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1.  ELECTROSPRAY IONIZATION (ESI) FRAGMENTATIONS AND DIMETHYLDIOXIRANE REACTIVITIES OF THREE DIVERSE LACTAMS HAVING FULL, HALF, AND ZERO RESONANCE ENERGIES 
The Journal of organic chemistry  2013;79(2):517-528.
Three lactams having respectively ~20 kcal/mol, ~10 kcal/mol, and 0 kcal/mol of resonance energy have been subjected to electrospray ionization mass spectrometry (ESI/MS) as well as to attempted reaction with dimethyldioxirane (DMDO). The ESI/MS for all three lactams are consistent with fragmentation from the N-protonated, rather than the O-protonated tautomer. Each exhibits a unique fragmentation pathway. DFT calculations are employed to provide insights concerning these pathways. N-Ethyl-2-pyrrolidinone and 1-azabicyclo[3.3.1]nonan-2-one, the full- and half-resonance lactams, are unreactive with DMDO. The “Kirby lactam” (3,5,7-trimethyl-1-azaadamantan-2-one), has zero resonance energy and reacts rapidly with DMDO to generate a mixture of reaction products. The structure assigned to one of these is the 2,2-dihydroxy-N-oxide, thought to be stabilized by intramolecular hydrogen bonding and buttressing by the methyl substituents. A reasonable pathway to this derivative might involve formation of an extremely labile N-oxide, in a purely formal sense an example of the hithertounknown amide N-oxides, followed by hydration with traces of moisture.
doi:10.1021/jo402041u
PMCID: PMC3959984  PMID: 24313276
2.  The Role of Variation at AβPP, PSEN1, PSEN2, and MAPT in Late Onset Alzheimer’s Disease 
Gerrish, Amy | Russo, Giancarlo | Richards, Alexander | Moskvina, Valentina | Ivanov, Dobril | Harold, Denise | Sims, Rebecca | Abraham, Richard | Hollingworth, Paul | Chapman, Jade | Hamshere, Marian | Pahwa, Jaspreet Singh | Dowzell, Kimberley | Williams, Amy | Jones, Nicola | Thomas, Charlene | Stretton, Alexandra | Morgan, Angharad R. | Lovestone, Simon | Powell, John | Proitsi, Petroula | Lupton, Michelle K. | Brayne, Carol | Rubinsztein, David C. | Gill, Michael | Lawlor, Brian | Lynch, Aoibhinn | Morgan, Kevin | Brown, Kristelle S. | Passmore, Peter A. | Craig, David | McGuinness, Bernadette | Todd, Stephen | Johnston, Janet A. | Holmes, Clive | Mann, David | Smith, A. David | Love, Seth | Kehoe, Patrick G. | Hardy, John | Mead, Simon | Fox, Nick | Rossor, Martin | Collinge, John | Maier, Wolfgang | Jessen, Frank | Kölsch, Heike | Heun, Reinhard | Schürmann, Britta | van den Bussche, Hendrik | Heuser, Isabella | Kornhuber, Johannes | Wiltfang, Jens | Dichgans, Martin | Frölich, Lutz | Hampel, Harald | Hüll, Michael | Rujescu, Dan | Goate, Alison M. | Kauwe, John S. K. | Cruchaga, Carlos | Nowotny, Petra | Morris, John C. | Mayo, Kevin | Livingston, Gill | Bass, Nicholas J. | Gurling, Hugh | McQuillin, Andrew | Gwilliam, Rhian | Deloukas, Panagiotis | Davies, Gail | Harris, Sarah E. | Starr, John M. | Deary, Ian J. | Al-Chalabi, Ammar | Shaw, Christopher E. | Tsolaki, Magda | Singleton, Andrew B. | Guerreiro, Rita | Mühleisen, Thomas W. | Nöthen, Markus M. | Moebus, Susanne | Jöckel, Karl-Heinz | Klopp, Norman | Wichmann, H-Erich | Carrasquillo, Minerva M | Pankratz, V Shane | Younkin, Steven G. | Jones, Lesley | Holmans, Peter A. | O’Donovan, Michael C. | Owen, Michael J. | Williams, Julie
Rare mutations in AβPP, PSEN1, and PSEN2 cause uncommon early onset forms of Alzheimer’s disease (AD), and common variants in MAPT are associated with risk of other neurodegenerative disorders. We sought to establish whether common genetic variation in these genes confer risk to the common form of AD which occurs later in life (>65 years). We therefore tested single-nucleotide polymorphisms at these loci for association with late-onset AD (LOAD) in a large case-control sample consisting of 3,940 cases and 13,373 controls. Single-marker analysis did not identify any variants that reached genome-wide significance, a result which is supported by other recent genome-wide association studies. However, we did observe a significant association at the MAPT locus using a gene-wide approach (p = 0.009). We also observed suggestive association between AD and the marker rs9468, which defines the H1 haplotype, an extended haplotype that spans the MAPT gene and has previously been implicated in other neurodegenerative disorders including Parkinson’s disease, progressive supranuclear palsy, and corticobasal degeneration. In summary common variants at AβPP, PSEN1, and PSEN2 and MAPT are unlikely to make strong contributions to susceptibility for LOAD. However, the gene-wide effect observed at MAPT indicates a possible contribution to disease risk which requires further study.
doi:10.3233/JAD-2011-110824
PMCID: PMC4118466  PMID: 22027014
Alzheimer’s disease; amyloid-β protein precursor; genetics; human; MAPT protein; PSEN1 protein; PSEN2 protein
3.  Modelling the Interplay between Childhood and Adult Adversity in Pathways to Psychosis 
Psychological medicine  2013;44(2):407-419.
Background
There is evidence that a range of socio-environmental exposures are associated with an increased risk of psychosis. However, despite the fact that such factors probably combine in complex ways to increase risk, the majority of studies have tended to consider each exposure separately. In light of this, we sought to extend previous analyses of data from the ÆSOP study on childhood and adult markers of disadvantage to examine how they combine to increase risk of psychosis, testing both mediation (path) models and synergistic effects.
Method
All patients with a first episode of psychosis who made contact with psychiatric services in defined catchment areas in London and Nottingham, UK (n = 390) and a series of community controls (n = 391) were included in the ÆSOP study. Data relating to clinical and social variables, including parental separation and loss, education and adult disadvantage, were collected from cases and controls.
Results
There was evidence that the effect of separation from, but not death of, a parent in childhood on risk of psychosis was partially mediated through subsequent poor educational attainment (no qualifications), adult social disadvantage and, to a lesser degree, low self-esteem. In addition, there was strong evidence that separation from, but not death of, a parent combined synergistically with subsequent disadvantage to increase risk. These effects held for all ethnic groups in the sample.
Conclusions
Exposure to childhood and adult disadvantage may combine in complex ways to push some individuals along a predominantly socio-developmental pathway to psychosis.
doi:10.1017/S0033291713000767
PMCID: PMC4081841  PMID: 23590972
4.  Biology of primary breast cancer in older women treated by surgery: with correlation with long-term clinical outcome and comparison with their younger counterparts 
British Journal of Cancer  2013;108(5):1042-1051.
Background:
As age advances breast cancer appears to change its biological characteristics, however, very limited data are available to define the precise differences between older and younger patients.
Methods:
Over 36 years (1973–2009), 1758 older (⩾70 years) women with early operable primary breast cancer were managed in a dedicated clinic. In all, 813 underwent primary surgery and 575 good quality tumour samples were available for biological analysis. The pattern of biomarkers was analysed using indirect immunohistochemistry on tissue microarrays. Comparison was made with a previously characterised series of younger (<70 years) patients.
Results:
There was high expression of oestrogen receptor (ER), PgR, Bcl2, Muc1, BRCA1 and 2, E-cadherin, luminal cytokeratins, HER3, HER4, MDM2 and 4 and low expression of human epidermal growth factor receptor (HER)-2, Ki67, p53, EGFR and CK17. Oestrogen receptor and axillary stage appeared as independent prognostic factors. Unsupervised partitional clustering showed six biological clusters in older patients, five of which were common in the younger patients, whereas the low ER luminal cluster was distinct in the older series. The luminal phenotype showed better breast cancer-specific survival, whereas basal and HER2-overexpressing tumours were associated with poor outcome.
Conclusion:
Early operable primary breast cancer in older women appears as a distinct biological entity, with existence of a novel cluster. Overall older women showed less aggressive tumour biology and ER appeared as an independent prognostic factor alongside the time-dependent axillary stage. These biological characteristics may explain the differences in clinical outcome and should be considered in making therapeutic decisions.
doi:10.1038/bjc.2012.601
PMCID: PMC3619059  PMID: 23462719
biology; breast cancer; older women; clinical outcome
5.  Interplay Between Childhood Physical Abuse and Familial Risk in the Onset of Psychotic Disorders 
Schizophrenia Bulletin  2014;40(6):1443-1451.
Background: Childhood abuse is considered one of the main environmental risk factors for the development of psychotic symptoms and disorders. However, this association could be due to genetic factors influencing exposure to such risky environments or increasing sensitivity to the detrimental impact of abuse. Therefore, using a large epidemiological case-control sample, we explored the interplay between a specific form of childhood abuse and family psychiatric history (a proxy for genetic risk) in the onset of psychosis. Methods: Data were available on 172 first presentation psychosis cases and 246 geographically matched controls from the Aetiology and Ethnicity of Schizophrenia and Other Psychoses study. Information on childhood abuse was obtained retrospectively using the Childhood Experience of Care and Abuse Questionnaire and occurrence of psychotic and affective disorders in first degree relatives with the Family Interview for Genetic Studies. Results: Parental psychosis was more common among psychosis cases than unaffected controls (adjusted OR = 5.96, 95% CI: 2.09–17.01, P = .001). Parental psychosis was also associated with physical abuse from mothers in both cases (OR = 3.64, 95% CI: 1.06–12.51, P = .040) and controls (OR = 10.93, 95% CI: 1.03–115.90, P = .047), indicative of a gene-environment correlation. Nevertheless, adjusting for parental psychosis did not measurably impact on the abuse-psychosis association (adjusted OR = 3.31, 95% CI: 1.22–8.95, P = .018). No interactions were found between familial liability and maternal physical abuse in determining psychosis caseness. Conclusions: This study found no evidence that familial risk accounts for associations between childhood physical abuse and psychotic disorder nor that it substantially increases the odds of psychosis among individuals reporting abuse.
doi:10.1093/schbul/sbt201
PMCID: PMC4193698  PMID: 24399191
family history; gene-environment correlation; gene-environment interaction; liability; schizophrenia; trauma
6.  Exhaled Breath Condensate Detects Baseline Reductions in Chloride and Increases in Response to Albuterol in Cystic Fibrosis Patients 
Impaired ion regulation and dehydration is the primary pathophysiology in cystic fibrosis (CF) lung disease. A potential application of exhaled breath condensate (EBC) collection is to assess airway surface liquid ionic composition at baseline and in response to pharmacological therapy in CF. Our aims were to determine if EBC could detect differences in ion regulation between CF and healthy and measure the effect of the albuterol on EBC ions in these populations. Baseline EBC Cl−, DLCO and SpO2 were lower in CF (n = 16) compared to healthy participants (n = 16). EBC Cl− increased in CF subjects, while there was no change in DLCO or membrane conductance, but a decrease in pulmonary-capillary blood volume in both groups following albuterol. This resulted in an improvement in diffusion at the alveolar-capillary unit, and removal of the baseline difference in SpO2 by 90-minutes in CF subjects. These results demonstrate that EBC detects differences in ion regulation between healthy and CF individuals, and that albuterol mediates increases in Cl− in CF, suggesting that the benefits of albuterol extend beyond simple bronchodilation.
doi:10.4137/CCRPM.S12882
PMCID: PMC3869628  PMID: 24367235
diffusion capacity of the lungs for carbon monoxide and nitric oxide (DLCO/DLNO); peripheral oxygen saturation (SpO2); exhaled sodium; exhaled chloride
7.  Genetic Variation of SCNN1A Influences Lung Diffusing Capacity in Cystic Fibrosis 
Introduction
Epithelial Na+ Channels (ENaC) play a crucial role in ion and fluid regulation in the lung. In cystic fibrosis (CF) Na+ hyperabsorption results from ENaC over activity, leading to airway dehydration. Previous work has demonstrated functional genetic variation of SCNN1A (the gene encoding the ENaC α-subunit), manifesting as an alanine (A) to threonine (T) substitution at amino acid 663, with the αT663 variant resulting in a more active channel.
Methods
We assessed the influence of genetic variation of SCNN1A on the diffusing capacity of the lungs for carbon monoxide (DLCO) and nitric oxide (DLNO), together with alveolar capillary membrane conductance (DM), pulmonary capillary blood volume (VC), and alveolar volume (VA) at rest and during peak exercise in 18 patients with CF [10 homozygous for αA663 (AA group) and 8 with at least one T663 allele (AT/TT group)]. Due to the more active channel we hypothesized that the AT/TT group would show a greater increase in DLCO, DLNO, and DM with exercise due to exercise-mediated ENaC inhibition and subsequent attenuation of Na+ hyperabsorption.
Results
The AT/TT group had significantly lower pulmonary function, weight and BMI than the AA group. Both groups had similar peak workloads, relative peak oxygen consumptions, and cardiopulmonary responses to exercise. The AT/TT group demonstrated a greater increase in DLNO, DLNO/VA, and DM in response to exercise (% increases: DLNO= 18±11vs.41±38; DLNO/VA= 14±21vs.40±37; DM= 15±11vs.41±38, AAvs.AT/TT, respectively). There were no differences between groups in absolute diffusing capacity measures at peak exercise.
Conclusion
These results suggest that genetic variation of the alpha-subunit of ENaC differentially affects the diffusing capacity response to exercise in patients with CF.
doi:10.1249/MSS.0b013e318266ebc3
PMCID: PMC3501594  PMID: 22776878
exercise; cystic fibrosis; diffusing capacity; DLNO; DLCO; ENaC polymorphism
8.  Assessment of posttraumatic symptoms in patients with first-episode psychosis 
The Journal of nervous and mental disease  2011;199(11):10.1097/NMD.0b013e318234a037.
Posttraumatic Stress Disorder (PTSD) is common among patients with psychotic disorders. The present study examined the internal reliability and comparability of the Impact of Event Scale (IES) in a sample of 38 patients with first-episode psychosis and 47 controls exposed to severe physical and/or sexual abuse. The IES total score and both subscales showed high internal consistency in both groups (Cronbach alpha coefficients of approximately .9 or above). Given their equivalent trauma reporting, the lack of differences in IES scores between patients and controls seems to indicate that patients are likely to report accurately and neither exaggerate nor minimize their posttraumatic symptoms. Overall, the findings suggest that the IES can be used to assess symptoms of posttraumatic stress in patients with psychotic disorders as in other populations.
doi:10.1097/NMD.0b013e318234a037
PMCID: PMC3825662  PMID: 22048144
trauma; post-traumatic stress; first-episode psychosis; reliability
9.  Gender Differences in Neuropsychological Performance across Psychotic Disorders – a Multi-Centre Population Based Case-Control Study 
PLoS ONE  2013;8(10):e77318.
Background
Patients with schizophrenia and other psychoses exhibit a wide range of neuropsychological deficits. An unresolved question concerns whether there are gender differences in cognitive performance.
Methods
Data were derived from a multi-centre population based case-control study of patients with first-episode psychosis. A neuropsychological test battery was administered to patients with a diagnosis of schizophrenia or schizoaffective disorder (N=70, 36% females), bipolar/mania (N=34, 60% females), depressive psychosis (N=36, 58% females) and healthy controls (N=148, 55% females). Generalized and specific cognitive deficits were compared.
Results
There was strong evidence for disorder-specific gender differences in neuropsychological performance. Males and females with schizophrenia showed similar pervasive neuropsychological impairments. In psychotic depressive disorder females performed worse than males across neuropsychological measures. Differences in neuropsychological performance between males and females with bipolar/manic disorder were restricted to language functions. Symptom severity did not contribute to the observed gender differences.
Conclusions
Early in the course of psychotic illness, gender related factors appear to moderate the severity of cognitive deficits in depressive psychosis and bipolar/mania patients.
doi:10.1371/journal.pone.0077318
PMCID: PMC3810462  PMID: 24204806
10.  Quantitative assays for new families of esterified oxylipins generated by immune cells 
Nature protocols  2010;5(12):1919-1931.
Phospholipid-esterified oxylipins are newly described families of bioactive lipids generated by lipoxygenases in immune cells. Until now, assays for their quantitation were not well developed or widely available. Here, we describe a mass spectrometric protocol that enables accurate measurement of several, in particular hydro(pero)xyeicosatetraenoic acids (H(p)ETEs), hydroxyoctadecadienoic acids (HODEs), hydroxydocosahexaenoic acids (HDOHEs) and keto-eicosatetraenoic acids (KETEs), attached to either phosphatidylethanolamine (PE) or phosphatidylcholine (PC). Lipids are isolated from cells or tissue using a liquid phase organic extraction, then analyzed by HPLC-tandem mass spectrometry (LC/MS/MS) in multiple reaction monitoring (MRM) mode. The protocol can simultaneously monitor up to 23 different species. Generation of standards takes 2 days approximately. Following this, extraction of 30 samples takes approximately 3 hrs, with LC/MS/MS run time of 50 min per sample.
doi:10.1038/nprot.2010.162
PMCID: PMC3678246  PMID: 21127486
Lipid biochemistry; eicosanoid; phospholipid; mass spectrometry; macrophage; neutrophil; platelet
11.  Pcp4l1 contains an auto-inhibitory element that prevents its IQ motif from binding to calmodulin 
Journal of Neurochemistry  2012;121(6):843-851.
Purkinje cell protein 4-like 1 (Pcp4l1) is a small neuronal IQ motif protein closely related to the calmodulin binding protein Pcp4/PEP-19. PEP-19 interacts with calmodulin via its IQ motif to inhibit calmodulin-dependent enzymes and we hypothesized Pcp4l1 would have similar properties. Surprisingly, full length Pcp4l1 does not interact with calmodulin in yeast two-hybrid or pulldown experiments yet a synthetic peptide constituting only the IQ motif of Pcp4l1 binds calmodulin and inhibits calmodulin-dependent kinase II. A nine-residue glutamic acid rich sequence in Pcp4l1 confers these unexpected properties. This element lies outside the IQ motif and its deletion or exchange with the homologous region of PEP-19 restores calmodulin binding. Conversion of a single isoleucine (Ile36) within this motif to phenylalanine, the residue present in PEP-19, imparts calmodulin binding onto Pcp4l1. Moreover, only aromatic amino acid substitutions at position 36 in Pcp4l1 allow binding. Thus, despite their sequence similarities PEP-19 and Pcp4l1 have distinct properties with the latter harboring an element that can functionally suppress an IQ motif. We speculate Pcp4l1 may be a latent calmodulin inhibitor regulated by post-translational modification and/or co-factor interactions.
doi:10.1111/j.1471-4159.2012.07745.x
PMCID: PMC3371134  PMID: 22458599
Calmodulin; Calcium; IQ motif; Pcp4l1; PEP-19
12.  Protocol for “Seal or Varnish?” (SoV) trial: a randomised controlled trial to measure the relative cost and effectiveness of pit and fissure sealants and fluoride varnish in preventing dental decay 
BMC Oral Health  2012;12:51.
Background
Dental caries remains a significant public health problem, prevalence being linked to social and economic deprivation. Occlusal surfaces of first permanent molars are the most susceptible site in the developing permanent dentition. Cochrane reviews have shown pit and fissure sealants (PFS) and fluoride varnish (FV) to be effective over no intervention in preventing caries. However, the comparative cost and effectiveness of these treatments is uncertain. The primary aim of the trial described in this protocol is to compare the clinical effectiveness of PFS and FV in preventing dental caries in first permanent molars in 6-7 year-olds. Secondary aims include: establishing the costs and the relative cost-effectiveness of PFS and FV delivered in a community/school setting; examining the impact of PFS and FV on children and their parents/carers in terms of quality of life/treatment acceptability measures; and examining the implementation of treatment in a community setting.
Methods/design
The trial design comprises a randomised, assessor-blinded, two-arm, parallel group trial in 6–7 year old schoolchildren. Clinical procedures and assessments will be performed at 66 primary schools, in deprived areas in South Wales. Treatments will be delivered via a mobile dental clinic. In total, 920 children will be recruited (460 per trial arm). At baseline and annually for 36 months dental caries will be recorded using the International Caries Detection and Assessment System (ICDAS) by trained and calibrated dentists. PFS and FV will be applied by trained dental hygienists. The FV will be applied at baseline, 6, 12, 18, 24 and 30 months. The PFS will be applied at baseline and re-examined at 6, 12, 18, 24, and 30 months, and will be re-applied if the existing sealant has become detached/is insufficient. The economic analysis will estimate the costs of providing the PFS versus FV. The process evaluation will assess implementation and acceptability through acceptability scales, a schools questionnaire and interviews with children, parents, dentists, dental nurses and school staff. The primary outcome measure will be the proportion of children developing new caries on any one of up to four treated first permanent molars.
Discussion
The objectives of this study have been identified by the National Institute for Health Research as one of importance to the National Health Service in the UK. The results of this trial will provide guidance on which of these technologies should be adopted for the prevention of dental decay in the most susceptible tooth-surface in the most at risk children.
Trial registrations
ISRCTN ref: ISRCTN17029222 EudraCT: 2010-023476-23 UKCRN ref: 9273
doi:10.1186/1472-6831-12-51
PMCID: PMC3534529  PMID: 23167481
Dental caries; Clinical trial; Pit and fissure sealants; Fluoride varnish; Preventive dentistry; Oral health
13.  BETAINE FEEDING PREVENTS THE BLOOD ALCOHOL CYCLE IN RATS FED ALCOHOL CONTINUOUSLY FOR 1 MONTH USING THE RAT INTRAGASTRIC TUBE FEEDING MODEL 
Background
Blood alcohol levels (BAL) cycle up and down over a 7–8 day period when ethanol is fed continuously for one month in the intragastric tube feeding rat model (ITFRM) of alcoholic liver disease. The cycling phenomenon is due to an alternating increase and decrease in the metabolic rate. Recently, we found that S-adenosyl-methionine (SAMe) fed with alcohol prevented the BAL cycle.
Method
Using the ITFRM we fed rats betaine (2 g/kg/day) with ethanol for 1 month and recorded the daily 24 h urine ethanol level (UAL) to measure the BAL cycle. UAL is equivalent to BAL because of the constant ethanol infusion. Liver histology, steatosis and BAL were measured terminally after 1 month of treatment. Microarray analysis was done on the mRNA extracted from the liver to determine the effects of betaine and alcohol on changes in gene expression.
Results
Betaine fed with ethanol completely prevented the BAL cycle similar to SAMe. Betaine also significantly reduced the BAL compared to ethanol fed rats without betaine. This was also observed when SAMe was fed with ethanol. The mechanism involved in both cases is that SAMe is required for the conversion of epinephrine from norepinephrine by phenylethanolamine methyltransferase (PNMT). Epinephrine is 5 to 10 fold more potent than norepinephrine in increasing the metabolic rate. The increase in the metabolic rate generates NAD, permitting ADH to increase the oxidation of alcohol. NAD is the rate limiting factor in oxidation of alcohol by alcohol dehydrogenase (ADH). This explains how SAMe and betaine prevented the cycle. Microarray analysis showed that betaine feeding prevented the up regulation of a large number of genes including TLR2/4, Il-1b, Jax3, Sirt3, Fas, Ifngr1, Tgfgr2, Tnfrsf21, Lbp and Stat 3 which could explain how betaine prevented fatty liver.
Conclusion
Betaine feeding lowers the BAL and prevents the BAL cycle by increasing the metabolic rate. This increases the rate of ethanol elimination by generating NAD.
doi:10.1016/j.yexmp.2011.05.009
PMCID: PMC3185137  PMID: 21708146
S-adenosylmethionine (SAMe); Betaine; Blood Alcohol Cycle (BAL); Microarray Analysis; NAD
14.  No consistent evidence for association between mtDNA variants and Alzheimer disease 
Hudson, G. | Sims, R. | Harold, D. | Chapman, J. | Hollingworth, P. | Gerrish, A. | Russo, G. | Hamshere, M. | Moskvina, V. | Jones, N. | Thomas, C. | Stretton, A. | Holmans, P.A. | O'Donovan, M.C. | Owen, M.J. | Williams, J. | Chinnery, P.F. | Harold, Denise | Abraham, Richard | Hollingworth, Paul | Sims, Rebecca | Gerrish, Amy | Chapman, Jade | Russo, Giancarlo | Hamshere, Marian | Pahwa, Jaspreet Singh | Moskvina, Valentina | Dowzell, Kimberley | Williams, Amy | Jones, Nicola | Thomas, Charlene | Stretton, Alexandra | Morgan, Angharad | Lovestone, Simon | Powell, John | Proitsi, Petroula | Lupton, Michelle K | Brayne, Carol | Rubinsztein, David C. | Gill, Michael | Lawlor, Brian | Lynch, Aoibhinn | Morgan, Kevin | Brown, Kristelle | Passmore, Peter | Craig, David | McGuinness, Bernadette | Todd, Stephen | Johnston, Janet | Holmes, Clive | Mann, David | Smith, A. David | Love, Seth | Kehoe, Patrick G. | Hardy, John | Mead, Simon | Fox, Nick | Rossor, Martin | Collinge, John | Maier, Wolfgang | Jessen, Frank | Heun, Reiner | Kölsch, Heike | Schürmann, Britta | van den Bussche, Hendrik | Heuser, Isabella | Kornhuber, Johannes | Wiltfang, Jens | Dichgans, Martin | Frölich, Lutz | Hampel, Harald | Hüll, Michael | Rujescu, Dan | Goate, Alison | Kauwe, John S.K. | Cruchaga, Carlos | Nowotny, Petra | Morris, John C. | Mayo, Kevin | Livingston, Gill | Bass, Nicholas J. | Gurling, Hugh | McQuillin, Andrew | Gwilliam, Rhian | Deloukas, Panagiotis | Holmans, Peter | O'Donovan, Michael | Owen, Michael J. | Williams, Julie
Neurology  2012;78(14):1038-1042.
Objective:
Although several studies have described an association between Alzheimer disease (AD) and genetic variation of mitochondrial DNA (mtDNA), each has implicated different mtDNA variants, so the role of mtDNA in the etiology of AD remains uncertain.
Methods:
We tested 138 mtDNA variants for association with AD in a powerful sample of 4,133 AD case patients and 1,602 matched controls from 3 Caucasian populations. Of the total population, 3,250 case patients and 1,221 elderly controls met the quality control criteria and were included in the analysis.
Results:
In the largest study to date, we failed to replicate the published findings. Meta-analysis of the available data showed no evidence of an association with AD.
Conclusion:
The current evidence linking common mtDNA variations with AD is not compelling.
doi:10.1212/WNL.0b013e31824e8f1d
PMCID: PMC3317529  PMID: 22442439
15.  Comparison of KRAS Mutation Assessment in Tumor DNA and Circulating Free DNA in Plasma and Serum Samples 
Testing for mutations in the KRAS oncogene for patients with metastatic colorectal cancer (mCRC) is generally performed using DNA from formalin-fixed paraffin-embedded tumor tissue; however, access to specimens can be limited and analysis challenging. This study assessed the identification of KRAS mutations in circulating free DNA (cfDNA) using a commercially available KRAS polymerase chain reaction (PCR) kit. Matched plasma, serum and tumor samples were available from 71 patients with mCRC who had received prior therapy but whose disease progressed following therapy. Yields of cfDNA from plasma and serum samples were comparable. Analyses were successful in 70/71 plasma-extracted samples (specificity: 97%, sensitivity: 31%) and 67/71 serum- extracted samples (specificity: 100%, sensitivity: 25%). This study demonstrates that KRAS mutations can be detected in cfDNA using a commercially available KRAS PCR kit, confirming cfDNA as a potential alternative source of tumor DNA in a diagnostic setting if access to archival tumor specimens is limited.
doi:10.4137/CPath.S8798
PMCID: PMC3362326  PMID: 22661904
KRAS; mutation; cfDNA; colorectal cancer
16.  Reliability and Comparability of Psychosis Patients’ Retrospective Reports of Childhood Abuse 
Schizophrenia Bulletin  2009;37(3):546-553.
An increasing number of studies are demonstrating an association between childhood abuse and psychosis. However, the majority of these rely on retrospective self-reports in adulthood that may be unduly influenced by current psychopathology. We therefore set out to explore the reliability and comparability of first-presentation psychosis patients’ reports of childhood abuse. Psychosis case subjects were drawn from the Aetiology and Ethnicity of Schizophrenia and Other Psychoses (ÆSOP) epidemiological study and completed the Childhood Experience of Care and Abuse Questionnaire to elicit abusive experiences that occurred prior to 16 years of age. High levels of concurrent validity were demonstrated with the Parental Bonding Instrument (antipathy: rs = 0.350–0.737, P < .001; neglect: rs = 0.688–0.715, P < .001), and good convergent validity was shown with clinical case notes (sexual abuse: κ = 0.526, P < .001; physical abuse: κ = 0.394, P < .001). Psychosis patients’ reports were also reasonably stable over a 7-year period (sexual abuse: κ = 0.590, P < .01; physical abuse: κ = 0.634, P < .001; antipathy: κ = 0.492, P < .01; neglect: κ = 0.432, P < .05). Additionally, their reports of childhood abuse were not associated with current severity of psychotic symptoms (sexual abuse: U = 1768.5, P = .998; physical abuse: U = 2167.5, P = .815; antipathy: U = 2216.5, P = .988; neglect: U = 1906.0, P = .835) or depressed mood (sexual abuse: χ2 = 0.634, P = .277; physical abuse: χ2 = 0.159, P = .419; antipathy: χ2 = 0.868, P = .229; neglect: χ2 = 0.639, P = .274). These findings provide justification for the use in future studies of retrospective reports of childhood abuse obtained from individuals with psychotic disorders.
doi:10.1093/schbul/sbp103
PMCID: PMC3080697  PMID: 19776204
psychotic disorders; child abuse; trauma; schizophrenia; psychometrics
17.  The varying impact of type, timing and frequency of exposure to childhood adversity on its association with adult psychotic disorder 
Psychological medicine  2010;40(12):1967-1978.
Background
Childhood adversity has been associated with onset of psychosis in adulthood but these studies have used only general definitions of this environmental risk indicator. Therefore, we sought to explore the prevalence of more specific adverse childhood experiences amongst those with and without psychotic disorders using detailed assessments in a large epidemiological case-control sample (ÆSOP).
Method
Data were collected on 182 first-presentation psychosis cases and 246 geographically-matched controls in two UK centres. Information relating to the timing and frequency of exposure to different types of childhood adversity (neglect, antipathy, physical and sexual abuse, local authority care, disrupted living arrangements and lack of supportive figure) was obtained using the Childhood Experience of Care and Abuse Questionnaire.
Results
Psychosis cases were three times more likely to report severe physical abuse from mother that commenced prior to 12 years of age, even after adjustment for other significant forms of adversity and demographic confounders. A non-significant trend was also evident for greater prevalence of reported severe maternal antipathy amongst those with psychosis. Associations with maternal neglect and childhood sexual abuse disappeared after adjusting for maternal physical abuse and antipathy. Paternal maltreatment and other forms of adversity were not associated with psychosis nor was there evidence of a dose-response effect.
Conclusions
These findings suggest that only specific adverse childhood experiences are associated with psychotic disorders and only in a minority of cases. If replicated, this greater precision will ensure that research into the mechanisms underlying the pathway from childhood adversity to psychosis is more fruitful.
doi:10.1017/S0033291710000231
PMCID: PMC3272393  PMID: 20178679
child abuse; psychotic disorders; childhood trauma; aetiology; psychosis
18.  Serum Neopterin Levels as a Diagnostic Marker of Hemophagocytic Lymphohistiocytosis Syndrome ▿ 
The objective of this study was to retrospectively evaluate the utility of serum neopterin as a diagnostic marker of hemophagocytic lymphohistiocytosis (HLH). The medical records of patients diagnosed with HLH (familial and secondary) between January 2000 and May 2009 were reviewed retrospectively, and clinical and laboratory information related to HLH criteria, in addition to neopterin levels, was recorded. A group of 50 patients with active juvenile dermatomyositis (JDM) (who routinely have neopterin levels assessed) served as controls for the assessment of the accuracy, sensitivity, and specificity of neopterin as a diagnostic test for HLH. The Pearson correlation was used to measure the association between serum neopterin levels and established HLH-related laboratory data. Serum neopterin levels were measured using a competitive enzyme immunoassay. During the time frame of the study, 3 patients with familial HLH and 18 patients with secondary HLH were identified as having had serum neopterin measured (all HLH patients were grouped together). The mean neopterin levels were 84.9 nmol/liter (standard deviation [SD], 83.4 nmol/liter) for patients with HLH and 21.5 nmol/liter (SD, 10.13 nmol/liter) for patients with JDM. A cutoff value of 38.9 nmol/liter was 70% sensitive and 95% specific for HLH. For HLH patients, neopterin levels correlated significantly with ferritin levels (r = 0.76, P = 0.0007). In comparison to the level in a control group of JDM patients, elevated serum neopterin was a sensitive and specific marker for HLH. Serum neopterin has value as a diagnostic marker of HLH, and prospective studies are under way to further evaluate its role as a marker for early diagnosis and management of patients.
doi:10.1128/CVI.00306-10
PMCID: PMC3122569  PMID: 21270283
19.  Correction: Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer's Disease 
Jones, Lesley | Holmans, Peter A. | Hamshere, Marian L. | Harold, Denise | Moskvina, Valentina | Ivanov, Dobril | Pocklington, Andrew | Abraham, Richard | Hollingworth, Paul | Sims, Rebecca | Gerrish, Amy | Pahwa, Jaspreet Singh | Jones, Nicola | Stretton, Alexandra | Morgan, Angharad R. | Lovestone, Simon | Powell, John | Proitsi, Petroula | Lupton, Michelle K. | Brayne, Carol | Rubinsztein, David C. | Gill, Michael | Lawlor, Brian | Lynch, Aoibhinn | Morgan, Kevin | Brown, Kristelle S. | Passmore, Peter A. | Craig, David | McGuinness, Bernadette | Todd, Stephen | Holmes, Clive | Mann, David | Smith, A. David | Love, Seth | Kehoe, Patrick G. | Mead, Simon | Fox, Nick | Rossor, Martin | Collinge, John | Maier, Wolfgang | Jessen, Frank | Schürmann, Britta | van den Bussche, Hendrik | Heuser, Isabella | Peters, Oliver | Kornhuber, Johannes | Wiltfang, Jens | Dichgans, Martin | Frölich, Lutz | Hampel, Harald | Hüll, Michael | Rujescu, Dan | Goate, Alison M. | Kauwe, John S. K. | Cruchaga, Carlos | Nowotny, Petra | Morris, John C. | Mayo, Kevin | Livingston, Gill | Bass, Nicholas J. | Gurling, Hugh | McQuillin, Andrew | Gwilliam, Rhian | Deloukas, Panos | Al-Chalabi, Ammar | Shaw, Christopher E. | Singleton, Andrew B. | Guerreiro, Rita | Mühleisen, Thomas W. | Nöthen, Markus M. | Moebus, Susanne | Jöckel, Karl-Heinz | Klopp, Norman | Wichmann, H.-Erich | Rüther, Eckhard | Carrasquillo, Minerva M. | Pankratz, V. Shane | Younkin, Steven G. | Hardy, John | O'Donovan, Michael C. | Owen, Michael J. | Williams, Julie
PLoS ONE  2011;6(2):10.1371/annotation/a0bb886d-d345-4a20-a82e-adce9b047798.
doi:10.1371/annotation/a0bb886d-d345-4a20-a82e-adce9b047798
PMCID: PMC3039022
20.  Enhancement of In Vivo and In Vitro Immune Functions by a Conformationally-Biased, Response-Selective Agonist of Human C5a: Implications for a Novel Adjuvant in Vaccine Design 
Vaccine  2009;28(2):463-469.
A conformationally-biased, agonist of human C5a65–74 (EP67) was assessed for its adjuvant activities in vitro and in vivo. EP67 induced the release of the inflammatory (Th1) type cytokines from C5a receptor (CD88)-bearing antigen presenting cells (APC). Serum from mice immunized with EP67-ovalbumin (OVA) contained high OVA-specific antibody (Ab) titers [IgG1, IgG2a (IGg2c), IgG2b]. Mice receiving OVA alone produced only IgG1 Abs, indicating the ability of EP67 to induce a Th1-like antibody (A)b class switch. Spleen cell cultures from wild type mice but not CD88−/− mice showed an enhanced OVA-specific proliferative response in vitro. These results indicate the ability of EP67 to drive a Th1-mediated immune response and its potential use as a unique adjuvant
doi:10.1016/j.vaccine.2009.10.029
PMCID: PMC2789185  PMID: 19836478
21.  Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer's Disease 
Jones, Lesley | Holmans, Peter A. | Hamshere, Marian L. | Harold, Denise | Moskvina, Valentina | Ivanov, Dobril | Pocklington, Andrew | Abraham, Richard | Hollingworth, Paul | Sims, Rebecca | Gerrish, Amy | Pahwa, Jaspreet Singh | Jones, Nicola | Stretton, Alexandra | Morgan, Angharad R. | Lovestone, Simon | Powell, John | Proitsi, Petroula | Lupton, Michelle K. | Brayne, Carol | Rubinsztein, David C. | Gill, Michael | Lawlor, Brian | Lynch, Aoibhinn | Morgan, Kevin | Brown, Kristelle S. | Passmore, Peter A. | Craig, David | McGuinness, Bernadette | Todd, Stephen | Holmes, Clive | Mann, David | Smith, A. David | Love, Seth | Kehoe, Patrick G. | Mead, Simon | Fox, Nick | Rossor, Martin | Collinge, John | Maier, Wolfgang | Jessen, Frank | Schürmann, Britta | van den Bussche, Hendrik | Heuser, Isabella | Peters, Oliver | Kornhuber, Johannes | Wiltfang, Jens | Dichgans, Martin | Frölich, Lutz | Hampel, Harald | Hüll, Michael | Rujescu, Dan | Goate, Alison M. | Kauwe, John S. K. | Cruchaga, Carlos | Nowotny, Petra | Morris, John C. | Mayo, Kevin | Livingston, Gill | Bass, Nicholas J. | Gurling, Hugh | McQuillin, Andrew | Gwilliam, Rhian | Deloukas, Panos | Al-Chalabi, Ammar | Shaw, Christopher E. | Singleton, Andrew B. | Guerreiro, Rita | Mühleisen, Thomas W. | Nöthen, Markus M. | Moebus, Susanne | Jöckel, Karl-Heinz | Klopp, Norman | Wichmann, H.-Erich | Rüther, Eckhard | Carrasquillo, Minerva M. | Pankratz, V. Shane | Younkin, Steven G. | Hardy, John | O'Donovan, Michael C. | Owen, Michael J. | Williams, Julie
PLoS ONE  2010;5(11):e13950.
Background
Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes.
Methodology
We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset.
Principal Findings
We found a significant overrepresentation of association signals in pathways related to cholesterol metabolism and the immune response in both of the two largest genome-wide association studies for LOAD.
Significance
Processes related to cholesterol metabolism and the innate immune response have previously been implicated by pathological and epidemiological studies of Alzheimer's disease, but it has been unclear whether those findings reflected primary aetiological events or consequences of the disease process. Our independent evidence from two large studies now demonstrates that these processes are aetiologically relevant, and suggests that they may be suitable targets for novel and existing therapeutic approaches.
doi:10.1371/journal.pone.0013950
PMCID: PMC2981526  PMID: 21085570
22.  Urethral Sphincter Morphology and Function With and Without Stress Incontinence 
The Journal of urology  2009;182(1):203-209.
Purpose
Using magnetic resonance images we analyzed the relationship between urethral sphincter anatomy, urethral function and pelvic floor function.
Materials and Methods
A total of 103 women with stress incontinence and 108 asymptomatic continent controls underwent urethral profilometry, urethral axis measurement with a cotton swab, vaginal closure force measurement with an instrumented speculum and magnetic resonance imaging. Striated urogenital sphincter length was determined and its thickness was measured in the proximal sphincter, where its circular shape enables estimation of striated urogenital sphincter area. A length-area index was calculated as a proxy for volume.
Results
The striated urogenital sphincter in women with stress incontinence was 12.5% smaller than that in asymptomatic continent women (mean ± SD length-area index 766.4 ± 294.3 vs 876.2 ± 407.3 mm3, p = 0.04). The groups did not differ significantly in striated urogenital sphincter length (13.2 ± 3.4 vs 13.7 ±3.9 mm, p = 0.40), thickness (2.83 ± 0.8 vs 3.11± 1.4 mm, p = 0.09) or area (59.1 ± 18.4 vs 62.9 ± 24.7 mm2, p = 0.24). Striated urogenital sphincter length and area, and the length-area index were associated during voluntary pelvic muscle contraction with more urethral axis elevation and increased vaginal closure force augmentation.
Conclusions
A smaller striated urogenital sphincter is associated with stress incontinence and poorer pelvic floor muscle function.
doi:10.1016/j.juro.2009.02.129
PMCID: PMC2752958  PMID: 19450822
urethra; urinary incontinence, stress; magnetic resonance imaging; female; muscle, striated
23.  Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease, and shows evidence for additional susceptibility genes 
Harold, Denise | Abraham, Richard | Hollingworth, Paul | Sims, Rebecca | Gerrish, Amy | Hamshere, Marian | Singh Pahwa, Jaspreet | Moskvina, Valentina | Dowzell, Kimberley | Williams, Amy | Jones, Nicola | Thomas, Charlene | Stretton, Alexandra | Morgan, Angharad | Lovestone, Simon | Powell, John | Proitsi, Petroula | Lupton, Michelle K | Brayne, Carol | Rubinsztein, David C. | Gill, Michael | Lawlor, Brian | Lynch, Aoibhinn | Morgan, Kevin | Brown, Kristelle | Passmore, Peter | Craig, David | McGuinness, Bernadette | Todd, Stephen | Holmes, Clive | Mann, David | Smith, A. David | Love, Seth | Kehoe, Patrick G. | Hardy, John | Mead, Simon | Fox, Nick | Rossor, Martin | Collinge, John | Maier, Wolfgang | Jessen, Frank | Schürmann, Britta | van den Bussche, Hendrik | Heuser, Isabella | Kornhuber, Johannes | Wiltfang, Jens | Dichgans, Martin | Frölich, Lutz | Hampel, Harald | Hüll, Michael | Rujescu, Dan | Goate, Alison | Kauwe, John S.K. | Cruchaga, Carlos | Nowotny, Petra | Morris, John C. | Mayo, Kevin | Sleegers, Kristel | Bettens, Karolien | Engelborghs, Sebastiaan | De Deyn, Peter | van Broeckhoven, Christine | Livingston, Gill | Bass, Nicholas J. | Gurling, Hugh | McQuillin, Andrew | Gwilliam, Rhian | Deloukas, Panagiotis | Al-Chalabi, Ammar | Shaw, Christopher E. | Tsolaki, Magda | Singleton, Andrew | Guerreiro, Rita | Mühleisen, Thomas W. | Nöthen, Markus M. | Moebus, Susanne | Jöckel, Karl-Heinz | Klopp, Norman | Wichmann, H-Erich | Carrasquillo, Minerva M. | Pankratz, V. Shane | Younkin, Steven G. | Holmans, Peter | O'Donovan, Michael | Owen, Michael J. | Williams, Julie
Nature genetics  2009;41(10):1088-1093.
We undertook a two-stage genome-wide association study of Alzheimer's disease involving over 16,000 individuals. In stage 1 (3,941 cases and 7,848 controls), we replicated the established association with the APOE locus (most significant SNP: rs2075650, p= 1.8×10−157) and observed genome-wide significant association with SNPs at two novel loci: rs11136000 in the CLU or APOJ gene (p= 1.4×10−9) and rs3851179, a SNP 5′ to the PICALM gene (p= 1.9×10−8). Both novel associations were supported in stage 2 (2,023 cases and 2,340 controls), producing compelling evidence for association with AD in the combined dataset (rs11136000: p= 8.5×10−10, odds ratio= 0.86; rs3851179: p= 1.3×10−9, odds ratio= 0.86). We also observed more variants associated at p< 1×10−5 than expected by chance (p=7.5×10−6), including polymorphisms at the BIN1, DAB1 and CR1 loci.
doi:10.1038/ng.440
PMCID: PMC2845877  PMID: 19734902
24.  Evaluation of the rheumatoid arthritis susceptibility loci HLA-DRB1, PTPN22, OLIG3/TNFAIP3, STAT4 and TRAF1/C5 in an inception cohort 
Introduction
This study investigated five confirmed rheumatoid arthritis (RA) susceptibility genes/loci (HLA-DRB1, PTPN22, STAT4, OLIG3/TNFAIP3 and TRAF1/C5) for association with susceptibility and severity in an inception cohort.
Methods
The magnitude of association for each genotype was assessed in 1,046 RA subjects from the Yorkshire Early RA cohort and in 5,968 healthy UK controls. Additional exploratory subanalyses were undertaken in subgroups defined by autoantibody status (rheumatoid factor and anti-cyclic citrullinated peptide) or disease severity (baseline articular erosions, Health Assessment Questionnaire (HAQ) score and swollen joint count (SJC)).
Results
In the total RA inception cohort, the HLA-DRB1 shared epitope (per-allele odds ratio (OR) = 2.1, trend P < 0.0001), PTPN22 (per-allele OR = 1.5, trend P < 0.0001), OLIG3/TNFAIP3 locus (per-allele OR = 1.2, trend P = 0.009) and TRAF1/C5 locus (per-allele OR = 1.1, trend P = 0.04) were associated with RA. The magnitude of association for these loci was increased in those patients who were autoantibody-positive. PTPN22 was associated with autoantibody-negative RA (per-allele OR = 1.3, trend P = 0.04). There was no evidence of association between these five genetic loci and baseline erosions or SJC in the total RA cohort, after adjustment for symptom duration. TRAF1/C5 was significantly associated with baseline HAQ, however, following adjustment for symptom duration (P trend = 0.03).
Conclusions
These findings support the mounting evidence that different genetic loci are associated with autoantibody-positive and autoantibody-negative RA, possibly suggesting that many of the genes identified to date are associated with autoantibody production. Additional studies with a specific focus on autoantibody-negative RA will be needed to identify the genes predisposing to this RA subgroup. The TRAF1/C5 locus in particular warrants further investigation in RA as a potential disease severity locus.
doi:10.1186/ar2969
PMCID: PMC2888207  PMID: 20353580
25.  Examining evidence for neighbourhood variation in the duration of untreated psychosis 
Health & Place  2010;16(2):219-225.
Background
Family involvement in help-seeking is associated with a shorter duration of untreated psychoses [DUP], but it is unknown whether neighbourhood-level factors are also important.
Methods
DUP was estimated for all cases of first-episode psychoses identified over 2 years in 33 Southeast London neighbourhoods (n=329). DUP was positively skewed and transformed to the natural logarithm scale. We fitted various hierarchical models, adopting different assumptions with regard to spatial variability of DUP, to assess whether there was evidence of neighbourhood heterogeneity in DUP, having accounted for a priori individual-level confounders.
Results
Neighbourhood-level variation in DUP was negligible compared to overall variability. A non-hierarchical model with age, sex and ethnicity covariates, but without area-level random effects, provided the best fit to the data.
Discussion
Neighbourhood factors do not appear to be associated with DUP, suggesting its predictors lie at individual and family levels. Our results inform mental healthcare planning, suggesting that in one urbanised area of Southeast London, where you live does not affect duration of untreated psychosis.
doi:10.1016/j.healthplace.2009.09.013
PMCID: PMC2812704  PMID: 19875323
Neighbourhood; DUP; Spatial epidemiology; Psychosis; Geography

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