Evaluation of a Push-Pull Strategy for Spotted-Wing Drosophila Management in Highbush Blueberry

We evaluated a novel push-pull control strategy for protecting highbush blueberry, Vaccinium corymbosum, against spotted-wing drosophila (SWD), Drosophila suzukii. Methyl benzoate (MB) was used as the pushing agent and a previously tested SWD attractive blend of lure-scents was used as the pulling agent. MB dispensers (push) were hung in the canopy and lure-scent dispensers (pull) were hung in yellow jacket traps filled with soapy water around the blueberry bushes. Blueberries were sampled weekly, and any infestation was inspected by examining the breathing tubes of SWD eggs which protrude through the skin of infested fruit. The frequency of infestation, i.e., the proportion of berries infested with at least one egg, and the extent of infestation, i.e., the mean number of eggs in infested berries, were significantly reduced in treatments receiving MB dispensers as a pushing agent when infestation rates were very high. However, the mass trapping devices as a pulling agent did not provide comparable protection on their own and did not produce additive protection when used in combination with the MB dispensers in push-pull trials. We conclude that MB has the potential to be implemented as a spatial repellent/oviposition deterrent to reduce SWD damage in blueberry under field conditions and does not require the SWD attractant as a pulling agent to achieve crop protection.

Time-resolved X-ray diffraction diagnostic development for the National Ignition Facility

We present the development of an experimental platform that can collect four frames of x-ray diffraction data along a single line of sight during laser-driven, dynamic-compression experiments at the National Ignition Facility. The platform is comprised of a diagnostic imager built around ultrafast sensors with a 2-ns integration time, a custom target assembly that serves also to shield the imager, and a 10-ns duration, quasi-monochromatic x-ray source produced by laser-generated plasma. We demonstrate the performance with diffraction data for Pb ramp compressed to 150 GPa and illuminated by a Ge x-ray source that produces ∼7 × 1011, 10.25-keV photons/ns at the 400 μm diameter sample.

Thermal biology and overwintering behavior of the red sunflower seed weevil (Coleoptera: Curculionidae)

Most natural mortality of the red sunflower seed weevil, Smicronyx fulvus LeConte (Coleoptera: Curculionidae), occurs while larvae overwinter in the soil. To test the hypothesis that S. fulvus mortality is related to low temperatures, experiments were used to (i) evaluate the temperature at which larvae freeze (= supercooling point [SCP]), (ii) assess possible vertical movement between entry into the soil in fall and adult emergence in summer, and (iii) determine if realistic soil temperatures could explain patterns of overwintering mortality. Mean SCP for groups of S. fulvus larvae differed between years and months, but only ranged from -20.93 to -22.68 °C. Most overwintering larvae were found within 6 cm of the soil surface, but larvae appeared to move 1-2 cm deeper between pairs of successive sample dates (September to January, January to April). Significant larval mortality that occurred between January and April 2021 was tentatively attributed to a period in February where daily minimum soil temperatures ranged from -8 to -12 °C. When overwintering under control conditions (constant 4 °C) was interrupted with week-long exposure to -4, -8, or -12 °C in a cold bath, significant S. fulvus mortality was seen for temperatures at or below -8 °C. Combined results suggest that mortality of overwintering S. fulvus is likely caused by continuous exposure to low temperatures that may not be cold enough to freeze larvae. Additionally, the shallow overwintering by S. fulvus supports the idea that routine farm management, including tillage and herbicide incorporation, may help limit populations of this sunflower pest.

Developing a platform for Fresnel diffractive radiography with 1 μm spatial resolution at the National Ignition Facility

An x-ray Fresnel diffractive radiography platform was designed for use at the National Ignition Facility. It will enable measurements of micron-scale changes in the density gradients across an interface between isochorically heated warm dense matter materials, the evolution of which is driven primarily through thermal conductivity and mutual diffusion. We use 4.75 keV Ti K-shell x-ray emission to heat a 1000 μm diameter plastic cylinder, with a central 30 μm diameter channel filled with liquid D₂, up to 8 eV. This leads to a cylindrical implosion of the liquid D₂ column, compressing it to ∼2.3 g/cm³. After pressure equilibration, the location of the D₂/plastic interface remains steady for several nanoseconds, which enables us to track density gradient changes across the material interface with high precision. For radiography, we use Cu He-α x rays at 8.3 keV. Using a slit aperture of only 1 μm width increases the spatial coherence of the source, giving rise to significant diffraction features in the radiography signal, in addition to the refraction enhancement, which further increases its sensitivity to density scale length changes at the D₂/plastic interface.

Increased Ion Temperature and Neutron Yield Observed in Magnetized Indirectly Driven D_{2}-Filled Capsule Implosions on the National Ignition Facility

The application of an external 26 Tesla axial magnetic field to a D_{2} gas-filled capsule indirectly driven on the National Ignition Facility is observed to increase the ion temperature by 40% and the neutron yield by a factor of 3.2 in a hot spot with areal density and temperature approaching what is required for fusion ignition [1]. The improvements are determined from energy spectral measurements of the 2.45 MeV neutrons from the D(d,n)^{3}He reaction, and the compressed central core B field is estimated to be ∼4.9  kT using the 14.1 MeV secondary neutrons from the D(T,n)^{4}He reactions. The experiments use a 30 kV pulsed-power system to deliver a ∼3  μs current pulse to a solenoidal coil wrapped around a novel high-electrical-resistivity AuTa_{4} hohlraum. Radiation magnetohydrodynamic simulations are consistent with the experiment.

Trade-offs between succulent and non-succulent epiphytes underlie variation in drought tolerance and avoidance

Epiphyte communities comprise important components of many forest ecosystems in terms of biomass and diversity, but little is known regarding trade-offs that underlie diversity and structure in these communities or the impact that microclimate has on epiphyte trait allocation. We measured 22 functional traits in vascular epiphyte communities across six sites that span a microclimatic gradient in a tropical montane cloud forest region in Costa Rica. We quantified traits that relate to carbon and nitrogen allocation, gas exchange, water storage, and drought tolerance. Functional diversity was high in all but the lowest elevation site where drought likely limits the success of certain species with particular trait combinations. For most traits, variation was explained by relationships with other traits, rather than differences in microclimate across sites. Although there were significant differences in microclimate, epiphyte abundance, and diversity, we found substantial overlap in multivariate trait space across five of the sites. We found significant correlations between functional traits, many of which related to water storage (leaf water content, leaf thickness, hydrenchymal thickness), drought tolerance (turgor loss point), and carbon allocation (specific leaf area, leaf dry matter content). This suite of trait correlations suggests that the epiphyte community has evolved functional strategies along with a drought avoidance versus drought tolerance continuum where leaf succulence emerged as a pivotal overall trait.

Fatty Acid Data and Crop Surveys Indicate Sources of Red Sunflower Seed Weevil (Coleoptera: Curculionidae), Populations and Suggest Strategies for Management

The red sunflower seed weevil, Smicronyx fulvus L., is a univoltine seed-feeding pest of cultivated sunflower, Helianthus annuus L. Artificial infestations of S. fulvus onto sunflowers with traditional (<25% oleic acid), mid-oleic (55-75%), or high oleic (>80%) fatty acid profiles were used to test if fatty acids could be used as natural markers to estimate the proportion of weevils developing on oilseed sunflowers rather than wild Helianthus spp. and confection (non-oil) types. Oleic acid (%) in S. fulvus confirmed the fatty acid compositions of mature larvae and weevil adults reflected their diets, making primary (oleic or linoleic) fatty acids feasible as natural markers for this crop-insect combination. Oleic acid in wild S. fulvus populations in North Dakota suggests at least 84 and 90% of adults originated from mid-oleic or high oleic sunflower hybrids in 2017 and 2018, respectively. Surveys in 2017 (n = 156 fields) and 2019 (n = 120 fields) extended information provided by S. fulvus fatty acid data; no significant spatial patterns of S. fulvus damage were detected in samples, damage to oilseed sunflowers was greater than confection (non-oil) types, and the majority of damage occurred in ≈10% of surveyed fields. Combined, data suggest a few unmanaged or mismanaged oilseed sunflower fields are responsible for producing most S. fulvus in an area. Improved management seems possible with a combination of grower education and expanded use of non-insecticidal tactics, including cultural practices and S. fulvus-resistant hybrids.

Assessment of the threatened carnivore community in the recently expanded rainforest protected area Anjanaharibe-Sud Special Reserve, Madagascar

Madagascar is an island nation renowned for its biodiversity and species endemism, yet it is still largely understudied despite intense anthropogenic threats including forest loss and edge effects. Anjanaharibe-Sud Special Reserve is a recently expanded rainforest protected area that is lacking detailed surveys and assessments of the native carnivore community of the endemic family Eupleridae. To identify which terrestrial carnivores occupy the reserve and what anthropogenic disturbances and factors best explain their occurrence patterns, we deployed 35 motion-activated cameras to detect native and introduced carnivores. From November 2018 to February 2019, we collected 2918 unique capture events (all species) and confirmed the presence of 5 euplerids: Galidia elegans, Galidictis fasciata, Eupleres goudotii, Fossa fossana, and Cryptoprocta ferox. These results extend the known range of E. goudotii and G. fasciata. In the reserve, F. fossana and G. elegans were the most common and widespread native carnivores, while E. goudotii was the rarest. We highlight the negative impact of edge effects on G. fasciata and F. fossana and the threat posed by the free-ranging non-native carnivore C. familiaris. This study represents the first detailed survey and occurrence estimates of the carnivore community of this protected area, allowing comparison with other protected areas in Madagascar. Our empirical findings show that anthropogenic disturbance negatively impacts carnivore existence within the Anjanaharibe-Sud Special Reserve and provide important management recommendations for protecting the carnivore community and the co-occurring wildlife living within this area.

Seed and floret size parameters of sunflower are determined by partially overlapping sets of quantitative trait loci with epistatic interactions

KEY MESSAGE

Floret and seed traits are moderately correlated phenotypically in modern sunflower cultivars, but the underlying genetics are mostly independent. Seed traits in particular are governed in part by epistatic effects among quantitative trait loci. Seed size is an important quality component in marketing commercial sunflower (Helianthus annuus L.), particularly for the in-shell confectionery market, where long and broad seed types are preferred as a directly consumed snack food globally. Floret size is also important because corolla tube length was previously shown to be inversely correlated with pollinator visitation, impacting bee foraging potential and pollinator services to the plant. Commercial sunflower production benefits from pollinator visits, despite being self-compatible, and bees are required in hybrid seed production, where "female" and "male" inbred lines are crossed at field scale. Issues with pollination of long-seed confectionery sunflower suggest that there may be an unfavorable correlation between seed and floret traits; thus, our objective was to determine the strength of the correlation between seed and floret traits, and confirm any co-localization of seed and floret trait loci using genome-wide association analysis in the SAM diversity panel of sunflower. Our results indicate that phenotypic correlations between seed and floret traits are generally low to moderate, regardless of market class, a component of population substructure. Association mapping results mirror the correlations: while a few loci overlap, many loci for the two traits are not overlapping or even adjacent. The genetics of these traits, while modestly quantitative and influenced by epistatic effects, are not a barrier to simultaneous improvement of seed length and pollinator-friendly floret traits. We conclude that breeding for large seed size, which is required for the confectionery seed market, is possible without producing florets too long for efficient use by pollinators, which promotes bee foraging and associated pollination services.

1254. Outbreak of Mycobacterium chelonae Skin Infections Associated With Human Chorionic Gonadotropin Injections at Weight Loss Clinics

Background

In December 2016, a dermatologist notified the Minnesota Department of Health (MDH) of three patients with skin lesions after self-administration of human chorionic gonadotropin (HCG) injections supplied by same weight loss clinic chain (Chain X); one lesion had been diagnosed as a nontuberculous mycobacteria (NTM) infection. We investigated to identify the etiology, determine contributing transmission factors, and to prevent additional cases.

Methods

We defined a case as a skin or soft tissue lesion with a suspected infectious etiology in a Minnesota resident occurring within three months after HCG injection at or near an injection site. To find cases we sent health alerts to clinicians and clinical laboratories throughout Minnesota with diagnostic guidance, and we requested Chain X to notify all exposed patients. We visited two Chain X clinics to assess infection control practices, to collect invoices for product traceback, and to collect products for microbiological testing. All NTM isolates were identified by line probe assay and subtyped by pulsed-field gel electrophoresis (PFGE) at MDH.

Results

We identified six cases with illness onset dates ranging from April to November 2016. All patients were adult women who did not share HCG vials. Four patients had clinical specimens that grew NTM; all isolates were identified as Mycobacterium chelonae that were indistinguishable by PFGE. Three patients with confirmed M. chelonae infection obtained HCG at Clinic A, and one from Clinic B, but sharing of reconstituted HCG by the two clinics could not be excluded. We identified several infection control breaches at both clinics including improper reconstitution of HCG and incorrect use of single use vials. The most likely source of the HCG was an unregistered out-of-state compounding pharmacy.

Conclusion

This common source outbreak was likely due to contamination introduced either at a weight loss clinic or a compounding pharmacy. HCG injections are not US FDA-approved for weight loss, and their use may involve compounded products dispensed by alternative care settings that lack infection control expertise and regulatory oversight. This outbreak highlights the important role physician reporting of disease clusters plays in uncovering unsafe practices.

Disclosures

All authors: No reported disclosures.

Alcohol-dose-dependent DNA methylation and expression in the nucleus accumbens identifies coordinated regulation of synaptic genes

Alterations in DNA methylation have been associated with alcohol exposure and proposed to contribute to continued alcohol use; however, the molecular mechanisms involved remain obscure. We investigated the escalating effects of alcohol use on DNA methylation, gene expression and predicted neural effects in the nucleus accumbens of rhesus macaques that self-administered 4% alcohol for over 12 months. Using an exploratory approach to identify CpG-rich regions, followed by bisulfite sequencing, the methylation levels of 2.7 million CpGs were compared between seven low-binge drinkers and nine heavy-very heavy drinking subjects. We identified 17 significant differential methylation regions (DMRs), including 14 with methylation levels that were correlated with average daily alcohol consumption. The size of the DMRs ranged from 29 to 158 bp (mean=63.7), included 4-19 CpGs per DMR (mean=8.06) and spanned a range of average methylation values from 5 to 34%. Eight of the DMRs mapped to genes implicated in modulating synaptic plasticity. Six of the synaptic genes have not previously been linked to alcohol use. Validation studies of these eight DMRs using bisulfite amplicon sequencing and an expanded set of 30 subjects confirmed the significant alcohol-dose-associated methylation of the DMRs. Expression analysis of three of the DMR-associated genes, LRP5, GPR39 and JAKMIP1, revealed significant correlations between DMR methylation and whole-gene or alternative transcript expression, supporting a functional role in regulating gene expression. Together, these studies suggest that alcohol-associated synaptic remodeling may be regulated and coordinated at the level of DNA methylation.

Screening attendance, age group and diabetic retinopathy level at first screen

AIMS

To report on the relationships between age at diagnosis of diabetes, time from registration with the screening programme to first diabetic eye screening and severity of diabetic retinopathy.

METHODS

Data were extracted from four English screening programmes and from the Scottish, Welsh and Northern Irish programmes. Time from diagnosis of diabetes to first screening and age at diagnosis were calculated.

RESULTS

Time from registration with the screening programme to first screening episode is strongly related to age at registration. Within 18 months of registration 89% of 3958 young people under 18 years of age and 81% of 391 293 people over 35 years of age were seen. In 19 058 people between 18 and 34 years of age, 80% coverage was not reached until 2 years and 9 months. The time from diagnosis of diabetes to first screening is positively associated with severity of disease (P < 0.0001).

CONCLUSIONS

This report is the first that to demonstrate that those in the 18-34 year age group are least likely to attend promptly for screening after registration with a higher risk of referable diabetic retinopathy being present at the time of first screen. Date of diagnosis should be recorded and prodigious efforts made to screen all people promptly after diagnosis. Screening programmes should collect data on those who have not attended within one year of registration.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Effects of ecstasy on cooperative behaviour and perception of trustworthiness: a naturalistic study

BACKGROUND

Acute recreational use of 3,4-methylenedioxymethamphetamine (MDMA; 'ecstasy') can promote pro-social effects which may alter interpersonal perceptions.

AIMS

To explore such effects, this study investigated whether acute recreational use of ecstasy was associated with changes in individual perception of trustworthiness of people's faces and co-operative behaviours.

METHOD

An independent group, repeated measures design was used in which 17 ecstasy users were tested on the night of drug use (day 0) and again three days later (day 3); 22 controls were tested on parallel days. On each day, participants rated the trustworthiness of 66 faces, carried out three co-operative behaviour tasks (public good; dictator; ultimatum game) and completed mood self-ratings.

RESULTS

Acute ecstasy use was associated with increased face trustworthiness ratings and increased cooperative behaviour on the dictator and ultimatum games; on day 3 there were no group differences on any task. Self-ratings showed the standard acute ecstasy effects (euphoria, energy, jaw clenching) with negative effects (less empathy, compassion, more distrust, hostility) emerging on day 3.

CONCLUSIONS

Our findings of increased perceived trustworthiness and co-operative behaviours following use of ecstasy suggest that a single dose of the drug enhances aspects of empathy. This may in turn contribute to its popularity as a recreational drug and potentially to its enhancement of the therapeutic alliance in psychotherapy.

Learning rate and temperament in a high predation risk environment

Living in challenging environments can influence the behavior of animals in a number of ways. For instance, populations of prey fish that experience frequent, nonlethal interactions with predators have a high proportion of individuals that express greater reaction to risk and increased activity and exploration—collectively known as temperament traits. Temperament traits are often correlated, such that individuals that are risk-prone also tend to be active and explore more. Spatial learning, which requires the integration of many sensory cues, has also been shown to vary in fish exposed to different levels of predation threat. Fish from areas of low predation risk learn to solve spatial tasks faster than fish from high predation areas. However, it is not yet known whether simpler forms of learning, such as learning associations between two events, are similarly influenced. Simple forms of associative learning are likely to be affected by temperament because a willingness to approach and explore novel situations could provide animals with a learning advantage. However, it is possible that routine-forming and inflexible traits associated with risk-prone and increased exploratory behavior may act in the opposite way and make risk-prone individuals poorer at learning associations. To investigate this, we measured temperament in Panamanian bishop fish (Brachyrhaphis episcopi) sampled from a site known to contain many predators. The B. episcopi were then tested with an associative learning task. Within this population, fish that explored more were faster at learning a cue that predicted access to food, indicating a link between temperament and basic learning abilities.

T-ray Imaging and Tomography

We demonstrate two algorithms used forreconstructing the target's structure basedon the diffracted pulses and additionallyshow that a three-dimensional target can bereconstructed using the broadband pulsesand a Fresnel lens by virtue of itsfrequency dependent focal length. Oneadvantage of T-ray imaging is the abilityto measure the far-infrared spectralresponse of the target. To highlight theimportance of this spectral information, wedemonstrate T-ray classification imagingwith different biological samples using asimple classification algorithm and twodimensional T-ray spectroscopic images.

Genetic load is associated with hypothalamic-pituitary-adrenal axis dysregulation in macaques

Dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis pathway is associated with several neuropsychiatric disorders, including post-traumatic stress disorder (PTSD), major depressive disorder (MDD), schizophrenia and alcohol abuse. Studies have demonstrated an association between HPA axis dysfunction and gene variants within the cortisol, serotonin and opioid signaling pathways. We characterized polymorphisms in genes linked to these three neurotransmitter pathways and tested their potential interactions with HPA axis activity, as measured by dexamethasone (DEX) suppression response. We determined the percent DEX suppression of adrenocorticotropic hormone (ACTH) and cortisol in 62 unrelated, male rhesus macaques. While DEX suppression of cortisol was robust amongst 87% of the subjects, ACTH suppression levels were broadly distributed from -21% to 66%. Thirty-seven monkeys from the high and low ends of the ACTH suppression distribution (18 'high' and 19 'low' animals) were genotyped at selected polymorphisms in five unlinked genes (rhCRH, rhTPH2, rhMAOA, rhSLC6A4 and rhOPRM). Associations were identified between three variants (rhCRH-2610C>T, rhTPH2 2051A>C and rh5-HTTLPR) and level of DEX suppression of ACTH. In addition, a significant additive effect of the 'risk' genotypes from these three loci was detected, with an increasing number of 'risk' genotypes associated with a blunted ACTH response (P = 0.0009). These findings suggest that assessment of multiple risk alleles in serotonin and cortisol signaling pathway genes may better predict risk for HPA axis dysregulation and associated psychiatric disorders than the evaluation of single gene variants alone.

Childcare use and inequalities in breastfeeding: findings from the UK Millennium Cohort Study

BACKGROUND

UK breastfeeding rates are low and socially distributed. Childcare provides a potential setting for breastfeeding promotion. However, little is known about the association between childcare and breastfeeding in different socio-economic groups.

METHODS

Using data from a contemporary UK cohort of infants (n=18,050) the authors calculated RR for breastfeeding for at least 4 months according to informal childcare (care by friends, grandparents, other relatives, etc) and formal childcare (eg, nurseries, crèches), both lasting at least 10 h a week and commencing before the age of 4 months, compared to being cared for 'only by a parent' (this includes childcare for less than 10 h a week), overall and by socio-economic group.

RESULTS

Compared to being looked after only by a parent, informal (RR 0.51 (95% CI 0.43 to 0.59)) and formal (0.84 (0.72 to 0.99)) childcare was associated with a reduced likelihood of breastfeeding. For informal childcare, both part-time and full-time care was associated with a reduced risk of breastfeeding, whereas for formal care, only full-time formal childcare was associated with a reduced likelihood of breastfeeding. The reduced likelihood of breastfeeding in informal childcare was similar across all socio-economic groups, whereas for formal childcare the reduced likelihood was only seen for mothers from managerial and professional backgrounds (0.76 (0.62 to 0.94)), those who had a degree (0.71 (0.58 to 0.86)) and couple families (0.79 (0.66 to 0.94)). In contrast, lone mothers were more likely to breastfeed if their infant was cared for in formal childcare (1.65 (1.04 to 2.63)).

CONCLUSIONS

Informal childcare was associated with a reduced likelihood of breastfeeding for all groups of mothers. Formal childcare arrangements were only associated with a reduced likelihood of breastfeeding if used full-time by more advantaged families.

Does the home environment influence inequalities in unintentional injury in early childhood? Findings from the UK Millennium Cohort Study

BACKGROUND

Children from disadvantaged backgrounds are more likely to experience unintentional injuries and poor home environments. The aim of this study was to explore the home environment as a potential mediator between socioeconomic circumstances and unintentional injuries, in the UK Millennium Cohort Study (n=14 378).

METHODS

RRs and 95% CIs for being injured in the home between age 9 months and 3 years were estimated according to four measures of socioeconomic circumstances: social class, maternal education, lone parenthood status and tenure. Proxy indicators of housing quality (build type, storey, garden access, rooms per capita, central heating and presence of damp) and safety equipment use (use of fireguards, safety gates, electric socket covers and smoke alarms) were then controlled for in order to observe potential mediation.

RESULTS

Children from routine and manual backgrounds were more likely to be injured than those from managerial and professional backgrounds (RR=1.33, 95% CI 1.21 to 1.47), as were children of lone parents (compared with couple families) (RR=1.23, 95% CI 1.12 to 1.36), those whose mothers had no educational qualifications (compared with a degree) (RR=1.42, 95% CI 1.24 to 1.63) and those living in socially rented accommodation (compared with owned/mortgaged homes) (RR=1.35, 95% CI 1.24 to 1.46). However, controlling for the indicators of housing quality and safety equipment use did not alter the elevated risk of injury experienced by children from less advantaged backgrounds.

CONCLUSIONS

In this contemporary UK cohort, proxy indicators of the home environment did not appear to explain socioeconomic inequalities in injuries. Research exploring alternative explanations for inequalities in injuries could help contribute to the design or adaptation of policies to reduce them.

Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs)

The National Primate Research Centers (NPRCs) established Working Groups (WGs) for developing resources and mechanisms to facilitate collaborations among non-human primate (NHP) researchers. Here we report the progress of the Genome Banking and the Genetics and Genomics WGs in developing resources to advance the exchange, analysis and comparison of NHP genetic and genomic data across the NPRCs. The Genome Banking WG has established a National NHP DNA bank comprising 1250 DNA samples from unrelated animals and family trios from the 10 NHP species housed within the NPRC system. The Genetics and Genomics WG is developing SNP arrays that will provide a uniform, highly informative, efficient and low-cost method for rhesus and long-tailed macaque genotyping across the eight NPRCs. This WG is also establishing a Biomedical Informatics Research Network-based portal for shared bioinformatics resources including vital statistics, genotype and population data and information on the National NHP DNA bank.

Does childcare influence socioeconomic inequalities in unintentional injury? Findings from the UK Millennium Cohort Study

BACKGROUND

In recent decades the proportion of infants and young children being cared for in childcare has increased. Little is known about the impact that non-parental care has on childhood unintentional injury and whether this varies by socioeconomic group.

METHODS

Using data from a contemporary UK cohort of children at age 9 months (N = 18 114) and 3 years (N = 13 718), Poisson regression was used to explore the association between childcare type (parental, informal, formal) and the risk of unintentional injury, overall and by socioeconomic group.

RESULTS

At age 9 months there was no overall association between childcare and injury. However, when stratifying the analyses, infants from higher socioeconomic groups were less likely to be injured if they were cared for in formal childcare (compared with being cared for only by a parent), whereas those from lower social groups were more likely to be injured. At age 3 years informal childcare was associated with an increased risk of injury overall; in the stratified analyses this increased risk occurred only in less affluent groups. Formal childcare was no longer associated with injury at age 3 in any strata.

CONCLUSIONS

Previous findings have shown that childcare can have a positive influence on childhood injury; however, a recent Unicef report highlighted that a lack of access to high-quality childcare could lead to a widening of inequalities. Our analyses indicate that childcare does have the potential to widen inequalities in injury; further research is required to understand why childcare has a differential impact on unintentional injury and how this might be prevented.

Evidence for the receipt of DNA damage stimuli by PML nuclear domains

Promyelocytic leukaemia nuclear domains (PML-NDs) comprise a shell of PML protein and many labile cargo proteins. The nature of their cargo, their juxtaposition to foci of damaged DNA following ionizing radiation (IR), and the altered DNA damage responses in PML null cells all implicate PML-NDs in the DNA damage response. In this work, the propensity of PML-NDs to increase in number and decrease in size following IR has been studied. Serial quantitative studies of endogenous PML-NDs prove that the PML-ND response to IR is not the result of the asymmetry in cell cycle distribution that can follow IR, but reflects more directly the process of DNA damage. The response is swift, sensitive (evident after 1 Gy), and potentially reversible in untransformed fibroblasts. In these cells and in HCT116 colon cancer cells, failure to restore PML-ND number within 24 h correlates with later loss of growth potential--in fibroblasts, through prolonged cell cycle arrest and in HCT116 cells, through apoptosis. Failure to express an intact ATM/CHK2 DNA damage signalling pathway in either cell type leads to a delay in the PML-ND response to IR. Conversely, cell cycle progression following IR in cells that detect damaged DNA accelerates PML-ND reorganization. Collectively, these data show that the increase in PML-ND number seen after irradiation is, in part, triggered by the receipt of the DNA damage stimulus. The senescent cell state is also associated with chronic DNA damage and Hayflick-limited fibroblasts were found to express nuclei with elevated numbers of PML-NDs before IR that remained unresponsive to IR. Though the underlying reasons for damage-induced PML alteration remain obscure, it is noteworthy that significant numbers of PML-NDs juxtapose with ionizing radiation-induced foci after IR. The co-regulation of these structures may necessitate the stereotyped increases in PML-ND number following damage.

Enhanced T-ray signal classification using wavelet preprocessing

This study demonstrates the application of one-dimensional discrete wavelet transforms in the classification of T-ray pulsed signals. Fast Fourier transforms (FFTs) are used as a feature extraction tool and a Mahalanobis distance classifier is employed for classification. Soft threshold wavelet shrinkage de-noising is used and plays an important role in de-noising and reconstruction of T-ray pulsed signals. An iterative algorithm is applied to obtain three optimal frequency components and to achieve preferred classification performance.

Endoscopic ultrasonography in the diagnosis and staging of neoplasms of the head and neck

BACKGROUND AND STUDY AIMS

Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is a minimally invasive and highly accurate method of detecting mediastinal lymph-node metastases in gastrointestinal and lung cancer. Little information is available regarding the use of EUS-FNA to stage tumors in the head and neck region. This study reports experience with EUS in the diagnosis and staging of these tumors and their mediastinal spread.

PATIENTS AND METHODS

The records of patients who underwent EUS for diagnosis and/or staging of head and neck tumors were reviewed. Referral criteria were suspected invasion of the esophagus by a lower-neck mass on cervical computed tomography (CT) or magnetic resonance imaging (MRI), or mediastinal lymphadenopathy > 10 mm on a chest CT.

RESULTS

Thirty-two patients (23 men, nine women; mean age 65 years, range 44 - 80) were referred and underwent 35 EUS examinations. In one patient, EUS was not possible due to a benign esophageal stricture. In 17 patients with suspected esophageal invasion on CT scans, EUS demonstrated invasion of the esophagus in four cases and of the pleura in one; 12 tumors showed no visible invasion of adjacent structures. The other 17 examinations were carried out for suspected mediastinal metastatic disease. In eight cases, EUS-FNA confirmed metastatic disease, whereas only benign changes were shown in the other nine cases. EUS-FNA also provided the first tissue diagnosis in two primary tumors and identified malignancy in one patient with no CT suspicion of positive mediastinal lymph nodes. EUS avoided the need for more invasive investigations in all patients with mediastinal lymphadenopathy, and it changed the management in 12 of the 17 patients (71 %) with suspected esophageal invasion and in eight of the 17 patients (47 %) with suspected mediastinal disease.

CONCLUSIONS

EUS with FNA provides a viable approach to the diagnosis and staging of tumors in the head and neck region when there is a suggestion of esophageal invasion on CT or MRI, or enlarged mediastinal lymph nodes. EUS with FNA may avoid the need for mediastinoscopy or other more invasive techniques for staging of these neoplasms.

New algorithms for multi-class cancer diagnosis using tumor gene expression signatures

MOTIVATION

The increasing use of DNA microarray-based tumor gene expression profiles for cancer diagnosis requires mathematical methods with high accuracy for solving clustering, feature selection and classification problems of gene expression data.

RESULTS

New algorithms are developed for solving clustering, feature selection and classification problems of gene expression data. The clustering algorithm is based on optimization techniques and allows the calculation of clusters step-by-step. This approach allows us to find as many clusters as a data set contains with respect to some tolerance. Feature selection is crucial for a gene expression database. Our feature selection algorithm is based on calculating overlaps of different genes. The database used, contains over 16 000 genes and this number is considerably reduced by feature selection. We propose a classification algorithm where each tissue sample is considered as the center of a cluster which is a ball. The results of numerical experiments confirm that the classification algorithm in combination with the feature selection algorithm perform slightly better than the published results for multi-class classifiers based on support vector machines for this data set.

AVAILABILITY

Available on request from the authors.

Randomized controlled trial of brief cognitive behaviour therapy versus treatment as usual in recurrent deliberate self-harm: the POPMACT study

BACKGROUND

We carried out a large randomized trial of a brief form of cognitive therapy, manual-assisted cognitive behaviour therapy (MACT) versus treatment as usual (TAU) for deliberate self-harm.

METHOD

Patients presenting with recurrent deliberate self-harm in five centres were randomized to either MACT or (TAU) and followed up over 1 year. MACT patients received a booklet based on cognitive behaviour therapy (CBT) principles and were offered up to five plus two booster sessions of CBT from a therapist in the first 3 months of the study. Ratings of parasuicide risk, anxiety, depression, social functioning and global function, positive and negative thinking, and quality of life were measured at baseline and after 6 and 12 months.

RESULTS

Four hundred and eighty patients were randomized. Sixty per cent of the MACT group had both the booklet and CBT sessions. There were seven suicides, five in the TAU group. The main outcome measure, the proportion of those repeating deliberate self-harm in the 12 months of the study, showed no significant difference between those treated with MACT (39%) and treatment as usual (46%) (OR 0.78, 95% CI 0.53 to 1.14, P=0.20).

CONCLUSION

Brief cognitive behaviour therapy is of limited efficacy in reducing self-harm repetition, but the findings taken in conjunctin with the economic evaluation (Byford et al. 2003) indicate superiority of MACT over TAU in terms of cost and effectiveness combined.

"Cold calling" in psychiatric follow up studies: is it justified?

BACKGROUND

The ethics of cold calling-visiting subjects at home without prior appointment agreed-in follow up research studies has received little attention although it is perceived to be quite common. We examined the ethical implications of cold calling in a study of subjects with defined neurotic disorders followed up 12 years after initial assessment carried out to determine outcome in terms of symptoms, social functioning, and contact with health services. The patients concerned were asked at original assessment if they would agree to be followed up subsequently and although they agreed no time limit was put on this.

OBJECTIVES

To decide if cold calling was ethically justifiable and, if so, to set guidelines for researchers.

DESIGN

The study was a cohort study of patients with neurotic disorder treated initially for 10 weeks in a randomised controlled trial.

FINDINGS

At follow up by a research medical practitioner 18 of the 210 patients had died and of the remaining 192 patients 186 (97%) were seen or had a telephone interview. Four patients refused and two others did not have interviews but agreed to some data being obtained. However, only 104 patients (54%) responded to letters inviting them to make an appointment or to refuse contact and the remainder were followed up by cold calling, with most patients agreeing readily to the research interview. The findings illustrate the dilemma of the need to get the maximum possible data from such studies to achieve scientific validity (and thereby justify the ethics of the study) and the protection of subjects' privacy and autonomy.

CONCLUSIONS

More attention needs to be paid to consent procedures if cold calling is to be defended on ethical grounds but it is unreasonable to expect this to be obtained at the beginning of a research study in a way that satisfies the requirements for informed consent. A suggested way forward is to obtain written consent for the research at the time that cold calling takes place before beginning the research.