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1. Spatial variation and antecedent sea surface temperature conditions influence Hawaiian intertidal community structure

Author

Ward, Rebecca J, Cox, T Erin, Faucci, Anuschka, La Valle, Florybeth Flores, Philippoff, Joanna, Schaefer, Jessica LB, Ware, Ian M, Knope, Matthew L, and Ummenhofer, Caroline

Subjects
Hot Temperature, General Science & Technology, Temperature, Ecosystem, Hawaii
Abstract

Global sea surface temperatures (SSTs) are increasing, and in Hawai'i, rates of ocean warming are projected to double by the end of the 21st century. However, current nearshore warming trends and their possible impacts on intertidal communities are not well understood. This study represents the first investigation into the possible effects of rising SST on intertidal algal and invertebrate communities across the Main Hawaiian Islands (MHI). By utilizing citizen-science data coupled with high-resolution, daily SST satellite measurements from 12 intertidal sites across the MHI from 2004-2019, the response of intertidal algal and invertebrate abundance and community diversity to changes in SST was investigated across multiple spatial scales. Results show high rates of SST warming (0.40°C Decade-1) over this study's timeframe, similar to predicted rates of warming for Hawai'i by the end of the 21st century. Changes in abundance and diversity in response to SST were variable among intertidal sites, but differences in antecedent SST among intertidal sites were significantly associated with community dissimilarity. In addition, a statistically significant positive relationship was found between SST and Simpson's diversity index, and a significant relationship was also found between SST and the abundance of six dominant taxa. For five of these six dominant taxa, antecedent SSTs over the 6-12 months preceding sampling were the most influential for describing changes to abundance. The increase in community diversity in response to higher SSTs was best explained by temperatures in the 10 months preceding sampling, and the resultant decreased abundance of dominant turf algae. These results highlight rapidly warming nearshore SSTs in Hawai'i and the longer-term effects of antecedent SSTs as significant drivers of change within Hawaiian intertidal communities. Therefore, we suggest that future research and management should consider the possibility of lagging effects of antecedent SST on intertidal communities in Hawai'i and elsewhere.

Published
2023

2. Patient centered guidelines for the laboratory diagnosis of Gaucher disease type 1

Author

Dardis, A, Michelakakis, H, Rozenfeld, P, Fumic, K, Wagner, J, Pavan, E, Fuller, M, Revel-Vilk, S, Hughes, D, Cox, T, Aerts, J, International Working Group Of Gaucher Disease (IWGGD), Dardis, A [0000-0001-7024-8181], and Apollo - University of Cambridge Repository

Subjects
Genetic testing, Gaucher Disease, Clinical Laboratory Techniques, Patient-Centered Care, Lysosomal storage diseases, Humans, Glucosylceramidase, Review, Enzyme activity, Glucosylceramides, Biomarkers
Abstract

Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder due to the deficient activity of the acid beta-glucosidase (GCase) enzyme, resulting in the progressive lysosomal accumulation of glucosylceramide (GlcCer) and its deacylated derivate, glucosylsphingosine (GlcSph). GCase is encoded by the GBA1 gene, located on chromosome 1q21 16 kb upstream from a highly homologous pseudogene. To date, more than 400 GBA1 pathogenic variants have been reported, many of them derived from recombination events between the gene and the pseudogene. In the last years, the increased access to new technologies has led to an exponential growth in the number of diagnostic laboratories offering GD testing. However, both biochemical and genetic diagnosis of GD are challenging and to date no specific evidence-based guidelines for the laboratory diagnosis of GD have been published. The objective of the guidelines presented here is to provide evidence-based recommendations for the technical implementation and interpretation of biochemical and genetic testing for the diagnosis of GD to ensure a timely and accurate diagnosis for patients with GD worldwide. The guidelines have been developed by members of the Diagnostic Working group of the International Working Group of Gaucher Disease (IWGGD), a non-profit network established to promote clinical and basic research into GD for the ultimate purpose of improving the lives of patients with this disease. One of the goals of the IWGGD is to support equitable access to diagnosis of GD and to standardize procedures to ensure an accurate diagnosis. Therefore, a guideline development group consisting of biochemists and geneticists working in the field of GD diagnosis was established and a list of topics to be discussed was selected. In these guidelines, twenty recommendations are provided based on information gathered through a systematic review of the literature and two different diagnostic algorithms are presented, considering the geographical differences in the access to diagnostic services. Besides, several gaps in the current diagnostic workflow were identified and actions to fulfill them were taken within the IWGGD. We believe that the implementation of recommendations provided in these guidelines will promote an equitable, timely and accurate diagnosis for patients with GD worldwide.

Published
2022

3. Radiographic cortical thickness index predicts fragility fracture in Gaucher disease

Author

D’Amore, S., Sano, H., Chappell, D., Chiarugi, D., Baker, O., Page, K., Ramaswami, U., Johannesdottir, F., Cox, T., Deegan, P., Poole, K., Platt, F., Banka, S., Chakrapani, A., Geberhiwot, T., Hughes, D., Jones, S., Lachmann, R., Santra, S., Sharma, R., and Vellodi, A.

Subjects
Radiology, Nuclear Medicine and imaging, Article
Abstract

Background Patients with Gaucher disease (GD) have a high risk of fragility fractures. Routine evaluation of bone involvement in these patients includes radiography and repeated dual-energy x-ray absorptiometry (DXA). However, osteonecrosis and bone fracture may affect the accuracy of DXA. Purpose To assess the utility of DXA and radiographic femoral cortical thickness measurements as predictors of fragility fracture in patients with GD with long-term follow-up (up to 30 years). Materials and Methods Patients with GD age 16 years and older with a detailed medical history, at least one bone image (DXA and/or radiographs), and minimum 2 years follow-up were retrospectively identified using three merged UK-based registries (Gaucherite study, enrollment 2015-2017; Clinical Bone Registry, enrollment 2003-2006; and Mortality Registry, enrollment 1993-2019). Cortical thickness index (CTI) and canal-to-calcar ratio (CCR) were measured by two independent observers, and inter- and intraobserver reliability was calculated. The fracture-predictive value of DXA, CTI, CCR, and cutoff values were calculated using receiver operating characteristic curves. Statistical differences were assessed using univariable and multivariable analysis. Results Bone imaging in 247 patients (123 men, 124 women; baseline median age, 39 years; IQR, 27-50 years) was reviewed. The median follow-up period was 11 years (IQR, 7-19 years; range, 2-30 years). Thirty-five patients had fractures before or at first bone imaging, 23 patients had fractures after first bone imaging, and 189 patients remained fracture-free. Inter- and intraobserver reproducibility for CTI/CCR measurements was substantial (range, 0.96-0.98). In the 212 patients with no baseline fracture, CTI (cutoff, ≤0.50) predicted future fractures with higher sensitivity and specificity (area under the receiver operating characteristic curve [AUC], 0.96; 95% CI: 0.84, 0.99; sensitivity, 92%; specificity, 96%) than DXA T-score at total hip (AUC, 0.78; 95% CI: 0.51, 0.91; sensitivity, 64%; specificity, 93%), femoral neck (AUC, 0.73; 95% CI: 0.50, 0.86; sensitivity, 64%; specificity, 73%), lumbar spine (AUC, 0.69; 95% CI: 0.49, 0.82; sensitivity, 57%; specificity, 63%), and forearm (AUC, 0.78; 95% CI: 0.59, 0.89; sensitivity, 70%; specificity, 70%). Conclusion Radiographic cortical thickness index of 0.50 or less was a reliable independent predictor of fracture risk in Gaucher disease. Clinical trial registration no. NCT03240653 © RSNA, 2022

Published
2022

5. An exploration of the impact that continuous, summative assessment has on how university mathematics students spend their study time

Author

Howard, E., Meehan, M., Cox, T., Kingston, M., and Grimes, P.

Abstract

A move to modularisation has seen an increase in the amount of continuous, summative assessments undergraduate students must complete. Students advocate for these assessments as it encourages them to remain engaged, and lecturers feel compelled to give them to ensure students do not neglect their modules. This phenomenon has been dubbed “the assessment arms race”. In this study we examine the impact that continuous, summative assessment has on how Stage 3 mathematics undergraduate students in University College Dublin choose to spend their study time. Students completed weekly timesheets reporting how much time they spent on activities in their six modules in trimester 2, 2019-20. They were asked to describe the factors that influenced how they spent their study time, and if there were other activities they would have liked to complete. Although data collection was cut short owing to COVID-19, an analysis of the data up to that point provides clear evidence of the assessment arms race in action and highlights the behavioural impact that it has on how students approach their learning. We examine recommendations, and discuss possible solutions, to address this.

Published
2021
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6. In-depth phenotyping for clinical stratification of Gaucher disease

Author

D’Amore, Simona, Page, Kathleen, Donald, Aimée, Taiyari, Khadijeh, Tom, Brian, Deegan, Patrick, Tan, Chong Y., Poole, Kenneth, Jones, Simon A., Mehta, Atul, Hughes, Derralynn, Sharma, Reena, Lachmann, Robin H., Chakrapani, Anupam, Geberhiwot, Tarekegn, Santra, Saikat, Banka, Siddarth, Cox, Timothy M., Cox, T. M., Platt, F. M., Banka, S., Chakrapani, A., Deegan, P. B., Geberhiwot, T., Hughes, D. A., Jones, S., Lachmann, R. H., Santra, S., Sharma, R., Vellodi, A., Cox, Timothy M [0000-0002-4951-9941], Apollo - University of Cambridge Repository, and Cox, Timothy M. [0000-0002-4951-9941]

Subjects
Pediatrics, medicine.medical_specialty, medicine.medical_treatment, Splenectomy, Disease, Cohort Studies, Lysosomal storage diseases, medicine, Humans, Disease-modifying therapies, GAUCHERITE, Pharmacology (medical), Substrate reduction therapy, Prospective Studies, Bone pain, Genetics (clinical), Retrospective Studies, Gaucher Disease, business.industry, Research, Cohort, Genetic disorder, General Medicine, Enzyme replacement therapy, medicine.disease, Orthopedic surgery, Medicine, Glucosylceramidase, Nervous System Diseases, medicine.symptom, business
Abstract

Background The Gaucher Investigative Therapy Evaluation is a national clinical cohort of 250 patients aged 5–87 years with Gaucher disease in the United Kingdom—an ultra-rare genetic disorder. To inform clinical decision-making and improve pathophysiological understanding, we characterized the course of Gaucher disease and explored the influence of costly innovative medication and other interventions. Retrospective and prospective clinical, laboratory and radiological information including molecular analysis of the GBA1 gene and comprising > 2500 variables were collected systematically into a relational database with banking of collated biological samples in a central bioresource. Data for deep phenotyping and life-quality evaluation, including skeletal, visceral, haematological and neurological manifestations were recorded for a median of 17.3 years; the skeletal and neurological manifestations are the main focus of this study. Results At baseline, 223 of the 250 patients were classified as type 1 Gaucher disease. Skeletal manifestations occurred in most patients in the cohort (131 of 201 specifically reported bone pain). Symptomatic osteonecrosis and fragility fractures occurred respectively in 76 and 37 of all 250 patients and the first osseous events occurred significantly earlier in those with neuronopathic disease. Intensive phenotyping in a subgroup of 40 patients originally considered to have only systemic features, revealed neurological involvement in 18: two had Parkinson disease and 16 had clinical signs compatible with neuronopathic Gaucher disease—indicating a greater than expected prevalence of neurological features. Analysis of longitudinal real-world data enabled Gaucher disease to be stratified with respect to advanced therapies and splenectomy. Splenectomy was associated with an increased hazard of fragility fractures, in addition to osteonecrosis and orthopaedic surgery; there were marked gender differences in fracture risk over time since splenectomy. Skeletal disease was a heavy burden of illness, especially where access to specific therapy was delayed and in patients requiring orthopaedic surgery. Conclusion Gaucher disease has been explored using real-world data obtained in an era of therapeutic transformation. Introduction of advanced therapies and repeated longitudinal measures enabled this heterogeneous condition to be stratified into obvious clinical endotypes. The study reveals diverse and changing phenotypic manifestations with systemic, skeletal and neurological disease as inter-related sources of disability.

Published
2021

7. Patient-delivered tDCS on chronic neuropathic pain in prior responders to TMS (a randomized controlled pilot study)

Author

O'Neill F, Sacco P, Bowden E, Asher R, Burnside G, Cox T, and Nurmikko T

Subjects
lcsh:R5-920, Transcranial magnetic stimulation (TMS), Brain stimulation, Neuropathic pain, lcsh:Medicine (General), Motor cortex (M1), Transcranial direct current stimulation (tDCS)
Abstract

Francis O’Neill,1 Paul Sacco,1 Eleanor Bowden,1 Rebecca Asher,2 Girvan Burnside,3 Trevor Cox,2 Turo Nurmikko1 1The Pain Research Institute, Faculty of Health and Life Sciences, Clinical Sciences Centre, University of Liverpool, Liverpool, UK;2Cancer Research UK Liverpool Cancer Trials Unit, Liverpool, UK; 3Department of Biostatistics,University of Liverpool, Liverpool, UK Background: Successful response to repetitive transcranial magnetic stimulation (rTMS) of the motor cortex requires continued maintenance treatments. Transcranial Direct Current Stimulation (tDCS) may provide a more convenient alternative.Methods: This pilot study aimed to examine the feasibility of a randomized, double-blind, double-crossover pilot study for patients to self-administer tDCS motor cortex stimulation for 20 minutes/day over five consecutive days. Primary outcomes were as follows: usability of patient-administered tDCS, compliance with device, recruitment, and retention rates. Secondary outcomes were as follows: effect on overall pain levels and quality of life via Short Form-36 anxiety and depression via Hospital Anxiety and Depression Scale, and Mini-Mental State scores.Results: A total of 24 subjects with neuropathic pain, who had previously experienced rTMS motor cortex stimulation (13 with reduction in pain scores, 11 nonresponders) were recruited at the Pain Research Institute, Fazakerley, UK. A total of 21 subjects completed the study. Recruitment rate was 100% but retention rate was only 87.5%. All patients reported satisfactory usability of the tDCS device.No significant difference was shown between Sham vs Anodal (–0.16, 95% CI: –0.43 to 0.11) P=0.43, Sham vs Cathodal (0.11, 95% CI: –0.16 to 0.37) P=0.94, or Cathodal vs Anodal (–0.27, 95% CI: –0.54 to 0.00) P=0.053 treatments. Furthermore, no significant changes were demonstrated in anxiety, depression, or quality of life measurements. The data collected to ­estimate sample size for a definitive study suggested that the study’s sample size was already large enough to detect a change of 15% in pain levels at 90% power for the overall group of 21 patients.Conclusion: This study did not show a beneficial effect of tDCS in this group of patients and does not support the need for a larger definitive study using the same experimental paradigm.Trial registration: ISRCTN56839387 Keywords: neuropathic pain, brain stimulation, motor cortex, M1, transcranial direct current stimulation, tDCS, transcranial magnetic stimulation, TMS

Published
2018

8. The visual lightcurve of comet C/1995 O1 (Hale-Bopp) from 1995-1999

Author

Womack, M., Curtis, O., Rabson, D. A., Pinto, O. Harrington, Wierzchos, K., Gonzalez, S. Cruz, Sarid, G., Mentzer, C., Lastra, N., Pichette, N., Ruffini, N., Cox, T., Rivera, I., Micciche, A., Jackson, C., Homich, A., Escoto, S. Rosslyn, Erdahl, T., Goldschen-Ohm, Marcel P., Tollison, A., Reed, S., Zilka, J., Henning, B., Spinar, M., and Uhl, W. T.

Subjects
Earth and Planetary Astrophysics (astro-ph.EP), FOS: Physical sciences, Astrophysics - Earth and Planetary Astrophysics
Abstract

The long-term brightness evolution of the great comet C/1995 O1 (Hale-Bopp) presented a remarkable opportunity to study the behavior of its coma over four years. We used approximately 2200 total visual magnitudes published in the International Comet Quarterly taken from 17 observers during the period of 1995 July - 1999 September to create a secular lightcurve. In order to account for observer differences, we present a novel algorithm to reduce scatter and increase precision in a lightcurve compiled from many sources. It is implemented in a publicly available code, ICQSPLITTER. This code addresses the differences among observers by using a self-consistent statistical approach, leading to a sharper lightcurve, and improving the precision of the measured slopes. To first order, the comet's lightcurve approximately follows a r$^{-4}$ response for both pre- and post-perihelion distances. Interestingly, the pre-perihelion data are better fit with a fifth-order polynomial with inflection points at 4.0, 2.6, 2.1 and 1.1 au. We analyze these specific regions and find that they are associated with physical phenomena in the comet's evolution. Contrary to other reports, the lightcurve shows no evidence for the comet having been in outburst at discovery. Afrho values derived from the visual lightcurve data are consistent with a r$^{-1.5}$ dependence on heliocentric distance, which is similar in shape to those derived from spectroscopy and narrow-band photometry. We present correlation equations for visual magnitudes and CO and H2O production rates, which are consistent with the pre-perihelion visual magnitudes increasing almost entirely due to CO outgassing until a heliocentric distance of about 2.6 - 3.0 au. We also present two correlation equations that should prove highly useful for observation planning and data analysis, and can be generalized to be applicable to other comets., 30 pages, 7 figures, 4 tables, submitted to the AAS Journals

Published
2020

9. Ensembl 2008

Author

Flicek, P, Aken, BL, Beal, K, Ballester, B, Caccamo, M, Chen, Y, Clarke, L, Coates, G, Cunningham, F, Cutts, T, Down, T, Dyer, SC, Eyre, T, Fitzgerald, S, Fernandez-Banet, J, Gräf, S, Haider, S, Hammond, M, Holland, R, Howe, KL, Howe, K, Johnson, N, Jenkinson, A, Kähäri, A, Keefe, D, Kokocinski, F, Kulesha, E, Lawson, D, Longden, I, Megy, K, Meidl, P, Overduin, B, Parker, A, Pritchard, B, Prlic, A, Rice, S, Rios, D, Schuster, M, Sealy, I, Slater, G, Smedley, D, Spudich, G, Trevanion, S, Vilella, AJ, Vogel, J, White, S, Wood, M, Birney, E, Cox, T, Curwen, V, Durbin, R, Fernandez-Suarez, XM, Herrero, J, Hubbard, TJP, Kasprzyk, A, Proctor, G, Smith, J, Ureta-Vidal, A, and Searle, S

Subjects
Internet, Mice, User-Computer Interface, ComputingMethodologies_PATTERNRECOGNITION, Databases, Genetic, Computer Graphics, Animals, Humans, Genomics, Regulatory Elements, Transcriptional, Software
Abstract

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Published
2020
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10. Spatial and temporal patterns in Hawai'i's intertidal: decadal changes in benthic community composition

Author

La Valle, Florybeth F., Schaefer, Jessica L.B., Cox, T. Erin, and Philippoff, Joanna

Subjects
Global and local factors, Decadal changes, Turbinaria ornata, Crustose coralline algae, Physically resilient
Abstract

Spatially broad and long-term monitoring studies are lacking in tropical intertidal systems yet are necessary to test predictions regarding community assembly. To fill this gap, we examined spatial and decadal temporal patterns in benthic community structure at rocky intertidal sites along the main islands of Hawai‘i. Quantitative community surveys done in 2017 across nine sites and five islands showed that organismal composition differed by site, substrate type, and island. Secondly, we leveraged an earlier dataset collected using the same methods and analyzed intertidal communities at five sites on three Hawaiian islands for temporal changes in organismal abundance and composition from 2006 and 2007 vs. 2016 and 2017. Overall community structure differed significantly across years and decades. Most decadal differences were site specific, such as the fivefold increase in turf algae at one site. Crustose coralline algae and Turbinaria ornata increased significantly across five sites; both are physically resilient algae and similar increases in their abundances have been observed in tropical systems worldwide. This increase in physically resilient macroalgal species is potentially caused by global drivers, such as rising temperatures and changing land uses. In conclusion, there is evidence that both local and regional factors contribute to structuring tropical intertidal communities.

Published
2020

11. The Evolution of an Invasive Plant, Sorghum halepense L. ('Johnsongrass')

Author

Paterson, Andrew H., Kong, Wenqian, Johnston, Robyn M., Nabukalu, Pheonah, Wu, Guohong, Poehlman, William L., Goff, Valorie H., Isaacs, Krista, Lee, Tae-Ho, Guo, Hui, Zhang, Dong, Sezen, U. Uzay, Kennedy, Megan, Bauer, Diane, Feltus, Frank A., Weltzien, Eva, Rattunde, Henry Frederick, Barney, Jacob, Barry, Kerrie, Cox, T. Stan, and Scanlon, Michael J.

Subjects
Genetics & Heredity, 0604 Genetics, 1801 Law, TOPHAT, GENETICS, rhizome, food and beverages, 1103 Clinical Sciences, evolutionary novelty, SUGGESTS, READ ALIGNMENT, GENOME, SORGHUM-BICOLOR, crop, RECONSTRUCTION, PLANTS, invasion biology, Life Sciences & Biomedicine, polyploidy, weed, perennial
Abstract

From noble beginnings as a prospective forage, polyploid Sorghum halepense (‘Johnsongrass’) is both an invasive species and one of the world’s worst agricultural weeds. Formed by S. bicolor x S. propinquum hybridization, we show S. halepense to have S. bicolor-enriched allele composition and striking mutations in 5,957 genes that differentiate it from representatives of its progenitor species and an outgroup. The spread of S. halepense may have been facilitated by introgression from closely-related cultivated sorghum near genetic loci affecting rhizome development, seed size, and levels of lutein, a photochemical protectant and abscisic acid precursor. Rhizomes, subterranean stems that store carbohydrates and spawn clonal propagules, have growth correlated with reproductive rather than other vegetative tissues, and increase survival of both temperate cold seasons and tropical dry seasons. Rhizomes of S. halepense are more extensive than those of its rhizomatous progenitor S. propinquum, with gene expression including many alleles from its non-rhizomatous S. bicolor progenitor. The first surviving polyploid in its lineage in ∼96 million years, its post-Columbian spread across six continents carried rich genetic diversity that in the United States has facilitated transition from agricultural to non-agricultural niches. Projected to spread another 200–600 km northward in the coming century, despite its drawbacks S. halepense may offer novel alleles and traits of value to improvement of sorghum. Published version

Published
2020

12. Personal protection and delivery of rhinologic and endoscopic skull base procedures during the COVID-19 outbreak: ERS endorsed advises

Author

Van Gerven, L., Hellings, P. W., Cox, T., Fokkens, W., Hopkins, C., Hox, V, Jorissen, M., Schuermans, A., Sinonquel, P., Speleman, K., Vander Poorten, V., Van Gool, K., Van Zele, T., Alobid, I, Ear, Nose and Throat, AII - Inflammatory diseases, COX, Tony, Vander Poorten, V, Alobid, I, Van Gerven, L, Van Gool, K, Schuermans, A, Van Zele, T, Jorissen, M, Hopkins, C, Hox, V, Speleman, K, Sinonquel, P, Hellings, PW, and Fokkens, W

Subjects
SARS-CoV-2, Infection prevention, Personal protective equipment, COVID-19, Skull base surgery, Human medicine, Rhinology, Endoscopic surgery
Abstract

On March 11th 2020, the World Health Organization (WHO) declared COVID-19 pandemic, with subsequent profound impact on the entire health care system. During the COVID-19 outbreak, activities in the rhinology outpatient clinic and operation rooms are limited to emergency care only. Health care practitioners are faced with the need to perform rhinological and skull base emergency procedures in patients with a positive or unknown COVID-19 status. This article aims to provide recommendations and relevant information for rhinologists, based on the limited amount of (anecdotal) data, to guarantee high-quality patient care and adequate levels of infection prevention in the rhinology clinic.

Published
2020

13. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author

Haworth, S, Shapland, CY, Hayward, C, Prins, BP, Felix, JF, Medina-Gomez, C, Rivadeneira, F, Wang, C, Ahluwalia, TS, Vrijheid, M, Guxens, M, Sunyer, J, Tachmazidou, I, Walter, K, Iotchkova, V, Jackson, A, Cleal, L, Huffmann, J, Min, JL, Sass, L, Timmers, PRHJ, Al Turki, S, Anderson, CA, Anney, R, Antony, D, Artigas, MS, Ayub, M, Bala, S, Barrett, JC, Barroso, I, Beales, P, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, PF, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, DA, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Danecek, P, Day, INM, Day-Williams, A, Dominiczak, A, Down, T, Du, Y, Dunham, I, Durbin, R, Edkins, S, Ekong, R, Ellis, P, Evans, DM, Farooqi, IS, Fitzpatrick, DR, Flicek, P, Floyd, J, Foley, AR, Franklin, CS, Futema, M, Gallagher, L, Gaunt, TR, Geihs, M, Geschwind, D, Greenwood, CMT, Griffin, H, Grozeva, D, Guo, X, Gurling, H, Hart, D, Hendricks, AE, Holmans, P, Howie, B, Huang, J, Huang, L, Hubbard, T, Humphries, SE, Hurles, ME, Hysi, P, Jackson, DK, Jamshidi, Y, Joyce, C, Karczewski, KJ, Kaye, J, Keane, T, Kemp, JP, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, van Kogelenberg, M, Kolb-Kokocinski, A, Lachance, G, Langford, C, Lawson, D, Lee, I, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lonnqvist, J, Lopes, LR, Lopes, M, MacArthur, DG, Mangino, M, Marchini, J, Marenne, G, Maslen, J, Mathieson, I, McCarthy, S, McGuffin, P, McIntosh, AM, McKechanie, AG, McQuillin, A, Memari, Y, Metrustry, S, Migone, N, Mitchison, HM, Moayyeri, A, Morris, A, Morris, J, Muddyman, D, Muntoni, F, Northstone, K, O'Donovan, MC, O'Rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, MJ, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, JR, Paternoster, L, Paunio, T, Payne, F, Payne, SJ, Perry, JRB, Pietilainen, O, Plagnol, V, Pollitt, RC, Porteous, DJ, Povey, S, Quail, MA, Quaye, L, Raymond, FL, Rehnstrom, K, Richards, JB, Ridout, CK, Ring, S, Ritchie, GRS, Roberts, N, Robinson, RL, Savage, DB, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, RH, Semple, RK, Serra, E, Sharp, SI, Shaw, A, Shihab, HA, Shin, S-Y, Skuse, D, Small, KS, Smee, C, Smith, BH, Soranzo, N, Southam, L, Spasic-Boskovic, O, Spector, TD, St Clair, D, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Taylor, R, Tian, J, Tobin, MD, Valdes, AM, Vandersteen, AM, Vijayarangakannan, P, Visscher, PM, Wain, LV, Walters, JTR, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whyte, T, Williams, HJ, Williamson, KA, Wilson, C, Wilson, SG, Wong, K, Xu, C, Yang, J, Zhang, F, Zhang, P, Zheng, H-F, Smith, GD, Fisher, SE, Wilson, JF, Cole, TJ, Fernandez-Orth, D, Bonnelykke, K, Bisgaard, H, Pennell, CE, Jaddoe, VWV, Dedoussis, G, Timpson, N, Zeggini, E, Vitart, V, St Pourcain, B, UK10K Consortium, Epidemiology, Erasmus MC other, Pediatrics, Internal Medicine, and Child and Adolescent Psychiatry / Psychology

Abstract

Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The underlying genetic influences shaping these traits during the transition from childhood to adulthood are little understood, but might include both age-specific genetic factors and low-frequency genetic variation. Here, we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV + HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood, suggesting a previously unrecognized role of TP53 transcripts in human cranial development.

Published
2019

14. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author

Haworth, S., Shapland, C.Y., Hayward, C., Prins, B.P., Felix, J.F., Medina-Gomez, C., Rivadeneira, F., Wang, C., Ahluwalia, T.S., Vrijheid, M., Guxens, M., Sunyer, J., Tachmazidou, I., Walter, K., Iotchkova, V., Jackson, A., Cleal, L., Huffmann, J., Min, J.L., Sass, L., Timmers, P.R.H.J., Turki, S.A., Anderson, C.A., Anney, R., Antony, D., Artigas, M.S., Ayub, M., Bala, S., Barrett, J.C., Barroso, I., Beales, P., Bentham, J., Bhattacharya, S., Birney, E., Blackwood, D., Bobrow, M., Bochukova, E., Bolton, P.F., Bounds, R., Boustred, C., Breen, G., Calissano, M., Carss, K., Charlton, R., Chatterjee, K., Chen, L., Ciampi, A., Cirak, S., Clapham, P., Clement, G., Coates, G., Cocca, M., Collier, D.A., Cosgrove, C., Cox, T., Craddock, N., Crooks, Lucy, Curran, S., Curtis, D., Daly, A., Danecek, P., Day, I.N.M., Day-Williams, A., Dominiczak, A., Down, T., Du, Y., Dunham, I., Durbin, R., Edkins, S., Ekong, R., Ellis, P., Evans, D.M., Farooqi, I.S., Fitzpatrick, D.R., Flicek, P., Floyd, J., Foley, A.R., Franklin, C.S., Futema, M., Gallagher, L., Gaunt, T.R., Geihs, M., Geschwind, D., Greenwood, C.M.T., Griffin, H., Grozeva, D., Guo, X., Gurling, H., Hart, D., Hendricks, A.E., Holmans, P., Howie, B., Huang, J., Huang, L., Hubbard, T., Humphries, S.E., Hurles, M.E., Hysi, P., and Jackson, D.K.

Abstract

© 2019, The Author(s). Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The underlying genetic influences shaping these traits during the transition from childhood to adulthood are little understood, but might include both age-specific genetic factors and low-frequency genetic variation. Here, we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV + HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood, suggesting a previously unrecognized role of TP53 transcripts in human cranial development.

Published
2019

15. Is percutaneous tracheotomy safe in the context of anticoagulant therapy?

Author

Colpaert, Cecile, Cox, T., Janssens de Varebeke, Sebastien, Dubois, J., Jamaer, P., Ihtijarevic, B., Cox, C., Ketelslagers, K., and Deben, K.

Subjects
Human medicine
Abstract

Objectives: Tracheotomy is one of the most frequent procedures performed in intensive care unit patients. The percutaneous procedure presents many advantages, such as cost-effectiveness and feasibility as a bedside technique which is time-saving in skilled hands. Material and methods: All tracheotomies that were accomplished between January 2008 and December 2015 at Jessa Hospital, Hasselt, Belgium, were retrospectively reviewed. In our department, this percutaneous technique is always executed by two otolaryngologists using bronchoscopic guidance. Results: We identified 231 patients who underwent tracheotomy in our hospital between January 2008 and December 2015. Sixty-five percent were male patients, the mean age at time of tracheotomy was 66 +/- 14 years, and the percutaneous technique was used in 87% of these cases. Tracheotomy was required at a mean endotracheal intubation period of 15 +/- 9 days. Results show that 80% of patients were already under anticoagulant therapy at the time of intervention, making them high-risk patients. Minor complications were observed in 7.5% of patients: minor bleeding during tracheotomy (1%), minor postoperative bleeding (4.5%), creation of false passage (1%), and tracheocutaneous fistula (1%). No major complications were noted. Conclusions: Percutaneous tracheotomy is a safe technique in skilled hands and when performed on well-selected patients. The result shows that this technique is feasible and safe in patients with moderate to severe coagulation problems. The main contraindications in our center are obesity and difficult neck/chest anatomy.

Published
2019

18. Erratum to:Methods for evaluating medical tests and biomarkers

Author

Gopalakrishna, G, Langendam, M, Scholten, R, Bossuyt, P, Leeflang, M, Noel-Storr, A, Thomas, J, Marshall, I, Wallace, B, Whiting, P, Davenport, C, GopalaKrishna, G, De Salis, I, Mallett, S, Wolff, R, Riley, R, Westwood, M, Kleinen, J, Collins, G, Reitsma, H, Moons, K, Zapf, A, Hoyer, A, Kramer, K, Kuss, O, Ensor, J, Deeks, JJ, Martin, EC, Riley, RD, Rücker, G, Steinhauser, S, Schumacher, M, Snell, K, Willis, B, Debray, T, Deeks, J, Di Ruffano, LF, Taylor-Phillips, S, Hyde, C, Taylor, SA, Batnagar, G, STREAMLINE COLON Investigators, STREAMLINE LUNG Investigators, METRIC Investigators, Seedat, F, Clarke, A, Byron, S, Nixon, F, Albrow, R, Walker, T, Deakin, C, Zhelev, Z, Hunt, H, Yang, Y, Abel, L, Buchanan, J, Fanshawe, T, Shinkins, B, Wynants, L, Verbakel, J, Van Huffel, S, Timmerman, D, Van Calster, B, Zwinderman, A, Oke, J, O'Sullivan, J, Perera, R, Nicholson, B, Bromley, HL, Roberts, TE, Francis, A, Petrie, D, Mann, GB, Malottki, K, Smith, H, Billingham, L, Sitch, A, Gerke, O, Holm-Vilstrup, M, Segtnan, EA, Halekoh, U, Høilund-Carlsen, PF, Francq, BG, Dinnes, J, Parkes, J, Gregory, W, Hewison, J, Altman, D, Rosenberg, W, Selby, P, Asselineau, J, Perez, P, Paye, A, Bessede, E, Proust-Lima, C, Naaktgeboren, C, De Groot, J, Rutjes, A, Reitsma, J, Ogundimu, E, Cook, J, Le Manach, Y, Vergouwe, Y, Pajouheshnia, R, Groenwold, R, Peelen, L, Nieboer, D, De Cock, B, Pencina, MJ, Steyerberg, EW, Cooper, J, Parsons, N, Stinton, C, Smith, S, Dickens, A, Jordan, R, Enocson, A, Fitzmaurice, D, Adab, P, Boachie, C, Vidmar, G, Freeman, K, Connock, M, Court, R, Moons, C, Harris, J, Mumford, A, Plummer, Z, Lee, K, Reeves, B, Rogers, C, Verheyden, V, Angelini, GD, Murphy, GJ, Huddy, J, Ni, M, Good, K, Cooke, G, Hanna, G, Ma, J, Moons, KGMC, De Groot, JAH, Altman, DG, Reitsma, JB, Collins, GS, Moons, KGM, Kamarudin, AN, Kolamunnage-Dona, R, Cox, T, Borsci, S, Pérez, T, Pardo, MC, Candela-Toha, A, Muriel, A, Zamora, J, Sanghera, S, Mohiuddin, S, Martin, R, Donovan, J, Coast, J, Seo, MK, Cairns, J, Mitchell, E, Smith, A, Wright, J, Hall, P, Messenger, M, Calder, N, Wickramasekera, N, Vinall-Collier, K, Lewington, A, Damen, J, Cairns, D, Hutchinson, M, Sturgeon, C, Mitchel, L, Kift, R, Christakoudi, S, Rungall, M, Mobillo, P, Montero, R, Tsui, T-L, Kon, SP, Tucker, B, Sacks, S, Farmer, C, Strom, T, Chowdhury, P, Rebollo-Mesa, I, Hernandez-Fuentes, M, Damen, JAAG, Debray, TPA, Heus, P, Hooft, L, Scholten, RJPM, Schuit, E, Tzoulaki, I, Lassale, CM, Siontis, GCM, Chiocchia, V, Roberts, C, Schlüssel, MM, Gerry, S, Black, JA, Van der Schouw, YT, Peelen, LM, Spence, G, McCartney, D, Van den Bruel, A, Lasserson, D, Hayward, G, Vach, W, De Jong, A, Burggraaff, C, Hoekstra, O, Zijlstra, J, De Vet, H, Graziadio, S, Allen, J, Johnston, L, O'Leary, R, Power, M, Johnson, L, Waters, R, Simpson, J, Fanshawe, TR, Phillips, P, Plumb, A, Helbren, E, Halligan, S, Gale, A, Sekula, P, Sauerbrei, W, Forman, JR, Dutton, SJ, Takwoingi, Y, Hensor, EM, Nichols, TE, Kempf, E, Porcher, R, De Beyer, J, Hopewell, S, Dennis, J, Shields, B, Jones, A, Henley, W, Pearson, E, Hattersley, A, MASTERMIND consortium, Scheibler, F, Rummer, A, Sturtz, S, Großelfinger, R, Banister, K, Ramsay, C, Azuara-Blanco, A, Burr, J, Kumarasamy, M, Bourne, R, Uchegbu, I, Murphy, J, Carter, A, Marti, J, Eatock, J, Robotham, J, Dudareva, M, Gilchrist, M, Holmes, A, Monaghan, P, Lord, S, StJohn, A, Sandberg, S, Cobbaert, C, Lennartz, L, Verhagen-Kamerbeek, W, Ebert, C, Horvath, A, Test Evaluation Working Group of the European Federation of Clinical Chemistry and Laboratory Medicine, Jenniskens, K, Peters, J, Grigore, B, Ukoumunne, O, Levis, B, Benedetti, A, Levis, AW, Ioannidis, JPA, Shrier, I, Cuijpers, P, Gilbody, S, Kloda, LA, McMillan, D, Patten, SB, Steele, RJ, Ziegelstein, RC, Bombardier, CH, Osório, FDL, Fann, JR, Gjerdingen, D, Lamers, F, Lotrakul, M, Loureiro, SR, Löwe, B, Shaaban, J, Stafford, L, Van Weert, HCPM, Whooley, MA, Williams, LS, Wittkampf, KA, Yeung, AS, Thombs, BD, Cooper, C, Nieto, T, Smith, C, Tucker, O, Dretzke, J, Beggs, A, Rai, N, Bayliss, S, Stevens, S, Mallet, S, Sundar, S, Hall, E, Porta, N, Estelles, DL, De Bono, J, CTC-STOP protocol development group, and National Institute for Health Research

Subjects
medicine.medical_specialty, Astrophysics::High Energy Astrophysical Phenomena, MEDLINE, 030204 cardiovascular system & hematology, BTC (Bristol Trials Centre), MASTERMIND consortium, 03 medical and health sciences, 0302 clinical medicine, medicine, 030212 general & internal medicine, Intensive care medicine, CTC-STOP protocol development group, lcsh:R5-920, business.industry, Test Evaluation Working Group of the European Federation of Clinical Chemistry and Laboratory Medicine, Published Erratum, STREAMLINE COLON Investigators, 3. Good health, STREAMLINE LUNG Investigators, Centre for Surgical Research, Family medicine, METRIC Investigators, High Energy Physics::Experiment, Erratum, business, lcsh:Medicine (General)
Abstract

[This corrects the article DOI: 10.1186/s41512-016-0001-y.].

Published
2017

19. Landscape scale conservation: incentives for cross-property action

Author

Ampt, P, Baumber, AP, Berry, E, Cox, T, Cross, R, Metternicht, G, and Pfeiffer, H

Abstract

Production landscapes are critical for biodiversity conservation. Individual landholders can contribute but the real challenge is coordinated cross-property action at a landscape scale. This paper describes 2 projects through which we have attempted to better understand that challenge. The ‘Communities in Landscapes’ project (Caring for Our Country 2009-2012) provided coordinated advice and training to develop cross-property biodiversity plans and $70k for each of 7 landholder groups for the initial phase of the implementation. The project generated collaboration on landscape scale biodiversity conservation, but without ongoing support the benefits achieved could be soon lost. The ‘Increasing landholder collaboration for landscape scale conservation’ project (NSW Environmental Trust 2016-2017) is exploring the nature and extent of collaboration, and the opportunities provided by collaboration for public and private benefit. The vision is for landholders to develop ‘Landscape Corporations’ which are the vehicle for integrating production and conservation for landholders sharing the same landscape.

Published
2017

20. Inguinal Hernia: Mesh Fixation

Author

Sun, P, Hu, S. B, Cheng, X, Li, M, Guo, B, Song, Z. F, Zhang, Y, Zheng, Q. C, Hoyuela, C, Vega, L, Carvajal, F, Blay, L, Juvany, M, Camps, J, Veres, A, Besora, P, Trias, M, Feliu, X, Bellanova, G, Viel, G, Fabris, L, Valduga, P, Ciarleglio, F. A, Beltempo, P, Prezzi, C, Berlanda, G, Marcucci, S, Bondioli, P, Brolese, A, Agresta, F, Verza, L. A, Azabdaftari, A, Prando, D, Roveran, M. A, Rubinato, L, Vacca, U, Cesana, G, Ciccarese, F, Uccelli, M, Carrieri, D, Castello, G, Grava, G, Bonfanti, G, Legnani, G, Olmi, S, Chiaretti, M, Martinelli, A, Carru, G. A, Fegatelli, D. Alunni, Chiaretti, A. M, Consentino, P, Chiaretti, A. I, Procacciante, F, Blair, L, Huntington, C, Cox, T, Lincourt, A, Prasad, T, Matthews, B, Augenstein, V, Heniford, B. T, Verhagen, T, Loos, M. J. A, Scheltinga, M. R. M, Roumen, R. M. H, Magalhães, C, Pereira, S, Cardoso, G, Flores, A, Marcos, M, Lionetti, R, Cesaro, A, Napolitano, E, Caruso, L, Neola, B, Rutigliano, M, Pecic, V, Jovanovic, S, Filipovic, N, Trenkic, M, Pavlovic, A, Jovanovc, B, Tatic, M, Jovanovic, A, Khan, A, Tansawet, A, Lerdsirisopon, S, Techapongsatorn, S, Kasetsermwirija, W, Srimontayamas, S, Loapeamthong, C. U. S, Teawprasert, P, Bellomo, M. P, Bona, A, Borasi, A, Borreca, D, Filippa, C, Manfredi, S, De Paolis, P, Teng, A, Yu, J. W, Hu, Y, Sun, C. L, Zhou, J, Zha, X. G, Li, Y, Wu, J. Z, Abbonante, F, Kosai, N, Yussra, Y, Sutton, P. A, Shabbar, H. F, Razrim, R, Mustaffa, T, Tamil, A, Reynu, R, Abusalih, A, Shen, Y, Chen, J, Yang, S, Wang, M. G, Chen, F. Q, Fenger, A, Helvind, N. M, Pommergaard, H. C, Burcharth, J, Rosenberg, J., FERULANO, GIUSEPPE PAOLO, RABIN, MATTHEW, Sun, P, Hu, S B, Cheng, X, Li, M, Guo, B, Song, Z F, Zhang, Y, Zheng, Q C, Hoyuela, C, Vega, L, Carvajal, F, Blay, L, Juvany, M, Camps, J, Veres, A, Besora, P, Trias, M, Feliu, X, Bellanova, G, Viel, G, Fabris, L, Valduga, P, Ciarleglio, F A, Beltempo, P, Prezzi, C, Berlanda, G, Marcucci, S, Bondioli, P, Brolese, A, Agresta, F, Verza, L A, Azabdaftari, A, Prando, D, Roveran, M A, Rubinato, L, Vacca, U, Cesana, G, Ciccarese, F, Uccelli, M, Carrieri, D, Castello, G, Grava, G, Bonfanti, G, Legnani, G, Olmi, S, Chiaretti, M, Martinelli, A, Carru, G A, Fegatelli, D Alunni, Chiaretti, A M, Consentino, P, Chiaretti, A I, Procacciante, F, Blair, L, Huntington, C, Cox, T, Lincourt, A, Prasad, T, Matthews, B, Augenstein, V, Heniford, B T, Verhagen, T, Loos, M J A, Scheltinga, M R M, Roumen, R M H, Magalhães, C, Pereira, S, Cardoso, G, Flores, A, Marcos, M, Lionetti, R, Cesaro, A, Napolitano, E, Caruso, L, Neola, B, Rutigliano, M, Ferulano, G P, Pecic, V, Jovanovic, S, Filipovic, N, Trenkic, M, Pavlovic, A, Jovanovc, B, Tatic, M, Jovanovic, A, Khan, A, Tansawet, A, Lerdsirisopon, S, Techapongsatorn, S, Kasetsermwirija, W, Srimontayamas, S, Loapeamthong, C U S, Teawprasert, P, Bellomo, M P, Bona, A, Borasi, A, Borreca, D, Filippa, C, Manfredi, S, De Paolis, P, Teng, A, Yu, J W, Hu, Y, Sun, C L, Zhou, J, Zha, X G, Li, Y, Wu, J Z, Abbonante, F, Kosai, N, Yussra, Y, Sutton, P A, Shabbar, H F, Razrim, R, Mustaffa, T, Tamil, A, Reynu, R, Abusalih, A, Shen, Y, Chen, J, Yang, S, Wang, M G, Chen, F Q, Fenger, A, Helvind, N M, Pommergaard, H-C, Burcharth, J, Rosenberg, J, Hu, S. B, Song, Z. F, Zheng, Q. C, Ciarleglio, F. A, Verza, L. A, Roveran, M. A, Carru, G. A, Fegatelli, D. Alunni, Chiaretti, A. M, Chiaretti, A. I, Heniford, B. T, Loos, M. J. A, Scheltinga, M. R. M, Roumen, R. M. H, Ferulano, GIUSEPPE PAOLO, Loapeamthong, C. U. S, Bellomo, M. P, Yu, J. W, Sun, C. L, Zha, X. G, Wu, J. Z, Sutton, P. A, Shabbar, H. F, Wang, M. G, Chen, F. Q, Helvind, N. M, Pommergaard, H. C, Rosenberg, J., and Rabin, Matthew

Subjects
medicine.medical_specialty, Polypropylene suture, business.industry, Postoperative pain, Inguinal hernia, Chronic pain, Skin staples, medicine.disease, Lichtenstein technique, Lichtenstein inguinal hernioplasty, Surgery, Mesh fixation, medicine, Mean operative time, business, Abdominal surgery
Abstract

FIBRIN GLUE MESH FIXATION UNDER LOCAL ANAESTHESIA FOR THE TREATMENT OF INGUINAL HERNIA IN ELDERLY PATIENTS R LionettF, A Cesaro 1 , E NapolitanoI, L Caruso 1 , B Neola1, M Rutigliano1, 0 P Ferulano1 iDpt. Specialistic Surgeries and Nephrology Policlinic Federico II, Naples, ITALY Introduction: Inguinal hernia repair is one of the most common operations performed in general surgery, especially among elderly patients, due to age-related loss of muscle mass and increase of co-morbidities associated with high intra-abdominal pressure. The purpose of our trial was to assess the safeness and the impact on quality of life of tension free, sutureless hernia repair technique with the use of fibrin glue under local anesthesia in elderly patients. Methods: From January 2010 to December 2012,53 male patients aged 70 and above (mean age 73.9 years) were enrolled; complicated, recurrent, scrotal hernia and ASA IV patients were excluded. Furthermore diabetic patients with glycated hemoglobin level 7% or more were ruled out for presumable neuropathy. Informed consent and data from SF36 questionnaire were collected preoperatively. The Visual Analogue Scale (VAS) for postoperative pain and a new SF36 questionnaire for overall satisfaction at one year, were administered postoperatively. Chronic pain was classified according to Cunningham's criteria. Operative time, length of hospitalization, postoperative use of nonsteroidal anti-inflammatory drugs, complications and recurrences were also assessed. Results: All patients were operated under local anaesthesia (2% Mepivacaine Cloridrate and 7,5mg!ml Ropivacaine) with light sedation; in all cases partially absorbable mesh and plug (polypropylene! polyglecaprone 25) have been implanted and fixed with I ml of fibrin glue. 50 out of 53 patients completed the 2 years follow-up, one died for not related comorbidity. Mean operative time was 54.8 minutes; 46 patients were discharged at home the same day, 5 the following day, 2 patients had to stay one more day for postoperative complications (I haematoma, I urinary retention), no major complications were observed; at two years follow-up, 2 recurrences (4%) have been observed; mean VAS score for post-operative pain, assessed at 6, 12, 24 hours and 7 days after surgery, was 4 or less for 50 (94,3%) patients, only 3 (5,6%) patients referred a score> 4. At one year follow up only 2 (4%) patients suffered of chronic postoperative pain (I mild and I moderate), no severe chronic postoperative pain has been reported. Data from pre and postoperative SF36 questionnaires, analysed by using the Student's t test, showed significant increase of the score both in the Physical Component Summery (PCM) and in the Mental Component Summary (MCS) with a p-value < 0.0001. Conclusion: Inguinal hernia repair with use of fibrin glue and partially absorbable prosthesis under local anaesthesia is a safe technique in elderly patients

Published
2015

21. Solving the enigma: the digging adaptation of Mesoscalops montanensis (Mammalia, Proscalopidae) unveiled by Geometric Morphometrics and Finite Element Analysis

Author

PIRAS P., SANSALONE G., TERESI, Luciano, MOSCATO M., PROFICO A., ENG R., COX T. C., LOY A., COLANGELO P., KOTSAKIS, Anastassios, Piras, P., Sansalone, G., Teresi, Luciano, Moscato, M., Profico, A., Eng, R., Cox, T. C., Loy, A., Colangelo, P., and Kotsakis, Anastassios

Subjects
Proscalopidae, Talpidae, Chrysochloridae, functional morphology, comparative methods, biomechanical simulation
Abstract

The enigmatic Early Miocene fossorial mammal Mesoscalops montanensis shows one of the most modified humeri among terrestrial mammals. It has been suggested, on qualitative considerations, that this species has no extant homologues for humerus kinematics and that, functionally, the closest extant group is represented by Chrysochloridae. We combine here three dimensional geometric morphometrics, finite element analysis and phylogenetic comparative methods to explore the shape and mechanical stress states of Mesoscalops montanensis as well as of extant and extinct Talpidae and Chrysochloridae under realistic digging simulations. Evolutionary convergence analyses reveal that the shape of Mesoscalops montanensis represents a unique morphology in the context of fossorial mammals and that its functional performance, albeit superficially similar to that of extant Chrysochloridae, still represents a nonconvergent optimum for adaptation to digging.

Published
2015

25. Ensembl 2008

Author

Flicek, P., Aken, B., Beal, K., Ballester, Benoit, Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, S., Eyre, T., Fitzgerald, S., Fernandez-Banet, J., Gräf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Johnson, N., Jenkinson, A., Kähäri, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wood, M., Birney, E., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, J., Kasprzyk, A., Proctor, G., Smith, J., Ureta-Vidal, A., Searle, S., Graf, S., Kahari, A., Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Expert and Training Centre for Breast Cancer Screening, Radboud University Medical Center [Nijmegen], Techniques de l'Informatique et de la Microélectronique pour l'Architecture des systèmes intégrés (TIMA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS), Institut de physique du globe de Strasbourg (IPGS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Dep. of Energy, Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Techniques of Informatics and Microelectronics for integrated systems Architecture (TIMA), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)

Subjects
Internet, 0303 health sciences, 030302 biochemistry & molecular biology, Articles, Genomics, Mice, User-Computer Interface, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, Databases, Genetic, Computer Graphics, Genetics, Animals, Humans, Regulatory Elements, Transcriptional, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software, 030304 developmental biology
Abstract

International audience; The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Published
2007

27. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Author

Huang, J, Howie, B, Mccarthy, S, Memari, Y, Walter, K, Min, Jl, Danecek, P, Malerba, Giovanni, Trabetti, Elisabetta, Zheng, Hf, Gambaro, G, Richards, Jb, Durbin, R, Timpson, Nj, Marchini, J, Soranzo, N, Al Turki, S, Amuzu, A, Anderson, Ca, Anney, R, Antony, D, Artigas, Ms, Ayub, M, Bala, S, Barrett, Jc, Barroso, I, Beales, P, Benn, M, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, Pf, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Casas, Jp, Chambers, Jc, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, Da, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Day, In, Day Williams, A, Dedoussis, G, Down, T, Du, Y, van Duijn, Cm, Dunham, I, Edkins, S, Ekong, R, Ellis, P, Evans, Dm, Farooqi, Is, Fitzpatrick, Dr, Flicek, P, Floyd, J, Foley, Ar, Franklin, Cs, Futema, M, Gallagher, L, Gasparini, P, Gaunt, Tr, Geihs, M, Geschwind, D, Greenwood, C, Griffin, H, Grozeva, D, Guo, X, Gurling, H, Hart, D, Hendricks, Ae, Holmans, P, Huang, L, Hubbard, T, Humphries, Se, Hurles, Me, Hysi, P, Iotchkova, V, Isaacs, A, Jackson, Dk, Jamshidi, Y, Johnson, J, Joyce, C, Karczewski, Kj, Kaye, J, Keane, T, Kemp, Jp, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, Kleber, Me, van Kogelenberg, M, Kolb Kokocinski, A, Kooner, Js, Lachance, G, Langenberg, C, Langford, C, Lawson, D, Lee, I, van Leeuwen, Em, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lönnqvist, J, Lopes, Lr, Lopes, M, Luan, J, Macarthur, Dg, Mangino, M, Marenne, G, März, W, Maslen, J, Matchan, A, Mathieson, I, Mcguffin, P, Mcintosh, Am, Mckechanie, Ag, Mcquillin, A, Metrustry, S, Migone, N, Mitchison, Hm, Moayyeri, A, Morris, J, Morris, R, Muddyman, D, Muntoni, F, Nordestgaard, Bg, Northstone, K, O'Donovan, Mc, O'Rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, Mj, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, Jr, Paternoster, L, Paunio, T, Payne, F, Payne, Sj, Perry, Jr, Pietilainen, O, Plagnol, V, Pollitt, Rc, Povey, S, Quail, Ma, Quaye, L, Raymond, L, Rehnström, K, Ridout, Ck, Ring, S, Ritchie, Gr, Roberts, N, Robinson, Rl, Savage, Db, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, Rh, Scott, Ra, Semple, Rk, Serra, E, Sharp, Si, Shaw, A, Shihab, Ha, Shin, Sy, Skuse, D, Small, Ks, Smee, C, Smith, Gd, Southam, L, Spasic Boskovic, O, Spector, Td, St Clair, D, St Pourcain, B, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Tachmazidou, I, Taylor, R, Tian, J, Tobin, Md, Toniolo, D, Traglia, M, Tybjaerg Hansen, A, Valdes, Am, Vandersteen, Am, Varbo, A, Vijayarangakannan, P, Visscher, Pm, Wain, Lv, Walters, Jt, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whincup, P, Whyte, T, Williams, Hj, Williamson, Ka, Wilson, C, Wilson, Sg, Wong, K, Xu, C, Yang, J, Zaza, Gianluigi, Zeggini, E, Zhang, F, Zhang, P, Zhang, W., Clinicum, Department of Psychiatry, Jie, Huang, Bryan, Howie, Shane, Mccarthy, Yasin, Memari, Klaudia, Walter, Josine L., Min, Petr, Danecek, Giovanni, Malerba, Elisabetta, Trabetti, Hou Feng, Zheng, Saeed Al, Turki, Antoinette, Amuzu, Carl A., Anderson, Richard, Anney, Dinu, Antony, María Soler, Artiga, Muhammad, Ayub, Senduran, Bala, Jeffrey C., Barrett, Inês, Barroso, Phil, Beale, Marianne, Benn, Jamie, Bentham, Shoumo, Bhattacharya, Ewan, Birney, Douglas, Blackwood, Martin, Bobrow, Elena, Bochukova, Patrick F., Bolton, Rebecca, Bound, Chris, Boustred, Gerome, Breen, Mattia, Calissano, Keren, Car, Juan Pablo, Casa, John C., Chamber, Ruth, Charlton, Krishna, Chatterjee, Lu, Chen, Antonio, Ciampi, Sebahattin, Cirak, Peter, Clapham, Gail, Clement, Guy, Coate, Cocca, Massimiliano, David A., Collier, Catherine, Cosgrove, Tony, Cox, Nick, Craddock, Lucy, Crook, Sarah, Curran, David, Curti, Allan, Daly, Ian N. M., Day, Aaron Day, William, George, Dedoussi, Thomas, Down, Yuanping, Du, Cornelia M., van Duijn, Ian, Dunham, Sarah, Edkin, Rosemary, Ekong, Peter, Elli, David M., Evan, I., Sadaf Farooqi, David R., Fitzpatrick, Paul, Flicek, James, Floyd, A., Reghan Foley, Christopher S., Franklin, Marta, Futema, Louise, Gallagher, Gasparini, Paolo, Tom R., Gaunt, Matthias, Geih, Daniel, Geschwind, Celia, Greenwood, Heather, Griffin, Detelina, Grozeva, Xiaosen, Guo, Xueqin, Guo, Hugh, Gurling, Deborah, Hart, Audrey E., Hendrick, Peter, Holman, Liren, Huang, Tim, Hubbard, Steve E., Humphrie, Matthew E., Hurle, Pirro, Hysi, Valentina, Iotchkova, Aaron, Isaac, David K., Jackson, Yalda, Jamshidi, Jon, Johnson, Chris, Joyce, Konrad J., Karczewski, Jane, Kaye, Thomas, Keane, John P., Kemp, Karen, Kennedy, Alastair, Kent, Julia, Keogh, Farrah, Khawaja, Marcus E., Kleber, Margriet van, Kogelenberg, Anja Kolb, Kokocinski, Jaspal S., Kooner, Genevieve, Lachance, Claudia, Langenberg, Cordelia, Langford, Daniel, Lawson, Irene, Lee, Elisabeth M., van Leeuwen, Monkol, Lek, Rui, Li, Yingrui, Li, Jieqin, Liang, Hong, Lin, Ryan, Liu, Jouko, Lönnqvist, Luis R., Lope, Margarida, Lope, Jian'An, Luan, Daniel G., Macarthur, Massimo, Mangino, Gaëlle, Marenne, Winfried, März, John, Maslen, Angela, Matchan, Iain, Mathieson, Peter, Mcguffin, Andrew M., Mcintosh, Andrew G., Mckechanie, Andrew, Mcquillin, Sarah, Metrustry, Nicola, Migone, Hannah M., Mitchison, Alireza, Moayyeri, James, Morri, Richard, Morri, Dawn, Muddyman, Francesco, Muntoni, Børge G., Nordestgaard, Kate, Northstone, Michael C., O'Donovan, Stephen, O'Rahilly, Alexandros, Onoufriadi, Karim, Oualkacha, Michael J., Owen, Aarno, Palotie, Kalliope, Panoutsopoulou, Victoria, Parker, Jeremy R., Parr, Lavinia, Paternoster, Tiina, Paunio, Felicity, Payne, Stewart J., Payne, John R. B., Perry, Olli, Pietilainen, Vincent, Plagnol, Rebecca C., Pollitt, Sue, Povey, Michael A., Quail, Lydia, Quaye, Lucy, Raymond, Karola, Rehnström, Cheryl K., Ridout, Susan, Ring, Graham R. S., Ritchie, Nicola, Robert, Rachel L., Robinson, David B., Savage, Peter, Scambler, Stephan, Schiffel, Miriam, Schmidt, Nadia, Schoenmaker, Richard H., Scott, Robert A., Scott, Robert K., Semple, Eva, Serra, Sally I., Sharp, Adam, Shaw, Hashem A., Shihab, So Youn, Shin, David, Skuse, Kerrin S., Small, Carol, Smee, George Davey, Smith, Lorraine, Southam, Olivera Spasic, Boskovic, Timothy D., Spector, David St, Clair, Beate St, Pourcain, Jim, Stalker, Elizabeth, Steven, Jianping, Sun, Gabriela, Surdulescu, Jaana, Suvisaari, Petros, Syrri, Ioanna, Tachmazidou, Rohan, Taylor, Jing, Tian, Martin D., Tobin, Daniela, Toniolo, Michela, Traglia, Anne Tybjaerg, Hansen, Ana M., Valde, Anthony M., Vandersteen, Anette, Varbo, Parthiban, Vijayarangakannan, Peter M., Visscher, Louise V., Wain, James T. R., Walter, Guangbiao, Wang, Jun, Wang, Yu, Wang, Kirsten, Ward, Eleanor, Wheeler, Peter, Whincup, Tamieka, Whyte, Hywel J., William, Kathleen A., Williamson, Crispian, Wilson, Scott G., Wilson, Kim, Wong, Changjiang, Xu, Jian, Yang, Gianluigi, Zaza, Eleftheria, Zeggini, Feng, Zhang, Pingbo, Zhang, Weihua, Zhang, Giovanni, Gambaro, J., Brent Richard, Richard, Durbin, Nicholas J., Timpson, Jonathan, Marchini, and Nicole, Soranzo

Subjects
Computer science, General Physics and Astronomy, Genome-wide association study, 0302 clinical medicine, Gene Frequency, Haplotype, Genetics,Biological sciences, Settore MED/14 - NEFROLOGIA, Aged, 80 and over, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, TWINSUK, Middle Aged, single-nucleotide polymorphism, Whole-genome sequencing, WGS imputation panel, single-nucleotide polymorphism, Biological sciences, Italy, MAP, Adult, Adolescent, Genotype, WGS imputation panel, Population, Single-nucleotide polymorphism, FORMAT, Computational biology, GENOTYPE IMPUTATION, Polymorphism, Single Nucleotide, Article, White People, General Biochemistry, Genetics and Molecular Biology, Young Adult, 03 medical and health sciences, Humans, GENOME-WIDE ASSOCIATION, 1000 Genomes Project, education, Allele frequency, Alleles, Aged, 030304 developmental biology, Whole-genome sequencing, Models, Statistical, Models, Genetic, Genome, Human, Genetic Variation, General Chemistry, United Kingdom, Minor allele frequency, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], Haplotypes, 3111 Biomedicine, 030217 neurology & neurosurgery, Imputation (genetics)
Abstract

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants., Imputation uses genotype information from SNP arrays to infer the genotypes of missing markers. Here, the authors show that an imputation reference panel derived from whole-genome sequencing of 3,781 samples from the UK10K project improves the imputation accuracy and coverage of low frequency variants compared to existing methods.

Published
2015

28. Mi-1-mediated nematode resistance in tomatoes is broken by short-term heat stress but recovers over time

Author

CARVALHO, L. M. de, BENDA, N. D., VAUGHAN, M. M., CABRERA, A. R., HUNG, K., COX, T., ABDO, Z., ALLEN, L. H., TEAL, P. E. A., and LUCIANA MARQUES DE CARVALHO, CPATC.

Subjects
Meloidogyne, Nematoda, Tomato (solanum lycopersicum L)
Abstract

Tomato (Solanum lycopersicum L.) is among the most valuable agricultural products, but Meloidogyne spp. (root-knot nematode) infestations result in serious crop losses. In tomato, resistance to root-knot nematodes is controlled by the gene Mi-1, but heat stress interferes with Mi-1-associated resistance. Inconsistent results in published field and greenhouse experiments led us to test the effect of short-term midday heat stress on tomato susceptibility to Meloidogyne incognita race 1. Under controlled day/night temperatures of 258C/218C, ?Amelia?, which was verified as possessing the Mi-1 gene, was deemed resistant (4.1 ± 0.4 galls/plant) and Rutgers, which does not possess the Mi-1 gene, was susceptible (132 ± 9.9 galls/plant) to M. incognita infection. Exposure to a single 3 hr heat spike of 358C was sufficient to increase the susceptibility of ?Amelia? but did not affect Rutgers. Despite this change in resistance, Mi-1 gene expression was not affected by heat treatment, or nematode infection. The heat-induced breakdown of Mi-1 resistance in ?Amelia? did recover with time regardless of additional heat exposures and M. incognita infection. These findings would aid in the development of management strategies to protect the tomato crop at times of heightened M. incognita susceptibility.'

Published
2015

29. Stable or improved neurological manifestations during miglustat therapy in patients from the international disease registry for Niemann-Pick disease type C: An observational cohort study

Author

Patterson, M. C, Mengel, E, Vanier, M. T, Schwierin, B, Muller, A, Cornelisse, P, Pineda, M, Amado-Fondo, A, Amraoui, Y, Andria, G, Arellano, M, Audoin, B, Azcona, C, Barr, C, Baruteau, J, Baumgartner, C, Bell, L, Bembi, B, Benneddif, K, Bernard, G, Bobocea, N, Bodzioch, M, Boettcher, T, Bonnan, M, Broue, P, Bruni, A, Caceres, M, Camino, R, Campbell, E, Cances, C, Cannell, P, Cesar, J, Chabrol, B, Chakrapani, A, Colao, R, Collet, A, Corsetti, T, Cousins, A, Covanis, A, Cox, T, Cuisset, J. M, Dardis, A, Das, A, Deegan, P, Dengler, T, Deodato, F, Derralynn, H, Di Donato, I, Di Rocco, M, Dinopoulos, A, Pakiela, D, Eckehard, S, Engelen, M, Eyer, D, Fecarotta, S, Federico, A, Filla, A, Fiumara, A, Fonseca, M. J, Gabrielli, O, Garcia, T, Garrote, J, Gissen, P, Giugliani, L, Greenberg, C, Heron, B, Hertzberg, C, Higgins, F, Hill, A, Hiwot, T, Hlavata, A, Hörbe-Blindt, A, Howley, E, Hussain, N, Illsinger, S, Imrie, J, Jacklin, E, Jones, S, Jovanovic, A, Kaczmarek, V, Kaphan, E, Kibaek, M, Kleinhans, P, Klünemann, Kh, Koch, S. M, Koegl-Wallner, W, Kolnikova, M, Korenke, G. C, Korinthenberg, R, Kumari, S, Lachmann, R, Lee Ann, L, Likopoulou, L, Lilienthal, E, Link, B, Lippold, M, Lopez-Laso, E, Luecke, T, Lundgren, J, Mackrell, M, Madruga, M, Maletta, R, Malinova, V, Manners, J, Marinei, R, Marquardt, T, Martins, E, Martins, A. M, Martins, N, Mcalister, L, Mccabe, A, Mckie, M, Mcmahon, S, Meehan, M, Meldgaard Lund, A, Mendozah, C, Meyer, A, Mielke, S, Milligan, A, Mir, P, Moisa, M, Mombelli, C, Morris, L, Müller Vom Hagen, J, Munoz, B, Murphy, E, Nagarajan, L, Neto, P. B, Nevsimalova, S, Nia, S, Nicolai, J, Niemann, D, Niktari, G, O'Callaghan, M. D. M, Paucar-Arce, M, Peers, K, Peintinger, L, Peralta, M, Pérez, J, Perez-Poyato, M, Petrariu, A, Puschmann, A, Raiman, J, Rask, O, Rataj, J, Raymond-Gaynor, C, Reichelt, G, Ribeiro, E, Riches, V, Roberts, A, Roelants, J, Rohrbach, M, Rokicki, D, Rolfs, A, Russo, C, Rutsch, F, Saleem, R, Santos, M, Schmutz, P, Schwahn, B, Sedel, F, Semotok, J, Sharma, R, Silska, S, Silva, A, Simmons, L, Sivera, R, Skorpen, J, Sole, G, Souza, C, Stadlober-Degwerth, M, Starling, J, Temudo, T, Tomas, M, Tranchant, C, Uziel, G, Valayannopoulous, V, Van Den Hout, H, Van Der Tol, L, Van Spronsen, F, Vellodi, A, Verdu, A, Vilchez, J. J, Vinaixa, A, Visser, G, Voelker, J, Waldek, S, Walter, A, Walterfang, M, Wein, U, Widner, H, Wilcke, C, Wildish, L, Wraith, E, Wright, N, Xaidara, A, Yamamoto, M, Zallocco, F, Zielke, S, Patterson, Mc, Mengel, E, Vanier, Mt, Schwierin, B, Muller, A, Cornelisse, P, Pineda, M, Registry investigators, Npc, Filla, Alessandro, Russo, CINZIA VALERIA, Neurology, Paediatric Neurology, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, ANS - Amsterdam Neuroscience, and Graduate School

Subjects
Male, Pediatrics, Neurology, Cohort Studies, 0302 clinical medicine, Miglustat, Medicine, Enzyme Inhibitor, Genetics(clinical), Pharmacology (medical), Prospective Studies, Young adult, Enzyme Inhibitors, Prospective cohort study, Child, Genetics (clinical), Medicine(all), 0303 health sciences, Medicine (all), Niemann-Pick disease type C, Niemann-Pick Disease, Type C, General Medicine, 3. Good health, Treatment Outcome, Child, Preschool, Cohort, Disease Progression, Female, medicine.drug, Cohort study, Human, Adult, medicine.medical_specialty, Registry, 1-Deoxynojirimycin, Adolescent, 03 medical and health sciences, Young Adult, Disease registry, Swallowing, Humans, 030304 developmental biology, business.industry, Research, Prospective Studie, Cohort Studie, business, 030217 neurology & neurosurgery
Abstract

BACKGROUND: Niemann-Pick disease type C (NP-C) is a rare neurovisceral disease characterised by progressive neurological degeneration, where the rate of neurological disease progression varies depending on age at neurological onset. We report longitudinal data on functional disease progression and safety observations in patients in the international NPC Registry who received continuous treatment with miglustat. METHODS: The NPC Registry is a prospective observational cohort of NP-C patients. Enrolled patients who received ≥1 year of continuous miglustat therapy (for ≥90 % of the observation period, with no single treatment interruption >28 days) were included in this analysis. Disability was measured using a scale rating the four domains, ambulation, manipulation, language and swallowing from 0 (normal) to 1 (worst). Neurological disease progression was analysed in all patients based on: 1) annual progression rates between enrolment and last follow up, and; 2) categorical analysis with patients categorised as 'improved/stable' if ≥3/4 domain scores were lower/unchanged, and as 'progressed' if

Published
2015

31. Secondary non-Hodgkin lymphoma of the ethmoid sinus after temozolomide

Author

Broes, K., Van Ginderachter, L., Joosens, E., Maes, A., Theunissen, K., Schepers, S., Deben, K., Claes, Jozef, Mebis, J., and Cox, T.

Subjects
hemic and lymphatic diseases, otorhinolaryngologic diseases, Human medicine
Abstract

The paranasal sinuses are rarely the site of malignancy, especially non-Hodgkin lymphoma. In such cases, the ethmoid sinus is the second most frequently involved paranasal sinus. Diagnosis of these malignancies is difficult because the early symptoms often mimic benign sinus pathology. Thus, most cases are diagnosed at an advanced stage, and their prognosis is poor. Here we describe the case of a 58-year-old man with a secondary high-grade B-cell non-Hodgkin lymphoma of the ethmoid sinus. This malignancy was diagnosed two years after the patient had received treatment with temozolomide for a glioblastoma multiforme. This case highlights that malignant tumours of the paranasal sinuses should always be included in the differential diagnosis of sinus disease. Additionally, patients treated with temozolomide should receive regular follow-up care including vigilant evaluation for secondary tumours, such as non-Hodgkin lymphoma.

Published
2015

34. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Author

Delaneau O., Marchini J., McVeanh G.A., Donnelly P., Lunter G., Marchini J.L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson I., Rimmer, A., Xifara, D.K., Kerasidou, A., Churchhouse, C., Altshuler, D.M., Gabriel, S.B., Lander, E.S., Gupta, N., Daly, M.J., DePristo, M.A., Banks, E., Bhatia G., Carneiro, M.O., Del Angel G., Genovese G., Handsaker, R.E., Hartl, C., McCarroll, S.A., Nemesh J.C., Poplin, R.E., Schaffner, S.F., Shakir, K., Sabeti P.C., Grossman, S.R., Tabrizi, S., Tariyal, R., Li H., Reich, D., Durbin, R.M., Hurles, M.E., Balasubramaniam, S., Burton J., Danecek P., Keane, T.M., Kolb-Kokocinski, A., McCarthy, S., Stalker J., Quail, M., Ayub Q., Chen, Y., Coffey, A.J., Colonna V., Huang, N., Jostins L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S.J., Ning, Z., Frankish, A., Harrow J., Chris, T.-S., Abecasis G.R., Kang H.M., Anderson P., Blackwell, T., Busonero F., Fuchsberger, C., Jun G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M.K., Bentley, D.R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R.K., Cox, T., Eberle, M., Murray L., Shaw, R., Chakravarti, A., Clark, A.G., Keinan, A., Rodriguez-Flores J.L., De LaVega F.M., Degenhardt J., Eichler, E.E., Flicek P., Clarke L., Leinonen, R., Smith, R.E., Zheng-Bradley X., Beal, K., Cunningham F., Herrero J., McLaren W.M., Ritchie G.R.S., Barker J., Kelman G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter I., Toneva I., Gibbs, R.A., Dinh H., Kovar, C., Lee, S., Lewis L., Muzny, D., Reid J., Wang, M., Yu F., Bainbridge, M., Challis, D., Evani, U.S., Lu J., Nagaswamy, U., Sabo, A., Wang, Y., Yu J., Fowler G., Hale W., Kalra, D., Green, E.D., Knoppers, B.M., Korbel J.O., Rausch, T., Sttz, A.M., Lee, C., Griffin L., Hsieh, C.-H., Mills, R.E., Von Grotthuss, M., Zhang, C., Shi X., Lehrach H., Sudbrak, R., Amstislavskiy V.S., Lienhard, M., Mertes F., Sultan, M., Timmermann, B., Yaspo, M.L., Herwig, S.R., Mardis, E.R., Wilson, R.K., Fulton L., Fulton, R., Weinstock G.M., Chinwalla, A., Ding L., Dooling, D., Koboldt, D.C., McLellan, M.D., Wallis J.W., Wendl, M.C., Zhang Q., Marth G.T., Garrison, E.P., Kural, D., Lee W.-P., Leong W.F., Ward, A.N., Wu J., Zhang, M., Nickerson, D.A., Alkan, C., Hormozdiari F., Ko, A., Sudmant P.H., Schmidt J.P., Davies, C.J., Gollub J., Webster, T., Wong, B., Zhan, Y., Sherry, S.T., Xiao, C., Church, D., Ananiev V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner J., Hefferon, T., Kimelman, M., Liu, C., Lopez J., Meric P., Ostapchuk, Y., Phan L., Ponomarov, S., Schneider V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang H., Wang J., Fang X., Guo X., Jian, M., Jiang H., Jin X., Li G., Li J., Li, Y., Liu X., Lu, Y., Ma X., Tai, S., Tang, M., Wang, B., Wang G., Wu H., Wu, R., Yin, Y., Zhang W., Zhao J., Zhao, M., Zheng X., Lachlan H., Fang L., Li Q., Li, Z., Lin H., Liu, B., Luo, R., Shao H., Xie, Y., Ye, C., Yu, C., Zheng H., Zhu H., Cai H., Cao H., Su, Y., Tian, Z., Yang H., Yang L., Zhu J., Cai, Z., Albrecht, M.W., Borodina, T.A., Auton, A., Yoon, S.C., Lihm J., Makarov V., Jin H., Kim W., Kim, K.C., Gottipati, S., Jones, D., Cooper, D.N., Ball, E.V., Stenson P.D., Barnes, B., Kahn, S., Ye, K., Batzer, M.A., Konkel, M.K., Walker J.A., MacArthur, D.G., Lek, M., Shriver, M.D., Bustamante, C.D., Gravel, S., Kenny, E.E., Kidd J.M., Lacroute P., Maples, B.K., Moreno-Estrada, A., Zakharia F., Henn, B., Sandoval, K., Byrnes J.K., Halperin, E., Baran, Y., Craig, D.W., Christoforides, A., Izatt, T., Kurdoglu, A.A., Sinari, S.A., Homer, N., Squire, K., Sebat J., Bafna V., Burchard, E.G., Hernandez, R.D., Gignoux, C.R., Haussler, D., Katzman, S.J., Kent W.J., Howie, B., Ruiz-Linares, A., Dermitzakis, E.T., Lappalainen, T., Devine, S.E., Maroo, A., Tallon L.J., Rosenfeld J.A., Michelson L.P., Angius, A., Cucca F., Sanna, S., Bigham, A., Jones, C., Reinier F., Lyons, R., Schlessinger, D., Awadalla P., Hodgkinson, A., Oleksyk, T.K., Martinez-Cruzado J.C., Fu, Y., Xiong, M., Jorde L., Witherspoon, D., Xing J., Browning, B.L., Hajirasouliha I., Chen, K., Albers, C.A., Gerstein, M.B., Abyzov, A., Chen J., Habegger L., Harmanci, A.O., Mu X.J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson J.J., OSullivan, C., Barnes, K.C., Gharani, N., Toji L.H., Gerry, N., Kaye J.S., Kent, A., Mathias, R., Ossorio P.N., Parker, M., Rotimi, C.N., Royal, C.D., Tishkoff, S., Via, M., Bodmer W., Bedoya G., Yang G., You, C.J., Garcia-Montero, A., Orfao, A., Dutil J., Brooks L.D., Felsenfeld, A.L., McEwen J.E., Clemm, N.C., Guyer, M.S., Peterson J.L., Duncanson, A., Dunn, M., Peltonen L., and 1000 Genomes Project Consortium

Subjects
haplotype, genetic association, genotype, General Physics and Astronomy, Genome-wide association study, genetic analysis, gene sequence, Biology, gene frequency, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, polymorphism, Gene Frequency, single nucleotide polymorphism, Humans, chromosome, human, 1000 Genomes Project, indel mutation, genome, Alleles, Genetic association, Genetics, Whole genome sequencing, Multidisciplinary, accuracy, Genome, Human, Haplotype, allele, article, reference database, General Chemistry, Microarray Analysis, chromosome 20, Haplotypes, Human genome, microarray analysis, Imputation (genetics), Algorithms, SNP array, Genome-Wide Association Study
Abstract

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved.

Published
2014

38. The spectrum of hemojuvelin gene mutations in 1q-linked Juvenile Hemochromatosis

Author

LANZARA C, ROETTO A, DARAIO F, PIVARD S, FICARELLA R, SIMARD H, COX T, CAZZOLA M, PIPERNO A. GIMENEZ ROQUEPLO AP, GRAMMATICO, VOLINIA S, GASPARINI P, CAMASCHELLA, CLARA, Lanzara, C, Roetto, A, Daraio, F, Pivard, S, Ficarella, R, Simard, H, Cox, T, Cazzola, M, PIPERNO A., GIMENEZ ROQUEPLO AP, Grammatico, Volinia, S, Gasparini, P, and Camaschella, Clara

Abstract

Juvenile or type 2 hemochromatosis (JH) is transmitted as a recessive trait that leads to severe iron overload and organ damage typically before age 30 years. Linkage to a locus on chromosome 1q has been found in most patients with JH. The recently identified causal gene encodes hemojuvelin, a protein with a proposed crucial role in iron metabolism. A second, rare type of JH, with clinical expression identical to the 1q-linked form, is due to inactivation of hepcidin, the key regulator of iron homeostasis. Here we report the spectrum of mutations of the hemojuvelin gene (HJV) in 34 patients who did not show hepcidin mutations. This represents the largest cohort of patients with JH collected worldwide. We identified 17 different (16 novel) mutations of HJV, both at the homozygous and at the compound heterozygous state. Mutations either generate premature termination codons or were missense substitutions, affecting highly conserved residues, relevant to the protein structure and/or function.

Published
2004

39. The spectrum of hemojuvelin gene mutations in 1q-linked juvenile hemochromatosis

Author

LANZARA C, ROETTO A, DARAIO F, RIVARD S, FICARELLA R, SIMARD H, COX T, CAZZOLA M, PIPERNO A, GIMENEZROQUEPLO AP, GRAMMATICO P, VOLINIA S, CAMASCHELLA C., GASPARINI, PAOLO, Lanzara, C, Roetto, A, Daraio, F, Rivard, S, Ficarella, R, Simard, H, Cox, T, Cazzola, M, Piperno, A, Gimenezroqueplo, Ap, Grammatico, P, Volinia, S, Gasparini, Paolo, and Camaschella, C.

Published
2004

40. Tropospheric Aerosol: Formation, Trasformation, Fate and Impacts. General Discussion

Author

Wahner, A., Pandis, S., Allan, J., Mc Figgans, G., Abbatt, J., Freedman, M., Johnston, M., Harrison, R., Donahue, N., Percival, C., Heard, D., Carslaw, K., Jacobson, M., Olenius, T., Vehkamaki, H., Nizkorodov, S., Kiendler Scharr, A., Cappelletti, David Michele, Herrmann, H., Cox, T., Mcneill, V. F., Lewis, A., Colomer Ortega, I. K., Krieger, U., Colussi, A., Aumont, B., Kroll, J., Volkamer, R., Noziere, B., Abbat, J., Rudich, Y., Knopf, D., Held, A., and Villenave, E.

Published
2013

41. General discussion. Tropospheric aerosol - formation, transformation, fate and impacts

Author

Wahner, A., Pandis, S., Allan, J., Mcfiggans, G., Abbatt, J., Freedman, M., Johnston, M., Harrison, R., Donahue, N., Percival, C., Heard, D., Carslaw, K., Jacobson, M., Olenius, T., Vehkamaki, H., Nizkorodov, S., Kiendler Scharr, A., Cappelletti, David Michele, Herrmann, H., Cox, T., Mcneill, Vf, Lewis, A., Colomer Ortega, Ik, Krieger, U., Colussi, A., Aumont, A., Kroll, J., Volkamer, R., Noziere, B., Rudich, Y., Knopf, D., Held, A, and Villenave, E.

Published
2013

42. Ensembl 2004

Author

Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, X. M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M., and Hubbard, T.

Subjects
Internet, ComputingMethodologies_PATTERNRECOGNITION, Genome, Databases, Genetic, Genetics, Animals, Computational Biology, Humans, Information Storage and Retrieval, Articles, Genomics, Software
Abstract

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Published
2004

43. Natural history of hemochromatosis

Author

De Gobbi M, Roetto A, Piperno A, Mariani R, Alberti F, Papanikolaou G, Politou M, Lockitch G, Girelli D, Fargion S, Cox T. M, Gasparini P, Cazzola M, CAMASCHELLA , CLARA, De Gobbi, M, Roetto, A, Piperno, A, Mariani, R, Alberti, F, Papanikolaou, G, Politou, M, Lockitch, G, Girelli, D, Fargion, S, Cox T., M, Gasparini, P, Cazzola, M, and Camaschella, Clara

Published
2002

45. An integrated map of genetic variation from 1,092 human genomes

Author

Altshuler, DM, Durbin, RM, Abecasis, GR, Bentley, DR, Chakravarti, A, Clark, AG, Donnelly, P, Eichler, EE, Flicek, P, Gabriel, SB, Gibbs, RA, Green, ED, Hurles, ME, Knoppers, BM, Korbel, JO, Lander, ES, Lee, C, Lehrach, H, Mardis, ER, Marth, GT, McVean, GA, Nickerson, DA, Schmidt, JP, Sherry, ST, Wang, J, Wilson, RK, Dinh, H, Kovar, C, Lee, S, Lewis, L, Muzny, D, Reid, J, Wang, M, Fang, X, Guo, X, Jian, M, Jiang, H, Jin, X, Li, G, Li, J, Li, Y, Li, Z, Liu, X, Lu, Y, Ma, X, Su, Z, Tai, S, Tang, M, Wang, B, Wang, G, Wu, H, Wu, R, Yin, Y, Zhang, W, Zhao, J, Zhao, M, Zheng, X, Zhou, Y, Gupta, N, Clarke, L, Leinonen, R, Smith, RE, Zheng-Bradley, X, Grocock, R, Humphray, S, James, T, Kingsbury, Z, Sudbrak, R, Albrecht, MW, Amstislavskiy, VS, Borodina, TA, Lienhard, M, Mertes, F, Sultan, M, Timmermann, B, Yaspo, M-L, Fulton, L, Fulton, R, Weinstock, GM, Balasubramaniam, S, Burton, J, Danecek, P, Keane, TM, Kolb-Kokocinski, A, McCarthy, S, Stalker, J, Quail, M, Davies, CJ, Gollub, J, Webster, T, Wong, B, Zhan, Y, Auton, A, Yu, F, Bainbridge, M, Challis, D, Evani, US, Lu, J, Nagaswamy, U, Sabo, A, Wang, Y, Yu, J, Coin, LJM, Fang, L, Li, Q, Lin, H, Liu, B, Luo, R, Qin, N, Shao, H, Xie, Y, Ye, C, Yu, C, Zhang, F, Zheng, H, Zhu, H, Garrison, EP, Kural, D, Lee, W-P, Leong, WF, Ward, AN, Wu, J, Zhang, M, Griffin, L, Hsieh, C-H, Mills, RE, Shi, X, Von Grotthuss, M, Zhang, C, Daly, MJ, DePristo, MA, Banks, E, Bhatia, G, Carneiro, MO, Del Angel, G, Genovese, G, Handsaker, RE, Hartl, C, McCarroll, SA, Nemesh, JC, Poplin, RE, Schaffner, SF, Shakir, K, Yoon, SC, Lihm, J, Makarov, V, Jin, H, Kim, W, Kim, KC, Rausch, T, Beal, K, Cunningham, F, Herrero, J, McLaren, WM, Ritchie, GRS, Gottipati, S, Keinan, A, Rodriguez-Flores, JL, Sabeti, PC, Grossman, SR, Tabrizi, S, Tariyal, R, Cooper, DN, Ball, EV, Stenson, PD, Barnes, B, Bauer, M, Cheetham, RK, Cox, T, Eberle, M, Kahn, S, Murray, L, Peden, J, Shaw, R, Ye, K, Batzer, MA, Konkel, MK, Walker, JA, MacArthur, DG, Lek, M, Herwig, R, Shriver, MD, Bustamante, CD, Byrnes, JK, De la Vega, FM, Gravel, S, Kenny, EE, Kidd, JM, Lacroute, P, Maples, BK, Moreno-Estrada, A, Zakharia, F, Halperin, E, Baran, Y, Craig, DW, Christoforides, A, Homer, N, Izatt, T, Kurdoglu, AA, Sinari, SA, Squire, K, Xiao, C, Sebat, J, Bafna, V, Burchard, EG, Hernandez, RD, Gignoux, CR, Haussler, D, Katzman, SJ, Kent, WJ, Howie, B, Ruiz-Linares, A, Dermitzakis, ET, Lappalainen, T, Devine, SE, Maroo, A, Tallon, LJ, Rosenfeld, JA, Michelson, LP, Kang, HM, Anderson, P, Angius, A, Bigham, A, Blackwell, T, Busonero, F, Cucca, F, Fuchsberger, C, Jones, C, Jun, G, Lyons, R, Maschio, A, Porcu, E, Reinier, F, Sanna, S, Schlessinger, D, Sidore, C, Tan, A, Trost, MK, Awadalla, P, Hodgkinson, A, Lunter, G, Marchini, JL, Myers, S, Churchhouse, C, Delaneau, O, Gupta-Hinch, A, Iqbal, Z, Mathieson, I, Rimmer, A, Xifara, DK, Oleksyk, TK, Fu, Y, Xiong, M, Jorde, L, Witherspoon, D, Xing, J, Browning, BL, Alkan, C, Hajirasouliha, I, Hormozdiari, F, Ko, A, Sudmant, PH, Chen, K, Chinwalla, A, Ding, L, Dooling, D, Koboldt, DC, McLellan, MD, Wallis, JW, Wendl, MC, Zhang, Q, Tyler-Smith, C, Albers, CA, Ayub, Q, Chen, Y, Coffey, AJ, Colonna, V, Huang, N, Jostins, L, Li, H, Scally, A, Walter, K, Xue, Y, Zhang, Y, Gerstein, MB, Abyzov, A, Balasubramanian, S, Chen, J, Clarke, D, Habegger, L, Harmanci, AO, Jin, M, Khurana, E, Mu, XJ, Sisu, C, Degenhardt, J, Stuetz, AM, Church, D, Michaelson, JJ, Ben, B, Lindsay, SJ, Ning, Z, Frankish, A, Harrow, J, Fowler, G, Hale, W, Kalra, D, Barker, J, Kelman, G, Kulesha, E, Radhakrishnan, R, Roa, A, Smirnov, D, Streeter, I, Toneva, I, Vaughan, B, Ananiev, V, Belaia, Z, Beloslyudtsev, D, Bouk, N, Chen, C, Cohen, R, Cook, C, Garner, J, Hefferon, T, Kimelman, M, Liu, C, Lopez, J, Meric, P, O'Sullivan, C, Ostapchuk, Y, Phan, L, Ponomarov, S, Schneider, V, Shekhtman, E, Sirotkin, K, Slotta, D, Zhang, H, Barnes, KC, Beiswanger, C, Cai, H, Cao, H, Gharani, N, Henn, B, Jones, D, Kaye, JS, Kent, A, Kerasidou, A, Mathias, R, Ossorio, PN, Parker, M, Reich, D, Rotimi, CN, Royal, CD, Sandoval, K, Su, Y, Tian, Z, Tishkoff, S, Toji, LH, Via, M, Yang, H, Yang, L, Zhu, J, Bodmer, W, Bedoya, G, Ming, CZ, Yang, G, You, CJ, Peltonen, L, Garcia-Montero, A, Orfao, A, Dutil, J, Martinez-Cruzado, JC, Brooks, LD, Felsenfeld, AL, McEwen, JE, Clemm, NC, Duncanson, A, Dunn, M, Guyer, MS, Peterson, JL, 1000 Genomes Project Consortium, Dermitzakis, Emmanouil, Universitat de Barcelona, Massachusetts Institute of Technology. Department of Biology, Altshuler, David, and Lander, Eric S.

Subjects
Natural selection, LOCI, Genome-wide association study, Evolutionary biology, Continental Population Groups/genetics, Human genetic variation, VARIANTS, Genoma humà, Binding Sites/genetics, 0302 clinical medicine, RARE, Sequence Deletion/genetics, WIDE ASSOCIATION, ddc:576.5, Copy-number variation, MUTATION, Exome sequencing, transcription factor, Conserved Sequence, Human evolution, Sequence Deletion, Genetics, RISK, 0303 health sciences, Multidisciplinary, Continental Population Groups, 1000 Genomes Project Consortium, Genetic analysis, Genomics, Polymorphism, Single Nucleotide/genetics, Research Highlight, 3. Good health, Algorithm, Multidisciplinary Sciences, Genetic Variation/genetics, Map, Science & Technology - Other Topics, Conserved Sequence/genetics, Integrated approach, General Science & Technology, Genetics, Medical, Haplotypes/genetics, Biology, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, Genetic variation, Humans, Transcription Factors/metabolism, POPULATION-STRUCTURE, 1000 Genomes Project, Polymorphism, Nucleotide Motifs, Alleles, 030304 developmental biology, COPY NUMBER VARIATION, Science & Technology, Binding Sites, Human genome, Genome, Human, Racial Groups, Genetic Variation, Genetics, Population, Haplotypes, Genome, Human/genetics, untranslated RNA, 030217 neurology & neurosurgery, Transcription Factors, Genome-Wide Association Study
Abstract

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations., National Institutes of Health (U.S.) (Grant RC2HL102925), National Institutes of Health (U.S.) (Grant U54HG3067)

Published
2012

47. The Role of Dwarf Galaxy Interactions in Shaping the Magellanic System and Implications for Magellanic Irregulars

Author

Besla, Gurtina, Kallivayalil, Nitya, Hernquist, Lars, van der Marel, Roeland P., Cox, T. J., and Keres, Dusan

Subjects
Astrophysics of Galaxies (astro-ph.GA), FOS: Physical sciences, Astrophysics::Solar and Stellar Astrophysics, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics::Galaxy Astrophysics
Abstract

We present a novel pair of numerical models of the interaction history between the Large and Small Magellanic Clouds (LMC and SMC, respectively) and our Milky Way (MW) in light of recent high precision proper motions (Kallivayalil et al. 2006a,b). Given the new velocities, cosmological simulations of structure formation favor a scenario where the Magellanic Clouds (MCs) are currently on their first infall towards our Galaxy (Boylan-Kolchin et al. 2011, Busha et al. 2011). We illustrate here that the observed irregular morphology and internal kinematics of the MCs (in gas and stars) are naturally explained by interactions between the LMC and SMC, rather than gravitational interactions with the MW. This picture further supports a first infall scenario (Besla et a. 2007). In particular, we demonstrate that the Magellanic Stream, a band of HI gas trailing behind the MCs 150 degrees across the sky, can be accounted for by the action of LMC tides on the SMC before the system was accreted by the MW. We further demonstrate that the off-center, warped stellar bar of the LMC and its one-armed spiral, can be naturally explained by a recent direct collision with the SMC. Such structures are key morphological characteristics of a class of galaxies referred to as Magellanic Irregulars (de Vaucouleurs & Freeman 1972), the majority of which are not associated with massive spiral galaxies. We infer that dwarf-dwarf galaxy interactions are important drivers for the morphological evolution of Magellanic Irregulars and can dramatically affect the efficiency of baryon removal from dwarf galaxies via the formation of extended tidal bridges and tails. Such interactions are important not only for the evolution of dwarf galaxies but also have direct consequences for the buildup of baryons in our own MW, as LMC-mass systems are believed to be the dominant building blocks of MW-type halos., 33 pages, 21 figures, Accepted for publication in MNRAS, Dec 23 2011

Published
2012

48. Motivation for employers to carry out workplace health promotion: literature review

Author

Hassard, J, Wang, D, Cox, T, Muylaert, K, Namysł, A, Kazenas, A, Flaspöler, E, Podniece, Z, and European Agency for Safety and Health at Work - EU-OSHA

Abstract

Workplace health promotion (WHP) is the combined efforts of employers, workers and society to improve the health and wellbeing of people at work. This can be achieved by: improving the work organisation and the work environment; promoting the active participation of all stakeholders in the process, and encouraging personal development. It is important to note that WHP aims to be a complementary support for, but not a replacement of, workplace risk management. Proper risk management is an essential foundation for a successful WHP programme. Developing and sustaining a healthy work environment and workforce has clear benefits for companies and employees, but can also lead to an improvement in social and economic development at local, regional, national and European level. This report presents the findings of a literature review that aims to identify the key reasons, arguments and motivation for employers to carry out workplace health promotion initiatives, and discusses some of the associated challenges and obstacles. This knowledge can be used to encourage and motivate employers to start WHP.

Published
2012

49. Search for pair produced fourth-generation up-type quarks in pp collisions at √s = 7 TeV with a lepton in the final state

Author

Chatrchyan, S, Khachatryan, V, Sirunyan, M, Tumasyan, A, Adam, W, Aguilo, E, Bergauer, T, Dragicevic, M, Erăś, J, Fabjan, C, Friedl, M, Frăźhwirth, R, Ghete, M, Hammer, J, Hăśrmann, N, Hrubec, J, Jeitler, M, Kiesenhofer, W, Knăźnz, V, Krammer, M, Kră¤tschmer, I, Liko, D, Mikulec, I, Pernicka, M, Rahbaran, B, Rohringer, C, Rohringer, H, Schăśfbeck, R, Strauss, J, Taurok, A, Waltenberger, W, Walzel, G, Wulz, C. E., Mossolov, V, Shumeiko, N, Gonzalez, Suarez, Bansal, M, Bansal, S, Cornelis, T, Wolf, De, Janssen, X, Luyckx, S, Mucibello, L, Ochesanu, S, Roland, B, Rougny, R, Selvaggi, M, Haevermaet, Van, Mechelen, Van, Remortel, Van, Spilbeeck, Van, Blekman, F, Blyweert, S, Dęźhondt, J, Suarez, Gonzalez, Kalogeropoulos, A, Maes, M, Olbrechts, A, Doninck, Van, Mulders, Van, Onsem, Van, Villella, I, Clerbaux, B, Lentdecker, De, Dero, V, Gay, R, Hreus, T, Lăšonard, A, Marage, E, Reis, T, Thomas, L, Velde, Vander, Vanlaer, P, Wang, J, Adler, V, Beernaert, K, Cimmino, A, Costantini, S, Garcia, G, Grunewald, M, Klein, B, Lellouch, J, Marinov, A, Mccartin, J, Rios, Ocampo, Ryckbosch, D, Strobbe, N, Thyssen, F, Tytgat, M, Walsh, S, Yazgan, E, Zaganidis, N, Basegmez, S, Bruno, G, Castello, R, Ceard, L, Delaere, C, Pree, Du, Favart, D, Forthomme, L, Giammanco, A, Hollar, J, Lemaitre, V, Liao, J, Militaru, O, Nuttens, C, Pagano, D, Pin, A, Piotrzkowski, K, Schul, N, Garcia, Vizan, Beliy, N, Caebergs, T, Daubie, E, Hammad, H, Alves, A, Junior, Martins, Martins, T, Pol, E, Souza, G, Jăşnior, Aldăą, Carvalho, W, Custăłdio, A, Costa, Da, Damiao, Jesus, Martins, Oliveira, Souza, De, Malbouisson, H, Malek, M, Figueiredo, Matos, Mundim, L, Nogima, H, Silva, Da, Santoro, A, Jorge, Soares, Sznajder, A, Pereira, Vilela, Anjos, S, Bernardes, A, Dias, A, Tomei, Perez, Gregores, M, Lagana, C, Marinho, F, Mercadante, G, Novaes, F, Padula, S, Genchev, V, Iaydjiev, P, Piperov, S, Rodozov, M, Stoykova, S, Sultanov, G, Tcholakov, V, Trayanov, R, Vutova, M, Dimitrov, A, Hadjiiska, R, Kozhuharov, V, Litov, L, Pavlov, B, Petkov, P, Bian, G, Chen, M, Chen, S, Jiang, H, Liang, D, Liang, S, Meng, X, Tao, J, Wang, X, Wang, Z, Xiao, H, Xu, M, Zang, J, Zhang, Z, Asawatangtrakuldee, C, Ban, Y, Guo, Y, Li, W, Liu, S, Mao, Y, Qian, J, Teng, H, Wang, D, Zhang, L, Zou, W, Avila, C, Gomez, P, Moreno, Gomez, Oliveros, Osorio, Sanabria, C, Godinovic, N, Lelas, D, Plestina, R, Polic, D, Puljak, I, Antunovic, Z, Kovac, M, Brigljevic, V, Duric, S, Kadija, K, Luetic, J, Mekterovic, D, Morovic, S, Attikis, A, Galanti, M, Mavromanolakis, G, Mousa, J, Nicolaou, C, Ptochos, F, Razis, A, Finger, M, Finger, J. r. M., Assran, Y, Elgammal, S, Kamel, Ellithi, Khalil, S, Mahmoud, A, Radi, A, Kadastik, M, Măźntel, M, Raidal, M, Rebane, L, Tiko, A, Eerola, P, Fedi, G, Voutilainen, M, Hă¤rkăśnen, J, Heikkinen, A, Karimă¤ki, V, Kinnunen, R, Kortelainen, J, Lampăšn, T, Lassila Perini, K, Lehti, S, Lindăšn, T, Luukka, P, Mă¤enpă¤ă¤, T, Peltola, T, Tuominen, E, Tuominiemi, J, Tuovinen, E, Ungaro, D, Wendland, L, Banzuzi, K, Karjalainen, A, Korpela, A, Tuuva, T, Besancon, M, Choudhury, S, Dejardin, M, Denegri, D, Fabbro, B, Faure, L, Ferri, F, Ganjour, S, Givernaud, A, Gras, P, Monchenault, De, Jarry, P, Locci, E, Malcles, J, Millischer, L, Nayak, A, Rander, J, Rosowsky, A, Shreyber, I, Titov, M, Baffioni, S, Beaudette, F, Benhabib, L, Bianchini, L, Bluj, M, Broutin, C, Busson, P, Charlot, C, Daci, N, Dahms, T, Dalchenko, M, Dobrzynski, L, Florent, A, Cassagnac, De, Haguenauer, M, Minăš, P, Mironov, C, Naranjo, N, Nguyen, M, Ochando, C, Paganini, P, Sabes, D, Salerno, R, Sirois, Y, Veelken, C, Zabi, A, Agram, J. L., Andrea, J, Bloch, D, Bodin, D, Brom, J. M., Cardaci, M, Chabert, C, Collard, C, Conte, E, Drouhin, F, Fontaine, J. 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2012

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