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Search Results: 1 - 10 of 137558 matches for " Patrick CK Li "
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Comparison of predicted susceptibility between genotype and virtual phenotype HIV drug resistance interpretation systems among treatment-naive HIV-infected patients in Asia: TASER-M cohort analysis
Awachana Jiamsakul, Rami Kantor, Patrick CK Li, Sunee Sirivichayakul, Thira Sirisanthana, Pacharee Kantipong, Christopher KC Lee, Adeeba Kamarulzaman, Winai Ratanasuwan, Rossana Ditangco, Thida Singtoroj, Somnuek Sungkanuparph, On behalf of the TREAT Asia Studies to Evaluate Resistance – Monitoring Study (TASER-M)
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-582
Abstract: Sequences from 1301 ARV-naive patients enrolled in the TREAT Asia Studies to Evaluate Resistance – Monitoring Study (TASER-M) were analysed by both interpreting systems. Interpretations from both Stanford HIVdb and vircoTYPE? HIV-1 were initially grouped into 2 levels: susceptible and non-susceptible. Discrepancy was defined as a discordant result between the susceptible and non-susceptible interpretations from the two systems for the same ARV. Further analysis was performed when interpretations from both systems were categorised into 3 levels: susceptible, intermediate and resistant; whereby discrepancies could be categorised as major discrepancies and minor discrepancies. Major discrepancy was defined as having a susceptible result from one system and resistant from the other. Minor discrepancy corresponded to having an intermediate interpretation in one system, with a susceptible or resistant result in the other. The level of agreement was analysed using the prevalence adjusted bias adjusted kappa (PABAK).Overall, the agreement was high, with each ARV being in “almost perfect agreement”, using Landis and Koch’s categorisation. Highest discordance was observed for efavirenz (75/1301, 5.8%), all arising from susceptible Stanford HIVdb versus non-susceptible vircoTYPE? HIV-1 predictions. Protease Inhibitors had highest level of concordance with PABAKs all above 0.99, followed by Nucleoside Reverse Transcriptase Inhibitors with PABAKs above 0.97 and non-NRTIs with the lowest PABAK of 0.88. The 68/75 patients with discordant efavirenz results harboured the V179D/E mutations compared to 7/1226 with no efavirenz discrepancy (p-value <0.001). In the 3-level comparison, all but one of the discrepancies was minor.The two systems agreed well with lowest concordance observed for efavirenz. When interpreting HIVDR, especially in non-B subtypes, clinical correlation is crucial, in particular when efavirenz resistance is interpreted based on V179D/E.In recent years, developing
K-theory for ring C*-algebras - the case of number fields with higher roots of unity
Xin Li,Wolfgang Lück
Mathematics , 2012, DOI: 10.2140/agt.2013.13.1
Abstract: We compute K-theory for ring C*-algebras in the case of higher roots of unity and thereby completely determine the K-theory for ring C*-algebras attached to rings of integers in arbitrary number fields.
Automated Masking of AFLP Markers Improves Reliability of Phylogenetic Analyses
Patrickck, Carola Greve, Bernhard Misof, France Gimnich
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049119
Abstract: The amplified fragment length polymorphisms (AFLP) method has become an attractive tool in phylogenetics due to the ease with which large numbers of characters can be generated. In contrast to sequence-based phylogenetic approaches, AFLP data consist of anonymous multilocus markers. However, potential artificial amplifications or amplification failures of fragments contained in the AFLP data set will reduce AFLP reliability especially in phylogenetic inferences. In the present study, we introduce a new automated scoring approach, called “AMARE” (AFLP MAtrix REduction). The approach is based on replicates and makes marker selection dependent on marker reproducibility to control for scoring errors. To demonstrate the effectiveness of our approach we record error rate estimations, resolution scores, PCoA and stemminess calculations. As in general the true tree (i.e. the species phylogeny) is not known, we tested AMARE with empirical, already published AFLP data sets, and compared tree topologies of different AMARE generated character matrices to existing phylogenetic trees and/or other independent sources such as morphological and geographical data. It turns out that the selection of masked character matrices with highest resolution scores gave similar or even better phylogenetic results than the original AFLP data sets.
Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life
Patrickck, Francisco Hita Garcia, Bernhard Misof, Karen Meusemann
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021031
Abstract: Martialinae are pale, eyeless and probably hypogaeic predatory ants. Morphological character sets suggest a close relationship to the ant subfamily Leptanillinae. Recent analyses based on molecular sequence data suggest that Martialinae are the sister group to all extant ants. However, by comparing molecular studies and different reconstruction methods, the position of Martialinae remains ambiguous. While this sister group relationship was well supported by Bayesian partitioned analyses, Maximum Likelihood approaches could not unequivocally resolve the position of Martialinae. By re-analysing a previous published molecular data set, we show that the Maximum Likelihood approach is highly appropriate to resolve deep ant relationships, especially between Leptanillinae, Martialinae and the remaining ant subfamilies. Based on improved alignments, alignment masking, and tree reconstructions with a sufficient number of bootstrap replicates, our results strongly reject a placement of Martialinae at the first split within the ant tree of life. Instead, we suggest that Leptanillinae are a sister group to all other extant ant subfamilies, whereas Martialinae branch off as a second lineage. This assumption is backed by approximately unbiased (AU) tests, additional Bayesian analyses and split networks. Our results demonstrate clear effects of improved alignment approaches, alignment masking and data partitioning. We hope that our study illustrates the importance of thorough, comprehensible phylogenetic analyses using the example of ant relationships.
How do patients with inflammatory bowel disease want their biological therapy administered?
Patrick B Allen, Hannah Lindsay, Tony CK Tham
BMC Gastroenterology , 2010, DOI: 10.1186/1471-230x-10-1
Abstract: The aims of this study were to compare preferences in Inflammatory Bowel Disease (IBD) patients for two currently available anti-TNF agents and the reasons for their choices.An anonymous questionnaire was distributed to IBD patients who had attended the Gastroenterology service (Ulster Hospital, Dundonald, Belfast, N. Ireland. UK) between January 2007 and December 2007. The patients were asked in a hypothetical situation if the following administering methods of anti-TNF drugs (intravenous or subcutaneous) were available, which drug route of administration would they choose.One hundred and twenty-five patients fulfilled the inclusion criteria and were issued questionnaires, of these 78 questionnaires were returned (62 percent response). The mean age of respondent was 44 years. Of the total number of respondents, 33 patients (42 percent) preferred infliximab and 19 patients (24 percent) preferred adalimumab (p = 0.07). Twenty-six patients (33 percent) did not indicate a preference for either biological therapy and were not included in the final analysis. The commonest reason cited for those who chose infliximab (iv) was: "I do not like the idea of self-injecting," (67 percent). For those patients who preferred adalimumab (sc) the commonest reason cited was: "I prefer the convenience of injecting at home," (79 percent). Of those patients who had previously been treated with an anti-TNF therapy (n = 10, all infliximab) six patients stated that they would prefer infliximab if given the choice in the future (p = 0.75).There was a trend towards patient preference for infliximab (iv) treatment as opposed to adalimumab (sc) in patients with IBD. This difference may be due to the frequency of administration, mode of administration or differing 'times in the market-place', as infliximab had been approved for a longer period of time in Crohn's disease. Further studies are required in IBD patients to investigate whether patient choice will affect compliance, patient satisfactio
Local breaking of the spin-orbit interaction: the microscopic origin of exchange bias in Co/FeMn
Sebastian Brück,Patrick Audehm,Gisela Schütz,Eberhard Goering
Physics , 2009,
Abstract: Modern magnetic thin film devices owe their success in large part to effects emerging from interlayer coupling and exchange interaction at interfaces. A prominent example is exchange bias (EB), a magnetic coupling phenomenon found in ferromagnet (F)/antiferromagnet (AF) systems. Uncompensated pinned moments in the AF couple to the F via the interface causing an additional unidirectional anisotropy. As a result, the hysteresis of the F is shifted. The existence of such pinned moments is nowadays accepted although their physical nature and origin is still unknown. Here we present a thorough spectroscopic investigation based on X-ray magnetic circular dichroism which does for the first time provide direct information about the physics of pinned magnetic moments. Our data clearly shows that the orbital magnetic moment, which is usually widely quenched in transition metal systems, is the driving force behind exchange bias in Co/FeMn.
Risk and prognostic significance of tuberculosis in patients from The TREAT Asia HIV Observational Database
Jialun Zhou, Julian Elliott, Patrick CK Li, Poh Lim, Sasisopin Kiertiburanakul, Nagalingeswaran Kumarasamy, Tuti Merati, Sanjay Pujari, Yi-Ming A Chen, Praphan Phanuphak, Saphonn Vonthanak, Thira Sirisanthana, Somnuek Sungkanuparph, Christopher KC Lee, Adeeba Kamarulzaman, Shinichi Oka, Fujie Zhang, Goa Tau, Rossana Ditangco
BMC Infectious Diseases , 2009, DOI: 10.1186/1471-2334-9-46
Abstract: The risk of TB diagnosis after recruitment was assessed in patients with prospective follow-up. TB diagnosis was fitted as a time-dependent variable in assessing overall survival.At baseline, 22% of patients were diagnosed with TB. TB incidence was 1.98 per 100 person-years during follow up, with predictors including younger age, lower recent CD4 count, duration of antiretroviral treatment, and living in high TB burden countries. Among 3279 patients during 6968 person-years, 142 died (2.04 per 100 person-years). Compared to patients with CDC category A or B illness only, mortality was marginally higher in patients with single Non-TB AIDS defining illness (ADI), or TB only (adjusted HR 1.35, p = 0.173) and highest in patients with multiple non-TB AIDS or both TB and other ADI (adjusted HR 2.21, p < 0.001).The risk of TB diagnosis was associated with increasing immunodeficiency and partly reduced by antiretroviral treatment. The prognosis of developing TB appeared to be similar to that following a diagnosis of other non-TB ADI.The use of highly active antiretroviral therapy (HAART) has led to dramatic reductions in morbidity and mortality in HIV patients [1,2]. However, tuberculosis (TB) remains a common opportunistic infections and a major cause of death among patients with HIV, especially in sub-Saharan African and Asian countries [3-5], where there is a high background prevalence of TB [5-7].The risk of TB in HIV-infected patients and the impact of TB diagnosis on disease progression in HIV infected patients have been well described in Africa [3,8-10]. The Asia-Pacific region has a large burden of both tuberculosis [7], with nearly 5 million prevalent cases and over 3 million new cases in 2006, and HIV, with an estimated 5 million people living with HIV and 380,000 new infections occurring in 2007 [11]. It is estimated that 2.5 million people are living with both infections in the region [5]. Despite the importance of these inter-related epidemics in the region, fe
Trends in CD4 counts in HIV-infected patients with HIV viral load monitoring while on combination antiretroviral treatment: results from The TREAT Asia HIV Observational Database
Jialun Zhou, Thira Sirisanthana, Sasisopin Kiertiburanakul, Yi-Ming A Chen, Ning Han, Poh_Lian Lim, Nagalingeswaran Kumarasamy, Jun Choi, Tuti Merati, Evy Yunihastuti, Shinichi Oka, Adeeba Kamarulzaman, Praphan Phanuphak, Christopher KC Lee, Patrick CK Li, Sanjay Pujari, Vanthanak Saphonn, Matthew G Law
BMC Infectious Diseases , 2010, DOI: 10.1186/1471-2334-10-361
Abstract: Treatment-naive HIV-infected patients who started cART with three or more and had three or more CD4 count and HIV VL tests were included. CD4 count slopes were expressed as changes of cells per microliter per year. Predictors of CD4 count slopes from 6 months after initiation were assessed by random-effects linear regression models.A total of 1676 patients (74% male) were included. The median time on cART was 4.2 years (IQR 2.5-5.8 years). In the final model, CD4 count slope was associated with age, concurrent HIV VL and CD4 count, disease stage, hepatitis B or C co-infection, and time since cART initiation. CD4 count continues to increase with HIV VL up to 20 000 copies/mL during 6-12 months after cART initiation. However, the HIV VL has to be controlled below 5 000, 4 000 and 500 copies/mL for the CD4 count slope to remain above 20 cells/microliter per year during 12-18, 18-24, and beyond 24 months after cART initiation.After cART initiation, CD4 counts continued to increase even when the concurrent HIV VL was detectable. However, HIV VL needed to be controlled at a lower level to maintain a positive CD4 count slope when cART continues. The effect on long-term outcomes through the possible development of HIV drug resistance remains uncertain.Studies show that latent infection of CD4 cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective anti-retroviral therapy [1]. To suppress viral replication so that the VL is below the level of detection with standard assays is thus one of the aims at the start of antiretroviral treatment. Maximal and durable suppression of HIV VL prevents or delays development of drug resistant mutations, preserves CD4 cells, and eventually results in better clinical outcomes. According to the US guidelines, if HIV VL suppression is not achieved, it is necessary to change to a new regimen, a second or third line regimen, with at least two active drugs [2].HIV-infected patients in most developing countries h
Risk Identification and Assessment in PPP Infrastructure Projects using Fuzzy Analytical Hierarchy Process and Life-Cycle Methodology
Jie Li,Patrick Zou
Australasian Journal of Construction Economics and Building , 2012,
Abstract: To fulfil the increasing demands of the public,Public Private Partnership (PPP) has beenincreasingly used to procure infrastructureprojects, such as motor ways, bridges, tunnelsand railways. However, the risks involved inPPP projects are unique and dynamic due tolarge amount of investment and longconcession period. This paper aims to developa risk identification framework from theperspectives of project life cycle, and anassessment framework for risks associatedwith PPP project using fuzzy analyticalhierarchy process (AHP). First the paperreviews the current literature to identifycommon risks in PPP infrastructure projectsand classification methods used. The risksidentified from the literature were classifiedusing project life cycle perspectives. Followingthat, the paper presents the advantages offuzzy AHP. Furthermore, the paper provides aframework for assessment of risks in PPPprojects followed by an illustrative examplewhere the data was obtained from surveyquestionnaires. The paper concludes that risksassociated in PPP infrastructure projects areunique and therefore it is beneficial to classifythem from project life cycle perspectives, andthe proposed fuzzy AHP method is suitable forthe assessment of these risks.
Kernel-Based Aggregation of Marker-Level Genetic Association Tests Involving Copy-Number Variation
Yinglei Li,Patrick Breheny
Microarrays , 2013, DOI: 10.3390/microarrays2030265
Abstract: Genetic association tests involving copy-number variants (CNVs) are complicated by the fact that CNVs span multiple markers at which measurements are taken. The power of an association test at a single marker is typically low, and it is desirable to pool information across the markers spanned by the CNV. However, CNV boundaries are not known in advance, and the best way to proceed with this pooling is unclear. In this article, we propose a kernel-based method for aggregation of marker-level tests and explore several aspects of its implementation. In addition, we explore some of the theoretical aspects of marker-level test aggregation, proposing a permutation-based approach that preserves the family-wise error rate of the testing procedure, while demonstrating that several simpler alternatives fail to do so. The empirical power of the approach is studied in a number of simulations constructed from real data involving a pharmacogenomic study of gemcitabine and compares favorably with several competing approaches.
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