GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Iowa Immunization Program Annual Report 2010, March 31, 2011

The Bureau of Immunization is part of the Division of Acute Disease Prevention and Emergency Response (ADPER) at the Iowa Department of Public Health (IDPH). The ADPER division provides support, technical assistance and consultation to local hospitals, public health agencies, community health centers, emergency medical service programs and local health care providers regarding infectious diseases, disease prevention and control, injury prevention and public health and health care emergency preparedness and response. The division encompasses the Center for Acute Disease Epidemiology (CADE), the Bureau of Immunization and Tuberculosis (ITB), the Bureau of Emergency Medical Services (EMS), the Bureau of Communication and Planning (CAP), the Office of Health Information Technology (HIT), and the Center for Disaster Operations and Response (CDOR). The Bureau of Immunization and Tuberculosis includes the Immunization Program, the Tuberculosis Control Program, and the Refugee Health Program. The mission of the Immunization Program is to decrease vaccine‐preventable diseases through education, advocacy and partnership. While there has been major advancement in expanding immunizations to many parts of Iowa’s population, work must continue with public and private health care providers to promote the program���s vision of healthy Iowans living in communities free of vaccine‐preventable diseases. Accomplishing this goal will require achieving and maintaining high vaccination coverage levels, improving vaccination strategies among under‐vaccinated populations, prompt reporting and thorough investigation of suspected disease cases, and rapid institution of control measures. The Immunization Program is comprised of multiple programs that provide immunization services throughout the state: Adolescent Immunization Program, Adult Immunization Program, Immunization Registry Information System (IRIS), Vaccines for Children Program (VFC), Perinatal Hepatitis B Program, and Immunization Assessment Program.

Iowa Immunization Program Annual Report 2011, February 20, 2012

The Bureau of Immunization is part of the Division of Acute Disease Prevention and Emergency Response (ADPER) at the Iowa Department of Public Health (IDPH). The ADPER division provides support, technical assistance and consultation to local hospitals, public health agencies, community health centers, emergency medical service programs and local health care providers regarding infectious diseases, disease prevention and control, injury prevention and public health and health care emergency preparedness and response. The division encompasses the Center for Acute Disease Epidemiology (CADE), the Bureau of Immunization and Tuberculosis (ITB), the Bureau of Emergency Medical Services (EMS), the Bureau of Communication and Planning (CAP), the Office of Health Information Technology (HIT), and the Center for Disaster Operations and Response (CDOR). The Bureau of Immunization and Tuberculosis includes the Immunization Program, the Tuberculosis Control Program, and the Refugee Health Program. The mission of the Immunization Program is to decrease vaccine‐preventable diseases through education, advocacy and partnership. While there has been major advancement in expanding immunizations to many parts of Iowa’s population, work must continue with public and private health care providers to promote the program���s vision of healthy Iowans living in communities free of vaccine‐preventable diseases. Accomplishing this goal will require achieving and maintaining high vaccination coverage levels, improving vaccination strategies among under‐vaccinated populations, prompt reporting and thorough investigation of suspected disease cases, and rapid institution of control measures. The Immunization Program is comprised of multiple programs that provide immunization services throughout the state: Adolescent Immunization Program, Adult Immunization Program, Immunization Registry Information System (IRIS), Vaccines for Children Program (VFC), Perinatal Hepatitis B Program, and Immunization Assessment Program.

Iowa Immunization Program Annual Report 2012, February 20, 2012

The Bureau of Immunization is part of the Division of Acute Disease Prevention and Emergency Response (ADPER) at the Iowa Department of Public Health (IDPH). The ADPER division provides support, technical assistance and consultation to local hospitals, public health agencies, community health centers, emergency medical service programs and local health care providers regarding infectious diseases, disease prevention and control, injury prevention and public health and health care emergency preparedness and response. The division encompasses the Center for Acute Disease Epidemiology (CADE), the Bureau of Immunization and Tuberculosis (ITB), the Bureau of Emergency Medical Services (EMS), the Bureau of Communication and Planning (CAP), the Office of Health Information Technology (HIT), and the Center for Disaster Operations and Response (CDOR). The Bureau of Immunization and Tuberculosis includes the Immunization Program, the Tuberculosis Control Program, and the Refugee Health Program. The mission of the Immunization Program is to decrease vaccine‐preventable diseases through education, advocacy and partnership. While there has been major advancement in expanding immunizations to many parts of Iowa’s population, work must continue with public and private health care providers to promote the program���s vision of healthy Iowans living in communities free of vaccine‐preventable diseases. Accomplishing this goal will require achieving and maintaining high vaccination coverage levels, improving vaccination strategies among under‐vaccinated populations, prompt reporting and thorough investigation of suspected disease cases, and rapid institution of control measures. The Immunization Program is comprised of multiple programs that provide immunization services throughout the state: Adolescent Immunization Program, Adult Immunization Program, Immunization Registry Information System (IRIS), Vaccines for Children Program (VFC), Perinatal Hepatitis B Program, and Immunization Assessment Program.

2014 Immunizations in Iowa, Iowa Immunization Program Annual Report, January 11, 2016

The Bureau of Immunization is part of the Division of Acute Disease Prevention and Emergency Response (ADPER) at the Iowa Department of Public Health (IDPH). The ADPER division provides support, technical assistance and consultation to local hospitals, public health agencies, community health centers, emergency medical service programs and local health care providers regarding infectious diseases, disease prevention and control, injury prevention and public health and health care emergency preparedness and response. The division encompasses the Center for Acute Disease Epidemiology (CADE), the Bureau of Immunization and Tuberculosis (ITB), the Bureau of Emergency Medical Services (EMS), the Bureau of Communication and Planning (CAP), the Office of Health Information Technology (HIT), and the Center for Disaster Operations and Response (CDOR). The Bureau of Immunization and Tuberculosis includes the Immunization Program, the Tuberculosis Control Program, and the Refugee Health Program. The mission of the Immunization Program is to decrease vaccine‐preventable diseases through education, advocacy and partnership. While there has been major advancement in expanding immunizations to many parts of Iowa’s population, work must continue with public and private health care providers to promote the program���s vision of healthy Iowans living in communities free of vaccine‐preventable diseases. Accomplishing this goal will require achieving and maintaining high vaccination coverage levels, improving vaccination strategies among under‐vaccinated populations, prompt reporting and thorough investigation of suspected disease cases, and rapid institution of control measures. The Immunization Program is comprised of multiple programs that provide immunization services throughout the state: Adolescent Immunization Program, Adult Immunization Program, Immunization Registry Information System (IRIS), Vaccines for Children Program (VFC), Perinatal Hepatitis B Program, and Immunization Assessment Program.

Estimation of age- and stage-specific Catalan breast cancer survival functions using US and Catalan survival data

Background: During the last part of the 1990s the chance of surviving breast cancer increased. Changes in survival functions reflect a mixture of effects. Both, the introduction of adjuvant treatments and early screening with mammography played a role in the decline in mortality. Evaluating the contribution of these interventions using mathematical models requires survival functions before and after their introduction. Furthermore, required survival functions may be different by age groups and are related to disease stage at diagnosis. Sometimes detailed information is not available, as was the case for the region of Catalonia (Spain). Then one may derive the functions using information from other geographical areas. This work presents the methodology used to estimate age- and stage-specific Catalan breast cancer survival functions from scarce Catalan survival data by adapting the age- and stage-specific US functions. Methods: Cubic splines were used to smooth data and obtain continuous hazard rate functions. After, we fitted a Poisson model to derive hazard ratios. The model included time as a covariate. Then the hazard ratios were applied to US survival functions detailed by age and stage to obtain Catalan estimations. Results: We started estimating the hazard ratios for Catalonia versus the USA before and after the introduction of screening. The hazard ratios were then multiplied by the age- and stage-specific breast cancer hazard rates from the USA to obtain the Catalan hazard rates. We also compared breast cancer survival in Catalonia and the USA in two time periods, before cancer control interventions (USA 1975–79, Catalonia 1980–89) and after (USA and Catalonia 1990–2001). Survival in Catalonia in the 1980–89 period was worse than in the USA during 1975–79, but the differences disappeared in 1990–2001. Conclusion: Our results suggest that access to better treatments and quality of care contributed to large improvements in survival in Catalonia. On the other hand, we obtained detailed breast cancer survival functions that will be used for modeling the effect of screening and adjuvant treatments in Catalonia.

Global surveillance of cancer survival 1995-2009 : analysis of individual data for 25 676 887 patients from 279 population-based registries in 67 countries (CONCORD-2)

BACKGROUND: Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control. METHODS: Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15-99 years) and 75 000 children (age 0-14 years) diagnosed with cancer during 1995-2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights. FINDINGS: 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005-09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15-19% in North America, and as low as 7-9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10-20% between 1995-99 and 2005-09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer, national estimates of 5-year survival range from less than 50% to more than 70%; regional variations are much wider, and improvements between 1995-99 and 2005-09 have generally been slight. For women diagnosed with ovarian cancer in 2005-09, 5-year survival was 40% or higher only in Ecuador, the USA, and 17 countries in Asia and Europe. 5-year survival for stomach cancer in 2005-09 was high (54-58%) in Japan and South Korea, compared with less than 40% in other countries. By contrast, 5-year survival from adult leukaemia in Japan and South Korea (18-23%) is lower than in most other countries. 5-year survival from childhood acute lymphoblastic leukaemia is less than 60% in several countries, but as high as 90% in Canada and four European countries, which suggests major deficiencies in the management of a largely curable disease. INTERPRETATION: International comparison of survival trends reveals very wide differences that are likely to be attributable to differences in access to early diagnosis and optimum treatment. Continuous worldwide surveillance of cancer survival should become an indispensable source of information for cancer patients and researchers and a stimulus for politicians to improve health policy and health-care systems. FUNDING: Canadian Partnership Against Cancer (Toronto, Canada), Cancer Focus Northern Ireland (Belfast, UK), Cancer Institute New South Wales (Sydney, Australia), Cancer Research UK (London, UK), Centers for Disease Control and Prevention (Atlanta, GA, USA), Swiss Re (London, UK), Swiss Cancer Research foundation (Bern, Switzerland), Swiss Cancer League (Bern, Switzerland), and University of Kentucky (Lexington, KY, USA).

Uses of cancer registries for public health and clinical research in Europe : results of the European Network of Cancer Registries survey among 161 population-based cancer registries during 2010-2012

AIM: To provide insight into cancer registration coverage, data access and use in Europe. This contributes to data and infrastructure harmonisation and will foster a more prominent role of cancer registries (CRs) within public health, clinical policy and cancer research, whether within or outside the European Research Area. METHODS: During 2010-12 an extensive survey of cancer registration practices and data use was conducted among 161 population-based CRs across Europe. Responding registries (66%) operated in 33 countries, including 23 with national coverage. RESULTS: Population-based oncological surveillance started during the 1940-50s in the northwest of Europe and from the 1970s to 1990s in other regions. The European Union (EU) protection regulations affected data access, especially in Germany and France, but less in the Netherlands or Belgium. Regular reports were produced by CRs on incidence rates (95%), survival (60%) and stage for selected tumours (80%). Evaluation of cancer control and quality of care remained modest except in a few dedicated CRs. Variables evaluated were support of clinical audits, monitoring adherence to clinical guidelines, improvement of cancer care and evaluation of mass cancer screening. Evaluation of diagnostic imaging tools was only occasional. CONCLUSION: Most population-based CRs are well equipped for strengthening cancer surveillance across Europe. Data quality and intensity of use depend on the role the cancer registry plays in the politico, oncomedical and public health setting within the country. Standard registration methodology could therefore not be translated to equivalent advances in cancer prevention and mass screening, quality of care, translational research of prognosis and survivorship across Europe. Further European collaboration remains essential to ensure access to data and comparability of the results.

Estimation of age- and stage-specific Catalan breast cancer survival functions using US and Catalan survival data

During the last part of the 1990s the chance of surviving breast cancer increased. Changes in survival functions reflect a mixture of effects. Both, the introduction of adjuvant treatments and early screening with mammography played a role in the decline in mortality. Evaluating the contribution of these interventions using mathematical models requires survival functions before and after their introduction. Furthermore, required survival functions may be different by age groups and are related to disease stage at diagnosis. Sometimes detailed information is not available, as was the case for the region of Catalonia (Spain). Then one may derive the functions using information from other geographical areas. This work presents the methodology used to estimate age- and stage-specific Catalan breast cancer survival functions from scarce Catalan survival data by adapting the age- and stage-specific US functions. Methods: Cubic splines were used to smooth data and obtain continuous hazard rate functions. After, we fitted a Poisson model to derive hazard ratios. The model included time as a covariate. Then the hazard ratios were applied to US survival functions detailed by age and stage to obtain Catalan estimations. Results: We started estimating the hazard ratios for Catalonia versus the USA before and after the introduction of screening. The hazard ratios were then multiplied by the age- and stage-specific breast cancer hazard rates from the USA to obtain the Catalan hazard rates. We also compared breast cancer survival in Catalonia and the USA in two time periods, before cancer control interventions (USA 1975–79, Catalonia 1980–89) and after (USA and Catalonia 1990–2001). Survival in Catalonia in the 1980–89 period was worse than in the USA during 1975–79, but the differences disappeared in 1990–2001. Conclusion: Our results suggest that access to better treatments and quality of care contributed to large improvements in survival in Catalonia. On the other hand, we obtained detailed breast cancer survival functions that will be used for modeling the effect of screening and adjuvant treatments in Catalonia

Press forming of paperboard – advancement of converting tools and process control

Press forming is nowadays one of the most common industrial methods in use for producing deeper trays from paperboard. Demands for material properties like recyclability and sustainability have increased also in the packaging industry, but there are still limitations related to the formability of paperboard. A majority of recent studies have focused on material development, but the potential of the package manufacturing process can also be improved by the development of tooling and process control. In this study, advanced converting tools (die cutting tools and the press forming mould) are created for production scale paperboard tray manufacturing. Also monitoring methods that enable the production of paperboard trays with enhanced quality, and can be utilized in process control are developed. The principles for tray blank preparation, including creasing pattern and die cutting tool design are introduced. The mould heating arrangement and determination of mould clearance are investigated to improve the quality of the press formed trays. The effect of the spring back of the tray walls on the tray dimensions can be managed by adjusting the heat-related process parameters and estimating it at the mould design stage. This enables production speed optimization as the process parameters can be adjusted more freely. Real-time monitoring of pressing force by using multiple force sensors embedded in the mould structure can be utilized in the evaluation of material characteristics on a modified production machinery. Comprehensive process control can be achieved with a combination of measurement of the outer dimensions of the trays and pressing force monitoring. The control method enables detection of defects and tracking changes in the material properties. The optimized converting tools provide a basis for effective operation of the control system.

Les inégalités sociales dans le dépistage du cancer du sein, quand le système s'en mêle...

Réalisé en cotutelle avec Dr. Béatrice Godard, Professeure titulaire à l'Université de Montréal.

La néphrectomie partielle chez les patients atteints du cancer du rein de stade T1b

Objectif : La néphrectomie partielle est reconnue actuellement comme le traitement de choix des tumeurs de moins de 7 cm. Le but de notre étude est de comparer le taux de mortalité lié au cancer du rein suite au traitement par néphrectomie partielle ou radicale chez les patients de stade T1b, de présenter la tendance temporelle du taux d'intervention par néphrectomie partielle pour les tumeurs de stade T1b et d’identifier les facteurs sociodémographiques et tumoraux qui influencent le choix thérapeutique entre les deux types de traitement chirurgical. Méthode : Il s’agit d’une étude épidémiologique de type rétrospective. La population de patients provient de la base de donnée SEER (Surveillance, Epidemiology, and End Results) qui regroupe une grande proportion de la population nord-américaine. Dans notre étude, nous avons utilisé l’analyse par régression logistique pour identifier les facteurs sociodémographiques associés à l'intervention par néphrectomie partielle. Dans un deuxième temps, nous avons comparé la mortalité liée au cancer entre les deux options chirurgicales, après association par score de tendance pour diminuer les différences de base entre les deux populations. Nos critères étaient l’âge, la race, le sexe, l’état civil, le niveau socioéconomique, la taille tumorale, le grade nucléaire, l’histologie et la localité du centre hospitalier. L’analyse des données a été faite par le logiciel SPSS. Résultats : Le taux d'interventions par néphrectomie partielle a augmenté de 1,2% en 1988 à 15,9% en 2008 (p <0,001). Les jeunes patients, les tumeurs de petite taille, les patients de race noire, ainsi que les hommes sont plus susceptibles d'être traités par néphrectomie partielle (tous les p < 0,002). Parmi le groupe ciblé, le taux de mortalité lié au cancer à 5 ans et à 10 ans est de 4,4 et de 6,1% pour les néphrectomies partielles et de 6,0 et 10,4% pour les néphrectomies radicales (p = 0,03). Après ajustement de toutes les autres variables, les analyses de régression montrent que le choix entre les deux types de néphrectomie n’est pas associé à la mortalité lié au cancer (hazard ratio: 0,89, p = 0,5). Conclusion : Malgré un contrôle oncologique équivalent, le taux d'intervention par néphrectomie partielle chez les patients ayant un cancer du rein T1b est faible en comparaison à la néphrectomie radicale.

Determinación de los efectos en la salud de los trabajadores del programa de control de vectores expuestos laboralmente a organoclorados en tres departamentos de Colombia 2013

Objetivo: Evaluar la exposición a plaguicidas organoclorados empleados en salud publica en la población trabajadora del programa de control de vectores en tres regiones de Colombia en 2013. Métodos: Se realizó un estudio descriptivo de corte transversal en el grupo de trabajadores del programa de control de enfermedades transmitidas por vectores -ETV- (coordinadores, técnicos, entomólogos, técnicos y auxiliares) de los departamentos de Meta, Nariño y Risaralda. A todos los participantes se les realizó una entrevista en la cual se recogió, mediante cuestionario, información de las tres variables de muestreo: sociodemográficas, ocupacionales, clínicas y toxicológicas. Se determinaron los niveles de 13 organoclorados en suero mediante cromatografía de gases en el Instituto Nacional de Salud. Se llevó a cabo un análisis descriptivo y se llevo a cabo un análisis para determinar la distribución de medias entre variables de exposición ocupacional (Ji2 para cualitativas y U de Mann-Whitney para cuantitativas). Posteriormente, se llevó a cabo un análisis multivariado para estimar la asociación controlando por variables de antigüedad, exposición laboral a organoclorados. Resultados: El reporte de manipulación de insecticidas organoclorados fue del 39,1%. El 100% de los trabajadores que usaron organoclorados refirieron el uso DDT. El 7,5% (n=3) refirieron el uso de Aldrin. Los organoclorados fueron hexaclorbenceno, hexaclorocicloexano, heptacloro, heptaclorepoxi, α-Clordano, 4,4-DDT, 4,4-DDE, β -endosulfan, 2,4- DDT, endosulfan sulfato y mirex. Los organoclorados con niveles pico más altos fueron β-HCH, 4,4- DDT y α –HCH. Los síntomas de mayor presentación fueron: cefalea 28,7%, mareo 29,9%, disminución de fuerza en MMSS 17,2% y síntomas neurosiquiátricos.

Cobertura de citología cervicouterina y factores asociados en mujeres mayores de 15 años, Kennedy, Bogotá D.C. 2005

Hace más de tres décadas existe en el mundo un programa para la prevención del cáncer de cérvix centrado en la práctica de la Citología Cervico Uterina. Aspectos como las bajas coberturas dadas por la realización de exámenes reiterados a mujeres de bajo riesgo y la no captación de mujeres de alto riesgo, pobres controles de calidad, no entrega de reportes y el bajo acceso a los servicios de diagnostico y tratamiento han impedido cambios del perfil epidemiológico de esta enfermedad en Colombia. Este estudio evalúa la cobertura, el conocimiento del reporte y los motivos para la realización o no del examen y el nivel de conocimientos con respecto a la prueba y a ésta patología.

Impacto de dos técnicas quirúrgicas sobre la recaída local de carcinoma de mama en pacientes de una clínica de Bogotá D.C.

Introducción: El carcinoma de mama es el tumor maligno más frecuente entre las mujeres y representa una significativa mortalidad en los países en vías de desarrollo. Según datos del Instituto Nacional de Cancerología en el 2010 se reportaron 672 nuevos casos de cáncer de mama, lo que representó el 18% de todos los tumores malignos en mujeres. Durante las últimas 3 décadas las técnicas quirúrgicas para el tratamiento del cáncer de mama han presentado un cambio significativo y proponen disminución de procedimientos agresivos y radicales, intervenciones como: mastectomía radical modificada, cirugía conservadora y la disección de ganglio centinela son ejemplos claros de esta evolución asociado al incremento de la reconstrucción mamaria inmediata. Metodología: Estudio observacional tipo cohorte retrospectivo en el cual se revisó una base de datos de pacientes con cáncer de mama de las cuales 632 fueron sometidas a mastectomía radical con preservación de piel y complejo areola-pezón y mastectomía radical con preservación de piel sin preservación del complejo areola-pezón, los dos procedimientos asociados a reconstrucción mamaria inmediata y se comparó la frecuencia de recaída local entre los dos grupos. Resultados: De las 632 pacientes estudiadas al 30.5% se les realizo preservación del complejo areola pezón. Las mujeres a quienes se les realizó preservación del complejo areola pezón presentaron menor sobrevida a la recaída local a 10 años (80.51%) comparado con las mujeres a quienes no se les preservó el complejo areola pezón (87.40%), sin embargo no se encontró diferencia estadísticamente significativa para determinar que las probabilidades de sobrevida sean diferentes. Discusión: No se evidenció diferencia estadísticamente significativa entre los 2 procedimientos quirúrgicos (con y sin preservación del complejo areola pezón) en relación a la recaída local, estudios retrospectivos no han evidenciado una mayor tasa de recaídas locales en pacientes a quienes se les preserva el complejo areola-pezón, sin embargo hacen falta estudios prospectivos y aleatorizados que puedan otorgar un mayor sustento científico que garantice la seguridad de la preservación del complejo areola-pezón.