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1.  Primary care and youth mental health in Ireland: qualitative study in deprived urban areas 
BMC Family Practice  2013;14:194.
Background
Mental disorders account for six of the 20 leading causes of disability worldwide with a very high prevalence of psychiatric morbidity in youth aged 15–24 years. However, healthcare professionals are faced with many challenges in the identification and treatment of mental and substance use disorders in young people (e.g. young people’s unwillingness to seek help from healthcare professionals, lack of training, limited resources etc.) The challenge of youth mental health for primary care is especially evident in urban deprived areas, where rates of and risk factors for mental health problems are especially common. There is an emerging consensus that primary care is well placed to address mental and substance use disorders in young people especially in deprived urban areas. This study aims to describe healthcare professionals’ experience and attitudes towards screening and early intervention for mental and substance use disorders among young people (16–25 years) in primary care in deprived urban settings in Ireland.
Methods
The chosen method for this qualitative study was inductive thematic analysis which involved semi-structured interviews with 37 healthcare professionals from primary care, secondary care and community agencies at two deprived urban centres.
Results
We identified three themes in respect of interventions to increase screening and treatment: (1) Identification is optimised by a range of strategies, including raising awareness, training, more systematic and formalised assessment, and youth-friendly practices (e.g. communication skills, ensuring confidentiality); (2) Treatment is enhanced by closer inter-agency collaboration and training for all healthcare professionals working in primary care; (3) Ongoing engagement is enhanced by motivational work with young people, setting achievable treatment goals, supporting transition between child and adult mental health services and recognising primary care’s longitudinal nature as a key asset in promoting treatment engagement.
Conclusions
Especially in deprived areas, primary care is central to early intervention for youth mental health. Identification, treatment and continuing engagement are likely to be enhanced by a range of strategies with young people, healthcare professionals and systems. Further research on youth mental health and primary care, including qualitative accounts of young people’s experience and developing complex interventions that promote early intervention are priorities. (350 words)
doi:10.1186/1471-2296-14-194
PMCID: PMC3880165  PMID: 24341616
Young people; Urban deprivation; Mental health; Substance use; Primary care; General practice
2.  Radiation-induced acid ceramidase confers prostate cancer resistance and tumor relapse 
The Journal of Clinical Investigation  2013;123(10):4344-4358.
Escape of prostate cancer (PCa) cells from ionizing radiation–induced (IR-induced) killing leads to disease progression and cancer relapse. The influence of sphingolipids, such as ceramide and its metabolite sphingosine 1-phosphate, on signal transduction pathways under cell stress is important to survival adaptation responses. In this study, we demonstrate that ceramide-deacylating enzyme acid ceramidase (AC) was preferentially upregulated in irradiated PCa cells. Radiation-induced AC gene transactivation by activator protein 1 (AP-1) binding on the proximal promoter was sensitive to inhibition of de novo ceramide biosynthesis, as demonstrated by promoter reporter and ChIP-qPCR analyses. Our data indicate that a protective feedback mechanism mitigates the apoptotic effect of IR-induced ceramide generation. We found that deregulation of c-Jun induced marked radiosensitization in vivo and in vitro, which was rescued by ectopic AC overexpression. AC overexpression in PCa clonogens that survived a fractionated 80-Gy IR course was associated with increased radioresistance and proliferation, suggesting a role for AC in radiotherapy failure and relapse. Immunohistochemical analysis of human PCa tissues revealed higher levels of AC after radiotherapy failure than those in therapy-naive PCa, prostatic intraepithelial neoplasia, or benign tissues. Addition of an AC inhibitor to an animal model of xenograft irradiation produced radiosensitization and prevention of relapse. These data indicate that AC is a potentially tractable target for adjuvant radiotherapy.
doi:10.1172/JCI64791
PMCID: PMC3784522  PMID: 24091326
3.  ATP and potassium ions: a deadly combination for astrocytes 
Scientific Reports  2014;4:4576.
The ATP release channel Pannexin1 (Panx1) is self-regulated, i.e. the permeant ATP inhibits the channel from the extracellular space. The affinity of the ATP binding site is lower than that of the purinergic P2X7 receptor allowing a transient activation of Panx1 by ATP through P2X7R. Here we show that the inhibition of Panx1 by ATP is abrogated by increased extracellular potassium ion concentration ([K+]o) in a dose-dependent manner. Since increased [K+]o is also a stimulus for Panx1 channels, it can be expected that a combination of ATP and increased [K+]o would be deadly for cells. Indeed, astrocytes did not survive exposure to these combined stimuli. The death mechanism, although involving P2X7R, does not appear to strictly follow a pyroptotic pathway. Instead, caspase-3 was activated, a process inhibited by Panx1 inhibitors. These data suggest that Panx1 plays an early role in the cell death signaling pathway involving ATP and K+ ions. Additionally, Panx1 may play a second role once cells are committed to apoptosis, since Panx1 is also a substrate of caspase-3.
doi:10.1038/srep04576
PMCID: PMC3974143
4.  RIG-1 receptor expression in the pathology of Alzheimer’s disease 
Background
Neuroinflammation plays a critical role in the pathogenesis of Alzheimer’s disease (AD) and involves activation of the innate immune response via recognition of diverse stimuli by pattern recognition receptors (PRRs). The inflammatory inducers and precise innate signaling pathway contributing to AD pathology remain largely undefined.
Results
In the present study we analyzed expression levels of innate immune proteins in temporal and occipital cortices from preclinical (no cognitive impairment, NCI, N = 22) to mild cognitive impairment (MCI, N = 20) associated with AD pathology (N = 20) and AD patients (N = 23). We found that retinoic acid-inducible gene-I (RIG-1) is significantly elevated in the temporal cortex and plasma in patients with MCI. In addition, primary human astrocytes stimulated with the RIG-1 ligand 5′ppp RNA showed increased expression of amyloid precursor protein (APP) and amyloid-β (Aβ), supporting the idea that RIG-1 is involved in the pathology of MCI associated with early progression to AD.
Conclusion
These findings suggest that RIG-1 may play a critical role in incipient AD.
doi:10.1186/1742-2094-11-67
PMCID: PMC3977677  PMID: 24694234
Innate immunity; Rig signaling; RLR; Inflammation; Alzheimer’s disease; Mild cognitive impairment
5.  Losing sight of the future: Impaired semantic prospection following medial temporal lobe lesions 
Hippocampus  2012;23(4):268-277.
The ability to imagine the future (prospection) relies on many of the same brain regions that support memory for the past. To date, scientific research has primarily focused on the neural substrates of episodic forms of prospection (mental simulation of spatiotemporally specific future events) whereas little is known about the neural substrates of semantic prospection (mental simulation of future nonpersonal facts). Of particular interest is the role of the medial temporal lobes, and specifically the hippocampus. While the hippocampus has been proposed to play a key role in episodic prospection, recent evidence suggests that it may not play a similar role in semantic prospection. To examine this possibility, amnesic patients with medial temporal lobe (MTL) lesions were asked to imagine future issues occurring in the public domain. The results showed that patients could list general semantic facts about the future, but when probed to elaborate, patients produced impoverished descriptions that lacked semantic detail. This impairment occurred despite intact performance on standard neuropsychological tests of semantic processing, and did not simply reflect deficits in narrative construction. The performance of a patient with damage limited to the hippocampus was similar to that of the remaining MTL patients and amnesic patients’ impaired elaboration of the semantic future correlated with their impaired elaboration of the semantic past. Together, these results provide novel evidence from MTL amnesia that memory and prospection are linked in the semantic domain and reveal that the medial temporal lobes play a critical role in the construction of detailed, multi-element semantic simulations.
doi:10.1002/hipo.22084
PMCID: PMC3628277  PMID: 23197413
semantic memory; episodic memory; hippocampus; amnesia; imagination
6.  HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes 
AIDS (London, England)  2013;27(6):10.1097/QAD.0b013e32835e1616.
Objective
To define the relative frequencies of different mechanisms of viral escape.
Design
A population-based approach to examine the distribution of HIV polymorphism associated with diverse population human leucocyte antigens (HLAs) at sites within and flanking CD8 T-cell epitopes as a correlate of likely mechanisms of viral escape.
Methods
Sequence windows surrounding 874 HLA allele-specific polymorphisms across the full HIV-1 proteomic consensus sequence were scanned by an epitope-prediction programme. Either already known or probable CD8 T-cell epitopes with HLA restriction matching that of the proximal HLA association were identified and synthesized. These peptides were used as stimulating antigens in automated enzyme-linked immunospot (ELISpot) assays. Peptide arrays were customized to each individual based on their HLA genotype.
Results
Among HLA-associated HIV polymorphisms detected in the viral sequences of a cohort of 800 individuals with chronic subtype B HIV infection, those which were likely to affect HLA peptide binding were significantly more common than polymorphisms at nonanchor HLA binding sites. HIV epitopes with such polymorphisms were associated with reduced IFNγ responses in ELISpot assays. HIV escape at sites affecting T-cell receptor (TCR) engagement and epitope processing were also evident.
Conclusion
HIV escape from HLA-peptide binding predominates as an effective viral evasion strategy and therefore has implications for inclusion of HLA-adapted epitopes in vaccine immunogens.
doi:10.1097/QAD.0b013e32835e1616
PMCID: PMC3818524  PMID: 23276808
CD8; epitope; escape mutation; HIV-1; HLA-driven; polymorphism; T-cell immunity
7.  The genomes of four tapeworm species reveal adaptations to parasitism 
Nature  2013;496(7443):57-63.
Summary
Tapeworms cause debilitating neglected diseases that can be deadly and often require surgery due to ineffective drugs. Here we present the first analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium and the laboratory model Hymenolepis microstoma as examples. The 115-141 megabase genomes offer insights into the evolution of parasitism. Synteny is maintained with distantly related blood flukes but we find extreme losses of genes and pathways ubiquitous in other animals, including 34 homeobox families and several determinants of stem cell fate. Tapeworms have species-specific expansions of non-canonical heat shock proteins and families of known antigens; specialised detoxification pathways, and metabolism finely tuned to rely on nutrients scavenged from their hosts. We identify new potential drug targets, including those on which existing pharmaceuticals may act. The genomes provide a rich resource to underpin the development of urgently needed treatments and control.
doi:10.1038/nature12031
PMCID: PMC3964345  PMID: 23485966
HSP70; parasitism; Cestoda; cysticercosis; echinococcosis; Platyhelminthes
8.  Go retro and get a GRIP 
Genome Biology  2013;14(3):108.
Gene retrocopy insertions are a source of new genes and new gene functions, and can now be identified using paired-end whole genome sequencing data.
See related Research article: http://genomebiology.com/2013/14/3/R22
doi:10.1186/gb-2013-14-3-108
PMCID: PMC3663096  PMID: 23514103
9.  Targeting of Slc25a21 Is Associated with Orofacial Defects and Otitis Media Due to Disrupted Expression of a Neighbouring Gene 
PLoS ONE  2014;9(3):e91807.
Homozygosity for Slc25a21tm1a(KOMP)Wtsi results in mice exhibiting orofacial abnormalities, alterations in carpal and rugae structures, hearing impairment and inflammation in the middle ear. In humans it has been hypothesised that the 2-oxoadipate mitochondrial carrier coded by SLC25A21 may be involved in the disease 2-oxoadipate acidaemia. Unexpectedly, no 2-oxoadipate acidaemia-like symptoms were observed in animals homozygous for Slc25a21tm1a(KOMP)Wtsi despite confirmation that this allele reduces Slc25a21 expression by 71.3%. To study the complete knockout, an allelic series was generated using the loxP and FRT sites typical of a Knockout Mouse Project allele. After removal of the critical exon and neomycin selection cassette, Slc25a21 knockout mice homozygous for the Slc25a21tm1b(KOMP)Wtsi and Slc25a21tm1d(KOMP)Wtsi alleles were phenotypically indistinguishable from wild-type. This led us to explore the genomic environment of Slc25a21 and to discover that expression of Pax9, located 3′ of the target gene, was reduced in homozygous Slc25a21tm1a(KOMP)Wtsi mice. We hypothesize that the presence of the selection cassette is the cause of the down regulation of Pax9 observed. The phenotypes we observed in homozygous Slc25a21tm1a(KOMP)Wtsi mice were broadly consistent with a hypomorphic Pax9 allele with the exception of otitis media and hearing impairment which may be a novel consequence of Pax9 down regulation. We explore the ramifications associated with this particular targeted mutation and emphasise the need to interpret phenotypes taking into consideration all potential underlying genetic mechanisms.
doi:10.1371/journal.pone.0091807
PMCID: PMC3958370  PMID: 24642684
10.  Systematic review of novel ablative methods in locally advanced pancreatic cancer 
Unresectable locally advanced pancreatic cancer with or without metastatic disease is associated with a very poor prognosis. Current standard therapy is limited to chemotherapy or chemoradiotherapy. Few regimens have been shown to have a substantial survival advantage and novel treatment strategies are urgently needed. Thermal and laser based ablative techniques are widely used in many solid organ malignancies. Initial studies in the pancreas were associated with significant morbidity and mortality, which limited widespread adoption. Modifications to the various applications, in particular combining the techniques with high quality imaging such as computed tomography and intraoperative or endoscopic ultrasound has enabled real time treatment monitoring and significant improvements in safety. We conducted a systematic review of the literature up to October 2013. Initial studies suggest that ablative therapies may confer an additional survival benefit over best supportive care but randomised studies are required to validate these findings.
doi:10.3748/wjg.v20.i9.2267
PMCID: PMC3942832  PMID: 24605026
Pancreatic cancer; Radiofrequency ablation; Photodynamic therapy; Cryoablation; Microwave ablation; High frequency focused ultrasound; Irreversible electroporation
11.  Hungry bone syndrome and normalisation of renal phosphorus threshold after total parathyroidectomy for tertiary hyperparathyroidism in X-linked hypophosphataemia: a case report 
Introduction
This is the first report of which the authors are aware to describe this c.2166delinsGG mutation in X-linked hypophosphataemia and to describe normalisation of renal threshold for phosphate excretion after parathyroidectomy for tertiary hyperparathyroidism in X-linked hypophosphataemia.
Case presentation
We present the case of a 34-year-old Caucasian woman with X-linked hypophosphataemia. She developed tertiary hyperparathyroidism with markedly high bone turnover requiring total parathyroidectomy and had prolonged requirement for intravenous calcium infusion after surgery. She had a novel mutation in her phosphate-regulating gene with homologies to endopeptidases on the X-chromosome and had an unusual degree of dependence on phosphate supplementation. Prior to operative intervention she had a trial of cinacalcet that improved bone turnover markers when used in isolation but which led to a paradoxical rise in parathyroid hormone levels when given with phosphate supplementation. After correction of hungry bone syndrome, the renal phosphorus threshold normalised as a manifestation of hypoparathyroid state despite marked elevation in level of fibroblast growth factor 23.
Conclusions
This case illustrates the risk of tertiary hyperparathyroidism as a complication of treatment for hypophosphataemia; it highlights the morbidity associated with hungry bone syndrome and provides novel insight into renal handling of phosphorus.
doi:10.1186/1752-1947-8-84
PMCID: PMC3946034  PMID: 24594262
Cinacalcet; Fibroblast growth factor 23; Hungry bone syndrome; Hyperparathyroidism; X-linked hypophosphataemia
12.  CHILE: An Evidence-Based Preschool Intervention for Obesity Prevention in Head Start 
The Journal of school health  2013;83(3):223-229.
BACKGROUND
Obesity is a major concern among American Indians and Hispanics. The Child Health Initiative for Lifelong Eating and Exercise (CHILE) is an evidence-based intervention to prevent obesity in children enrolled in 16 Head Start (HS) Centers in rural communities. The design and implementation of CHILE are described.
METHODS
CHILE uses a socio-ecological approach to improve dietary intake and increase physical activity. The intervention includes: a classroom curriculum; teacher and food service training; family engagement; grocery store participation; and health care provider support.
RESULTS
Lessons learned from CHILE include: the need to consider availability of recommended foods; the necessity of multiple training sessions for teachers and food service; the need to tailor the family events to local needs; consideration of the profit needs of grocery stores; and sensitivity to the time constraints of health care providers.
CONCLUSIONS
HS can play an important role in preventing obesity in children. CHILE is an example of a feasible intervention that addresses nutrition and physical activity for preschool children that can be incorporated into HS curricula and aligns with HS national performance standards.
doi:10.1111/josh.12018
PMCID: PMC3556909  PMID: 23343323
13.  Interspecific Competition between Aedes albopictus and A. sierrensis: Potential for Competitive Displacement in the Western United States 
PLoS ONE  2014;9(2):e89698.
The Asian tiger mosquito, Aedes albopictus, was first detected in North America twenty five years ago. It utilizes water-holding container habitats as immature development sites, and has rapidly spread throughout the eastern United States. Aedes albopictus has occasionally been detected in the western United States, but until recently no established populations of A. albopictus were reported. The western tree-hole mosquito, Aedes sierrensis, is the most common tree-hole mosquito throughout the western United States, and is expected to more frequently encounter A. albopictus. In this study, competition between A. albopictus from the eastern United States and A. sierrensis from the western United States was tested in order to better understand the potential for either competitive displacement of A. sierrensis by A. albopictus or competitive resistance of A. sierrensis to A. albopictus. Varying densities of each species were reared with limited resources in a response surface design. Consistent with a prior study, we found that A. albopictus was clearly a superior larval competitor than A. sierrensis. Aedes sierrensis λ′ (finite rate of increase) decreased with increasing A. albopictus density, but in contrast, A. albopictus λ′ actually increased with increasing A. sierrensis density; a result that was not reflected by individual fitness parameters. These results indicate that A. sierrensis will not be an effective barrier to A. albopictus invasion into tree-holes in the western United States.
doi:10.1371/journal.pone.0089698
PMCID: PMC3938465  PMID: 24586969
14.  Evaluation of Cystoid Change Phenotypes in Ocular Toxoplasmosis Using Optical Coherence Tomography 
PLoS ONE  2014;9(2):e86626.
Purpose
To present unique cystoid changes occurring in patients with ocular toxoplasmosis observed in spectral domain optical coherence tomography (OCT).
Methods
Forty-six patients (80 eyes) with a diagnosis of ocular toxoplasmosis, who underwent volume OCT examination between January 2005 and October 2012, were retrospectively collected. Review of clinical examination findings, fundus photographs, fluorescein angiograms (FA) and OCT image sets obtained at initial visits and follow-up. Qualitative and quantitative analyses of cystoid space phenotypes visualized using OCT.
Results
Of the 80 eyes included, 17 eyes (15 patients) demonstrated cystoid changes in the macula on OCT. Six eyes (7.5%) had cystoid macular edema (CME), 2 eyes (2.5%) had huge outer retinal cystoid space (HORC), 12 eyes (15%) had cystoid degeneration and additional 3 eyes (3.75%) had outer retinal tubulation due to age related macular degeneration. In one eye with HORC, the lesion was seen in the photoreceptor outer segment, accompanied by photoreceptor elongation and splitting. Three eyes presented with paravascular cystoid degeneration in the inner retina without other macular OCT abnormality.
Conclusions
In this study, different phenotypes of cystoid spaces seen in eyes with ocular toxoplasmosis using spectral domain OCT (SD-OCT) were demonstrated. CME presented as an uncommon feature, consistently with previous findings. Identification of rare morphological cystoid features (HORC with/without photoreceptor enlongation or splitting) on clinical examination had provided evidence to previous experimental models, which may also expand the clinical spectrum of the disease. Cystoid degeneration in the inner retina next to the retinal vessels in otherwise “normal” looking macula was observed, which may suggest more often clinical evaluation for those patients. Further studies are needed to verify the relevance of cystoid features seen on SD-OCT in assisting with the diagnosis and management of ocular toxoplasmosis.
doi:10.1371/journal.pone.0086626
PMCID: PMC3914795  PMID: 24505261
15.  Quality-assured screening for diabetic retinopathy delivered in primary care in Ireland: an observational study 
The British Journal of General Practice  2013;63(607):e134-e140.
Background
At present, there is no national population-based retinopathy screening programme for people in Ireland who have diabetes, such as those operating in the UK for over a decade.
Aim
To evaluate a community-based initiative that utilised existing resources in general practice and community optometry/ophthalmology services to provide screening for diabetic retinopathy.
Design and setting
Cross-sectional study using electronic ophthalmic patient screening records in community optometry clinics in Cork, Ireland.
Method
A purposive sample of 32 practices was recruited from Diabetes in General Practice, a general practice-led initiative in the South of Ireland. Practices invited all adult patients registered with diabetes to participate in free retinopathy screening (n = 3598), provided by 15 community optometry practices and two community ophthalmologists. Data were recorded on an electronic database used by optometrists and the performance was benchmarked against proposed national standards for retinopathy screening.
Result
In total, 30 practices participated (94%). After 6 months, 49% of patients (n = 1763) had been screened, following one invitation letter and no reminder. Forty-three per cent of those invited consented to their data being used in the study and subsequent analyses are based on that sample (n = 1542). The mean age of the patients screened was 65 years (standard deviation = 13.0 years), 57% were male (n = 884), and 86% had type 2 diabetes (n = 1320). In total, 26% had some level of retinopathy detected (n = 395); 21% had background retinopathy (n = 331), 3% had pre-proliferative retinopathy (n = 53), and 0.7% had proliferative retinopathy (n = 11).
Conclusion
The detection of retinopathy among 26% of those screened highlights the need for a national retinopathy screening programme in Ireland. Significant learning, derived from the implementation of this initiative, will inform the national programme.
doi:10.3399/bjgp13X663091
PMCID: PMC3553639  PMID: 23561692
diabetic retinopathy; general practice; optometry; quality assurance; primary care; screening
16.  RetroSeq: transposable element discovery from next-generation sequencing data 
Bioinformatics  2012;29(3):389-390.
Summary: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls.
Availabilty: RetroSeq is open-source and available from https://github.com/tk2/RetroSeq.
Contact: tk2@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts697
PMCID: PMC3562067  PMID: 23233656
17.  Financial Distress and Depressive Symptoms among African American Women: Identifying Financial Priorities and Needs and why it Matters for Mental Health 
Prior research found that financial hardship or distress is one of the most important underlying factors for depression/depressive symptoms, yet factors that contribute to financial distress remain unexplored or unaddressed. Given this, the goals of the present study were (1) to examine the relationship between perceived financial distress and depressive symptoms, and (2) to identify financial priorities and needs that may contribute to financial distress. Surveys from 111 African American women, ages 18–44, who reside in Allegheny County, PA, were used to gather demographic information and measures of depressive symptoms and financial distress/financial well-being. Correlation and regression analyses revealed that perceived financial distress was significantly associated with levels of depressive symptoms. To assess financial priorities and needs, responses to two open-ended questions were analyzed and coded for common themes: “Imagine you won a $10,000 prize in a local lottery. What would you do with this money?” and “What kinds of programs or other help would be beneficial to you during times of financial difficulties?” The highest five priorities identified by the participants were paying bills and debt, saving, purchasing a home or making home repairs, and/or helping others. The participant’s perceived needs during times of financial difficulty included tangible assistance and/or financial education. The findings from this study can be used to create new and/or enhance existing programs, services, and/or interventions that focus on the identified financial priorities and needs. Collaborative efforts among professionals in different disciplines are also needed, as ways to manage and alleviate financial distress should be considered and discussed when addressing the mental health of African American women.
doi:10.1007/s11524-012-9755-x
PMCID: PMC3579302  PMID: 22930003
African American women; Depression; Depressive symptoms; Risk factors for depression; Perceived financial distress; Financial strain; Economic strain; Financial priorities; Financial needs
18.  Genotoxicity of multi-walled carbon nanotubes at occupationally relevant doses 
Carbon nanotubes are commercially-important products of nanotechnology; however, their low density and small size makes carbon nanotube respiratory exposures likely during their production or processing. We have previously shown mitotic spindle aberrations in cultured primary and immortalized human airway epithelial cells exposed to single-walled carbon nanotubes (SWCNT). In this study, we examined whether multi-walled carbon nanotubes (MWCNT) cause mitotic spindle damage in cultured cells at doses equivalent to 34 years of exposure at the NIOSH Recommended Exposure Limit (REL). MWCNT induced a dose responsive increase in disrupted centrosomes, abnormal mitotic spindles and aneuploid chromosome number 24 hours after exposure to 0.024, 0.24, 2.4 and 24 μg/cm2 MWCNT. Monopolar mitotic spindles comprised 95% of disrupted mitoses. Three-dimensional reconstructions of 0.1 μm optical sections showed carbon nanotubes integrated with microtubules, DNA and within the centrosome structure. Cell cycle analysis demonstrated a greater number of cells in S-phase and fewer cells in the G2 phase in MWCNT-treated compared to diluent control, indicating a G1/S block in the cell cycle. The monopolar phenotype of the disrupted mitotic spindles and the G1/S block in the cell cycle is in sharp contrast to the multi-polar spindle and G2 block in the cell cycle previously observed following exposure to SWCNT. One month following exposure to MWCNT there was a dramatic increase in both size and number of colonies compared to diluent control cultures, indicating a potential to pass the genetic damage to daughter cells. Our results demonstrate significant disruption of the mitotic spindle by MWCNT at occupationally relevant exposure levels.
doi:10.1186/1743-8977-11-6
PMCID: PMC3923549  PMID: 24479647
19.  Predicting Weight Outcomes in Preadolescence: The Role of Toddlers’ Self-regulation Skills and the Temperament Dimension of Pleasure 
Objective
To investigate the role of toddlers’ self-regulation skills and temperament in predicting weight outcomes in preadolescence.
Method
Participants for this study included 195 children (114 girls) obtained from three different cohorts participating in a larger ongoing longitudinal study. At 2 years of age, participants participated in several laboratory tasks designed to assess their self-regulation abilities, including emotion regulation, sustained attention, and delay of gratification, while parents filled out a temperament questionnaire to assess toddlers’ pleasure expression. Height and weight measures were collected when children were 4, 5, 7, and 10 years of age. Children also filled out a body image and eating questionnaire at the 10 year visit.
Results
Self-regulation skills in toddlers were associated with both BMI development, pediatric obesity, and body image/eating concerns. The temperament dimension of pleasure was also associated with BMI development and pediatric obesity but not body image/eating concerns.
Conclusion
Self-regulation difficulties across domains as well as temperament based pleasure in toddlers represented significant individual risk factors for the development of pediatric obesity eight years later. Early self-regulation difficulties also contributed to body image and eating concerns that typically accompanied overweight children. The mechanisms by which early self-regulation skills and temperament based pleasure may contribute to the development of pediatric obesity and associated weight concerns are discussed.
doi:10.1038/ijo.2012.165
PMCID: PMC3543516  PMID: 23044856
pediatric obesity; BMI; body image; self-regulation; toddlerhood; preadolescence
20.  Combined sequence-based and genetic mapping analysis of complex traits in outbred rats 
Nature genetics  2013;45(7):10.1038/ng.2644.
Genetic mapping on fully sequenced individuals is transforming our understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating novel genes in models of anxiety, heart disease and multiple sclerosis. The relation between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show the extent and spatial pattern of variation in inbred rats differ significantly from those of inbred mice, and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species.
doi:10.1038/ng.2644
PMCID: PMC3821058  PMID: 23708188
22.  Quantitation of fibroblast activation protein (FAP)-specific protease activity in mouse, baboon and human fluids and organs☆ 
FEBS Open Bio  2013;4:43-54.
The protease fibroblast activation protein (FAP) is a specific marker of activated mesenchymal cells in tumour stroma and fibrotic liver. A specific, reliable FAP enzyme assay has been lacking. FAP's unique and restricted cleavage of the post proline bond was exploited to generate a new specific substrate to quantify FAP enzyme activity. This sensitive assay detected no FAP activity in any tissue or fluid of FAP gene knockout mice, thus confirming assay specificity. Circulating FAP activity was ∼20- and 1.3-fold less in baboon than in mouse and human plasma, respectively. Serum and plasma contained comparable FAP activity. In mice, the highest levels of FAP activity were in uterus, pancreas, submaxillary gland and skin, whereas the lowest levels were in brain, prostate, leukocytes and testis. Baboon organs high in FAP activity included skin, epididymis, bladder, colon, adipose tissue, nerve and tongue. FAP activity was greatly elevated in tumours and associated lymph nodes and in fungal-infected skin of unhealthy baboons. FAP activity was 14- to 18-fold greater in cirrhotic than in non-diseased human liver, and circulating FAP activity was almost doubled in alcoholic cirrhosis. Parallel DPP4 measurements concorded with the literature, except for the novel finding of high DPP4 activity in bile. The new FAP enzyme assay is the first to be thoroughly characterised and shows that FAP activity is measurable in most organs and at high levels in some. This new assay is a robust tool for specific quantitation of FAP enzyme activity in both preclinical and clinical samples, particularly liver fibrosis.
Graphical abstract
Highlights
•A novel synthetic fluorogenic substrate is proven to be FAP-specific.•Mice have higher levels of circulating FAP activity compared to baboons or humans.•No FAP activity was detected in urine or bile but bile contained high DPP4 activity.•FAP activity is greatest in pancreas, uterus, salivary gland, skin and lymph node.•FAP activity and protein is elevated in both serum and liver in human liver disease.
doi:10.1016/j.fob.2013.12.001
PMCID: PMC3871272  PMID: 24371721
Fibroblast; Dipeptidyl peptidase; Protease substrates; Protease activity; Liver disease; Fibrosis; Biomarker; ALD, alcoholic liver disease; AMC, amino-4-methylcoumarin; DPP4, dipeptidyl peptidase 4; DMSO, dimethyl sulfoxide; EDTA, ethylene diamine tetra acetic acid; FAP, fibroblast activation protein-α; gko, gene knock out; HCV, hepatitis C virus; het, heterozygous; LDS, lithium dodecyl sulphate; LN, lymph node; mAb, monoclonal antibody; ND, non-diseased; PBC, primary biliary cirrhosis; PBMC, peripheral blood mononuclear cells; PBS, phosphate-buffered saline; PEP, prolyl endopeptidase; PVDF, polyvinylidene fluoride; STLV, simian T-cell lymphotrophic virus; wt, wild type; yrs, years
23.  Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents 
PLoS Genetics  2013;9(12):e1003995.
The contribution of regulatory versus protein change to adaptive evolution has long been controversial. In principle, the rate and strength of adaptation within functional genetic elements can be quantified on the basis of an excess of nucleotide substitutions between species compared to the neutral expectation or from effects of recent substitutions on nucleotide diversity at linked sites. Here, we infer the nature of selective forces acting in proteins, their UTRs and conserved noncoding elements (CNEs) using genome-wide patterns of diversity in wild house mice and divergence to related species. By applying an extension of the McDonald-Kreitman test, we infer that adaptive substitutions are widespread in protein-coding genes, UTRs and CNEs, and we estimate that there are at least four times as many adaptive substitutions in CNEs and UTRs as in proteins. We observe pronounced reductions in mean diversity around nonsynonymous sites (whether or not they have experienced a recent substitution). This can be explained by selection on multiple, linked CNEs and exons. We also observe substantial dips in mean diversity (after controlling for divergence) around protein-coding exons and CNEs, which can also be explained by the combined effects of many linked exons and CNEs. A model of background selection (BGS) can adequately explain the reduction in mean diversity observed around CNEs. However, BGS fails to explain the wide reductions in mean diversity surrounding exons (encompassing ∼100 Kb, on average), implying that there is a substantial role for adaptation within exons or closely linked sites. The wide dips in diversity around exons, which are hard to explain by BGS, suggest that the fitness effects of adaptive amino acid substitutions could be substantially larger than substitutions in CNEs. We conclude that although there appear to be many more adaptive noncoding changes, substitutions in proteins may dominate phenotypic evolution.
Author Summary
We present an analysis of the genome sequences of multiple wild house mice. Wild house mice are about ten times more genetically diverse than humans, reflecting the large effective population size of the species. This manifests itself as more effective natural selection acting against deleterious mutations and favouring advantageous mutations in mice than in humans. We show that there are strong signals of adaptive evolution at many sites in the genome. We estimate that 80% of adaptive changes in the genome are in gene regulatory elements and only 20% are in protein-coding genes. We find that nucleotide diversity is markedly reduced close to gene regulatory elements and protein-coding gene sequences. The reductions around regulatory elements can be explained by selection purging deleterious mutations that occur in the elements themselves, but this process only partially explains the diversity reductions around protein-coding genes. Recurrent adaptive evolution, which can also cause local reductions in diversity via selective sweeps, may be necessary to fully explain the patterns in diversity that we observe surrounding genes. Although most adaptive molecular evolution appears to be regulatory, adaptive phenotypic change may principally be driven by structural change in proteins.
doi:10.1371/journal.pgen.1003995
PMCID: PMC3854965  PMID: 24339797
24.  Pannexin: From discovery to bedside in 11±4 years? 
Brain research  2012;1487:150-159.
Pannexin1 (Panx1) originally was discovered as a gap junction related protein. However, rather than forming the cell-to-cell channels of gap junctions, Panx1 forms a mechanosensitive and highly ATP permeable channel in the cell membrane allowing the exchange of molecules between the cytoplasm and the extracellular space. The list of arguments for Panx1 representing the major ATP release channel includes: (1) Panx1 is expressed in (all?) cells releasing ATP in a non-vesicular fashion, such as erythrocytes; (2) in cells with polar release of ATP, Panx1 is expressed at the ATP release site, such as the apical membrane in airway epithelial cells; (3) the pharmacology of Panx1 channels matches that of ATP release; (4) mutation of Panx1 in strategic positions in the protein modifies ATP release; and (5) knockdown or knockout of Panx1 attenuates or abolishes ATP release. Panx1, in association with the purinergic receptor P2X7, is involved in the innate immune response and in apoptotic/pyroptotic cell death. Inflammatory processes are responsible for amplification of the primary lesion in CNS trauma and stroke. Panx1, as an early signal event and as a signal amplifier in these processes, is an obvious target for the prevention of secondary cell death due to inflammasome activity. Since Panx1 inhibitors such as probenecid are already clinically tested in different settings they should be considered for therapy in stroke and CNS trauma.
doi:10.1016/j.brainres.2012.04.058
PMCID: PMC3590907  PMID: 22771709
Pannexin; Probenecid; Glibenclamide; Inflammasome; Apoptosis; Gap junction
25.  Glucocorticoid-induced hyperglycemia is prevalent and unpredictable for patients undergoing cancer therapy: an observational cohort study 
Current Oncology  2013;20(6):e532-e538.
Background
Patients with cancer are often treated with glucocorticoids (gcs) as part of therapy, which may cause hyperglycemia. We sought to define the prevalence of, and risk factors for, hyperglycemia in this setting.
Methods
Adult patients taking gc as part of therapy protocols for primary brain tumour or metastasis, for lymphoma, or for bone marrow transplant (bmt) were screened with random glucometer measurements taken at least 3 hours after the last dose gcs.
Results
We screened 90 patients [44.4% women, 55.6% men; mean age: 59.6 years (range: 25–82 years); mean body mass index (bmi): 26.4 kg/m2 (range: 15.8–45.3 kg/m2)] receiving gc as part of cancer treatment. Mean total daily gc dose in the group was 238.5 mg (range: 30–1067 mg) hydrocortisone equivalents. Hyperglycemia (glucose ≥ 8.0 mmol/L) was found in 58.9% (53 of 90), and diabetes mellitus (dm)–range hyperglycemia (glucose ≥ 11.1 mmol/L) in 18.9% (17 of 90). The mean time from gc ingestion to glucometer testing was 5.5 hours (range: 3–20 hours). Presence of hyperglycemia did not correlate with traditional dm risk factors such as age, sex, bmi, and personal or family history of dm. A longer interval from gc dose to testing (p < 0.05), a higher gc dose (p = 0.04), and a shorter interval between the preceding meal and testing (p = 0.02) were risk factors for hyperglycemia in some patient groups.
Conclusions
Glucocorticoid-induced hyperglycemia is common in patients undergoing cancer treatment and cannot be predicted by traditional risk factors for dm. We recommend that all cancer patients receiving gc be screened for hyperglycemia at least 4–6 hours after gc administration.
doi:10.3747/co.20.1499
PMCID: PMC3851349  PMID: 24311953
Hyperglycemia; glucocorticoids; glucocorticoid-induced diabetes; diabetes mellitus

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