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Article ; Online: Development of a customised programme to standardise comorbidity diagnosis codes in a large-scale database

Adib A Abla / Robert C Osorio / Kunal P Raygor

BMJ Health & Care Informatics, Vol 29, Iss

2022 Volume 1

Abstract: Objectives The transition from ICD-9 to ICD-10 coding creates a data standardisation challenge for large-scale longitudinal research. We sought to develop a programme that automated this standardisation process.Methods A programme was developed to ... ...

Abstract	Objectives The transition from ICD-9 to ICD-10 coding creates a data standardisation challenge for large-scale longitudinal research. We sought to develop a programme that automated this standardisation process.Methods A programme was developed to standardise ICD-9 and ICD-10 terminology into one system. Code was improved to reduce runtime, and two iterations were tested on a joint ICD-9/ICD-10 database of 15.8 million patients.Results Both programmes successfully standardised diagnostic terminology in the database. While the original programme updated 100 000 cells in 12.5 hours, the improved programme translated 3.1 million cells in 38 min.Discussion While both programmes successfully translated ICD-related data into a standardised format, the original programme suffered from excessive runtimes. Code improvement with hash tables and parallelisation exponentially reduced these runtimes.Conclusion Databases with ICD-9 and ICD-10 codes require terminology standardisation for analysis. By sharing our programme’s implementation, we hope to assist other researchers in standardising their own databases.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	005
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Epstein–Barr Virus Infection in Lung Cancer

Julio C. Osorio / Rancés Blanco / Alejandro H. Corvalán / Juan P. Muñoz / Gloria M. Calaf / Francisco Aguayo

Pathogens, Vol 11, Iss 132, p

Insights and Perspectives

2022 Volume 132

Abstract: Lung cancer (LC) is the leading cause of cancer death worldwide. Tobacco smoke is the most frequent risk factor etiologically associated with LC, although exposures to other environmental factors such as arsenic, radon or asbestos are also involved. ... ...

Abstract	Lung cancer (LC) is the leading cause of cancer death worldwide. Tobacco smoke is the most frequent risk factor etiologically associated with LC, although exposures to other environmental factors such as arsenic, radon or asbestos are also involved. Additionally, the involvement of some viral infections such as high-risk human papillomaviruses (HR-HPVs), Merkel cell polyomavirus (MCPyV), Jaagsiekte Sheep Retrovirus (JSRV), John Cunningham Virus (JCV), and Epstein–Barr virus (EBV) has been suggested in LC, though an etiological relationship has not yet been established. EBV is a ubiquitous gamma herpesvirus causing persistent infections and some lymphoid and epithelial tumors. Since EBV is heterogeneously detected in LCs from different parts of the world, in this review we address the epidemiological and experimental evidence of a potential role of EBV. Considering this evidence, we propose mechanisms potentially involved in EBV-associated lung carcinogenesis. Additional studies are warranted to dissect the role of EBV in this very frequent malignancy.
Keywords	Epstein–Barr virus ; cancer ; lung ; Medicine ; R
Subject code	610
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Role of Epstein-Barr Virus and Human Papillomavirus Coinfection in Cervical Cancer

Rancés Blanco / Diego Carrillo-Beltrán / Julio C. Osorio / Gloria M Calaf / Francisco Aguayo

Pathogens, Vol 9, Iss 685, p

Epidemiology, Mechanisms and Perspectives

2020 Volume 685

Abstract: High-risk human papillomavirus (HR-HPV) is etiologically associated with the development and progression of cervical cancer, although other factors are involved. Epstein-Barr virus (EBV) detection in premalignant and malignant tissues from uterine cervix ...

Abstract	High-risk human papillomavirus (HR-HPV) is etiologically associated with the development and progression of cervical cancer, although other factors are involved. Epstein-Barr virus (EBV) detection in premalignant and malignant tissues from uterine cervix has been widely reported; however, its contribution to cervical cancer development is still unclear. Here, a comprehensive analysis regarding EBV presence and its potential role in cervical cancer, the frequency of EBV/HR-HPV coinfection in uterine cervix and EBV infection in tissue-infiltrating lymphocytes were revised. Overall, reports suggest a potential link of EBV to the development of cervical carcinomas in two possible pathways: (1) Infecting epithelial cells, thus synergizing with HR-HPV (direct pathway), and/or (2) infecting tissue-infiltrating lymphocytes that could generate local immunosuppression (indirect pathway). In situ hybridization (ISH) and/or immunohistochemical methods are mandatory for discriminating the cell type infected by EBV. However, further studies are needed for a better understanding of the EBV/HR-HPV coinfection role in cervical carcinogenesis.
Keywords	Epstein-Barr virus ; human papillomavirus ; coinfection ; cervical cancer ; tissue-infiltrating lymphocytes ; Medicine ; R
Subject code	610 ; 616
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phytotoxicity of plant extracts of Vismia japurensis cultivated in vivo and in vitro

L. M. Lima / L. S. Pedroza / M. I. C. Osório / J. C. Souza / C. V. Nunez

Brazilian Journal of Biology, Vol

2021 Volume 82

Abstract: Abstract Plants that produce secondary metabolites with allelopathic activity or phytotoxicity can be biotechnologically important, serving as sources of allelochemicals, and thus contributing to the agroindustrial sector. Vismia japurensis (Hypericaceae) ...

Abstract	Abstract Plants that produce secondary metabolites with allelopathic activity or phytotoxicity can be biotechnologically important, serving as sources of allelochemicals, and thus contributing to the agroindustrial sector. Vismia japurensis (Hypericaceae) is an Amazonian species that grows in clumps called vismiais, from which most other plants are absent. Accordingly, the objective of this study was to identify possible phytotoxicity effects of hexane and methanol extracts of Vismia japurensis leaves and branches in vivo and from seedlings grown in vitro on Lactuca sativa. In addition, fresh and dry leaves were assayed by the sandwich method in order to determine their ability to release allelochemicals. The hexanic extract from in vitro seedlings reduced germination by 10%, while the methanol extract produced a 16% reduction in germination speed. Root growth of Lactuca sativa was inhibited by 64.7% when subjected to hexane leaf extract, by 39.3% under the influence of hexane branch extract, and by 96.09% for in vitro seedling hexanic extract. When analysed by thin layer chromatography and 1H nuclear magnetic resonance, extracts showed evidence of terpenes, anthraquinones and flavonoids, with greater intensity of signals in the aromatic region of in vitro seedling hexanic extract. Clearly, Vismia japurensis has a high biotechnological potential in terms of the production of substances of low polarity with capacity to interfere in plant development.
Keywords	bioprospection ; plant tissue culture ; terpenes ; anthraquinones ; phytotoxicity ; Science ; Q ; Biology (General) ; QH301-705.5 ; Zoology ; QL1-991 ; Botany ; QK1-989
Subject code	580
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Instituto Internacional de Ecologia
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Characterization of High-Risk HPV/EBV Co-Presence in Pre-Malignant Cervical Lesions and Squamous Cell Carcinomas

Rancés Blanco / Diego Carrillo-Beltrán / Juan P. Muñoz / Julio C. Osorio / Julio C. Tapia / Verónica A. Burzio / Iván Gallegos / Gloria M. Calaf / Paola Chabay / Francisco Aguayo

Microorganisms, Vol 10, Iss 888, p

2022 Volume 888

Abstract: High-risk human papillomaviruses (HR-HPVs) are the etiological agents of cervical cancer. However, a low proportion of HR-HPV-infected women finally develop this cancer, which suggests the involvement of additional cofactors. Epstein–Barr virus (EBV) has ...

Abstract	High-risk human papillomaviruses (HR-HPVs) are the etiological agents of cervical cancer. However, a low proportion of HR-HPV-infected women finally develop this cancer, which suggests the involvement of additional cofactors. Epstein–Barr virus (EBV) has been detected in cervical squamous cell carcinomas (SCCs) as well as in low- (LSIL) and high-grade (HSIL) squamous intraepithelial lesions, although its role is unknown. In this study, we characterized HR-HPV/EBV co-presence and viral gene expression in LSIL ( n = 22), HSIL ( n = 52), and SCC ( n = 19) from Chilean women. Additionally, phenotypic changes were evaluated in cervical cancer cells ectopically expressing BamHI-A Rightward Frame 1 (BARF1). BARF1 is a lytic gene also expressed in EBV-positive epithelial tumors during the EBV latency program. HPV was detected in 6/22 (27.3%) LSIL, 38/52 (73.1%) HSIL, and 15/19 (78.9%) SCC cases ( p < 0.001). On the other hand, EBV was detected in 16/22 (72.7%) LSIL, 27/52 (51.9%) HSIL, and 13/19 (68.4%) SCC cases ( p = 0.177). HR-HPV/EBV co-presence was detected in 3/22 (13.6%) LSIL, 17/52 (32.7%) HSIL, and 11/19 (57.9%) SCC cases ( p = 0.020). Additionally, BARF1 transcripts were detected in 37/55 (67.3%) of EBV positive cases and in 19/30 (63.3%) of HR-HPV/EBV positive cases. Increased proliferation, migration, and epithelial-mesenchymal transition (EMT) was observed in cervical cancer cells expressing BARF1. Thus, both EBV and BARF1 transcripts are detected in low- and high-grade cervical lesions as well as in cervical carcinomas. In addition, BARF1 can modulate the tumor behavior in cervical cancer cells, suggesting a role in increasing tumor aggressiveness.
Keywords	Epstein–Barr virus ; human papillomavirus ; BamHI-A rightward frame 1 expression ; cervical cancer ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Seasonal Dynamics and Spatial Distribution of Aedes albopictus (Diptera

Hugo C. Osório / Jorge Rocha / Rita Roquette / Nélia M. Guerreiro / Líbia Zé-Zé / Fátima Amaro / Manuel Silva / Maria João Alves

International Journal of Environmental Research and Public Health, Vol 17, Iss 7083, p

Culicidae) in a Temperate Region in Europe, Southern Portugal

2020 Volume 7083

Abstract: Aedes albopictus is an invasive mosquito that has colonized several European countries as well as Portugal, where it was detected for the first time in 2017. To increase the knowledge of Ae. albopictus population dynamics, a survey was carried out in the ...

Abstract	Aedes albopictus is an invasive mosquito that has colonized several European countries as well as Portugal, where it was detected for the first time in 2017. To increase the knowledge of Ae. albopictus population dynamics, a survey was carried out in the municipality of Loulé, Algarve, a Southern temperate region of Portugal, throughout 2019, with Biogents Sentinel traps (BGS traps) and ovitraps. More than 19,000 eggs and 400 adults were identified from May 9 (week 19) and December 16 (week 50). A positive correlation between the number of females captured in the BGS traps and the number of eggs collected in ovitraps was found. The start of activity of A. albopictus in May corresponded to an average minimum temperature above 13.0 °C and an average maximum temperature of 26.2 °C. The abundance peak of this A. albopictus population was identified from September to November. The positive effect of temperature on the seasonal activity of the adult population observed highlight the importance of climate change in affecting the occurrence, abundance, and distribution patterns of this species. The continuously monitoring activities currently ongoing point to an established population of A. albopictus in Loulé, Algarve, in a dispersion process to other regions of Portugal and raises concern for future outbreaks of mosquito-borne diseases associated with this invasive mosquito species.
Keywords	Aedes albopictus ; invasive mosquitoes ; population dynamics ; arboviruses ; Portugal ; Medicine ; R
Subject code	590
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: First Report of Cadophora luteo-olivacea Causing Side Rot on Kiwifruit in Chile

Auger, J / C. Osorio-Navarro / I. Pérez / M. Esterio

Plant disease. 2018 Mar., v. 102, no. 3

2018

Abstract: Kiwifruit (Actinidia deliciosa [Chev] Ling et Ferguson cv. ‘Hayward’) can be stored for over 6 months at 0 ± 1°C. However, in recent years a postharvest disease of kiwifruit, characterized by a side rot appearing during harvest or after 3 to 6 months ... ...

Abstract	Kiwifruit (Actinidia deliciosa [Chev] Ling et Ferguson cv. ‘Hayward’) can be stored for over 6 months at 0 ± 1°C. However, in recent years a postharvest disease of kiwifruit, characterized by a side rot appearing during harvest or after 3 to 6 months postharvest cold storage period, has been observed in several packinghouses in central Chile. Symptoms on kiwifruit were depressed and elliptical areas, associated with brown-violet skin and brown pulp. Symptomatic kiwifruit samples from different packinghouses were sterilized with 75% (v/v) ethanol, and infected tissue was placed onto potato dextrose agar (PDA) at 24°C in the dark for a 7-day period. Single spore colonies were flat, felty, and cottony in the middle, with smooth margins, with an even edge and varying in color from white turning to gray/black-olivaceous. Microscopically, straight, septate, short conidiophores had mostly cylindrical monophialides with hyaline collarettes. Conidia (n = 50) from four representative isolates recovered from naturally infected kiwifruit (2VCBC, 2VCBD, 2VCBF, and 2VCCD) were hyaline, unicellular, oblong elliptical or ovoid, and mostly biguttulated, measured 3.8 to 5.8 × 2.2 to 3.5 μm (mean, 2.9 × 4.8 μm). Cultural and morphological pathogen characteristics were similar to those described for Cadophora sp. (Gramaje et al. 2011). Three loci (ITS, β-tubulin, and EF1-α) of the four representative isolates were sequenced using the primers ITS1/ITS4, Bt2a/Bt2b, and EF1-728F/EF1-986R (Travadon et al. 2015). BLAST analysis revealed ITS, β-tubulin, and EF1-α sequences (accessions nos. MF464553, MF464555, MF464558, and MF464562) to share 99 to 100% identity with Cadophora luteo-olivacea isolates in GenBank (accession nos. KT350592, KT350591, and KU720079); the sequences (accession nos. MF464554, MF464556, MF464559, and MF464563) were compared with those of C. luteo-olivacea in the NCBI GenBank database and had 99% nucleotide sequence identity (accession nos. KF764682, KF764648, and KF764647), and the sequences (accession nos. MF772484, MF772481, MF772482, and MF772480) were 100% identical to C. luteo-olivacea sequences in GenBank (accession nos. KT350599, KT350598, and KT350597), respectively. Twenty ‘Hayward’ kiwifruits (per representative isolates) were wounded-inoculated in the fruit equatorial region with 20 μl of a spore suspension (106 conidia/ml) prepared from a 15-day-old PDA culture and incubated at 24°C in darkness. Typical symptoms appeared between 8 and 12 days. Kiwifruits inoculated with sterile distilled water remained symptomless. Fungi isolated from the lesions had morphological characteristics that resembled the original isolates from infected fruits. The identity of the reisolations was confirmed as C. luteo-olivacea by sequencing, thus completing Koch’s postulates. C. luteo-olivacea has been identified associated with a similar symptom (skin pitting) on kiwifruit stored long-term in Italy (Piano at al. 2001; Spadaro et al. 2010). In kiwifruit orchards, C. luteo-olivacea is normally a soil-borne microorganism and may be transported into packing houses on fruit skins or in harvest bins (Gilardi et al. 2007). Side rot caused by C. luteo-olivacea represents an economically significant problem for the kiwifruit packinghouses in Chile, owing to the lack of effective postharvest fungicides and the limited knowledge of the pathogen and disease epidemiology. To our knowledge, this is the first report of side rot of kiwifruit caused by C. luteo-olivacea in Chile.
Keywords	Actinidia deliciosa ; Cadophora ; cold storage ; color ; conidia ; conidiophores ; culture media ; epidemiology ; fruits ; fungi ; fungicides ; genetic databases ; internal transcribed spacers ; kiwifruit ; loci ; orchards ; packing houses ; pathogens ; postharvest diseases ; pulp ; sequence analysis ; storage time ; tubulin ; Chile ; Italy
Language	English
Dates of publication	2018-03
Size	p. 680.
Publishing place	Plant Disease
Document type	Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS-09-17-1349-PDN
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: West Nile virus transmission potential in Portugal

José Lourenço / Sílvia C. Barros / Líbia Zé-Zé / Daniel S. C. Damineli / Marta Giovanetti / Hugo C. Osório / Fátima Amaro / Ana M. Henriques / Fernanda Ramos / Tiago Luís / Margarida D. Duarte / Teresa Fagulha / Maria J. Alves / Uri Obolski

Communications Biology, Vol 5, Iss 1, Pp 1-

2022 Volume 12

Abstract: Lourenço et al. review historical data and quantify the transmission potential of West Nile virus in Portugal. They report a North-South divide in infection patterns, a higher ecological capacity in the south, and an increasing positive effect of climate ...

Abstract	Lourenço et al. review historical data and quantify the transmission potential of West Nile virus in Portugal. They report a North-South divide in infection patterns, a higher ecological capacity in the south, and an increasing positive effect of climate change over the last 40 years.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Feeding Calcium-Ammonium Nitrate to Lactating Dairy Goats

Kleves V. Almeida / Geraldo T. Santos / Jesus A. C. Osorio / Jean C. S. Lourenço / Monique Figueiredo / Thomer Durman / Francilaine E. Marchi / Claudete R. Alcalde / Ranulfo C. Silva-Junior / Camila C. B. F. Itavo / Rafael C. Araujo / Andre F. Brito

Animals, Vol 12, Iss 983, p

Milk Quality and Ruminal Fermentation Responses

2022 Volume 983

Abstract: We aimed to investigate the effects of calcium-ammonium nitrate (CAN) fed to lactating dairy goats on dry matter (DM) intake, digestibility of nutrients, milk properties (composition, antioxidant capacity, fatty acid profile, and nitrate residues), and ... ...

Abstract	We aimed to investigate the effects of calcium-ammonium nitrate (CAN) fed to lactating dairy goats on dry matter (DM) intake, digestibility of nutrients, milk properties (composition, antioxidant capacity, fatty acid profile, and nitrate residues), and ruminal fermentation parameters. Twelve lactating Saanen goats averaging 98.5 ± 13.1 days in milk, 53.5 ± 3.3 kg of body weight, and 2.53 ± 0.34 kg of milk/day were randomly assigned in four 3 × 3 Latin squares to receive the following diets: a control group (without CAN) with 7.3 g/kg DM of urea (URE), 10 g/kg DM of CAN (CAN10), and 20 g/kg DM of CAN (CAN20). Each period lasted 21 days, with 14 days for diet adaptation and seven days for data and sample collection. The DM intake, digestibility of nutrients, yields of milk, 3.5% fat-corrected milk, and energy-corrected milk were not affected by treatments. Similarly, there were no treatment effects on the yields and concentrations of milk fat, true protein, and lactose, along with minor effects on milk fatty acid profile. Total antioxidant capacity in milk was unaffected by treatments; however, concentration of conjugated dienes increased, while thiobarbituric acid reactive substances in milk decreased linearly. Nitrate and nitrite residues in milk were elevated by treatments, while the total of volatile fatty acids and ammonia-N concentration in the rumen were unaffected. Collectively, feeding CAN (up to 20 g/kg of DM) to lactating dairy goats did not affect feed intake, nutrient digestibility, and milk composition; however, it may increase milk lipid oxidation, as evidenced by increased conjugated diene concentration.
Keywords	antioxidant capacity ; feed additive ; hydrogen sink ; nitrite ; non-protein nitrogen ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	630 ; 660
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Simulación dinámica de una alternativa de generación de energía a partir de residuos

Giselle Ramírez Flórez / Luisa F. Giraldo Correa / Natalia Tabares Urrea / Juan C. Osorio Gómez

Mutis, Vol 7, Iss 1, Pp 66-

2017 Volume 77

Abstract: A nivel mundial, la creciente generación de residuos sólidos corre pareja con una demanda de energía eléctrica que aumenta continuamente. Estos dos problemas en conjunto impactan el ambiente incrementando las emisiones de CO2 a la atmósfera. Para manejar ...

Abstract	A nivel mundial, la creciente generación de residuos sólidos corre pareja con una demanda de energía eléctrica que aumenta continuamente. Estos dos problemas en conjunto impactan el ambiente incrementando las emisiones de CO2 a la atmósfera. Para manejar los residuos sólidos se han planteado alternativas como la reutilización, el reciclaje o el reúso. Adicionalmente, se ha propuesto el waste to energy como una alternativa para generar energía a partir de los residuos. En este documento se plantea la comparación de los efectos ambientales asociados a la incineración de residuos (waste to energy) con las alternativas de reúso o reciclaje. El modelo planteado mediante la dinámica de sistemas se valida confrontándolo con la información que se tiene en Colombia sobre los residuos de envases plásticos. El modelo de simulación compara los efectos en cinco indicadores ambientales, encontrándose que dichos indicadores se ven favorecidos en algunos escenarios, pero que es necesario continuar investigando en el tema para tener resultados concluyentes y definitivos. Los resultados y las conclusiones buscan aportar elementos para mejorar los procesos de toma de decisión en este aspecto y abren un camino para continuar la investigación en este tema. (Abstract. Both problems, the growing solid waste generation and electricity demand continually growing impact the environment by increasing emissions of CO2 to the atmosphere. In relation to the solid waste 8 • Revista electrónica editada por la Facultad de Ciencias Naturales e Ingeniería de la UJTL management, alternative as reuse, recycling or reuse have been raised. In addition, Waste to energy appears as an alternative to generate energy from waste. In this paper a comparison of the environmental effects associated with waste incineration (waste to energy) versus alternative reuse or recycling is proposed. The model proposed by system dynamics is validated with information related to plastic packaging waste in Colombia. The model compares the effects on five environmental indicators, finding that such indicators are favored in some scenarios, but is necessary more research on the subject to will be conclusive and definitive results. The results and conclusions provide elements to improve decision-making processes in this area and encourage future researches in the subject.)
Keywords	waste to energy ; dinámica de sistemas ; Colombia ; reciclaje ; envases plásticos ; Science ; Q ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Language	English
Publishing date	2017-05-01T00:00:00Z
Publisher	Universidad Jorge Tadeo Lozano
Document type	Article ; Online
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