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1. Are state-space stock assessment model confidence intervals accurate? Case studies with SAM and Barents Sea stocks

Author

Cadigan, Noel G., Albertsen, Christoffer Moesgaard, Zheng, Nan, Nielsen, Anders, Cadigan, Noel G., Albertsen, Christoffer Moesgaard, Zheng, Nan, and Nielsen, Anders

Abstract

Our main contribution is to examine the reliability of confidence intervals using the SAM state-space fish stock assessment model used for the assessment of many stocks by the International Council for the Exploration of the Seas. We focus on frequentist statistical inferences and more specifically on inference conditioned on specific values of the state-space model random effects drawn from their process distribution. This is somewhat consistent with simulation self-test procedures that are commonly used to examine the reliability of state-space assessment model results. However, recent research has indicated that some estimation bias may be expected in the conditional setting. Hence, we also investigate recently proposed bias corrected confidence intervals appropriate for the conditional inference setting. The SAM simulation coverage probabilities of 95% confidence intervals for SSB and Fbar were usually slightly larger than 95%, but in a small number of years these coverage probabilities could be much smaller than 95%. The bias corrected confidence intervals were more reliable. When averaged over years, the SAM and bias corrected confidence interval coverage probabilities were similar for the Northeast Artic cod and saithe case studies, but the bias corrected confidence intervals performed much better overall for the haddock case study.

Published
2024

2. FTO genetic variants, dietary intake and body mass index:insights from 177 330 individuals

Author

Qi, Qibin, Oskari Kilpeläinen, Tuomas, Downer, Mary K, Tanaka, Toshiko, Smith, Caren E, Sluijs, Ivonne, Sonestedt, Emily, Chu, Audrey Y, Renström, Frida, Lin, Xiaochen, Angquist, Lars H, Huang, Jinyan, Liu, Zhonghua, Li, Yanping, Asif Ali, Muhammad, Xu, Min, Ahluwalia, Tarun Veer Singh, Boer, Jolanda M A, Chen, Peng, Daimon, Makoto, Eriksson, Johan, Perola, Markus, Friedlander, Yechiel, Gao, Yu-Tang, Heppe, Denise H M, Holloway, John W, Houston, Denise K, Kanoni, Stavroula, Kim, Yu-Mi, Laaksonen, Maarit A, Jääskeläinen, Tiina, Lee, Nanette R, Lehtimäki, Terho, Lemaitre, Rozenn N, Lu, Wei, Luben, Robert N, Manichaikul, Ani, Männistö, Satu, Marques-Vidal, Pedro, Monda, Keri L, Ngwa, Julius S, Perusse, Louis, van Rooij, Frank J A, Xiang, Yong-Bing, Wen, Wanqing, Wojczynski, Mary K, Zhu, Jingwen, Borecki, Ingrid B, Bouchard, Claude, Cai, Qiuyin, Cooper, Cyrus, Dedoussis, George V, Deloukas, Panos, Ferrucci, Luigi, Forouhi, Nita G, Hansen, Torben, Christiansen, Lene, Hofman, Albert, Johansson, Ingegerd, Jørgensen, Torben, Karasawa, Shigeru, Khaw, Kay-Tee, Kim, Mi-Kyung, Kristiansson, Kati, Li, Huaixing, Lin, Xu, Liu, Yongmei, Lohman, Kurt K, Long, Jirong, Mikkilä, Vera, Mozaffarian, Dariush, North, Kari, Pedersen, Oluf, Raitakari, Olli, Rissanen, Harri, Tuomilehto, Jaakko, van der Schouw, Yvonne T, Uitterlinden, André G, Carola Zillikens, M, Franco, Oscar H, Shyong Tai, E, Ou Shu, Xiao, Siscovick, David S, Toft, Ulla, Monique Verschuren, W M, Vollenweider, Peter, Wareham, Nicholas J, Witteman, Jacqueline C M, Zheng, Wei, Ridker, Paul M, Kang, Jae H, Liang, Liming, Jensen, Majken K, Curhan, Gary C, Pasquale, Louis R, Hunter, David J, Mohlke, Karen L, Uusitupa, Matti, Adrienne Cupples, L, Rankinen, Tuomo, Orho-Melander, Marju, Wang, Tao, Chasman, Daniel I, Franks, Paul W, Sørensen, Thorkild I A, Hu, Frank B, Loos, Ruth J F, Nettleton, Jennifer A, Qi, Lu, Qi, Qibin, Oskari Kilpeläinen, Tuomas, Downer, Mary K, Tanaka, Toshiko, Smith, Caren E, Sluijs, Ivonne, Sonestedt, Emily, Chu, Audrey Y, Renström, Frida, Lin, Xiaochen, Angquist, Lars H, Huang, Jinyan, Liu, Zhonghua, Li, Yanping, Asif Ali, Muhammad, Xu, Min, Ahluwalia, Tarun Veer Singh, Boer, Jolanda M A, Chen, Peng, Daimon, Makoto, Eriksson, Johan, Perola, Markus, Friedlander, Yechiel, Gao, Yu-Tang, Heppe, Denise H M, Holloway, John W, Houston, Denise K, Kanoni, Stavroula, Kim, Yu-Mi, Laaksonen, Maarit A, Jääskeläinen, Tiina, Lee, Nanette R, Lehtimäki, Terho, Lemaitre, Rozenn N, Lu, Wei, Luben, Robert N, Manichaikul, Ani, Männistö, Satu, Marques-Vidal, Pedro, Monda, Keri L, Ngwa, Julius S, Perusse, Louis, van Rooij, Frank J A, Xiang, Yong-Bing, Wen, Wanqing, Wojczynski, Mary K, Zhu, Jingwen, Borecki, Ingrid B, Bouchard, Claude, Cai, Qiuyin, Cooper, Cyrus, Dedoussis, George V, Deloukas, Panos, Ferrucci, Luigi, Forouhi, Nita G, Hansen, Torben, Christiansen, Lene, Hofman, Albert, Johansson, Ingegerd, Jørgensen, Torben, Karasawa, Shigeru, Khaw, Kay-Tee, Kim, Mi-Kyung, Kristiansson, Kati, Li, Huaixing, Lin, Xu, Liu, Yongmei, Lohman, Kurt K, Long, Jirong, Mikkilä, Vera, Mozaffarian, Dariush, North, Kari, Pedersen, Oluf, Raitakari, Olli, Rissanen, Harri, Tuomilehto, Jaakko, van der Schouw, Yvonne T, Uitterlinden, André G, Carola Zillikens, M, Franco, Oscar H, Shyong Tai, E, Ou Shu, Xiao, Siscovick, David S, Toft, Ulla, Monique Verschuren, W M, Vollenweider, Peter, Wareham, Nicholas J, Witteman, Jacqueline C M, Zheng, Wei, Ridker, Paul M, Kang, Jae H, Liang, Liming, Jensen, Majken K, Curhan, Gary C, Pasquale, Louis R, Hunter, David J, Mohlke, Karen L, Uusitupa, Matti, Adrienne Cupples, L, Rankinen, Tuomo, Orho-Melander, Marju, Wang, Tao, Chasman, Daniel I, Franks, Paul W, Sørensen, Thorkild I A, Hu, Frank B, Loos, Ruth J F, Nettleton, Jennifer A, and Qi, Lu

Abstract

FTO is the strongest known genetic susceptibility locus for obesity. Experimental studies in animals suggest the potential roles of FTO in regulating food intake. The interactive relation among FTO variants, dietary intake and body mass index (BMI) is complex and results from previous often small-scale studies in humans are highly inconsistent. We performed large-scale analyses based on data from 177 330 adults (154 439 Whites, 5776 African Americans and 17 115 Asians) from 40 studies to examine: (i) the association between the FTO-rs9939609 variant (or a proxy single-nucleotide polymorphism) and total energy and macronutrient intake and (ii) the interaction between the FTO variant and dietary intake on BMI. The minor allele (A-allele) of the FTO-rs9939609 variant was associated with higher BMI in Whites (effect per allele = 0.34 [0.31, 0.37] kg/m(2), P = 1.9 × 10(-105)), and all participants (0.30 [0.30, 0.35] kg/m(2), P = 3.6 × 10(-107)). The BMI-increasing allele of the FTO variant showed a significant association with higher dietary protein intake (effect per allele = 0.08 [0.06, 0.10] %, P = 2.4 × 10(-16)), and relative weak associations with lower total energy intake (-6.4 [-10.1, -2.6] kcal/day, P = 0.001) and lower dietary carbohydrate intake (-0.07 [-0.11, -0.02] %, P = 0.004). The associations with protein (P = 7.5 × 10(-9)) and total energy (P = 0.002) were attenuated but remained significant after adjustment for BMI. We did not find significant interactions between the FTO variant and dietary intake of total energy, protein, carbohydrate or fat on BMI. Our findings suggest a positive association between the BMI-increasing allele of FTO variant and higher dietary protein intake and offer insight into potential link between FTO, dietary protein intake and adiposity.

Published
2014

3. FTO genetic variants, dietary intake and body mass index:insights from 177 330 individuals

Author

Qi, Qibin, Oskari Kilpeläinen, Tuomas, Downer, Mary K, Tanaka, Toshiko, Smith, Caren E, Sluijs, Ivonne, Sonestedt, Emily, Chu, Audrey Y, Renström, Frida, Lin, Xiaochen, Angquist, Lars H, Huang, Jinyan, Liu, Zhonghua, Li, Yanping, Asif Ali, Muhammad, Xu, Min, Ahluwalia, Tarun Veer Singh, Boer, Jolanda M A, Chen, Peng, Daimon, Makoto, Eriksson, Johan, Perola, Markus, Friedlander, Yechiel, Gao, Yu-Tang, Heppe, Denise H M, Holloway, John W, Houston, Denise K, Kanoni, Stavroula, Kim, Yu-Mi, Laaksonen, Maarit A, Jääskeläinen, Tiina, Lee, Nanette R, Lehtimäki, Terho, Lemaitre, Rozenn N, Lu, Wei, Luben, Robert N, Manichaikul, Ani, Männistö, Satu, Marques-Vidal, Pedro, Monda, Keri L, Ngwa, Julius S, Perusse, Louis, van Rooij, Frank J A, Xiang, Yong-Bing, Wen, Wanqing, Wojczynski, Mary K, Zhu, Jingwen, Borecki, Ingrid B, Bouchard, Claude, Cai, Qiuyin, Cooper, Cyrus, Dedoussis, George V, Deloukas, Panos, Ferrucci, Luigi, Forouhi, Nita G, Hansen, Torben, Christiansen, Lene, Hofman, Albert, Johansson, Ingegerd, Jørgensen, Torben, Karasawa, Shigeru, Khaw, Kay-Tee, Kim, Mi-Kyung, Kristiansson, Kati, Li, Huaixing, Lin, Xu, Liu, Yongmei, Lohman, Kurt K, Long, Jirong, Mikkilä, Vera, Mozaffarian, Dariush, North, Kari, Pedersen, Oluf, Raitakari, Olli, Rissanen, Harri, Tuomilehto, Jaakko, van der Schouw, Yvonne T, Uitterlinden, André G, Carola Zillikens, M, Franco, Oscar H, Shyong Tai, E, Ou Shu, Xiao, Siscovick, David S, Toft, Ulla, Monique Verschuren, W M, Vollenweider, Peter, Wareham, Nicholas J, Witteman, Jacqueline C M, Zheng, Wei, Ridker, Paul M, Kang, Jae H, Liang, Liming, Jensen, Majken K, Curhan, Gary C, Pasquale, Louis R, Hunter, David J, Mohlke, Karen L, Uusitupa, Matti, Adrienne Cupples, L, Rankinen, Tuomo, Orho-Melander, Marju, Wang, Tao, Chasman, Daniel I, Franks, Paul W, Sørensen, Thorkild I A, Hu, Frank B, Loos, Ruth J F, Nettleton, Jennifer A, Qi, Lu, Qi, Qibin, Oskari Kilpeläinen, Tuomas, Downer, Mary K, Tanaka, Toshiko, Smith, Caren E, Sluijs, Ivonne, Sonestedt, Emily, Chu, Audrey Y, Renström, Frida, Lin, Xiaochen, Angquist, Lars H, Huang, Jinyan, Liu, Zhonghua, Li, Yanping, Asif Ali, Muhammad, Xu, Min, Ahluwalia, Tarun Veer Singh, Boer, Jolanda M A, Chen, Peng, Daimon, Makoto, Eriksson, Johan, Perola, Markus, Friedlander, Yechiel, Gao, Yu-Tang, Heppe, Denise H M, Holloway, John W, Houston, Denise K, Kanoni, Stavroula, Kim, Yu-Mi, Laaksonen, Maarit A, Jääskeläinen, Tiina, Lee, Nanette R, Lehtimäki, Terho, Lemaitre, Rozenn N, Lu, Wei, Luben, Robert N, Manichaikul, Ani, Männistö, Satu, Marques-Vidal, Pedro, Monda, Keri L, Ngwa, Julius S, Perusse, Louis, van Rooij, Frank J A, Xiang, Yong-Bing, Wen, Wanqing, Wojczynski, Mary K, Zhu, Jingwen, Borecki, Ingrid B, Bouchard, Claude, Cai, Qiuyin, Cooper, Cyrus, Dedoussis, George V, Deloukas, Panos, Ferrucci, Luigi, Forouhi, Nita G, Hansen, Torben, Christiansen, Lene, Hofman, Albert, Johansson, Ingegerd, Jørgensen, Torben, Karasawa, Shigeru, Khaw, Kay-Tee, Kim, Mi-Kyung, Kristiansson, Kati, Li, Huaixing, Lin, Xu, Liu, Yongmei, Lohman, Kurt K, Long, Jirong, Mikkilä, Vera, Mozaffarian, Dariush, North, Kari, Pedersen, Oluf, Raitakari, Olli, Rissanen, Harri, Tuomilehto, Jaakko, van der Schouw, Yvonne T, Uitterlinden, André G, Carola Zillikens, M, Franco, Oscar H, Shyong Tai, E, Ou Shu, Xiao, Siscovick, David S, Toft, Ulla, Monique Verschuren, W M, Vollenweider, Peter, Wareham, Nicholas J, Witteman, Jacqueline C M, Zheng, Wei, Ridker, Paul M, Kang, Jae H, Liang, Liming, Jensen, Majken K, Curhan, Gary C, Pasquale, Louis R, Hunter, David J, Mohlke, Karen L, Uusitupa, Matti, Adrienne Cupples, L, Rankinen, Tuomo, Orho-Melander, Marju, Wang, Tao, Chasman, Daniel I, Franks, Paul W, Sørensen, Thorkild I A, Hu, Frank B, Loos, Ruth J F, Nettleton, Jennifer A, and Qi, Lu

Abstract

FTO is the strongest known genetic susceptibility locus for obesity. Experimental studies in animals suggest the potential roles of FTO in regulating food intake. The interactive relation among FTO variants, dietary intake and body mass index (BMI) is complex and results from previous often small-scale studies in humans are highly inconsistent. We performed large-scale analyses based on data from 177 330 adults (154 439 Whites, 5776 African Americans and 17 115 Asians) from 40 studies to examine: (i) the association between the FTO-rs9939609 variant (or a proxy single-nucleotide polymorphism) and total energy and macronutrient intake and (ii) the interaction between the FTO variant and dietary intake on BMI. The minor allele (A-allele) of the FTO-rs9939609 variant was associated with higher BMI in Whites (effect per allele = 0.34 [0.31, 0.37] kg/m(2), P = 1.9 × 10(-105)), and all participants (0.30 [0.30, 0.35] kg/m(2), P = 3.6 × 10(-107)). The BMI-increasing allele of the FTO variant showed a significant association with higher dietary protein intake (effect per allele = 0.08 [0.06, 0.10] %, P = 2.4 × 10(-16)), and relative weak associations with lower total energy intake (-6.4 [-10.1, -2.6] kcal/day, P = 0.001) and lower dietary carbohydrate intake (-0.07 [-0.11, -0.02] %, P = 0.004). The associations with protein (P = 7.5 × 10(-9)) and total energy (P = 0.002) were attenuated but remained significant after adjustment for BMI. We did not find significant interactions between the FTO variant and dietary intake of total energy, protein, carbohydrate or fat on BMI. Our findings suggest a positive association between the BMI-increasing allele of FTO variant and higher dietary protein intake and offer insight into potential link between FTO, dietary protein intake and adiposity.

Published
2014

4. SN 2022ann: a Type Icn supernova from a dwarf galaxy that reveals helium in its circumstellar environment

Author

Davis, KW, Taggart, K, Tinyanont, S, Foley, RJ, Villar, VA, Izzo, L, Angus, CR, Bustamante-Rosell, MJ, Coulter, DA, Earl, N, Farias, D, Hjorth, J, Huber, ME, Jones, DO, Kelly, PL, Kilpatrick, CD, Langeroodi, D, Miao, HY, Pellegrino, CM, Ramirez-Ruiz, E, Ransome, CL, Rest, S, Siebert, MR, Terreran, G, Thornton, IM, Yadavalli, SK, Zeimann, GR, Auchettl, K, Bom, CR, Brink, TG, Burke, J, Camacho-Neves, Y, Chambers, KC, De Boer, TJL, Demarchi, L, Filippenko, AV, Galbany, L, Gall, C, Gao, H, Herpich, FR, Howell, DA, Jacobson-Galan, WV, Jha, SW, Kanaan, A, Khetan, N, Kwok, LA, Lai, Z, Larison, C, Lin, CC, Loertscher, KC, Magnier, EA, Mccully, C, McGill, P, Newsome, M, Padilla Gonzalez, E, Pan, YC, Rest, A, Rho, J, Ribeiro, T, Santos, A, Schoenell, W, Sharief, SN, Smith, KW, Wainscoat, RJ, Wang, Q, Zenati, Y, Zheng, W, Davis, KW, Taggart, K, Tinyanont, S, Foley, RJ, Villar, VA, Izzo, L, Angus, CR, Bustamante-Rosell, MJ, Coulter, DA, Earl, N, Farias, D, Hjorth, J, Huber, ME, Jones, DO, Kelly, PL, Kilpatrick, CD, Langeroodi, D, Miao, HY, Pellegrino, CM, Ramirez-Ruiz, E, Ransome, CL, Rest, S, Siebert, MR, Terreran, G, Thornton, IM, Yadavalli, SK, Zeimann, GR, Auchettl, K, Bom, CR, Brink, TG, Burke, J, Camacho-Neves, Y, Chambers, KC, De Boer, TJL, Demarchi, L, Filippenko, AV, Galbany, L, Gall, C, Gao, H, Herpich, FR, Howell, DA, Jacobson-Galan, WV, Jha, SW, Kanaan, A, Khetan, N, Kwok, LA, Lai, Z, Larison, C, Lin, CC, Loertscher, KC, Magnier, EA, Mccully, C, McGill, P, Newsome, M, Padilla Gonzalez, E, Pan, YC, Rest, A, Rho, J, Ribeiro, T, Santos, A, Schoenell, W, Sharief, SN, Smith, KW, Wainscoat, RJ, Wang, Q, Zenati, Y, and Zheng, W

Abstract

We present optical and near-infrared (NIR) observations of the Type Icn supernova (SN Icn) 2022ann, the fifth member of its newly identified class of SNe. Its early optical spectra are dominated by narrow carbon and oxygen P-Cygni features with absorption velocities of ∼800 km s−1; slower than other SNe Icn and indicative of interaction with a dense, H/He-poor circumstellar medium (CSM) that is outflowing slower than typical Wolf–Rayet wind velocities of >1000 km s−1. We identify helium in NIR spectra 2 weeks after maximum and in optical spectra at 3 weeks, demonstrating that the CSM is not fully devoid of helium. Unlike other SNe Icn, the spectra of SN 2022ann never develop broad features from SN ejecta, including in the nebular phase. Compared to other SNe Icn, SN 2022ann has a low luminosity (o-band absolute magnitude of ∼−17.7), and evolves slowly. The bolometric light curve is well-modelled by 4.8 M⊙ of SN ejecta interacting with 1.3 M⊙ of CSM. We place an upper limit of 0.04 M⊙ of 56Ni synthesized in the explosion. The host galaxy is a dwarf galaxy with a stellar mass of 107.34 M⊙ (implied metallicity of log(Z/Z⊙) ≈ 0.10) and integrated star-formation rate of log (SFR) = −2.20 M⊙ yr−1; both lower than 97 per cent of galaxies observed to produce core-collapse supernovae, although consistent with star-forming galaxies on the galaxy Main Sequence. The low CSM velocity, nickel and ejecta masses, and likely low-metallicity environment disfavour a single Wolf–Rayet progenitor star. Instead, a binary companion is likely required to adequately strip the progenitor and produce a low-velocity outflow.

Published
2023

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