Cookies Policy
The website need some cookies and similar means to function. If you permit us, we will use those means to collect data on your visits for aggregated statistics to improve our service. Find out More
Accept Reject
  • Menu
Publications

2017

Genetic effects on gene expression across human tissues

Authors
Aguet, F; Brown, AA; Castel, SE; Davis, JR; He, Y; Jo, B; Mohammadi, P; Park, Y; Parsana, P; Segre, AV; Strober, BJ; Zappala, Z; Cummings, BB; Gelfand, ET; Hadley, K; Huang, KH; Lek, M; Li, X; Nedzel, JL; Nguyen, DY; Noble, MS; Sullivan, TJ; Tukiainen, T; MacArthur, DG; Getz, G; Management, NP; Addington, A; Guan, P; Koester, S; Little, AR; Lockhart, NC; Moore, HM; Rao, A; Struewing, JP; Volpi, S; Collection, B; Brigham, LE; Hasz, R; Hunter, M; Johns, C; Johnson, M; Kopen, G; Leinweber, WF; Lonsdale, JT; McDonald, A; Mestichelli, B; Myer, K; Roe, B; Salvatore, M; Shad, S; Thomas, JA; Walters, G; Washington, M; Wheeler, J; Bridge, J; Foster, BA; Gillard, BM; Karasik, E; Kumar, R; Miklos, M; Moser, MT; Jewell, SD; Montroy, RG; Rohrer, DC; Valley, D; Mash, DC; Davis, DA; Sobin, L; Barcus, ME; Branton, PA; Grp, EMW; Abell, NS; Balliu, B; Delaneau, O; Fresard, L; Gamazon, ER; Garrido Martin, D; Gewirtz, ADH; Gliner, G; Gloudemans, MJ; Han, B; He, AZ; Hormozdiari, F; Li, X; Liu, B; Kang, EY; McDowell, IC; Ongen, H; Palowitch, JJ; Peterson, CB; Quon, G; Ripke, S; Saha, A; Shabalin, AA; Shimko, TC; Sul, JH; Teran, NA; Tsang, EK; Zhang, H; Zhou, YH; Bustamante, CD; Cox, NJ; Guigo, R; Kellis, M; McCarthy, MI; Conrad, DF; Eskin, E; Li, G; Nobel, AB; Sabatti, C; Stranger, BE; Wen, X; Wright, FA; Ardlie, KG; Dermitzakis, ET; Lappalainen, T; Battle, A; Brown, CD; Engelhardt, BE; Montgomery, SB; Aguet, F; Ardlie, KG; Cummings, BB; Gelfand, ET; Getz, G; Hadley, K; Handsaker, RE; Huang, KH; Kashin, S; Karczewski, KJ; Lek, M; Li, X; MacArthur, DG; Nedzel, JL; Nguyen, DT; Noble, MS; Segre, AV; Trowbridge, CA; Tukiainen, T; Abell, NS; Balliu, B; Barshir, R; Basha, O; Battle, A; Bogu, GK; Brown, A; Brown, CD; Castel, SE; Chen, LS; Chiang, C; Conrad, DF; Cox, NJ; Damani, FN; Davis, JR; Delaneau, O; Dermitzakis, ET; Engelhardt, BE; Eskin, E; Ferreira, PG; Fresard, L; Gamazon, ER; Garrido Martin, D; Gewirtz, ADH; Gliner, G; Gloudemans, MJ; Guigo, R; Hall, IM; Han, B; He, Y; Hormozdiari, F; Howald, C; Im, HK; Jo, B; Kang, EY; Kim, Y; Kim Hellmuth, S; Lappalainen, T; Li, G; Li, X; Liu, B; Mangul, S; McCarthy, MI; McDowell, IC; Mohammadi, P; Monlong, J; Montgomery, SB; Munoz Aguirre, M; Ndungu, AW; Nicolae, DL; Nobel, AB; Oliva, M; Ongen, H; Palowitch, JJ; Panousis, N; Papasaikas, P; Park, Y; Parsana, P; Payne, AJ; Peterson, CB; Quan, J; Reverter, F; Sabatti, C; Saha, A; Sammeth, M; Scott, AJ; Shabalin, AA; Sodaei, R; Stephens, M; Stranger, BE; Strober, BJ; Sul, JH; Tsang, EK; Urbut, S; De Bunt, MV; Wang, G; Wen, X; Wright, FA; Xi, HS; Yeger Lotem, E; Zappala, Z; Zaugg, JB; Zhou, YH; Akey, JM; Bates, D; Chan, J; Chen, LS; Claussnitzer, M; Demanelis, K; Diegel, M; Doherty, JA; Feinberg, AP; Fernando, MS; Halow, J; Hansen, KD; Haugen, E; Hickey, PF; Hou, L; Jasmine, F; Jian, R; Jiang, L; Johnson, A; Kaul, R; Kellis, M; Kibriya, MG; Lee, K; Li, JB; Li, Q; Li, X; Lin, J; Lin, S; Linder, S; Linke, C; Liu, Y; Maurano, MT; Molinie, B; Montgomery, SB; Nelson, J; Neri, FJ; Oliva, M; Park, Y; Pierce, BL; Rinaldi, NJ; Rizzardi, LF; Sandstrom, R; Skol, A; Smith, KS; Snyder, MP; Stamatoyannopoulos, J; Stranger, BE; Tang, H; Tsang, EK; Wang, L; Wang, M; Van Wittenberghe, N; Wu, F; Zhang, R; Fund, NC; Nierras, CR; Nci, N; Branton, PA; Carithers, LJ; Guan, P; Moore, HM; Rao, A; Vaught, JB; Nhgri, N; Gould, SE; Lockart, NC; Martin, C; Struewing, JP; Volpi, S; Nimh, N; Addington, AM; Koester, SE; Nida, N; Little, AR; Brigham, LE; Hasz, R; Hunter, M; Johns, C; Johnson, M; Kopen, G; Leinweber, WF; Lonsdale, JT; McDonald, A; Mestichelli, B; Myer, K; Roe, B; Salvatore, M; Shad, S; Thomas, JA; Walters, G; Washington, M; Wheeler, J; Bridge, J; Foster, BA; Gillard, BM; Karasik, E; Kumar, R; Miklos, M; Moser, MT; Jewell, SD; Montroy, RG; Rohrer, DC; Valley, DR; Davis, DA; Mash, DC; Undale, AH; Smith, AM; Tabor, DE; Roche, NV; McLean, JA; Vatanian, N; Robinson, KL; Sobin, L; Barcus, ME; Valentino, KM; Qi, L; Hunter, S; Hariharan, P; Singh, S; Um, KS; Matose, T; Tomaszewski, MM; Study, E; Barker, LK; Mosavel, M; Siminoff, LA; Traino, HM; Flicek, P; Juettemann, T; Ruffier, M; Sheppard, D; Taylor, K; Trevanion, SJ; Zerbino, DR; Craft, B; Goldman, M; Haeussler, M; Kent, WJ; Lee, CM; Paten, B; Rosenbloom, KR; Vivian, J; Zhu, J;

Publication
NATURE

Abstract
Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.

2017

Gait analysis as a complementary tool in the levodopa dose decision in vascular Parkinson's disease

Authors
Gago, M; Ferreira, F; Mollaei, N; Rodrigues, M; Sousa, N; Bicho, E; Rodrigues, P;

Publication
MOVEMENT DISORDERS

Abstract

2017

Disinfection of simulated and real winery wastewater using sulphate radicals: Peroxymonosulphate/transition metal/UV-A LED oxidation

Authors
Rodriguez Chueca, J; Moreira, SI; Lucas, MS; Fernandes, JR; Tavares, PB; Sampaio, A; Peres, JA;

Publication
JOURNAL OF CLEANER PRODUCTION

Abstract
The inactivation of four different microorganisms, Escherichia coli, Bacillus mycoides, Staphylococcus aureus and Candida albicans, inoculated in simulated (SWW) and real winery wastewaters (RWW), was assessed by the first time using free sulphate and hydroxyl radicals from photolytic (UV-A LED radiation; 370 nm) and metal [Fe(II) or Co(II)] activation of peroxymonosulphate (PMS). The experimental conditions tested were [PMS] = 0.1 mM and [Fe(II) or Co(II)] = 0.1 mM and pH 5.0 for the inactivation of microorganisms in SWW. However, due to the complexity of the water matrix, not unexpectedly, a fivefold concentration of reagents was required to inactivate the same organisms in RWW. In addition, compared to the bacteria, the fungus C. albicans presented a higher oxidative stress resistance to the treatments, and different experimental conditions were necessary to inactivate these cells. After 90 min, the photolytic activation of PMS through UV-A LED radiation achieved complete inactivation of E. coli, followed by S. aureus (approximate to 4 log) and B. mycoides (approximate to 3 log). Total inactivation of C. albicans was also achieved, but with higher dosages of PMS (10 mM). The metal activation of PMS through the use of a transition metal [Fe(II) or Co(II)] accelerated the inactivation rate, particularly in the first minutes of exposure time. These treatments reached between 1 and 3 log inactivation of microorganisms in the first minute of the experiment. In addition, the use of Co(II) as promoter in the activation of PMS, was more effective in the inactivation of S. aureus and C. albicans than activation with Fe(II). Since linear mathematical models do not adjust satisfactorily to inactivation results in all cases, different mathematical models were tested to fit the experimental inactivation data. In general, the Hom model correctly fits the inactivation results of the four microorganisms in all applied treatments. However, other models such as Biphasic and Double Weibull fit acceptably as well.

2017

Progress in Artificial Intelligence - 18th EPIA Conference on Artificial Intelligence, EPIA 2017, Porto, Portugal, September 5-8, 2017, Proceedings

Authors
Oliveira, Eugenio; Gama, Joao; Vale, ZitaA.; Cardoso, HenriqueLopes;

Publication
EPIA

Abstract

2017

Comparative study of the optical properties of colon mucosa and colon precancerous polyps between 400 and 1000 nm

Authors
Carvalho, S; Gueiral, N; Nogueira, E; Henrique, R; Oliveira, L; Tuchin, VV;

Publication
DYNAMICS AND FLUCTUATIONS IN BIOMEDICAL PHOTONICS XIV

Abstract
Optical properties of biological tissues are unique and may be used for tissue identification, tissue discrimination or even to identify pathologies. Early stage colorectal cancer evolves from adenomatous polyps that arise in the inner layer of the colorectal tube - the mucosa. The identification of different optical properties between healthy and pathological colorectal tissues might be used to identify different tissue components and to develop an early stage diagnosis method using optical technologies. Since most of the biomedical optics techniques use light within the visible and near infrared wavelength ranges, we used the inverse adding-doubling method to make a fast estimation of the optical properties of colorectal mucosa and early stage adenocarcinoma between 400 and 1000 nm. The estimated wavelength dependencies have provided information about higher lipid content in healthy mucosa and higher blood content in pathological tissue. Such data has also indicated that the wavelength dependence of the scattering coefficient for healthy mucosa is dominated by Rayleigh scattering and for pathological mucosa it is dominated by Mie scattering. Such difference indicates smaller scatterer size in healthy mucosa tissue. Such information can now be used to develop new diagnosis or treatment methods for early cancer detection or removal. One possibility is to use optical clearing technique to improve tissue transparency and create localized and temporary tissue dehydration for image contrast improvement during diagnosis or polyp laser removal. Such techniques can now be developed based on the different results that we have found for healthy and pathological colorectal mucosa.

2017

Application of a Hybrid Neural Fuzzy Inference System to Forecast Solar Intensity

Authors
Silva, F; Teixeira, B; Teixeira, N; Pinto, T; Praca, I; Vale, Z;

Publication
Proceedings - International Workshop on Database and Expert Systems Applications, DEXA

Abstract
This paper presents a proposal for the use of the Hybrid Fuzzy Inference System algorithm (HyFIS) as solar intensity forecast mechanism. Fuzzy Inference Systems (FIS) are used to solve regression problems in various contexts. The HyFIS is a method based on FIS with the particular advantage of combining fuzzy concepts with Artificial Neural Networks (ANN), thus optimizing the learning process. This algorithm is part of several other FIS algorithms implemented in the Fuzzy Rule-Based Systems (FRBS) package of R. The ANN algorithms and Support Vector Machine (SVM), both widely used for solving regression problems, are also used in this study to allow the comparison of results. Results show that HyFIS presents higher performance when compared to the ANN and SVM, when applied to real data of Florianopolis, Brazil, which helps to reinforce the potential of this algorithm in solving the solar intensity forecasting problems. © 2016 IEEE.

  • 2045
  • 4312