Estimació de la incidència del càncer a totes les províncies d’Espanya

Treballs Finals de Grau en Estadística UB-UPC, Facultat d'Economia i Empresa (UB) i Facultat de Matemàtiques i Estadística (UPC), Curs: 2017-2018, Tutors: Alberto Ameijide; Xavier Puig(cat) El càncer és una de les malalties que més afecta actualment tant a la població catalana com espanyola, sent aquesta la segona causa de mort més comuna. En l'àmbit estadístic, l'estudi d'aquesta malaltia parteix d'una sèrie d'indicadors epidemiològics que permeten mesurar-ne l'impacte que genera el càncer en la societat, així com observar quina va sent la seva evolució al llarg del temps. D'aquests indicadors epidemiològics, el present treball se centra en l'anàlisi de la incidència, indicador que permet mesurar el nombre de nous casos que es registren sobre una població en una determinada zona i moment. La incidència del càncer en un territori és una dada desconeguda a excepció d’alguns territoris on existeixen Registres de Càncer de Base Poblacional (RCBP). L’objectiu d’aquest estudi és estimar la incidència del càncer a España a partir de les dades d’incidència i mortalitat conegudes i validar la idoneïtat d’aquest estimador. A partir de les dades d’incidència d’aquelles províncies i períodes en els que es disposen de dades dels registres de càncer de base poblacional i dades de mortalitat per aquelles mateixes zones i períodes, s’ha fet l’estimació de la raó entre la incidència i mortalitat (RIM) pel període 1994-2007, mitjançant models lineals generalitzats mixtes bayesians per a cada tipus de tumor i sexe. S’ha estimat al nombre de casos incidents durant el període 2009-2013 a les províncies de Tarragona i Girona en tres escenaris diferents que representaven diferents hipòtesis de la evolució del RIM, constant lineal i quadràtica, i s’han comparat i validat aquestes estimacions amb les dades reals de Tarragona i Girona per al mateix període seleccionant l’escenari que millor ajustava. A partir del escenaris triats, s’ha estimat la incidència per cada una de les províncies espanyoles pel període 2009-2013. En el cas dels homes dels 22 tipus de tumors estudiats, 8 han presentat estimacions no acceptables mentre que en el cas de les dones dels 24 tipus estudiats, 5 han presentat estimacions no acceptables. La conclusió final és que el model estudiat produeix estimacions acceptables en la majoria dels tumors, però té certes limitacions que poden produir estimacions no acceptables en determinades situacions, on seria necessari seguir estudiant nous mètodes i/o models d’estimacions que presentin uns valors de casos incidents més acurats.(eng) Cancer is one of the diseases that most affects both the Catalan and Spanish population, and this is the second most common cause of death. In the statistical field, the study of this disease presents a set of epidemiological indicators that allow us to measure the impact that cancer causes in society, as well as to observe the evolution of the disease over time. Of these epidemiological indicators, the present project focuses on the analysis of incidence, an indicator that allows to measure the number of new cases that are recorded on a population in a specific area and time. The incidence of cancer in one area is unknown, with the exception of some territories where there are Population-Based Cancer Registries (RCBP). The objective of this study is to estimate the incidence of cancer in Spain based on known incidence and mortality data and validate the suitability of this estimator. From the incidence data of those provinces and periods in which data on populationbased cancer registers and mortality data are available for those same zones and periods, the estimation of the ratio between incidence and mortality (RIM) for the period 1994-2007 it’s done using Bayesian mixed generalized linear models for each type of tumor and sex. The number of incidents in the period 2009-2013 has been estimated in the provinces of Tarragona and Girona in three different scenarios that represented different hypotheses of the evolution of RIM, linear and quadratic constant, and these estimates have been compared and validated with the real data of Tarragona and Girona for the same period, selecting the setting that best adjusted. Based on the scenarios chosen, the incidence was estimated for each of the Spanish provinces during the period 2009-2013. In the case of men from the 22 types of tumors studied, 8 have presented unacceptable estimates while in the case of women of the 24 types studied, 5 have presented non-acceptable estimates. The final conclusion is that the model studied produces acceptable estimates in most tumors, but it has certain limitations that can produce estimates not acceptable in certain situations, where it would be necessary to continue studying new methods and / or estimation models that present a more accurate incident case values

Cervical pessary and cerclage placement for preterm birth prevention and cervicovaginal microbiome changes

Cervical length; Microbial diversity; PessaryLongitud cervical; Diversidad microbiana; PesarioLongitud cervical; Diversitat microbiana; PessariIntroduction Our objective was to compare the vaginal microbiome in low-risk and high-risk pregnant women and to explore a potential association between vaginal microbiome and preterm birth. Material and methods A pilot, consecutive, longitudinal, multicenter study was conducted in pregnant women at 18–22 weeks of gestation. Participants were assigned to one of three groups: control (normal cervix), pessary (cervical length ≤25 mm) and cerclage (cervical length ≤25 mm or history of preterm birth). Analysis and comparison of vaginal microbiota as a primary outcome was performed at inclusion and at 30 weeks of gestation, along with a follow-up of pregnancy and perinatal outcomes. We assessed the vaginal microbiome of pregnant women presenting a short cervix with that of pregnant women having a normal cervix, and compared the vaginal microbiome of women with a short cervix before and after placement of a cervical pessary or a cervical cerclage. Results The microbiome of our control cohort was dominated by Lactobacillus crispatus and inners. Five community state types were identified and microbiome diversity did not change significantly over 10 weeks in controls. On the other hand, a short cervix was associated with a lower microbial load and higher microbial richness, and was not correlated with Lactobacillus relative abundance. After intervention, the cerclage group (n = 19) had a significant increase in microbial richness and a shift towards community state types driven by various bacterial species, including Lactobacillus mulieris, unidentified Bifidobacterium or Enterococcus. These changes were not significantly observed in the pessary (n = 26) and control (n = 35) groups. The cerclage group had more threatened preterm labor episodes and poorer outcomes than the control and pessary groups. Conclusions These findings indicate that a short cervix is associated with an altered vaginal microbiome community structure. The use of a cerclage for preterm birth prevention, as compared with a pessary, was associated with a microbial community harboring a relatively low abundance of Lactobacillus, with more threatened preterm labor episodes, and with poorer clinical outcomes.This study was supported by the Instituto de Salud Carlos III/FEDER FIS PI15/02043; Beca Dexeus Mujer 2015. Francisca Yáñez was supported by a grant from ANID, BECAS Chile, N° 72190278. Zixuan Xie received a fellowship from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Action, Innovative Training Network: FunHoMic; grant number 812969

Distribution of aminogenic activity among potential autochthonous starter cultures for dry fermented sausages

Any bacterial strain to be used as starter culture should have suitable characteristics, including a lack of amino acid decarboxylase activity. In this study, the decarboxylase activity of 76 bacterial strains, including lactic acid bacteria and gram-positive, catalase-positive cocci, was investigated. These strains were previously isolated from European traditional fermented sausages to develop autochthonous starter cultures. Of all the strains tested, 48% of the lactic acid bacteria strains and 13% of gram-positive, catalase-positive cocci decarboxylated one or more amino acids. Aminogenic potential was strain dependent, although some species had a higher proportion of aminogenic strains than did others. Thus, all Lactobacillus curvatus strains and 70% of Lactobacillus brevis strains had the capacity to produce tyramine and beta-phenylethylamine. Some strains also produced other aromatic amines, such as tryptamine and the diamines putrescine and cadaverine. All the enterococcal strains tested were decarboxylase positive, producing high amounts of tyramine and considerable amounts of beta-phenylethylamine. None of the staphylococcal strains had tyrosine-decarboxylase activity, but some produced other amines. From the aminogenic point of view, Lactobacillus plantarum, Lactobacillus sakei, and Staphylococcus xylosus strains would be the most suitable for use as autochthonous starter cultures for traditional fermented sausages

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Performance and Operation of the CMS Electromagnetic Calorimeter

The operation and general performance of the CMS electromagnetic calorimeter using cosmic-ray muons are described. These muons were recorded after the closure of the CMS detector in late 2008. The calorimeter is made of lead tungstate crystals and the overall status of the 75848 channels corresponding to the barrel and endcap detectors is reported. The stability of crucial operational parameters, such as high voltage, temperature and electronic noise, is summarised and the performance of the light monitoring system is presented

Pseudorapidity and transverse momentum dependence of flow harmonics in pPb and PbPb collisions

info:eu-repo/semantics/publishe