Teses / dissertações: "Severe Actute Respiratory Syndrome (SARS)"

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Chu, Chung-ming. "Clinical aspects of severe acute respiratory syndrome (SARS)". Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B31937925.

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Chu, Chung-ming, e 朱頌明. "Clinical aspects of severe acute respiratory syndrome (SARS)". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B31937925.

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Lau, Yik-Chung. "Numerical simulation of severe acute respiratory syndrome (SARS) epidemics /". View abstract or full-text, 2004. http://library.ust.hk/cgi/db/thesis.pl?PHYS%202004%20LAU.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004.
Includes bibliographical references (leaves 43-44). Also available in electronic version. Access restricted to campus users.

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Chauhan, Vinita Singh. "Molecular characterization of severe acute respiratory syndrome (SARS) coronavirus - nucleocapsid protein". Diss., Manhattan, Kan. : Kansas State University, 2006. http://hdl.handle.net/2097/152.

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Ching, Chi-yun Johannes. "Study of host genetic susceptibility to severe acute respiratory syndrome (SARS) infection". Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B40687648.

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Ching, Chi-yun Johannes, e 程子忻. "Study of host genetic susceptibility to severe acute respiratory syndrome (SARS) infection". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40687648.

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Chow, Yan-ching Ken, e 周恩正. "Characterization of the apoptotic properties of severe acute respiratory syndrome coronavirus (SARS-CoV) structural proteins". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30105493.

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Law, Ka-man. "Vaccine development against the severe acute respiratory syndrome-coronavirus (SARS-CoV) using SARS-CoV spike protein". Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36774480.

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Law, Ka-man, e 羅嘉敏. "Vaccine development against the severe acute respiratory syndrome-coronavirus (SARS-CoV) using SARS-CoV spike protein". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B36774480.

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Ng, Yuen-yi Fiona. "Assessment of quality of life in adults recovering from severe acute respiratory syndrome /". Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31972998.

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Xu, Meishu. "Association of DC-SIGN (CD209) gene polymorphisms with severe acute respiratory syndrome (SARS)". View the Table of Contents & Abstract, 2007. http://sunzi.lib.hku.hk/hkuto/record/B3723125X.

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Xu, Meishu, e 徐美術. "Association of DC-SIGN (CD209) gene polymorphisms with severe acute respiratory syndrome (SARS)". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B38616142.

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Yip, Ming-shum, e 葉名琛. "Severe acute respiratory syndrome coronavirus infection of human immune cells through antibody-mediated pathway". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46542139.

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Leung, Hiu-lan Nancy, e 梁曉灡. "Mechanism of antibody-dependent enhancement in severe acute respiratory syndrome coronavirus infection". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B47327066.

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Severe lymphopenia is a clinical feature of Severe Acute Respiratory Syndrome (SARS) patients. However, lymphocytes do not express receptor for SARS-CoV, neither the widely accepted viral receptor angiotensin converting enzyme 2 (ACE2) nor the putative receptors Dendritic Cell- and Liver/lymph-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin (DC-SIGN and L-SIGN). Our group previously showed in vitro that, SARS-CoV Spike pseudotyped particles (SARSCoVpp) could infect human B cells only when inoculated in presence of anti-SARSCoV Spike immune serum. Such observations raised concerns about the possible occurrence of antibody-dependent enhancement (ADE) of infection, a phenomenon during which a virus bounded by antibodies could gain entry into cells through mechanisms involving complement receptors or Fc receptors. Recently, we have demonstrated the participation of the human Fc gamma receptor II (hFcγRII) molecules in granting SARS-CoV an opportunity to infect human immune cells. The aim of this study was to decipher the molecular mechanism leading to antibodymediated, FcγRII-dependent infection of immune cells by SARS-CoV. By using transduction experiment, I highlighted that different members of the hFcγRII family (namely hFcγRIIA, hFcγRIIB1 and hFcγRIIB2) could confer susceptibility to ADE of SARS-CoVpp infection. I further demonstrated that purified anti-viral immunoglobulin G, but not other soluble factor(s) from heat-inactivated immune serum, was the determinant for occurrence of ADE infection. Additionally, with the development of a cell-cell fusion assay, I illustrated that in contrast to the ACE2- dependent pathway, ADE infection did not occur at the plasma membrane, but rather require internalization of virus/antibodies immune complexes by the target cells. In line with this hypothesis, my results using a panel of FcγRII-expressing mutants demonstrated that binding of immune complexes to cell surface FcγRII was a prerequisite but was not sufficient to trigger ADE infection. In these experiments, only FcγRII signaling-competent constructions conferred susceptibility to ADE of SARS-CoVpp infection. Altogether my results point toward a role of the anti-SARS-CoV Spike IgG in vitro in granting SARS-CoV an opportunity to infect cells bearing signaling-competent FcγRII receptors. If further confirmed, such observations could have implications for understanding SARS-CoV tropism and SARS pathogenesis, as well as warrant for careful design of SARS vaccines and immunotherapy based on anti-viral antibodies.
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Microbiology
Master
Master of Philosophy

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Yeung, Yin-shan. "Molecular characterization of apoptosis induced by severe acute respiratory syndrome coronavirus spike protein". Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B38302366.

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Yeung, Yin-shan, e 楊燕珊. "Molecular characterization of apoptosis induced by severe acute respiratory syndrome coronavirus spike protein". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B38302366.

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Ooi, Gaik Cheng, e 黃玉清. "Role of imaging in evaluation of lung involvement in severe acute respiratory syndrome (SARS)". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B47468713.

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Diagnostic imaging played a substantial role in the management and treatment of patients during the Severe Acute Respiratory Syndrome (SARS) outbreak when daily chest radiographs were performed as a measure of disease severity and respiratory status. This thesis was performed to address several issues relating to the radiological spectrum of SARS, its temporal pattern on chest radiograph and high resolution computed tomography (HRCT) during the course of disease, and relationships between severity of opacities quantified on chest radiographs and clinical parameters including treatment response. Radiological parameters that could discriminate SARS from non-SARS community-acquired pneumonia (CAP) were also studied. Unifocal unilateral ground glass opacities was the dominant radiographic abnormality at presentation that progressed rapidly to maximal disease within 9.35 ± 4.09 (median 9, range 3-21) days after onset of symptoms with bilateral consolidation in 62.5% of patients. Complete resolution and significant residual disease was noted in 50% and 20% of cases respectively at end of assessment period. There was a temporal pattern of lung abnormalities on HRCT with ground glass opacity and consolidation at presentation. Reticulation developed after the first week and was present in 50% of patients at ?four weeks. HRCT was useful in illustrating parenchymal abnormalities in patients with normal radiographs at presentation. Severity of lung abnormalities quantified on chest radiograph at different time points of disease correlated with clinical and laboratory parameters such as SaO2 and liver transaminases ALT and AST. Significant relationships were also found between radiographic parameters, and O2 supplementation and treatment response. There are discriminating differences in the radiographic pattern, rate of radiographic progression, and zone of involvement between SARS and non-SARS CAP.
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Medicine
Master
Doctor of Medicine

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Lam, Wai Yee. "Spatial dynamics of the severe acute respiratory syndrome (SARS) epidemic in Hong Kong in 2003". Thesis, Imperial College London, 2011. http://hdl.handle.net/10044/1/6332.

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The Severe Acute Respiratory Syndrome (SARS) epidemic in 2003 was the first infectious disease outbreak caused by a novel pathogen in the twenty-first century. The outbreak in Hong Kong was the second largest worldwide and was characterised by a large proportion of hospital infections and a super-spreading event caused by environmental factors in residential buildings. Hospitals treating SARS cases were at high risk for transmission. I found that hospital outbreaks triggered community transmission as well as the formation of spatial clusters of community cases. The size of the community outbreak in an area increased with the size of the outbreak in the nearest hospital treating SARS, and an area was more likely to have no community-infected cases if it was far from hospitals treating SARS, or had less hospital-infected cases within the area. To quantify the transmission between hospital and community, I developed a spatial epidemic-tree-reconstruction method that uses gravity models to spatially define the probability of contact between individuals in the community. From the reconstructed probabilistic infection tree, I estimated that 24% of community transmission was likely to be infected by cases infected in hospitals, with infected patients discharged during their incubation period and hospital visitors the most important drivers of transmission from healthcare settings to the community. Healthcare workers were key drivers of hospital transmission, with the hospital-to-hospital reproduction number, excluding a single hospital super-spreading event, estimated to be 0.8. A typical community-acquired case was estimated to generate 0.6 cases in the community and 0.2 cases in the hospital in which they were subsequently hospitalised. My findings suggest that hospital infection control could be improved. Restricted hospital visitor policies could have been imposed for longer time during the outbreak and quarantine could be considered for those who recently visited or have been discharged from hospitals treating SARS cases.

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Ng, Yuen-yi Fiona, e 吳婉兒. "Assessment of quality of life in adults: recovering from severe acute respiratory syndrome". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31972998.

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Wu, Ka-yin Christina. "An analysis of severe acute respiratory syndrome (SARS) and the management of Hong Kong's healthcare system". Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31967644.

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Ho, Sheng-sheng, e 何湘霜. "A study of the clinical course of Severe Acute Respiratory Syndrome ina community hospital in Hong Kong". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B45010031.

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Choi, Wai-yee Junet. "Serum neopterin for early assessment of severity of severe acute respiratory syndrome and Dengue virus infection". Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B32031579.

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Wu, Ka-yin Christina, e 鄔家燕. "An analysis of severe acute respiratory syndrome (SARS) and the management of Hong Kong's healthcare system". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31967644.

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Fong, Ho-ching. "Longitudinal changes in community psycho-behavioural responses and impact on outbreak control during severe acute respiratory syndrome (SARS) epidemic in Hong Kong". Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31971714.

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Glowacka, Ilona [Verfasser]. "Bedeutung von Wirtszellproteasen für die Infektion mit dem Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) / Ilona Glowacka". Hannover : Technische Informationsbibliothek und Universitätsbibliothek Hannover (TIB), 2011. http://d-nb.info/1013365224/34.

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Choi, Wai-yee Junet, e 蔡偉儀. "Serum neopterin for early assessment of severity of severe acute respiratory syndrome and Dengue virus infection". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B32031579.

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Wong, Shan. "Psychological reaction of healthcare workers in the outbreak and aftermath of severe acute respiratory syndrome". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B29760239.

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Wong, W. M. Wendy. "A survey of nurses' preventive measures and health status in relation to the severe acute respiratory syndrome (SARS) epidemic in Hong Kong /". View the Table of Contents & Abstract, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36397052.

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au, johnbott@westnet com, e John Arthur Bottomley. "A mediated crisis : news and the national mind". Murdoch University, 2008. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20081113.143044.

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The thesis examines a mediated crisis and how The Straits Times and The Australian approach the reporting of Severe Acute Respiratory Syndrome (SARS). It looks at how this mediated crisis exemplifies the culture of the national newspaper and in turn how the national newspaper has an historical influence on the national psyche. A total of 649 reports and headlines and 141 letters about SARS in The Straits Times (including The Straits Time Interactive) were examined from April 2003 to November 2003 as were 125 headlines from The Australian. The early sections of the thesis discuss how a crisis makes news; examine how the media report a crisis and what emphasis is given to aspects such as: actors, primary definers, vocabulary, lexical choices, subjects, themes, issues and value dimension or stance. The first chapter defines crisis, journalism and crisis journalism and discusses where the latter sits within the continuing expansion and development of major theoretical frameworks, including living in a risk society. The implication here is that crisis and risk have a symbiotic relationship. Historical perspectives of news are discussed in Chapter 2, and the newspaper is placed within the context of contemporary media. The chapter discusses how newspapers are aligned with the concept of the national mind and demonstrates the roles and formations of the two newspapers in relation to the SARS crisis. Chapter 3 codes the headlines, article titles and subtitles of The Straits Times and The Australian and using content analysis of the headlines, analyses the reporting of a serious health crisis SARS that lasted from March to November, 2003. The quantification within content analysis enables a researcher to read and interpret questions that relate to the intensity of meaning in texts, their social impact, the relationships between media texts and the realities and representations they reflect (Hansen et al, 1998). The theory and method of content analysis is used in this chapter to consider differences between The Straits Times and The Australian and to exemplify the medias representation of the narratives of SARS as it happened in the countries of Singapore and Australia. Aspects of crisis and risk, the newspaper and the national mind, narratives, presentations, and post SARS events are discussed in the last chapter. It is concluded from these discussions there is a world narrative that tells the story of how the human condition likes to live and rely on a safe social environment always being available. The relationship between a mediated crisis and risk are also discussed. In addition, it is maintained that reporting in 2003 was not just about SARS but a way of reporting that allowed one to view journalism as an aid to good governance, particularly with regard to living in a risk and crisis-ridden society.

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Chafekar, Aasiyah. "Production of cytokines in human whole blood after incubation with the nucleocapsid protein of the NL63 Coronavirus". University of the Western Cape, 2012. http://hdl.handle.net/11394/4037.

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Masters of Science
The Coronaviridae family consists of RNA viruses within the order Nidovirales. The family is classified into two genera, namely the corona- and toroviruses. Coronaviruses are enveloped, single stranded, positive sense RNA viruses with genomes ranging between 27-32kb in size. The 5’ two-thirds of the genome encodes for the 1a/b polyprotein, while the 3’ one-third of the genome encodes for the structural proteins that mediate viral entry into the host cell. These structural proteins include the spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins. The nucleocapsid protein is expressed at high levels within an infected cell. Studies have shown that this protein plays a key regulatory role in different cellular pathways, including the inhibition of interferon production and the up-regulation of the AP1 signal transduction pathway, amongst others. Also, the N protein is vital in the formation of the ribonucleocapsid core by binding to the viral RNA during virion assembly. The focus of this study is the immune response in whole blood cultures to the presence of human coronavirus (HCoV) NL63 N protein. To characterise the stimulation of the immune activity against HCoV-NL63 N in blood cultures, the HCoV-NL63 N gene was expressed in a bacterial system. In this pilot study, GSTtagged N constructs were then purified and used to treat whole blood cultures from three volunteers. ELISAs were used to measure the cytokine response in these treated whole blood cultures. Results showed that the nucleocapsid protein has an inflammatory response on whole blood cultures. These results have generated vital information in the potential function of the HCoV-NL63 N protein on the immune system. It is suffice to say that the HCoV-NL63 N protein is able to elicit an effective inflammatory response within the host cell. Future studies into the cellular pathways affected by the HCoV-NL63 N protein will clarify its exact role in stimulating the host immune system.

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Lam, Chun-yip. "Comparative molecular analysis of the binding between severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein and angiotensin converting enzyme 2(ACE2)". Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/HKUTO/record/B39557017.

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Fong, Ho-ching, e 方浩澄. "Longitudinal changes in community psycho-behavioural responses and impact on outbreak control during severe acute respiratory syndrome(SARS) epidemic in Hong Kong". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31971714.

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Lam, Chun-yip, e 林俊業. "Comparative molecular analysis of the binding between severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein andangiotensin converting enzyme 2(ACE2)". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B39557017.

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Chavez, Thomas David F. Luechai Sringernyuang. "The language of uncertainty in a new illness : hedging and modality in the biomedical discourse of severe acute respiratory syndrome (SARS) /". Abstract, 2004. http://mulinet3.li.mahidol.ac.th/thesis/2547/cd366/4537982.pdf.

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Gela, Anele. "Cloning and expression of human cyclophilin A and its interaction with human coronavirus NL63 nucleocapsid protein". University of the Western Cape, 2011. http://hdl.handle.net/11394/5360.

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Magister Scientiae (Medical Bioscience) - MSc(MBS)
Coronaviridae family is composed of a number of ribonucleic acid (RNA)-containing viruses currently classified into two genera, the coronavirus and torovirus. The family is classified together with the Arteviridae in the order Nidovirales. Coronaviruses are enveloped single stranded positive sense RNA viruses about 80-160 nm in diameter. The coronavirus is, as in the case of all positive sense RNA virus, a messenger, and the naked RNA is infectious. The 5′-two thirds of the genome encodes for a polyprotein that contains all the enzymes necessary for replication, whereas the 3′-one third encodes for all the structural proteins that mediate viral entry into the host cell. The structural proteins include spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins.Nucleocapsid protein is one of the most crucial structural components of coronaviruses;hence major attention has been focused on characterization of this protein. Some laboratories have demonstrated that this protein interferes with different cellular pathways, thus implying it to be a key regulatory component of the virus (Zakhartchouk, Viswanathan et al. 2005). Furthermore, it has been shown that severe acute respiratory syndrome (SARS)-N protein interacts with cellular proteins, including cyclophilin A (CypA), heterogenous nuclear ribonucleoprotein (hnRNP) A1, human ubiquitin-conjugating enzyme, cyclin dependent kinase (CDK)-cyclin complex protein, Ikappaßalpha (IkBα), cytochrome (Cyt) P450 etc. For the purpose of this study, the focus is based on CypA interaction with human coronavirus (HCoV) NL63-N protein. These interactions might play a role in the pathology of HCoV-NL63. Using glutathione-S-transferase (GST), the interaction of CypA with the nucleocapsid protein can be clearly demonstrated to be direct and specific. Since the N protein is involved in viral RNA packaging to form a helical core, it is suffice to say that both NL63-N and CypA are possibly within the HCoV-NL63 replication/transcription complex and NL63-N/human CypA interaction might function in the regulation of HCoV-NL63 RNA synthesis. In addition, the results will demonstrate that HCoV-NL63-N has only a specific domain for interacting with CypA.

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Wong, W. M. Wendy, e 黃慧雯. "A survey of nurses' preventive measures and health status in relation to the severe acute respiratory syndrome (SARS) epidemic in Hong Kong". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B45011941.

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Castaneda, Emily, e Cecilia Holmblad. "Sjuksköterskors upplevelser av att vårda personer med svår akut respiratorisk sjukdom [sars] på sjukhus : en litteraturöversikt". Thesis, Sophiahemmet Högskola, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:shh:diva-3900.

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Bakgrund Svår akut respiratorisk sjukdom [SARS] var en ny typ av atypisk lunginflammation som orsakades av ett coronavirus som tidigare enbart var känt att smittade mellan djur. År 2002 muterade detta virus och började infektera människor. 2000-talets första epidemi drog igång och över 8000 personer konstaterades smittade. Många personer som smittades blev svårt sjuka och behövde söka vård på grund av andningssvårigheter och hypoxi. Syfte Syftet var att belysa sjuksköterskans upplevelser av att vårda personer med svår akut respiratorisk sjukdom på sjukhus. Metod Den valda metoden för detta arbete var en icke-systematisk litteraturöversikt där 15 vetenskapliga artiklar inkluderades. Artiklarna som användes var både kvalitativa och kvantitativa och har kvalitetsgranskats med hjälp av Sophiahemmets Högskolas bedömningsunderlag. Insamling av artiklar har gjorts från databaserna Cinahl, PubMed och PsycINFO och analyserades med integrerad dataanalys. Resultat Resultatet visade att sjuksköterskorna upplevde stor stress, rädsla och maktlöshet. Adekvat skyddsutrustning och kunskap om smittan saknades. Sjuksköterskorna hamnade i en situation där de var tvungna att välja att antingen stanna kvar i sin profession eller leta efter arbete med mindre yrkesrisker. Många valde att stanna, detta för att de insåg att det inte fanns någon annan som kunde ta hand om dessa personer. Slutsats Trots de psykiska påfrestningarna som drabbade sjuksköterskorna kunde de med stöd av varandra ta sig igenom epidemin. Många kände att de växte i sin roll som sjuksköterska och kunde ta med sig nya lärdomar inför framtiden. Dock kunde stora brister uppdagas i sjukvården och dessa kunskapsluckor behöver fyllas med lärdomar från tidigare epidemier och pandemier inför framtida utbrott.
Background Severe acute respiratory syndrome was a new type of atypical pneumonia caused by a coronavirus that previously was known only to spread amongst animals. During late 2002 the virus mutated and started to infect people. The 21st century’s first epidemic began and over 8000 people were confirmed infected with the new disease. A lot of people became severely ill and had to seek medical care due to breathing difficulties and hypoxia. Aim The purpose was to shed light on the nurse's experiences of caring for persons with severe acute respiratory syndrome in hospitals. Method The chosen method for this paper was a non-systematic literature review in which 15 scientific articles were included. The articles included were both qualitative and quantitative and were quality reviewed with the help of Sophiahemmets University’s assessment tool. The articles were collected using the databases CINAHL, PubMed and PsycINFO and analyzed with an integrated data analysis. Results The results show that nurses experienced a high level of stress, fear and powerlessness. There was a lack of adequate protective equipment and knowledge about the disease. The nurses were forced to choose, either to stay in their profession or search for a different occupation with less risk of getting infected. A lot of nurses chose to stay, they realized that there were no one else who could take care of the patients. Conclusions Despite the psychological symptoms that affected the nurses, they realized that they could get through the epidemic with the support of each other. Many nurses felt a growth in their profession and could bring a lot of new knowledge with them for the future. A lack of knowledge was discovered in the healthcare system and there are a lot off lessons to be learned for future epidemic and pandemic outbreaks.

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Maguiña, Jorge L., Percy Soto-Becerra, Yamilee Hurtado-Roca e Roger V. Araujo-Castillo. "Laboratory tests for identification of sars-cov-2 during pandemic times in Peru: Some clarification regarding «diagnostic performance»". Instituto Nacional de Salud, 2020. http://hdl.handle.net/10757/655698.

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Attenborough, Frederick Thomas. "The singular case of SARS : medical microbiology and the vanishing of multifactorality". Thesis, Loughborough University, 2010. https://dspace.lboro.ac.uk/2134/22335.

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This thesis is about the politics and the possibilities of aetiology. Firstly, the possibilities. Does an infectious disease have one, single pathogenic cause or many, interacting causes? In the medical microbiological sciences, there is no definitive answer, one way or another, to this question: there, the conditions of aetiological possibility exist in a curious tension. Ever since the birth of the 'germ theory of disease' and the concomitant birth of the singular aetiological object, these conditions have allowed for the co-existence of a very different, and far less well understood kind of object: the multifactorial object. That SARS was caused by one, singular viral agent, a coronavirus (CoV), is now entrenched as microbiological fact. And yet, the curious thing about SARS is that the history of the 2003 outbreak is littered with moments at which the possibility of the multifactorial object presented itself to, and was actively considered by, medical microbiologists. So how did we get here - to SARS-CoV, an infectious disease that could be understood and storied in this, the most singular of ways? And what happened along the way to deny the multifactorial aetiological object any kind of existence at all? In an attempt to grapple with these questions, the thesis seeks to recover the possibility of the multifactorial object through a deep, ethnomethodological reading of the moments at which it flared up precise/y as a possibility for medical microbiologists investigating the outbreak. What emerges from that recovery operation is a sense that the multifactorial object was never actually ruled out or disproved in any way, but rather, was vanished. Put another way, the suggestion is that various medical microbiological practices and interventions, whilst establishing singularity, were serving, at the same time, to create an illusion of multifactorality's non-existence; an illusion behind which the issue of multifactorality, its possibility, could be discarded without ever having to be resolved, one way or the other. In the closing sections of this thesis a move is made towards suggesting that SARS-Co V, the singular disease, was the product of a choice-, a choice that was made to explore one aetiological possibility at the expense of another. And that is where the politics comes in. For if politics, the realm of the political, can be taken to arise in situations where various possibilities exist but not all possibilities can be chosen, then it follows that what this thesis provides is an opportunity to foreground the politics bound up with the practical doing of aetiology. As a result, and based on the experience of attempting to recover the vanished multifactorial object from the 2003 SARS outbreak, the thesis concludes with an attempt to inhabit the present in such a way as to make it possible to think, in a little more detail, about where aetiology, as understood by medical microbiologists, might be heading in the future: might recent shifts in practical, everyday, seemingly innocuous microbiological technique, have begun to make it easier to coax the multifactorial object out into a space of visibility? Might those shifts actually herald the crossing of an epistemological threshold in the medical sciences? And might the conditions of aetiological possibility be changing, and changing in ways that would drastically alter what it meant to speak of a 'disease', an 'infection' and a 'pathogen'?

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40

Mnyamana, Yanga Eddie. "Expression of human coronavirus NL63 and SARS-CoV nucleocapsid proteins for antibody production". University of the Western Cape, 2012. http://hdl.handle.net/11394/2989.

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>Magister Scientiae - MSc
Human Coronaviruses (HCoVs) are found within the family Coronaviridae (genus, Coronavirus) and are enveloped, single-stranded, positive-sense RNA viruses. Infections of humans by coronaviruses are not normally associated with severe diseases. However, the identification of the coronavirus responsible for the outbreak of severe acute respiratory syndrome (SARS-CoV) showed that highly pathogenic coronaviruses can enter the human population. The SARS-CoV epidemic resulted in 8 422 cases with 916 deaths globally (case fatality rate: 10.9%). In 2004 a group 1 Coronavirus, designated Human Coronavirus NL63 (HCoV-NL63), was isolated from a 7 month old Dutch child suffering from bronchiolitis. In addition, HCoV-NL63 causes disease in children (detected in approximately 10% of respiratory tract infections), the elderly and the immunocompromised. This study was designed to express the full length nucleocapsid (N) proteins of HCoV-NL63 and SARS-CoV for antibody production in an animal model. The NL63-N/pFN2A and SARSN/ pFN2A plasmid constructs were used for this study. The presence of the insert on the Flexi ® vector was confirmed by restriction endonuclease digest and sequence verification. The sequenced chromatographs obtained from Inqaba Biotec were consistent with sequences from the NCBI Gen_Bank. Proteins were expressed in a KRX Escherichia coli bacterial system and analysed using 15% SDS-PAGE and Western Blotting. Thereafter, GST-tagged proteins were purified ith an affinity column purification system. Purified fusion proteins were subsequently cleaved with Pro-TEV Plus protease, separated on 15% SDS-PAGE gel and stained with Coomassie Brilliant Blue R250. The viral fusion proteins were subsequently used to immunize Balbc mice in order to produce polyclonal antibodies. A direct ELISA was used to analyze and validate the production of polyclonal antibodies by the individual mice. This is a preliminary study for development of diagnostic tools for the detection of HCoV-NL63 from patient samples collected in the Western Cape.
South Africa

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41

Wu, Chia Jung. "Effectiveness of a specific infection control education program for Taiwanese nursing students". Thesis, Queensland University of Technology, 2007. https://eprints.qut.edu.au/16541/1/Chia-Jung_Wu_Thesis.pdf.

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The purpose of the study The purpose of this research project was to develop and test an educational program for preparing Taiwanese nursing students for clinical practice. Study background The SARS outbreak revealed that health care professionals were ill-prepared for coping with the disease epidemic in terms of the rapid transmission of the infection, the high mortality and morbidity rate among health care workers, and the significant impacts on the public and health care personnel. Frontline nurses were the group at highest risk of becoming infected, as they are the health care personally that provide direct health care to infected patients. However, to date the ability of Taiwanese frontline nurses to respond to such a disease epidemic has not been examined. Study design This research project incorporated a three phase design, presented in the form of two separate studies. A small qualitative exploratory study was undertaken to validate the assumptions emerging from international literature regarding the preparedness nurses in managing an infection outbreak. The information gained was used to construct an infection control education program (Study I). A quasi-experimental design, using pre- and post-tests and experimental and control groups was then used to test the effectiveness of the education intervention (Study II). Participants A purposive sampling technique was used in the qualitative exploratory study, whereby six Taiwanese nurses who had provided direct nursing care to patients with SARS were interviewed. A convenience sampling approach was utilised in the quantitative study, which aimed to test the effectiveness of educational intervention. This, second study, had 175 participants in total, 80 in the experimental group and 95 in the control group. All participants were enrolled in the first semester of their fourth year in a five-year nursing program in two selected junior nursing colleges. The education intervention The purpose-designed standard and additional precautions (SnAP) program was the intervention. The experimental group received a SnAP program which consisted of 16 hours of classes over 16 weeks. The control group received a conventional education program. Data collection and instrument Data were collected at three time points during the study (baseline, four months, six month) using validated instrument. The reliability and validity of the instrument was established in a pilot study with a Taiwanese population prior to the present study. Data analysis t-tests and chi-square analyses were performed to assess any differences across demographic variables and baseline outcome variables between the experimental and control groups. Two-way repeated measures ANOVAs were used to examine the scores of the intervention and control groups across three time points. Results The data revealed that, at six months following the education program, there was a statistically significant improvement in the knowledge (F [2,180] =13.53, p=0.001) and confidence (F [2,94] =4.88, p= 0.01) of infection precautions in the intervention group compared to the control group. Also, the means of knowledge and confidence in intervention group showed a consistently increased across three time points; whereas, the mean of confidence relating infection control management in the control group resulted a drop at time 3. Although the application skills relating to infection control procedures did not show a statistically significant change during this period (F [2, 174] = 2.54, p=0.081), there were minor improvements in these scores at the six-month follow-up assessment. Conclusion The SnAP program had a positive impact on Taiwanese nursing students' readiness for clinical placement and potential outbreak of disease epidemics. Participation increased their knowledge about infection control precautions, their ability to properly use these specific precautions, and their confidence in solving infection-related issues in clinical practice.

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42

Wu, Chia Jung. "Effectiveness of a specific infection control education program for Taiwanese nursing students". Queensland University of Technology, 2007. http://eprints.qut.edu.au/16541/.

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The purpose of the study The purpose of this research project was to develop and test an educational program for preparing Taiwanese nursing students for clinical practice. Study background The SARS outbreak revealed that health care professionals were ill-prepared for coping with the disease epidemic in terms of the rapid transmission of the infection, the high mortality and morbidity rate among health care workers, and the significant impacts on the public and health care personnel. Frontline nurses were the group at highest risk of becoming infected, as they are the health care personally that provide direct health care to infected patients. However, to date the ability of Taiwanese frontline nurses to respond to such a disease epidemic has not been examined. Study design This research project incorporated a three phase design, presented in the form of two separate studies. A small qualitative exploratory study was undertaken to validate the assumptions emerging from international literature regarding the preparedness nurses in managing an infection outbreak. The information gained was used to construct an infection control education program (Study I). A quasi-experimental design, using pre- and post-tests and experimental and control groups was then used to test the effectiveness of the education intervention (Study II). Participants A purposive sampling technique was used in the qualitative exploratory study, whereby six Taiwanese nurses who had provided direct nursing care to patients with SARS were interviewed. A convenience sampling approach was utilised in the quantitative study, which aimed to test the effectiveness of educational intervention. This, second study, had 175 participants in total, 80 in the experimental group and 95 in the control group. All participants were enrolled in the first semester of their fourth year in a five-year nursing program in two selected junior nursing colleges. The education intervention The purpose-designed standard and additional precautions (SnAP) program was the intervention. The experimental group received a SnAP program which consisted of 16 hours of classes over 16 weeks. The control group received a conventional education program. Data collection and instrument Data were collected at three time points during the study (baseline, four months, six month) using validated instrument. The reliability and validity of the instrument was established in a pilot study with a Taiwanese population prior to the present study. Data analysis t-tests and chi-square analyses were performed to assess any differences across demographic variables and baseline outcome variables between the experimental and control groups. Two-way repeated measures ANOVAs were used to examine the scores of the intervention and control groups across three time points. Results The data revealed that, at six months following the education program, there was a statistically significant improvement in the knowledge (F [2,180] =13.53, p=0.001) and confidence (F [2,94] =4.88, p= 0.01) of infection precautions in the intervention group compared to the control group. Also, the means of knowledge and confidence in intervention group showed a consistently increased across three time points; whereas, the mean of confidence relating infection control management in the control group resulted a drop at time 3. Although the application skills relating to infection control procedures did not show a statistically significant change during this period (F [2, 174] = 2.54, p=0.081), there were minor improvements in these scores at the six-month follow-up assessment. Conclusion The SnAP program had a positive impact on Taiwanese nursing students' readiness for clinical placement and potential outbreak of disease epidemics. Participation increased their knowledge about infection control precautions, their ability to properly use these specific precautions, and their confidence in solving infection-related issues in clinical practice.

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43

McBryde, Emma Sue. "Mathematical and statistical modelling of infectious diseases in hospitals". Queensland University of Technology, 2006. http://eprints.qut.edu.au/16330/.

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Antibiotic resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE), are an increasing burden on healthcare systems. Hospital acquired infections with these organisms leads to higher morbidity and mortality compared with the sensitive strains of the same species and both VRE and MRSA are on the rise worldwide including in Australian hospitals. Emerging community infectious diseases are also having an impact on hospitals. The Severe Acute Respiratory Syndrome virus (SARS Co-V) was noted for its propensity to spread throughout hospitals, and was contained largely through social distancing interventions including hospital isolation. A detailed understanding of the transmission of these and other emerging pathogens is crucial for their containment. The statistical inference and mathematical models used in this thesis aim to improve understanding of pathogen transmission by estimating the transmission rates of contagions and predicting the impact of interventions. Datasets used for these studies come from the Princess Alexandra Hospital in Brisbane, Australia and Shanxi province, mainland China. Epidemiological data on infection outbreaks are challenging to analyse due to the censored nature of infection transmission events. Most datasets record the time on symptom onset, but the transmission time is not observable. There are many ways of managing censored data, in this study we use Bayesian inference, with transmission times incorporated into the augmented dataset as latent variables. Hospital infection surveillance data is often much less detailed that data collected for epidemiological studies, often consisting of serial incidence or prevalence of patient colonisation with a resistant pathogen without individual patient event histories. Despite the lack of detailed data, transmission characteristics can be inferred from such a dataset using structured HiddenMarkovModels (HMMs). Each new transmission in an epidemic increases the infection pressure on those remaining susceptible, hence infection outbreak data are serially dependent. Statistical methods that assume independence of infection events are misleading and prone to over-estimating the impact of infection control interventions. Structured mathematical models that include transmission pressure are essential. Mathematical models can also give insights into the potential impact of interventions. The complex interaction of different infection control strategies, and their likely impact on transmission can be predicted using mathematical models. This dissertation uses modified or novel mathematical models that are specific to the pathogen and dataset being analysed. The first study estimates MRSA transmission in an Intensive Care Unit, using a structured four compartment model, Bayesian inference and a piecewise hazard methods. The model predicts the impact of interventions, such as changes to staff/patient ratios, ward size and decolonisation. A comparison of results of the stochastic and deterministic model is made and reason for differences given. The second study constructs a Hidden Markov Model to describe longitudinal data on weekly VRE prevalence. Transmission is assumed to be either from patient to patient cross-transmission or sporadic (independent of cross-transmission) and parameters for each mode of acquisition are estimated from the data. The third study develops a new model with a compartment representing an environmental reservoir. Parameters for the model are gathered from literature sources and the implications of the environmental reservoir are explored. The fourth study uses a modified Susceptible-Exposed-Infectious-Removed (SEIR) model to analyse data from a SARS outbreak in Shanxi province, China. Infectivity is determined before and after interventions as well as separately for hospitalised and community symptomatic SARS cases. Model diagnostics including sensitivity analysis, model comparison and bootstrapping are implemented.

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44

McBryde, Emma Sue. "Mathematical and statistical modelling of infectious diseases in hospitals". Thesis, Queensland University of Technology, 2006. https://eprints.qut.edu.au/16330/1/Emma_McBryde_Thesis.pdf.

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Antibiotic resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE), are an increasing burden on healthcare systems. Hospital acquired infections with these organisms leads to higher morbidity and mortality compared with the sensitive strains of the same species and both VRE and MRSA are on the rise worldwide including in Australian hospitals. Emerging community infectious diseases are also having an impact on hospitals. The Severe Acute Respiratory Syndrome virus (SARS Co-V) was noted for its propensity to spread throughout hospitals, and was contained largely through social distancing interventions including hospital isolation. A detailed understanding of the transmission of these and other emerging pathogens is crucial for their containment. The statistical inference and mathematical models used in this thesis aim to improve understanding of pathogen transmission by estimating the transmission rates of contagions and predicting the impact of interventions. Datasets used for these studies come from the Princess Alexandra Hospital in Brisbane, Australia and Shanxi province, mainland China. Epidemiological data on infection outbreaks are challenging to analyse due to the censored nature of infection transmission events. Most datasets record the time on symptom onset, but the transmission time is not observable. There are many ways of managing censored data, in this study we use Bayesian inference, with transmission times incorporated into the augmented dataset as latent variables. Hospital infection surveillance data is often much less detailed that data collected for epidemiological studies, often consisting of serial incidence or prevalence of patient colonisation with a resistant pathogen without individual patient event histories. Despite the lack of detailed data, transmission characteristics can be inferred from such a dataset using structured HiddenMarkovModels (HMMs). Each new transmission in an epidemic increases the infection pressure on those remaining susceptible, hence infection outbreak data are serially dependent. Statistical methods that assume independence of infection events are misleading and prone to over-estimating the impact of infection control interventions. Structured mathematical models that include transmission pressure are essential. Mathematical models can also give insights into the potential impact of interventions. The complex interaction of different infection control strategies, and their likely impact on transmission can be predicted using mathematical models. This dissertation uses modified or novel mathematical models that are specific to the pathogen and dataset being analysed. The first study estimates MRSA transmission in an Intensive Care Unit, using a structured four compartment model, Bayesian inference and a piecewise hazard methods. The model predicts the impact of interventions, such as changes to staff/patient ratios, ward size and decolonisation. A comparison of results of the stochastic and deterministic model is made and reason for differences given. The second study constructs a Hidden Markov Model to describe longitudinal data on weekly VRE prevalence. Transmission is assumed to be either from patient to patient cross-transmission or sporadic (independent of cross-transmission) and parameters for each mode of acquisition are estimated from the data. The third study develops a new model with a compartment representing an environmental reservoir. Parameters for the model are gathered from literature sources and the implications of the environmental reservoir are explored. The fourth study uses a modified Susceptible-Exposed-Infectious-Removed (SEIR) model to analyse data from a SARS outbreak in Shanxi province, China. Infectivity is determined before and after interventions as well as separately for hospitalised and community symptomatic SARS cases. Model diagnostics including sensitivity analysis, model comparison and bootstrapping are implemented.

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45

"Severe acute respiratory syndrome (SARS): from diagnosis to clinical management". Thesis, 2006. http://library.cuhk.edu.hk/record=b6074339.

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In part ONE of this thesis, including the most up to date information on SARS virology, disease transmission, pathogenesis and laboratory diagnosis will be summarized and presented, including the results of many studies in which I have participated (these references will be underlined as they appear in text). This of course summarizes knowledge that is now known in 2006 but was largely unknown during the initial outbreak. In part TWO, six original clinical studies performed at PWH will be presented: study (1) describes the clinical manifestations and severity of SARS, and its potential to cause major hospital outbreaks; (2) demonstrates the importance of epidemiological linkage in diagnosing SARS; (3) reports the clinical outcomes of a stepwise treatment protocol, which includes the use of corticosteroid therapy as an immunomodulant; (4) demonstrates that corticosteroid therapy can retard viral clearance, and should be used judiciously; (5) demonstrates that a more robust humoral response is associated with severe SARS, thus indicating that passive immunity treatment strategies seem only suitable either during early illness or as prophylaxis; and (6) shows that SARS has few early discriminating laboratory features compared to other causes of community-acquired pneumonia, thus a high index of suspicion is needed to recognize this infection in the absence of worldwide transmission. A thorough review of the relevant published material will be included in the discussion section of each study.
Severe Acute Respiratory Syndrome (SARS) is an emerging infectious disease caused by a novel coronavirus. It caused a global outbreak in 2003, resulting in more than 8000 infections, 700 deaths, and major social and economic disruption. In the initial phase of the SARS outbreak, the medical profession had no knowledge regarding the responsible pathogen, nor the clinical manifestations of SARS and the course of illness. There was no reliable diagnostic tool and no known effective therapy. But for the first time in medical history, we witnessed the rapid accumulation of knowledge on a disease as it evolved, which in turn assisted its management and control.
Since conducting randomized-controlled trials during the 2003 crisis was almost impossible, most of the presented studies are either descriptive or case-controlled in design. However, these studies have laid foundations for recent and future research into the clinical diagnosis and management of SARS. Moreover, the construction of the SARS clinical database has contributed to the work of other investigators, which has resulted in over thirty-six publications. It is my hope that these research endeavors can contribute to the understanding of this emerging, deadly disease.
Lee Lai Shun, Nelson.
"April 2006."
Source: Dissertation Abstracts International, Volume: 69-01, Section: B, page: 0205.
Thesis (M.D.)--Chinese University of Hong Kong, 2007.
Includes bibliographical references (p. 264-292).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Abstracts in English and Chinese.
School code: 1307.

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46

"Substrate specificity of severe acute respiratory syndrome coronavirus main protease". 2006. http://library.cuhk.edu.hk/record=b5896512.

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Chong Lin-Tat.
Thesis (M.Phil.)--Chinese University of Hong Kong, 2006.
Includes bibliographical references (leaves 76-78).
Abstracts in English and Chinese.
Chapter Chapter 1 --- introduction
Chapter 1.1 --- Severe acute respiratory syndrome Coronavirus (SARS CoV) --- p.13
Figure 1.1 Genome organization and putative functional ORFs of SARS CoV --- p.14
Chapter 1.2 --- SARS main protease
Chapter 1.2.1 --- Three dimensional structure --- p.15
Figure 1.2 Ribbon illustration of the SARS-coronavirus main protease --- p.17
Figure 1.3 Surface representations of P1 and P2 substrate-binding pocket of main protease --- p.18
Chapter 1.2.2 --- Substrate specificities --- p.19
Table 1.1. Eleven predicted cleavage sites of SARS CoV main protease --- p.21
Chapter 1.3 --- Protein-based FRET assay system --- p.22
Figure 1.4. The principle of fluorescent resonance energy transfer (FRET) --- p.24
Chapter 1.4 --- Objectives --- p.25
Chapter Chapter 2 --- Materials and Methods
Chapter 2.1 --- General Techniques
Chapter 2.1.1 --- Preparation and transformation of competent E. coli DH5a and23 BL21 (DE3)pLysS --- p.26
Chapter 2.1.2 --- Minipreparation of plasmid DNA (Invitrogen) --- p.27
Chapter 2.1.3 --- Spectrophotometric quantitation DNA --- p.28
Chapter 2.1.4 --- Agarose gel electrophoresis
Chapter 2.1.5 --- Purification of DNA from agarose gel (Invitrogen)
Chapter 2.1.6 --- Restriction digestion of DNA fragments --- p.29
Chapter 2.1.7 --- Ligation of DNA fragments into vector
Table 2.1. Standard recipe of ligation reaction --- p.30
Chapter 2.1.8 --- SDS-PAGE electrophoresis --- p.31
Table 2.2. Standard recipe of separating gel for SDS-PAGE --- p.32
Table 2.3. Standard recipe of stacking gel for SDS-PAGE --- p.33
Chapter 2.2 --- Sub-cloning and site-directed mutagenesis
Chapter 2.2.1 --- Sub-cloning of SARS Co V main protease --- p.34
Chapter 2.2.2 --- Sub-cloning of Substrate
Chapter 2.2.3 --- Site-directed mutagenesis of substrate variant --- p.35
Table 2.4 Primer sequence for generating substrate variants --- p.36
Table 2.5. Standard recipe of Polymerase Chain Reaction (PCR) --- p.40
Table 2.6. Polymerase Chain Reaction (PCR) profile --- p.41
Chapter 2.3 --- Sample preparation
Chapter 2.3.1 --- Expression of recombinant proteins --- p.42
SARS CoV main protease
Substrate and substrate variants
Chapter 2.3.2 --- Purification of recombinant proteins
SARS CoV main protease
Substrate and substrate variants
Chapter 2.4 --- Protein-based FRET kinetic analysis --- p.45
Chapter 2.5 --- A model for substrate-enzyme binding by docking simulation --- p.46
Chapter Chapter 3 --- Results
Chapter 3.1 --- Preparation of SARS CoV main protease and substrate
Chapter 3.1.1 --- Expression and purification of SARS main protease --- p.48
Figure 3.1. Purification profile of SARS CoV main protease --- p.49
Chapter 3.1.2 --- Expression and purification of substrate and substrate variants --- p.50
Figure 3.2. Purification profile of substrate and substrate variants --- p.51
Chapter 3.2 --- A novel protein-based FRET assay system was established
Chapter 3.2.1 --- "With the cleavage of active main protease, absorbance at 528nm dropped while signal at 485nm were slightly increased" --- p.52
Figure 3.3. Absorbance at 528nm dropped and 485nm increased with the substrate hydrolysis --- p.53
Chapter 3.2.2 --- FRET efficiency ratio (528/485) decreased over time --- p.54
Figure 3.4. FRET efficiency ratio (528/485) decreased over time --- p.55
Chapter 3.2.3 --- Comparable kcat/Km value of SARS CoV main protease was obtained --- p.56
Figure 3.5. Catalytic parameter (kcat/ Km) was determined from the slope of straight Line --- p.57
Chapter 3.3 --- Main protease activity towards substrate variants at different substrate-binding sites (S2'-S2) --- p.58
Table 3.1. Kinetic parameterrs of 76 substrate variants in descending order --- p.59
Chapter 3.3.1 --- S2'substrate-binding site --- p.60
Chapter 3.3.2 --- S1' substrate-b inding site
Chapter 3.3.3 --- S1 substrate-binding site
Chapter 3.3.4 --- S2 substrate-binding site
Figure 3.6. Kinetic analysis of some typical substrate variants against main protease --- p.62
Figure 3.7. SDS-PAGE analysis of some typical substrate variants against main protease --- p.63
Chapter Chapter 4 --- Discussion
Chapter 4.1 --- Quantitative and high-throughput analysis by protein-based FRET assay system --- p.64
Chapter 4.2 --- Substrate specificities of SARS CoV main protease at S2'-S2 subsites
Chapter 4.2.1 --- β-strand conformation was preferred at S2，subsite
Chapter 4.2.2 --- Residues with small aliphatic side chain were preferred at S1 ´ة subsite --- p.65
Chapter 4.2.3 --- "Glutamine at S1 subsite was absolutely conserved, but alternatives were disclosed" --- p.66
Figure 4.1. Glutamine was not absolutely conserved in S1 subsite --- p.67
Chapter 4.2.4 --- Hydrophilic residues were tolerated at S2 subsite --- p.68
Figure 4.2. Hydrophilic residues were tolerated at S2 subsite --- p.70
Table 4.1. Summary of types of residues preferred at individual subsites --- p.71
Chapter 4.3 --- Predicted conformation of substrate towards SARS CoV main protease at S2' and S1' subsites --- p.72
Figure 4.3. Small residues were preferred at S1´ة subsite and Val at S2' subsite was more favoured than the native one --- p.73
Chapter Chapter 5 --- Summary --- p.74
Chapter Chapter 6 --- Future work --- p.75
References --- p.76

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47

"Molecular characterization of the nucleocapsid protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV)". 2005. http://library.cuhk.edu.hk/record=b5892806.

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Poon Wing Ming Jodie.
Thesis (M.Phil.)--Chinese University of Hong Kong, 2005.
Includes bibliographical references (leaves 207-233).
Abstracts in English and Chinese.
Acknowledgements --- p.i
Abstract --- p.ii
論文摘要 --- p.iv
Abbreviations --- p.v
List of Figures --- p.x
List of Tables --- p.xiii
Contents --- p.xiv
Chapter CHAPTER ONE --- INTRODUCTION --- p.1
Chapter 1.1. --- Severe Acute Respiratory Syndrome (SARS) --- p.1
Chapter 1.1.1. --- Background of SARS --- p.1
Chapter 1.1.2. --- Etiology and pathology of SARS --- p.3
Chapter 1.1.3. --- Genome organization and expression of SARS-CoV --- p.5
Chapter 1.1.4. --- Current molecular advances of SARS-CoV --- p.13
Chapter 1.1.5. --- Current research advances on SARS-CoV nucleocapsid --- p.18
Chapter 1.1.6. --- Current diagnostic assays of SARS-CoV infection --- p.23
Chapter 1.1.7. --- Current treatment --- p.25
Chapter 1.1.8. --- Vaccine development --- p.27
Chapter 1.2. --- Aims of study --- p.30
Chapter CHAPTER TWO --- MATERIALS AND METHODS --- p.33
Chapter 2.1. --- Subcellular localization study of the SARS-CoV nucleocapsid protein --- p.33
Chapter 2.1.1. --- "Cloning of SARS-CoV nucleocapsid cDNA into the green fluorescence protein (GFP) mammalian expression vector, pEGFP-C1" --- p.33
Chapter 2.1.1.1. --- Amplification of SARS-CoV nucleocapsid gene by polymerase chain reaction (PCR) --- p.33
Chapter 2.1.1.2. --- Purification of PCR products --- p.35
Chapter 2.1.1.3. --- Restriction digestion of purified PCR products and the circular pEGFP-C 1 vector --- p.36
Chapter 2.1.1.4. --- Ligation --- p.36
Chapter 2.1.1.5. --- Preparation of chemically competent bacterial cell E.coli strain DH5a for transformation --- p.37
Chapter 2.1.1.6. --- Transformation of ligation product into chemically competent bacterial cells --- p.38
Chapter 2.1.1.7. --- Small-scale preparation of bacterial plasmid DNA --- p.39
Chapter 2.1.1.8. --- Screening for recombinant clones --- p.40
Chapter 2.1.1.9. --- DNA sequencing of cloned plasmid DNA --- p.41
Chapter 2.1.1.10. --- Midi-scale preparation of recombinant plasmid DNA --- p.42
Chapter 2.1.2. --- Cell culture --- p.44
Chapter 2.1.2.1. --- Sub-culture of VeroE6 and HepG2 cell lines --- p.44
Chapter 2.1.2.2. --- Transient transfection of GFP fusion construct --- p.45
Chapter 2.1.3. --- Epi-fluorescent microscopy --- p.46
Chapter 2.2. --- Study on differential gene expression patterns upon SARS-CoV nucleocpasid induction by cDNA microarray analysis --- p.48
Chapter 2.2.1. --- Cloning of SARS-CoV N gene into mammalian expression vector pCMV-Tagl --- p.48
Chapter 2.2.2. --- Cell culture --- p.50
Chapter 2.2.2.1. --- Sub-culture of VeroE6 cell line --- p.50
Chapter 2.2.2.2. --- Transient transfection of pCMV-Tag1 -SAR-CoV N construct --- p.50
Chapter 2.2.3. --- Total RNA isolation --- p.51
Chapter 2.2.3.1. --- Total RNA isolation by RNeasy Mini Kit --- p.51
Chapter 2.2.3.2. --- Checking of RNA integrity --- p.53
Chapter 2.2.3.3. --- Checking of RNA purity --- p.54
Chapter 2.2.3.4. --- Determinations of total RNA concentrations and precipitation --- p.54
Chapter 2.2.4. --- cDNA microarray (done by Affymetrix Inc. as a customer service) --- p.55
Chapter 2.2.4.1. --- Precipitation of RNA --- p.55
Chapter 2.2.4.2. --- Quantification of RNA --- p.56
Chapter 2.2.4.3. --- Synthesis of double-stranded cDNA from total RNA --- p.56
Chapter (i) --- First stand cDNA synthesis --- p.56
Chapter (ii) --- Second cDNA synthesis --- p.57
Chapter 2.2.4.4. --- Clean-up of double stranded cDNA --- p.58
Chapter (i) --- Phase lock gel-phenol/ chloroform extraction --- p.58
Chapter (ii) --- Ethanol precipitation --- p.58
Chapter 2.2.4.5. --- Synthesis of biotin-labeled cRNA --- p.59
Chapter 2.2.4.6. --- Clean-up and quantification of in vitro transcription (IVP) products --- p.59
Chapter (i) --- In vitro transcription clean-up --- p.59
Chapter (ii) --- Ethanol precipitation --- p.60
Chapter (iii) --- Quantitation of cRNA --- p.60
Chapter (iv) --- Sample checking --- p.60
Chapter 2.2.4.7. --- cRNA fragmentation for target preparation --- p.60
Chapter 2.2.4.8. --- Eukaryotic target hybridization --- p.61
Chapter 2.2.4.9. --- "Probe array washing, staining and scanning" --- p.62
Chapter 2.2.5. --- Confirmation of results by RT-PCR --- p.62
Chapter 2.2.5.1. --- First-strand cDNA synthesis --- p.62
Chapter 2.2.5.2. --- RT-PCR of candidate gene --- p.63
Chapter 2.3. --- In vitro RNA interference of SARS-CoV nucleocapsid --- p.66
Chapter 2.3.1. --- siRNA target site selection --- p.66
Chapter 2.3.2. --- Cloning of target siRNA sequences into pSilencer 3.1-H1 vector --- p.71
Chapter 2.3.3. --- Cell culture --- p.72
Chapter 2.2.3.1. --- Sub-culture ofVeroE6 cells --- p.72
Chapter 2.3.3.2. --- Transient co-transfection --- p.72
Chapter 2.3.4. --- Detection of SARS-CoV nucleocapsid mRNA expression level by RT-PCR --- p.73
Chapter 2.3.4.1. --- Total RNA isolation by TRIzol reagent --- p.73
Chapter 2.3.4.2. --- First-strand cDNA synthesis --- p.74
Chapter 2.3.4.3. --- RT-PCR assays --- p.74
Chapter 2.3.5. --- Detection of SARS-CoV nucleocapsid protein expression level by Western blotting --- p.75
Chapter 2.3.5.1. --- Total protein extraction --- p.75
Chapter 2.3.5.2. --- Protein quantification --- p.75
Chapter 2.3.5.3. --- Protein separation by SDS-PAGE and Western blot --- p.76
Chapter 2.3.5.4. --- Western blot analysis --- p.78
Chapter 2.4. --- Human fgl2 prothrombinase promoter analyses --- p.80
Chapter 2.4.1. --- Cloning of the full-length human fgl2 prothrombinase promoter construct into a promoterless mammalian expression vector-pGL3-Basic --- p.80
Chapter 2.4.2. --- Cloning of SARS-CoV Membrane gene into the mammalian expression vector pCMV-Tagl --- p.82
Chapter 2.4.3. --- Cell culture --- p.84
Chapter 2.4.3.1. --- Sub-culture of HepG2 and VeroE6 cell lines --- p.84
Chapter 2.4.3.2. --- "Transient co-transfection of the full-length human fgl2 prothrombinase promoter construct with the pCMV-Tagl empty vector, pCMV-Tagl-SARS-CoV M expression vector, or pCMV-Tag1 -SARS-CoV N expression vector" --- p.84
Chapter 2.4.4. --- Dual-luciferase reporter assay --- p.85
Chapter 2.4.5. --- Detection of fgl2 mRNA expression level under the induction of SARS-CoV nucleocapsid protein by RT-PCR --- p.86
Chapter 2.4.5.1. --- Total RNA isolation by TRIzol reagent --- p.86
Chapter 2.4.5.2. --- First strand cDNA synthesis --- p.86
Chapter 2.4.5.3. --- RT-PCR of fgl2 gene --- p.87
Chapter CHAPTER THREE --- RESULTS --- p.88
Chapter 3.1. --- Computer analysis of SARS-CoV Nucleocapsid --- p.88
Chapter 3.2. --- Subcellular localization of SARS-CoV nucleopcasid protein in VeroE6 cells and HepG2 cells --- p.102
Chapter 3.3. --- cDNA microarray analysis on differential gene expression pattern upon the over-expression of SARS-CoV Nucleocapsid gene --- p.114
Chapter 3.4. --- In vitro RNA Interference of SARS nucleocapsid --- p.129
Chapter 3.5. --- Transactivation of fgl2 prothrombinase gene promoter by SARS-CoV nucleocapsid protein in HepG2 and VE6 cells --- p.138
Chapter CHAPTER FOUR --- DISCUSSION --- p.155
Chapter 4.1. --- "The EGFP-tagged SARS-CoV N protein was localized in the cytoplasm only in VE6 cells, but translocated into both cytoplasm and nucleus in HepG2 cellsin the epi-fluorescence microscopy study" --- p.155
Chapter 4.2. --- cDNA microarray demonstrated alternations of mRNA transcript level on a number of genes belonging to various functional classes upon over expression of SARS-CoV nucleocapsid gene --- p.162
Chapter 4.3. --- RNA interference demonstrated effective gene silencing of SARS-CoV nucleocapsid gene --- p.171
Chapter 4.4. --- SASR-CoV nucleocapsid protein induced the promoter activity of the prothrombinase fibrinogen-like protein2/ fibroleukin (fgl2) gene --- p.191
Chapter 4.5. --- Conclusion --- p.196
Chapter 4.6. --- Future work --- p.198
Appendices --- p.199
References --- p.207

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48

Liu, Te-Chu, e 劉德菊. "Clinical Manifestations and Death Related Factors in Patients with Severe Acute Respiratory Syndrome (SARS)". Thesis, 2007. http://ndltd.ncl.edu.tw/handle/54845367517499395151.

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碩士
長庚大學
護理學研究所
95
The purpose of this study was to understand the clinical manifestations and death related factors in patients with severe acute respiratory syndrome (SARS). Between August 2003 and February 2004, 78 patients with probable SARS seen at some South, North Medical center included in this retrospective study. Utilize SARS structural questionnaire to collect the data. Data were analyzed using descriptive and inferential Statistics with the SPSS software package, version 10.0 for Windows. The main findings are as follows: (1) Of the 78 patients with probable SARS (Mean ages, 44 years; SD, 18 years; range, 13-84 years), 24 were male (30.8%) and 54 were female (69.2%). Nosomical infection (56.4%) is the major cause for SARS. (2)The earliest symptoms appearing as follows: fever (98.7%), cough (48.7%), myalgia (24.4%), short of breath(21.8%), chillness and weakness (20.5%). (3)The laboratory findings included leucopenia (on hospital admission, 23.4%; during hospitalization, 50%), leukocytosis (on hospital admission, 16.9%; during hospitalization, 53.1%), thrombocytopenia (on hospital admission, 35.1%; during hospitalization, 56%), elevated segment (on hospital admission, 58.4%; during hospitalization, 84.4%), lymphopenia (on hospital admission, 68.8%; during hospitalization, 84.4%), elevated CPK (on hospital admission, 27%; during hospitalization, 36.4%), LDH (on hospital admission, 28.4%; during hospitalization, 57.9%), GOT (on hospital admission, 35.3%; during hospitalization, 100%), GPT (on hospital admission, 21.2%; during hospitalization, 71.4%), CRP (on hospital admission, 77.8%; during hospitalization, 91.2%). (4)The patients had abnormal findings on chest radiographs (on hospital admission, 71.8%; during hospitalization, 97.4%) became serious at a mean time of 7.1± 6.6 days after hospitalized. (5)The sample for SARS-CoV was positive in 47 of the 78 patients (60.3%) in whom the test was performed. (6)Mortality was 24 of the 78 patients (30.8% ). (7)Age (t=-4.9,p<0.001), married (χ2=10.819,p=0.004), education background (χ2=13.200,p=0.040), the medical relevant personnel (p=0.004), the past history of cancer (p=0.003), the past history of pulmonary disease (p=0.002) , intubations (p<0.001), the first time of leukocyte and segment on the first week and second week , the first time of lymphocyte on the second week (t=2.998,p=0.004) during hospitalization, the second week (t=-4.393, p<0.001) and the third week(t=-2.796,p=0.008) on chest radiograph during hospitalization were associated with death. (8) Logistic regression analysis showed that intubations was the only significant predictor of death (OR=115,p＜0.001).

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49

Huang, Hsien-Hao, e 黃獻皞. "The Impact of Severe Acute Respiratory Syndrome (SARS) on Emergency Department Census and Cost". Thesis, 2006. http://ndltd.ncl.edu.tw/handle/99349343733494924853.

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碩士
國立陽明大學
急重症醫學研究所
94
Background and Purpose: The immediate and long-term impact of severe acute respiratory syndrome (SARS) outbreak on emergency department (ED) visits and hospital expenditures for these visits has not been thoroughly investigated. The objectives of this retrospective observational study investigated the impact of SARS outbreak on the ED visits and the cost of these visits in a designed SARS medical center. Methods: Data related to total ED visits and their costs were collected for the SARS epidemic period in 2003 and the same period in the preceding year in 2002. Data collected included total ED visits, services provided, triage categories, and total expenditures for all patients. Data were retrieved and compared before and during the outbreak. Results: In demographic data, there is a significant decreases in patients attendances with a mean reduction of 92.5 ± 8.3 (43.7% ± 3.9% in reduction rate, P< 0.01) during peak- versus pre-epidemic stages, but without changes in patients’ age and gender. The numbers of patient with ambulance transport, inter-hospital referral, and critical illness, including dead on arrival, categorized to triage 1 or admitted to intensive care unit after ED visits, were not influenced by SARS epidemics. There are statistically significant decreases in mean attendances of patients with cardiovascular diseases, inflammatory or functional bowel disease, endocrine diseases, dizziness or vertigo, and trauma (P< 0.05), respectively, in peak- as compared to those in pre- and early-epidemic stages. As compared with data from the same time in 2002, the reduction in daily ED visits reached 51.6% at the peak of SARS epidemic (p < 0.01). In pediatric, trauma and non-trauma patients, the maximum mean decreases in number of visits were 80.0% (p < 0.01), 57.6% (p < 0.01) and 40.8% (p < 0.01), respectively. In triage 1, 2 and 3 patients, the maximum mean decreases were 18.1% (p < 0.01), 55.9% (p < 0.01) and 53.7% (p < 0.01). The maximal decrease of total costs was 37.7% (p < 0.01). The maximum mean costs per patient increased 35.9% (p < 0.01). The proportions of increases in mean costs of each patient were attributed to laboratory investigations (31.4%), radiography (21.9%) and medications (29.5%). Conclusions: The SARS outbreak did not eliminate the need of critical illness patients for advanced medical supports but resulted in a marked reduction of ED visits which persisted for 3 months after the end of the epidemic. Total cost of treating individual patients showed a simultaneous marked increase, while overall operational costs in the ED showed a marked decrease. The increased total cost of each patient was attributed to the increased number of diagnostic procedures to screen for the possible SARS in the ED.

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50

Shen, Hsiao-Mei, e 沈孝梅. "Factors Associated with Strategic Management of Hospitals Response for Severe Acute Respiratory Syndrome (SARS)". Thesis, 2005. http://ndltd.ncl.edu.tw/handle/96639653888296645540.

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碩士
臺北醫學大學
醫務管理學系
93
In April 2003 is no doubt one of the most unforgettable month to all human beings living in this global village. Taiwanese was not fortunate enough to be the exception. The society was deeply shaken by acute respiratory syndrome (SARS). The calamity of SARS swept off the island with unexpected overwhelming speed. Furthermore, from the day when all patients, hospital workers and visitors were quarantined within the building of Ho-Pin hospital, no one on this island could escape from the dreadful SARS nightmare. SARS not only took high social medical cost but also exposed the problem of Taiwan hospitals’ emergency problem-solving ability. We hope SARS or other similar tragedy will never return. However, we should take the lesson and the story of SARS should be wisely investigated. Well —structured and thoughtful research is expected to serve as a preparation that if SARS return it can be used as proper reference. In this paper, we classify hospitals’ response strategy according to the theory of Shortell. There are three aspects analyzed: organization, management and technical aspects. We target on all hospitals in Taiwan and investigated them by implementing self-made structural surveys. After testing the effectiveness and completion pretest of the answering surveys, there are 475 surveys been sent out, 174 surveys returned and 6 surveys counted as invalid. The total rate of return is therefore 37.9 percent. The result of the analysis reveals that there are significant differences between different level of organization (p=0.001), accreditation level（p=0.001）, acturally general ward（p=0.001）, to accept SARS patient（p=0.001）, a isolation ward（p=0.017）, responsibility hospital（p=0.008）, level of impact（p=0.002）, and the satisfaction of emergency response ability（p=0.003）. On the aspect of management, there are also notable differences between different level of organization（p＝0.006）, accreditation level、acturally general ward（p＜0.001）, a burden isolation ward（p=0.008）, responsibility hospital（p=0.002）, to accept SARS patient（p=0.003）, and level of impact（p=0.037）. On the aspect of technique,different level of organization（p=0.002）, accreditation level（p=0.001）, acturally general ward（p=0.004）, responsibility hospital（p=0.007）, to accept SARS patient（p＜0.001）, and level of impact（p=0.021）, and the satisfaction of emergency response ability（p=0.024）. When we run the regression analysis, three main critical points are revealed. First, several significant variables that affect the response strategy of the organization are listed as follows: In general hospital 51-100 ward and 101-200ward,OPD service decrease 21-30 percent,IPD service decrease 31-40 percent,emergency service decrease 51-70 percent（R2=0.341, P＜0.05）. Secondly, main variables that influence management response strategy are as follows: ranking,general ward,OPD service decrease 31-40 percent, IPD service decrease 11-20 percent、21-30 percent、above 70 percent（R2 =0.496, P＜0.05）.Thirdly, significant variables on the issue of technical response strategy are emergency service decrease 11-20 percent and decrease 21-30 percent（R2=0.385, P＜0.05）respectively. According to the above research analysis, three critical suggestions are strongly recommended. （1）Recommendation to Taiwan’s main departments of health: They should take the lesson of SARS and work on the strategy of limiting transmission, and keep monitoring the performance of all hospitals. Educating the public and establishing a system that can effectively control potential SARS patients are both indispensably required. （2）Recommendation to chief executive officers of hospitals: Not only focus on contagious disease Control among hospital workers is crucial, thoughtful psychological communication between hospitals and their workers are also substantial. （3）Recommendation for future literature Future analysis can be further built on investigating hospital worker’s pressure when they face a dilemma between their career duty, moral problem and their own fear. For example, during the SARS period there were some hospital workers refused to be called back on duty, and some protests had been held by the families of people quarantined.

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