survival. This ability to monitor chemical changes at the molecular level can yield important insights into a wide range of adaptive responses.
- ItemAnalysis of persistence soil nutrient status in abandoned cattle kraals in a semi arid area in Botswana(2010-12) Kizza, Sarah; Otlogetswe, Totolo; Perkins, Jeremy; Olusegun, AreolaThe aim of this study was to analyze the depletion of soil nutrients with time on abandoned kraals in a peri-urban area of Botswana. Active kraals are enriched with nutrients through the accumulation of animal droppings and this study was aimed at assessing how long the impact of this soil nutrient enrichment persists after kraal abandonment. A total of 25 disused kraals, that had been abandoned for periods ranging from 1 to 45 years were sampled. The soil parameters analyzed included particle size distribution (%), bulk density (g/cm3), pore space (%), moisture content (%), pH in water and KCl solution, EC (µS/cm), organic matter (%), CEC (meq/100g), exchangeable Ca++ (cmolc/kg), Mg++ (cmolc/kg),K+ (cmolc/kg), Na+ (cmolc/kg), nitrogen [NH4-N (mg/kg), NO3-N (mg/kg), TKN (%), and Olsen P (mg/kg). Results showed that soil nutrient concentrations on abandoned kraals generally were significantly higher than at the control sites. Soil nutrient concentrations decreased with time as abandoned kraals retrogressed towards their pre-kraal conditions. However, the effects of soil nutrient enrichment from animal wastes persist long after kraal abandonment. For example, soil Olsen P, Ca++ and Mg++ levels in kraal sites that had been abandoned for over 45 years were still significantly higher than in the control sites. In a pastoral system such as is practiced in Botswana where kraal manure is not used as soil amendment, the whole ecosystem suffers as soil nutrients are transferred and concentrated at isolated spots (kraals).
- ItemInvestigating water meter performance in developing countries: A case study of Kampala, Uganda(2011) Mutikanga, Harrison E.; Sharma, Saroj K.; Vairavamoorthy, KalanithyHigh levels of water losses in distribution systems are the main challenge that water utilities in developing countries currently face. The water meter is an essential tool for both the utility and the customers to measure and monitor consumption. When metering is inefficient and coupled with low tariffs, the financial sustainability of utilities is at stake. Apparent water losses caused by metering inefficiencies can be reduced by assessing meters’ performance and identifying the main causes of inefficiency. This paper examines the performance of 3 meter models, on the basis of failure records for a developing world water utility in Kampala city, Uganda. The influence of sub-metering on meter accuracy is also examined. The results indicate a high meter failure rate (6.6%/year) in Kampala. Over 75% of failures were observed in the volumetric (oscillating-piston) meter types with the main cause of meter failure being particulates in water. The study also indicates an average reduction in revenue water registration of 18% due to sub-metering. The reduction was not because of water use efficiency but due to the combined effect of the metering errors of the sub-meters. This clearly implies that when properties are sub-metered, customers should be charged proportionately based on master meter readings, for accurate water accountability. The findings of this study will be useful for both utility managers and meter manufacturers who work in the water industry, especially in developing countries, to make appropriate metering and sub-metering decisions.
- ItemHerbaceous and Woody Plant Properties in Abandoned Kraal Areas in a Hardveld Botswana(2011) Kizza, SarahHerbaceous and woody plant species in abandoned traditional kraals were investigated. To achieve the aim of this study, nutrient status of soil in addition to vegetation composition and communities from the kraal sites were analyzed and results compared with those from control sites. A total of 25 kraals that had been abandoned between 5 and 45 years were sampled. Data were analyzed using multivariate procedures; a two-way indicator species analysis (TWINSPAN), detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) to establish classification of the plant communities. The significant environmental variables identified with t-values above 2.1 that determined the composition and patterns of the plant communities were organic matter, plant available nitrogen, calcium and moisture content. The results show major differences in soil physio-chemical properties and also in patterns and composition of vegetation communities between kraals and their surrounding areas. Evidence from the results show that kraal areas play an important role in determining key resource areas by influencing systematic distribution of nutrients. With kraals tending to increase the heterogeneity in the natural distribution of nutrients, it is apparent that animal waste deposited in the kraals modify vegetation patterns as high nutrient tolerant species gain competitive advantage over those that are not. The findings provide some important information that could explain herbaceous and woody species community patterns particularly in semi-arid environments where livestock management by the use of traditional kraals is a common practice.
- ItemEffect of the transposable element environment of human genes on gene length and expression(Oxford University Press, 2011-02-28) Jjingo, Daudi; Huda, Ahsan; Gundapuneni, Madhumati; Mariño-Ramǐrez, Leonardo; Jordan, I. KingIndependent lines of investigation have documented effects of both transposable elements (TEs) and gene length (GL) on gene expression. However, TE gene fractions are highly correlated with GL, suggesting that they cannot be considered independently. We evaluated the TE environment of human genes and GL jointly in an attempt to tease apart their relative effects. TE gene fractions and GL were compared with the overall level of gene expression and the breadth of expression across tissues. GL is strongly correlated with overall expression level but weakly correlated with the breadth of expression, confirming the selection hypothesis that attributes the compactness of highly expressed genes to selection for economy of transcription. However, TE gene fractions overall, and for the L1 family in particular, show stronger anti-correlations with expression level than GL, indicating that GL may not be the most important target of selection for transcriptional economy. These results suggest a specific mechanism, removal of TEs, by which highly expressed genes are selectively tuned for efficiency. MIR elements are the only family of TEs with gene fractions that show a positive correlation with tissue-specific expression, suggesting that they may provide regulatory sequences that help to control human gene expression. Consistent with this notion, MIR fractions are relatively enriched close to transcription start sites and associated with expression in specific sets of related tissues. Our results confirm the overall relevance of the TE environment to gene expression and point to distinct mechanisms by which different TE families may contribute to gene regulation.
- ItemAssessment of apparent losses in urban water systems(2011-08-17) Mutikanga, Harrison E.; Sharma, Saroj K.; Vairavamoorthy, KalanithyApparent losses relate to water that is consumed but not paid for. Most research carried out in the last decade particularly in the United Kingdom focused mainly on leakage. Until now, there are no set procedures and guidelines for assessment of apparent losses. Much work remains to bring it to par with the available tools and methodologies for leakage management. In the absence of adequate data and proper methodology, most developed countries use default values, which tend to be lowest values for well-managed water systems, for computation of apparent losses. These may not be appropriate for developing countries. This paper presents a methodology for the assessment of different components of apparent losses based on field audit and operational data for Kampala city’s water distribution system in Uganda. Metering inaccuracies and illegal use have been found to be significant components of apparent losses. Appropriate intervention strategies have been developed based on the assessment.
- ItemMulti-criteria Decision Analysis: A Strategic Planning Tool for Water Loss Management(2011-11) Mutikanga, Harrison E.; Sharma, Saroj K.; Vairavamoorthy, KalanithyWater utilities particularly in the developing countries continue to operate with considerable inefficiencies in terms of water and revenue losses. With increasing water demand and scarcity, utilities require effective strategies for optimum use of available water resources. Diverse water loss reduction options exist. Deciding on which option to choose amidst conflicting multiple criteria and different interests of stakeholders is a challenging task. In this paper, an integrated multi-criteria decision-aiding framework for strategic planning of water loss management is presented. The PROMETHEE II method was applied within the framework in prioritizing water loss reduction options for Kampala city. A strategic plan that combines selective mains and service lines replacement and pressure management as priorities is the best compromise based on preferences of the decision makers and seven evaluation criteria characterized by financial-economic, environmental, public health, technical and social impacts. The results show that the most preferred options are those that enhance water supply reliability, public health and water conservation measures. This study demonstrates how decision theory coupled with operational research techniques could be applied in practice to solve complex water management and planning problems.
- ItemPore pressure development in hybrid fibre – reinforced high strength concrete at elevated temperatures(2011-11) Mugume, Rodgers Bangi; Horiguchi, TakashiThe present experimental work investigates the build – up of pore pressure at different depths of High Strength Concrete (HSC) and Hybrid-Fibre-Reinforced High Strength Concrete (HFRHSC) when exposed to different heating rates. First, the effect of the measurement technique on maximum pore pressures measured was evaluated. The pressure measurement technique which utilized a sintered metal and silicon oil was found to be the most effective technique for pore pressure measurement. Pore pressure measurements carried out showed that addition of polypropylene fibres is very effective in mitigation of spalling and build – up of pore pressure inside heated HSC. Addition of steel fibres plays some role in pore pressure reduction at relatively higher pressures in deeper regions of concrete during fast heating. Pore pressure development is highly influenced by the rate of heating with fast heating leading to higher pore pressures in the deeper regions of concrete compared to slow heating.
- ItemPrediction of transposable element derived enhancers using chromatin modification profiles(PLoS ONE (Public Library of Science), 2011-11-07) Huda, Ahsan; Tyagi, Eishita; Marino-Ramırez, Leonardo; Bowen, Nathan J.; Jjingo, Daudi; King Jordan, I.Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.
- ItemOn the presence and role of human gene-body DNA methylation(International Multidisciplinary Publishing Academy for Computational Technologies, 2012-05-09) Jjingo, Daudi; Conley, Andrew B.; Yi, Soojin V.; Lunyak, Victoria V.; Jordan, I. KingDNA methylation of promoter sequences is a repressive epigenetic mark that down-regulates gene expression. However, DNA methylation is more prevalent within gene-bodies than seen for promoters, and gene-body methylation has been observed to be positively correlated with gene expression levels. This paradox remains unexplained, and accordingly, the role of DNA methylation in gene-bodies is poorly understood. We addressed the presence and role of human gene-body DNA methylation using a meta-analysis of human genome-wide methylation, expression and chromatin data sets. Methylation is associated with transcribed regions as genic sequences have higher levels of methylation than intergenic or promoter sequences. We also find that the relationship between gene-body DNA methylation and expression levels is non-monotonic and bell-shaped. Mid-level expressed genes have the highest levels of gene-body methylation, whereas the most lowly and highly expressed sets of genes both have low levels of methylation. While gene-body methylation can be seen to efficiently repress the initiation of intragenic transcription, the vast majority of methylated sites within genes are not associated with intragenic promoters. In fact, highly expressed genes initiate the most intragenic transcription, which is inconsistent with the previously held notion that gene-body methylation serves to repress spurious intragenic transcription to allow for efficient transcriptional elongation. These observations lead us to propose a model to explain the presence of human gene-body methylation. This model holds that the repression of intragenic transcription by gene-body methylation is largely epiphenomenal, and suggests that gene-body methylation levels are predominantly shaped via the accessibility of the DNA to methylating enzyme complexes.
- ItemReverse Logistics Related to Waste Management with Emphasis on Developing Countries—A Review Paper(2012-09-20) Kinobe, Joel R.; Gebresenbet, Girma; Vinnerås, BjörnThis paper provides an overview of the state of art of reverse logistics and current status of waste management problems with special emphasis on developing countries. Logistics activities have been practiced and played a fundamental role in the global economic development for over 5,000 years. It has then been transformed into different logistics branches and elaborates the emergency of reverse logistics as one of the most important. The paper presents the evolution of logistics into reverse logistics and how it relates to waste management both in the developed and developing world. Reverse logistics is a relatively new phenomenon in the research area which is mainly referring to damaged goods, the take back of products that should be returned to the manufacturers or distributors. Reverse logistics is relatively more practiced in an organized way in the developed world than in the developing countries in that the latter provided less value additions on reversed products.
- ItemPrediction of fire spalling in fibre-reinforced high strength concrete(2013) Mugume, Rodgers Bangi; Horiguchi, TakashiThis paper presents results of a study which investigates spalling in small scale specimens of fibre-reinforced high strength concrete exposed to elevated temperatures. A relationship to predict relative maximum pressures was developed, which takes into account parameters such as concrete strength, fibre type and fibre geometry. Also, a blowtorch spalling test method was utilized to investigate spalling in small scale specimens, and a clear relationship between relative maximum pore pressures and spalling was observed.
- ItemCalibrating an optimal condition model for solar water disinfection in peri-urban household water treatment in Kampala, Uganda(IWA Publishing, 2013) Okurut, Kenan; Wozei, Eleanor; Kulabako, Robinah; Nabasirye, Lillian; Kinobe, JoelIn low income settlements where the quality of drinking water is highly contaminated due to poor hygienic practices at community and household levels, there is need for appropriate, simple, affordable and environmentally sustainable household water treatment technology. Solar water disinfection (SODIS) that utilizes both the thermal and ultra-violet effect of solar radiation to disinfect water can be used to treat small quantities of water at household level to improve its bacteriological quality for drinking purposes. This study investigated the efficacy of the SODIS treatment method in Uganda and determined the optimal condition for effective disinfection. Results of raw water samples from the study area showed deterioration in bacteriological quality of water moved from source to the household; from 3 to 36 cfu/100 mL for tap water and 75 to 126 cfu/100 mL for spring water, using thermotolerant coliforms (TTCs) as indicator microorganisms. SODIS experiments showed over 99.9% inactivation of TTCs in 6 h of exposure, with a threshold temperature of 39.5± 0.7 WC at about 12:00 noon, in the sun during a clear sunny day. A mathematical optimal condition model for effective disinfection has been calibrated to predict the decline of the number of viable microorganisms over time.
- ItemFactors influencing selection of drinking water technologies for urban informal settlements in Kampala(2013-08-12) Isoke, Jennifer; Dijk, Meine Pieter vanAccess to drinking water in urban informal settlements of developing countries still remains a challenge for the poor and depends on technology selected. This paper determines the score on criteria used for technology selection by two major stakeholders in the water service delivery chain, the users and the utility. The criteria are: affordability to connect, affordability of consumption, method of payment, ease of operation, ease of spare parts acquisition, access distance, access time, generating sufficient water continuously, service coverage, the possibility of cost recovery and security of installation (SOI). The study was carried out in Bwaise II and Kisenyi III, two informal settlements in Kampala, the capital of Uganda. Through a household survey and semistructured interviews of key informants, data were collected for the score on these criteria of four piped water distribution technologies: public water points (PWPs) with conventional meters, PWPs with prepaid meters, house connections and yard taps. Using multicriteria methods and preference elicitation by pair wise ranking, the most preferred factor for technology selection from the users’ point of view is affordability to connect, while from the utility’s point of view, it is SOI. These preferences were confirmed by data from focus group discussions and in-depth interviews.
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