The relationship between deprivation, tumour stage and the systemic inflammatory response in patients with primary operable breast cancer

The extent of deprivation (Carstairs deprivation index) was directly associated with the magnitude of the systemic inflammatory response (reduced albumin and elevated C-reactive protein, P<0.01) in patients with primary operable breast cancer (n=314). Deprivation was not associated with age, tumour size, tumour type, grade, and the proportion of patients with involved lymph nodes and oestrogen receptor status

Controlled variations in stimulus similarity during learning determine visual discrimination capacity in freely moving mice

The mouse is receiving growing interest as a model organism for studying visual perception. However, little is known about how discrimination and learning interact to produce visual conditioned responses. Here, we adapted a two-alternative forced-choice visual discrimination task for mice and examined how training with equiprobable stimuli of varying similarity influenced conditioned response and discrimination performance as a function of learning. Our results indicate that the slope of the gradients in similarity during training determined the learning rate, the maximum performance and the threshold for successful discrimination. Moreover, the learning process obeyed an inverse relationship between discrimination performance and discriminative resolution, implying that sensitivity within a similarity range cannot be improved without sacrificing performance in another. Our study demonstrates how the interplay between discrimination and learning controls visual discrimination capacity and introduces a new training protocol with quantitative measures to study perceptual learning and visually-guided behavior in freely moving mice

Deployment of mating disruption dispensers before and after first seasonal male flights for the control of Aonidiella aurantii in citrus

The rejection of citrus fruit caused by infestations of the California red scale (CRS), Aonidiella aurantii (Maskell) (Hemiptera: Diaspididae), raises concerns about its management. This fact has led to the introduction of new integrated control methods in citrus orchards, including the implementation of techniques based on pheromones. Previous works described efficient mating disruption pheromone dispensers to control A. aurantii in the Mediterranean region. The main aims of the present study were to adjust the timing of dispenser applications and study the importance of controlling the early first generation of A. aurantii by testing two different application dates: before and after the first CRS male flight. The efficacy of the different mating disruption strategies was tested during 2010 in an experimental orchard and these results were confirmed during 2011 in a commercial citrus farm. Results showed that every mating disruption strategy achieved significantly lower male captures in monitoring pheromone traps compared with untreated plots, as well as mean fruit infestation reductions of about 80 %. The control of the first CRS generation is not essential for achieving a good efficacy as demonstrated in two locations with different pest pressure. The late application of MD dispensers before the second CRS male flight has proven to be effective, suggesting a new advantageous way to apply mating disruption.The authors want to thank Fernando Alfaro from Denia, Antonio Caballero, and Javier Macias from Rio Tinto Fruit S.A. (Huelva, Spain) for field support. We also thank Ecologia y Proteccion Agricola SL for the pheromone supply. This work has been funded by the Spanish Ministry of Science and Innovation (project AGL2009-10725) and Agroalimed Foundation. 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Ann Entomol Soc Am 52:354–362DeBach P, Argyriou L (1967) The colonization and success in Greece of some imported Aphytis spp. (Hymenoptera: Aphelinidae) parasitic on citrus scale insects (Homoptera: Diaspididae). Biocontrol 12:325–342Desneux N, Decourtye A, Delpuech JM (2007) The sublethal effects of pesticides on beneficial arthropods. Ann Rev Entomol 52:81–106Diari Oficial de la Comunitat Valenciana (DOCV) (2008) DOCV no. 5901, 26. Resolution 27 October 2008 of Consellería de Agricultura, Pesca y Alimentación; November 2008. http://www.docv.gva.es/datos/2008/11/26/pdf/2008_13692.pdfDomínguez-Ruiz J, Sanchis J, Navarro-Llopis V, Primo J (2008) A new long-life trimedlure dispenser for Mediterranean fruit fly. J Econ Entomol 101:1325–1330Eliahu M, Blumberg D, Horowitz AR, Ishaaya I (2007) Effect of pyriproxyfen on developing stages and embryogenesis of California red scale (CRS), Aonidiella aurantii. 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In: Proceeding 6th International Citrus Congress, Tel Aviv (Israel), pp 1121–1127Hernández-Penadés P, Rodríguez-Reina JM, García-Marí F (2002) Umbrales de tratamiento para cóccidos diaspídidos en cítricos. Bol San Veg Plagas 28:469–478Hothorn T, Bretz F, Westfall P (2008) Simultaneous Inference in General Parametric Models. Biometrical J 50:346–363Ioratti C, Anfora G, Tasin M, De Cristofaro A, Witzgall P, Lucchi A (2011) Chemical ecology and management of Lobesia botrana (Lepidoptera: Tortricidae). J Econ Entomol 104:1125–1137Kehat M, Anshelevich L, Harel M, Dunkelblum E (1995) Control of the codling moth (Cydia pomonella) in apple and pear orchards in Israel by mating disruption. Phytoparasitica 23:285–296Kennett CE, Hoffmann RW (1985) Seasonal development of the California red scale (Homoptera: Diaspididae) in San Joaquin Valley citrus based on degree-day accumulation. J Econ Entomol 78:73–79Levitin E, Cohen E (1998) The involvement of acetylcholinesterase in resistance of the California red scale shape Aonidiella aurantii to organophosphorus pesticides. Entomol Exp Appl 88:115–121Lykouressis D, Perdikis D, Samartzis D, Fantinou A, Toutouzas S (2005) Management of the pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) by mating disruption in cotton fields. Crop Prot 24:177–183McLaren IW, Buchanan GA (1973) Parasitism by Aphytis chrysomphali Mercet and A. melinus Debach of Californian red scale, Aonidiella aurantii (Maskell), in relation to seasonal availability of suitable stages of the scale. Austr J Zool 21:111–117Moreno DS, Kennett CE (1985) Predictive year-end California red scale (Homoptera: Diaspididae) orange fruit infestations based on catches of males in the San-Joaquin Valley. J Econ Entomol 78:1–9Moreno DS, Luck RF (1992) Augmentative releases of Aphytis melinus (Hymenoptera: Aphelinidae) to suppress California red scale (Homoptera: Diaspididae) in southern California lemon orchards. J Econ Entomol 85:1112–1119Pekas A, Aguilar A, Tena A, García-Marí F (2010) Influence of host size on parasitism by Aphytis chrysomphali and A. melinus (Hymenoptera: Aphelinidae) in Mediterranean populations of California red scale Aonidiella aurantii (Hemiptera: Diaspididae). Biol Control 55:132–140Rill S, Grafton-Cardwell EE, Morse JG (2007) Effects of pyriproxyfen on California red scale (Hemiptera: Diaspididae) development and reproduction. J Econ Entomol 100:1435–1443Rodrigo E, Troncho P, García-Marí F (1996) Parasitoids (Hymenoptera: Aphelinidae) of three scale insects (Homoptera: Diaspididae) in a citrus grove in Valencia, Spain. 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The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly

Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing

Disparate Associations of HLA Class I Markers with HIV-1 Acquisition and Control of Viremia in an African Population

BACKGROUND:Acquisition of human immunodeficiency virus type 1 (HIV-1) infection is mediated by a combination of characteristics of the infectious and the susceptible member of a transmission pair, including human behavioral and genetic factors, as well as viral fitness and tropism. Here we report on the impact of established and potential new HLA class I determinants of heterosexual HIV-1 acquisition in the HIV-1-exposed seronegative (HESN) partners of serodiscordant Zambian couples. METHODOLOGY/PRINCIPAL FINDINGS:We assessed the relationships of behavioral and clinically documented risk factors, index partner viral load, and host genetic markers to HIV-1 transmission among 568 cohabiting couples followed for at least nine months. We genotyped subjects for three classical HLA class I genes known to influence immune control of HIV-1 infection. From 1995 to December 2006, 240 HESNs seroconverted and 328 remained seronegative. In Cox proportional hazards models, HLA-A*68:02 and the B*42-C*17 haplotype in HESN partners were significantly and independently associated with faster HIV-1 acquisition (relative hazards = 1.57 and 1.55; p = 0.007 and 0.013, respectively) after controlling for other previously established contributing factors in the index partner (viral load and specific class I alleles), in the HESN partner (age, gender), or in the couple (behavioral and clinical risk score). Few if any previously implicated class I markers were associated here with the rate of acquiring infection. CONCLUSIONS/SIGNIFICANCE:A few HLA class I markers showed modest effects on acquisition of HIV-1 subtype C infection in HESN partners of discordant Zambian couples. However, the striking disparity between those few markers and the more numerous, different markers found to determine HIV-1 disease course makes it highly unlikely that, whatever the influence of class I variation on the rate of infection, the mechanism mediating that phenomenon is identical to that involved in disease control

Grading systems in head and neck dysplasia: their prognostic value, weaknesses and utility

Contains fulltext : 80594.pdf (publisher's version ) (Open Access)ABSTRACT: BACKGROUND: Grading of dysplasia, including head and neck lesions, continues to be a hotly debated subject. It is subjective and lacks intra- and inter-observer reproducibility due to the insufficiency of validated morphological criteria and the biological nature of dysplasia. Moreover, due to the absence of a consensus, several systems are currently employed. OBJECTIVES: The aims of this review are to:1) Highlight the significance of dysplasia and the importance of a valid method for assessing precursor lesions of the head and neck.2) Review the different histopathological classification systems for grading intraepithelial lesions of the head and neck.3) Discuss and review quality requirements for these grading systems. CONCLUSION: Regarding the different classification systems, data concerning the WHO classification system are the most available in current literature. There is no simple relationship or overlapping between the classification systems. Further studies should be done to see whether other systems have advantages above the current WHO system and to discover indications that could lead to an universal classification system for intraepithelial lesions of the head and neck

Gene Expression during the Generation and Activation of Mouse Neutrophils: Implication of Novel Functional and Regulatory Pathways

As part of the Immunological Genome Project (ImmGen), gene expression was determined in unstimulated (circulating) mouse neutrophils and three populations of neutrophils activated in vivo, with comparison among these populations and to other leukocytes. Activation conditions included serum-transfer arthritis (mediated by immune complexes), thioglycollate-induced peritonitis, and uric acid-induced peritonitis. Neutrophils expressed fewer genes than any other leukocyte population studied in ImmGen, and down-regulation of genes related to translation was particularly striking. However, genes with expression relatively specific to neutrophils were also identified, particularly three genes of unknown function: Stfa2l1, Mrgpr2a and Mrgpr2b. Comparison of genes up-regulated in activated neutrophils led to several novel findings: increased expression of genes related to synthesis and use of glutathione and of genes related to uptake and metabolism of modified lipoproteins, particularly in neutrophils elicited by thioglycollate; increased expression of genes for transcription factors in the Nr4a family, only in neutrophils elicited by serum-transfer arthritis; and increased expression of genes important in synthesis of prostaglandins and response to leukotrienes, particularly in neutrophils elicited by uric acid. Up-regulation of genes related to apoptosis, response to microbial products, NFkB family members and their regulators, and MHC class II expression was also seen, in agreement with previous studies. A regulatory model developed from the ImmGen data was used to infer regulatory genes involved in the changes in gene expression during neutrophil activation. Among 64, mostly novel, regulatory genes predicted to influence these changes in gene expression, Irf5 was shown to be important for optimal secretion of IL-10, IP-10, MIP-1α, MIP-1β, and TNF-α by mouse neutrophils in vitro after stimulation through TLR9. This data-set and its analysis using the ImmGen regulatory model provide a basis for additional hypothesis-based research on the importance of changes in gene expression in neutrophils in different conditions

Subclonal diversification of primary breast cancer revealed by multiregion sequencing.

The sequencing of cancer genomes may enable tailoring of therapeutics to the underlying biological abnormalities driving a particular patient's tumor. However, sequencing-based strategies rely heavily on representative sampling of tumors. To understand the subclonal structure of primary breast cancer, we applied whole-genome and targeted sequencing to multiple samples from each of 50 patients' tumors (303 samples in total). The extent of subclonal diversification varied among cases and followed spatial patterns. No strict temporal order was evident, with point mutations and rearrangements affecting the most common breast cancer genes, including PIK3CA, TP53, PTEN, BRCA2 and MYC, occurring early in some tumors and late in others. In 13 out of 50 cancers, potentially targetable mutations were subclonal. Landmarks of disease progression, such as resistance to chemotherapy and the acquisition of invasive or metastatic potential, arose within detectable subclones of antecedent lesions. These findings highlight the importance of including analyses of subclonal structure and tumor evolution in clinical trials of primary breast cancer

Household food insecurity and childhood overweight in Jamaica and Québec: a gender-based analysis

Background - Childhood overweight is not restricted to developed countries: a number of lower- and middle-income countries are struggling with the double burden of underweight and overweight. Another public health problem that concerns both developing and, to a lesser extent, developed countries is food insecurity. This study presents a comparative gender-based analysis of the association between household food insecurity and overweight among 10-to-11-year-old children living in the Canadian province of Québec and in the country of Jamaica. // Methods - Analyses were performed using data from the 2008 round of the Québec Longitudinal Study of Child Development and the Jamaica Youth Risk and Resiliency Behaviour Survey of 2007. Cross-sectional data were obtained from 1190 10-year old children in Québec and 1674 10-11-year-old children in Jamaica. Body mass index was derived using anthropometric measurements and overweight was defined using Cole's age- and sex-specific criteria. Questionnaires were used to collect data on food insecurity. The associations were examined using chi-square tests and multivariate regression models were used to estimate odds ratios (OR) and 95% confidence intervals. // Results - The prevalence of overweight was 26% and 11% (p < 0.001) in the Québec and Jamaican samples, respectively. In Québec, the adjusted odds ratio for being overweight was 3.03 (95% CI: 1.8-5.0) among children living in food-insecure households, in comparison to children living in food-secure households. Furthermore, girls who lived in food-insecure households had odds of 4.99 (95% CI: 2.4-10.5) for being overweight in comparison to girls who lived in food-secure households; no such differences were observed among boys. In Jamaica, children who lived in food-insecure households had significantly lower odds (OR 0.65, 95% CI: 0.4-0.9) for being overweight in comparison to children living in food-secure households. No gender differences were observed in the relationship between food-insecurity and overweight/obesity among Jamaican children. // Conclusions - Public health interventions which aim to stem the epidemic of overweight/obesity should consider gender differences and other family factors associated with overweight/obesity in both developed and developing countries

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

Esophageal adenocarcinoma (EAC) has a poor outcome, and targeted therapy trials have thus far been disappointing owing to a lack of robust stratification methods. Whole-genome sequencing (WGS) analysis of 129 cases demonstrated that this is a heterogeneous cancer dominated by copy number alterations with frequent large-scale rearrangements. Co-amplification of receptor tyrosine kinases (RTKs) and/or downstream mitogenic activation is almost ubiquitous; thus tailored combination RTK inhibitor (RTKi) therapy might be required, as we demonstrate in vitro. However, mutational signatures showed three distinct molecular subtypes with potential therapeutic relevance, which we verified in an independent cohort (n = 87): (i) enrichment for BRCA signature with prevalent defects in the homologous recombination pathway; (ii) dominant T>G mutational pattern associated with a high mutational load and neoantigen burden; and (iii) C>A/T mutational pattern with evidence of an aging imprint. These subtypes could be ascertained using a clinically applicable sequencing strategy (low coverage) as a basis for therapy selection.Whole-genome sequencing of esophageal adenocarcinoma samples was performed as part of the International Cancer Genome Consortium (ICGC) through the oEsophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium and was funded by Cancer Research UK. We thank the ICGC members for their input on verification standards as part of the benchmarking exercise. We thank the Human Research Tissue Bank, which is supported by the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre, from Addenbrooke’s Hospital and UCL. Also the University Hospital of Southampton Trust and the Southampton, Birmingham, Edinburgh and UCL Experimental Cancer Medicine Centres and the QEHB charities. This study was partly funded by a project grant from Cancer Research UK. R.C.F. is funded by an NIHR Professorship and receives core funding from the Medical Research Council and infrastructure support from the Biomedical Research Centre and the Experimental Cancer Medicine Centre. We acknowledge the support of The University of Cambridge, Cancer Research UK (C14303/A17197) and Hutchison Whampoa Limited. We would like to thank Dr. Peter Van Loo for providing the NGS version of ASCAT for copy number calling. We are grateful to all the patients who provided written consent for participation in this study and the staff at all participating centres. Some of the work was undertaken at UCLH/UCL who received a proportion of funding from the Department of Health’s NIHR Biomedical Research Centres funding scheme. The work at UCLH/UCL was also supported by the CRUK UCL Early Cancer Medicine Centre.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.365