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1.  Local structure order in Pd78Cu6Si16 liquid 
Scientific Reports  2015;5:8277.
The short-range order (SRO) in Pd78Cu6Si16 liquid was studied by high energy x-ray diffraction and ab initio molecular dynamics (MD) simulations. The calculated pair correlation functions at different temperatures agree well with the experimental results. The partial pair correlation functions from ab intio MD simulations indicate that Si atoms prefer to be uniformly distributed while Cu atoms tend to aggregate. By performing structure analysis using Honeycutt-Andersen index, Voronoi tessellation, and atomic cluster alignment method, we show that the icosahedron and face-centered cubic SRO increase upon cooling. The dominant SRO is the Pd-centered Pd9Si2 motif, namely the structure of which motif is similar to the structure of Pd-centered clusters in the Pd9Si2 crystal. The study further confirms the existence of trigonal prism capped with three half-octahedra that is reported as a structural unit in Pd-based amorphous alloys. The majority of Cu-centered clusters are icosahedra, suggesting that the presence of Cu is benefit to promote the glass forming ability.
doi:10.1038/srep08277
PMCID: PMC4317692  PMID: 25652079
2.  Spatially Resolved Distribution Function and the Medium-Range Order in Metallic Liquid and Glass 
Scientific Reports  2011;1:194.
The structural description of disordered systems has been a longstanding challenge in physical science. We propose an atomic cluster alignment method to reveal the development of three-dimensional topological ordering in a metallic liquid as it undercools to form a glass. By analyzing molecular dynamic (MD) simulation trajectories of a Cu64.5Zr35.5 alloy, we show that medium-range order (MRO) develops in the liquid as it approaches the glass transition. Specifically, around Cu sites, we observe “Bergman triacontahedron” packing (icosahedron, dodecahedron and icosahedron) that extends out to the fourth shell, forming an interpenetrating backbone network in the glass. The discovery of Bergman-type MRO from our order-mining technique provides unique insights into the topological ordering near the glass transition and the relationship between metallic glasses and quasicrystals.
doi:10.1038/srep00194
PMCID: PMC3245321  PMID: 22355709
3.  Incidence and risk factors for fatal pulmonary embolism after major trauma: a nested cohort study† 
BJA: British Journal of Anaesthesia  2010;105(5):596-602.
Background
Venous thromboembolism is common after major trauma. Strategies to prevent fatal pulmonary embolism (PE) are widely utilized, but the incidence and risk factors for fatal PE are poorly understood.
Methods
Using linked data from the intensive care unit, trauma registry, Western Australian Death Registry, and post-mortem reports, the incidence and risk factors for fatal PE in a consecutive cohort of major trauma patients, admitted between 1994 and 2002, were assessed. Non-linear relationships between continuous predictors and risk of fatal PE were modelled by logistic regression.
Results
Of the 971 consecutive trauma patients considered in the study, 134 (13.8%) died after their injuries. Fatal PE accounted for 11.9% of all deaths despite unfractionated heparin prophylaxis being used in 44% of these patients. Fatal PE occurred in those who were older (mean age 51- vs 37-yr-old, P=0.01), with more co-morbidities (Charlson's co-morbidity index 1.1 vs 0.2, P=0.01), had a larger BMI (31.8 vs 24.5, P=0.01), and less severe head and systemic injuries when compared with those who died of other causes. Sites of injuries were not significantly related to the risk of fatal PE. Fatal PE occurred much later than deaths from other causes (median 18 vs 2 days, P=0.01), and the estimated attributable mortality of PE was 49% (95% confidence interval 36–62%).
Conclusions
Fatal PE appeared to be a potential preventable cause of late mortality after major trauma. Severity of injuries, co-morbidity, and BMI were important risk factors for fatal PE after major trauma.
doi:10.1093/bja/aeq254
PMCID: PMC2955535  PMID: 20861095
mortality; prevention; thromboembolism; traumatic injuries
4.  A Polymorphism in IL28B Distinguishes Exposed, Uninfected Individuals From Spontaneous Resolvers of HCV Infection 
Gastroenterology  2011;141(1):320-325.e2.
Background & Aims
Polymorphisms in the interleukin-28B (IL28B) gene are associated with outcomes from infection with hepatitis C virus (HCV). However, the role of these polymorphisms in protecting injection drug users who are at high risk for HCV infection but do not have detectable antibodies against HCV or HCV RNA (exposed uninfected) has not been demonstrated. We investigated whether these individuals have the IL28B genotype rs12979860-CC, which protects some individuals against HCV infection.
Methods
Seventy-four exposed uninfected individuals, 89 spontaneous resolvers, and 234 chronically infected individuals were genotyped to determine single nucleotide polymorphisms at IL28B.rs12979860.
Results
Exposed, uninfected individuals had a significantly lower frequency of the protective genotype (rs12979860-CC) than anti-HCV-positive spontaneous resolvers (41.9% vs 69.7%, respectively; P = .0005; odds ratio [OR], 0.31; 95% confidence interval [CI]: 0.16–0.60) but a similar frequency to patients who were chronically infected (41.9% vs 43.6%, respectively; P = ns). However, exposed, uninfected individuals had a significantly higher frequency of homozygosity for killer cell immunoglobulin-like receptor 2DL3:group 1 HLA-C (KIR2DL3:HLA-C1) than those with chronic infection (31.1% vs 13.3%, respectively; P = .0008; OR, 2.95; 95% CI: 1.59–5.49). For patients who spontaneously resolved infection, IL28B and KIR:HLA protected, independently, against chronic HCV infection, based on logistic regression and synergy analyses (synergy factor, 1.3; 95% CI: 0.37–4.75; P synergy = .6).
Conclusions
IL28B and KIR2DL3:HLA-C1 are independently associated with spontaneous resolution of viremia following HCV exposure. Resistance to HCV infection in exposed uninfected cases is associated with homozygosity for KIR2DL3:HLA-C1 but not the single nucleotide polymorphism IL28B.rs12979860. Uninfected individuals are therefore a distinct population from patients who spontaneously resolve HCV infection. Distinct, nonsynergistic innate immune mechanisms can determine outcomes of HCV exposure.
doi:10.1053/j.gastro.2011.04.005
PMCID: PMC3194089  PMID: 21600205
Killer Cell Immunoglobulin-Like Receptor; Genetics; Liver Disease; Protective Mechanisms; EU, exposed but uninfected; HCV, hepatitis C virus; Hencore, Hepatitis C European Network for Cooperative Research collaboration; HLA, human leukocyte antigen; HLA-C1, group 1 HLA-C allotype; IDU, injection drug users; IFN, interferon; KIR, killer cell immunoglobulin-like receptor; NK, natural killer cells; SNP, single nucleotide polymorphism; SR, spontaneous resolvers
5.  Massive pulmonary embolism without haemodynamic compromise caused by the presence of a patent foramen ovale 
Heart  2006;92(1):109.
doi:10.1136/hrt.2005.063446
PMCID: PMC1860966  PMID: 16365360
Images in cardiology
6.  Dynamics of the Trimeric AcrB Transporter Protein Inferred From a B-Factor Analysis of the Crystal Structure 
Proteins  2006;62(1):152-158.
The Escherichia coli AcrB multi-drug transporter recognizes a wide range of toxic chemicals and actively extrudes them from cells. The molecular basis of multidrug transport in AcrB remains unknown. Herein, we describe normal mode analyses to study important regions for drug recognition and extrusion in this transporter. Based on the X-ray structure of AcrB, an elastic network model has been able to correct errors arising from crystal imperfection in the experimental B-factors. The results allow us to understand the functional dynamics of this membrane protein. It is expected that this technique can be applied to other membrane proteins with known structures.
doi:10.1002/prot.20743
PMCID: PMC2705243  PMID: 16288462
multidrug transporter; efflux pump; B-factors; anisotropic network model (ANM); normal mode analysis; membrane protein
7.  Ceftibuten Resistance and Treatment Failure of Neisseria gonorrhoeae Infection▿  
Antimicrobial Agents and Chemotherapy  2008;52(10):3564-3567.
Neisseria gonorrhoeae infections have been empirically treated in Hong Kong with a single oral 400-mg dose of ceftibuten since 1997. Following anecdotal reports of the treatment failure of gonorrhea with oral extended-spectrum cephalosporins, the current study was undertaken to determine the antimicrobial susceptibility pattern and molecular characteristics of isolates of N. gonorrhoeae among patients with putative treatment failure in a sexually transmitted disease clinic setting. Between October 2006 and August 2007, 44 isolates of N. gonorrhoeae were studied from patients identified clinically to have treatment failure with empirical ceftibuten. The ceftibuten MICs for three strains were found to have been 8 mg/liter. These strains were determined by N. gonorrhoeae multiantigen sequence typing to belong to sequence type 835 (ST835) or the closely related ST2469. The testing of an additional eight archived ST835 strains revealed similarly elevated ceftibuten MICs. The penA gene sequences of these 11 isolates all had the mosaic pattern previously described as pattern X. Of note is that the ceftriaxone susceptibility results of these strains all fell within the susceptible range. It is concluded that ceftibuten resistance may contribute to the empirical treatment failure of gonorrhea caused by strains harboring the mosaic penA gene, which confers reduced susceptibility to oral extended-spectrum cephalosporins. Screening for such resistance in the routine clinical laboratory may be undertaken by the disk diffusion test. The continued monitoring of antimicrobial resistance and molecular characteristics of N. gonorrhoeae isolates is important to ensure that control and prevention strategies remain effective.
doi:10.1128/AAC.00198-08
PMCID: PMC2565891  PMID: 18663018
9.  Interregional variations in measures of health from the Health and Lifestyle Survey and their relation with indicators of health care need in England. 
STUDY OBJECTIVE--The aim was to assess the extent to which a range of routinely available need indicators which have been suggested for use in NHS spatial resource allocation formulas were associated geographically in England with the different dimensions of population health status collected in the 1985/86 Health and Lifestyle Survey (HLS). DESIGN--Regional health authorities were ranked according to each of the HLS health variables which varied significantly between authorities. The HLS health variables were regressed on a selection from the range of routinely available morbidity and socioeconomic indicators available from the 1981 census. The potential need indicators were also regressed on the health variables. SETTING--The analyses were undertaken at individual level and at regional health authority level in England. SUBJECTS--The study comprised the English component of the HLS random sample representative of the population in private households in Great Britain. MAIN RESULTS--The different HLS health variables did not yield consistent regional health authority rankings. Among the variables, forced expiratory volume in one second (FEV1) and self assessed health appeared to be associated with most of the other health and need variables except longstanding illness. Longstanding illness was not strongly associated with any of the other HLS health variables but appeared to show some association with three deprivation indices constructed from the 1981 Census. CONCLUSIONS--There may be a case for including a measure of chronic ill health in the new NHS system of capitated finance in addition to the all cause standardised mortality ratio which is used currently as a measure of need for health care.
PMCID: PMC1059491  PMID: 1573358

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