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1. Comparison of isoprene chemical mechanisms under atmospheric night-time conditions in chamber experiments: evidence of hydroperoxy aldehydes and epoxy products from NO3 oxidation

Author

P. T. M. Carlsson, L. Vereecken, A. Novelli, F. Bernard, S. S. Brown, B. Brownwood, C. Cho, J. N. Crowley, P. Dewald, P. M. Edwards, N. Friedrich, J. L. Fry, M. Hallquist, L. Hantschke, T. Hohaus, S. Kang, J. Liebmann, A. W. Mayhew, T. Mentel, D. Reimer, F. Rohrer, J. Shenolikar, R. Tillmann, E. Tsiligiannis, R. Wu, A. Wahner, A. Kiendler-Scharr, and H. Fuchs

Subjects
Physics, QC1-999, Chemistry, QD1-999
Abstract

The gas-phase reaction of isoprene with the nitrate radical (NO3) was investigated in experiments in the outdoor SAPHIR chamber under atmospherically relevant conditions specifically with respect to the chemical lifetime and fate of nitrato-organic peroxy radicals (RO2). Observations of organic products were compared to concentrations expected from different chemical mechanisms: (1) the Master Chemical Mechanism, which simplifies the NO3 isoprene chemistry by only considering one RO2 isomer; (2) the chemical mechanism derived from experiments in the Caltech chamber, which considers different RO2 isomers; and (3) the FZJ-NO3 isoprene mechanism derived from quantum chemical calculations, which in addition to the Caltech mechanism includes equilibrium reactions of RO2 isomers, unimolecular reactions of nitrate RO2 radicals and epoxidation reactions of nitrate alkoxy radicals. Measurements using mass spectrometer instruments give evidence that the new reactions pathways predicted by quantum chemical calculations play a role in the NO3 oxidation of isoprene. Hydroperoxy aldehyde (HPALD) species, which are specific to unimolecular reactions of nitrate RO2, were detected even in the presence of an OH scavenger, excluding the possibility that concurrent oxidation by hydroxyl radicals (OH) is responsible for their formation. In addition, ion signals at masses that can be attributed to epoxy compounds, which are specific to the epoxidation reaction of nitrate alkoxy radicals, were detected. Measurements of methyl vinyl ketone (MVK) and methacrolein (MACR) concentrations confirm that the decomposition of nitrate alkoxy radicals implemented in the Caltech mechanism cannot compete with the ring-closure reactions predicted by quantum chemical calculations. The validity of the FZJ-NO3 isoprene mechanism is further supported by a good agreement between measured and simulated hydroxyl radical (OH) reactivity. Nevertheless, the FZJ-NO3 isoprene mechanism needs further investigations with respect to the absolute importance of unimolecular reactions of nitrate RO2 and epoxidation reactions of nitrate alkoxy radicals. Absolute concentrations of specific organic nitrates such as nitrate hydroperoxides would be required to experimentally determine product yields and branching ratios of reactions but could not be measured in the chamber experiments due to the lack of calibration standards for these compounds. The temporal evolution of mass traces attributed to product species such as nitrate hydroperoxides, nitrate carbonyl and nitrate alcohols as well as hydroperoxy aldehydes observed by the mass spectrometer instruments demonstrates that further oxidation by the nitrate radical and ozone at atmospheric concentrations is small on the timescale of one night (12 h) for typical oxidant concentrations. However, oxidation by hydroxyl radicals present at night and potentially also produced from the decomposition of nitrate alkoxy radicals can contribute to their nocturnal chemical loss.

Published
2023
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2. Investigation of the limonene photooxidation by OH at different NO concentrations in the atmospheric simulation chamber SAPHIR (Simulation of Atmospheric PHotochemistry In a large Reaction Chamber)

Author

J. Y. S. Pang, A. Novelli, M. Kaminski, I.-H. Acir, B. Bohn, P. T. M. Carlsson, C. Cho, H.-P. Dorn, A. Hofzumahaus, X. Li, A. Lutz, S. Nehr, D. Reimer, F. Rohrer, R. Tillmann, R. Wegener, A. Kiendler-Scharr, A. Wahner, and H. Fuchs

Subjects
Physics, QC1-999, Chemistry, QD1-999
Abstract

The oxidation of limonene by the hydroxyl (OH) radical and ozone (O3) was investigated in the atmospheric simulation chamber SAPHIR (Simulation of Atmospheric PHotochemistry In a large Reaction Chamber) in experiments performed at different nitric oxide (NO) mixing ratios from nearly 0 up to 10 ppbv. For the experiments dominated by OH oxidation, the formaldehyde (HCHO) yield was experimentally determined and found to be (12 ± 3), (13 ± 3), and (32 ± 5) % for experiments with low (∼ 0.1 ppbv), medium (∼ 0.3 ppbv), and high NO (5 to 10 ppbv), respectively. The yield in an ozonolysis-only experiment was (10 ± 1) %, which agrees with previous laboratory studies. The experimental yield of the first-generation organic nitrates from limonene–OH oxidation is calculated as (34 ± 5) %, about 11 % higher than the value in the Master Chemical Mechanism (MCM), which is derived from structure–activity relationships (SARs). Time series of measured radicals, trace-gas concentrations, and OH reactivity are compared to results from zero-dimensional chemical box model calculations applying MCM v3.3.1. Modeled OH reactivity is 5 to 10 s−1 (25 % to 33 % of the OH reactivity at the start of the experiment) higher than measured values at the end of the experiments under all chemical conditions investigated, suggesting either that there are unaccounted loss processes of limonene oxidation products or that products are less reactive toward OH. In addition, model calculations underestimate measured hydroperoxyl radical (HO2) concentrations by 20 % to 90 % and overestimate organic peroxyl radical (RO2) concentrations by 50 % to 300 %. The largest deviations are found in low-NO experiments and in the ozonolysis experiment. An OH radical budget analysis, which uses only measured quantities, shows that the budget is closed in most of the experiments. A similar budget analysis for RO2 radicals suggests that an additional RO2 loss rate constant of about (1–6) × 10−2 s−1 for first-generation RO2 is required to match the measured RO2 concentrations in all experiments. Sensitivity model runs indicate that additional reactions converting RO2 to HO2 at a rate constant of about (1.7–3.0) × 10−2 s−1 would improve the model–measurement agreement of NOx, HO2, and RO2 concentrations and OH reactivity. Reaction pathways that could lead to the production of additional OH and HO2 are discussed, which include isomerization reactions of RO2 from the oxidation of limonene, different branching ratios for the reaction of RO2 with HO2, and a faster rate constant for RO2 recombination reactions. As the exact chemical mechanisms of the additional HO2 and OH sources could not be identified, further work needs to focus on quantifying organic product species and organic peroxy radicals from limonene oxidation.

Published
2022
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3. Atmospheric photooxidation and ozonolysis of Δ3-carene and 3-caronaldehyde: rate constants and product yields

Author

L. Hantschke, A. Novelli, B. Bohn, C. Cho, D. Reimer, F. Rohrer, R. Tillmann, M. Glowania, A. Hofzumahaus, A. Kiendler-Scharr, A. Wahner, and H. Fuchs

Subjects
Physics, QC1-999, Chemistry, QD1-999
Abstract

The oxidation of Δ3-carene and one of its main oxidation products, caronaldehyde, by the OH radical and O3 was investigated in the atmospheric simulation chamber SAPHIR under atmospheric conditions for NOx mixing ratios below 2 ppbv. Within this study, the rate constants of the reaction of Δ3-carene with OH and O3 and of the reaction of caronaldehyde with OH were determined to be (8.0±0.5)×10-11 cm3 s−1 at 304 K, (4.4±0.2)×10-17 cm3 s−1 at 300 K and (4.6±1.6)×10-11 cm3 s−1 at 300 K, in agreement with previously published values. The yields of caronaldehyde from the reaction of OH and ozone with Δ3-carene were determined to be 0.30±0.05 and 0.06±0.02, respectively. Both values are in reasonably good agreement with reported literature values. An organic nitrate (RONO2) yield from the reaction of NO with RO2 derived from Δ3-carene of 0.25±0.04 was determined from the analysis of the reactive nitrogen species (NOy) in the SAPHIR chamber. The RONO2 yield of the reaction of NO with RO2 derived from the reaction of caronaldehyde with OH was found to be 0.10±0.02. The organic nitrate yields of Δ3-carene and caronaldehyde oxidation with OH are reported here for the first time in the gas phase. An OH yield of 0.65±0.10 was determined from the ozonolysis of Δ3-carene. Calculations of production and destruction rates of the sum of hydroxyl and peroxy radicals (ROx=OH+HO2+RO2) demonstrated that there were no unaccounted production or loss processes of radicals in the oxidation of Δ3-carene for conditions of the chamber experiments. In an OH-free experiment with added OH scavenger, the photolysis frequency of caronaldehyde was obtained from its photolytical decay. The experimental photolysis frequency was a factor of 7 higher than the value calculated from the measured solar actinic flux density, an absorption cross section from the literature and an assumed effective quantum yield of unity for photodissociation.

Published
2021
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4. Evolution of NO3 reactivity during the oxidation of isoprene

Author

P. Dewald, J. M. Liebmann, N. Friedrich, J. Shenolikar, J. Schuladen, F. Rohrer, D. Reimer, R. Tillmann, A. Novelli, C. Cho, K. Xu, R. Holzinger, F. Bernard, L. Zhou, W. Mellouki, S. S. Brown, H. Fuchs, J. Lelieveld, and J. N. Crowley

Subjects
Physics, QC1-999, Chemistry, QD1-999
Abstract

In a series of experiments in an atmospheric simulation chamber (SAPHIR,1 Forschungszentrum Jülich, Germany), NO3 reactivity (kNO3) resulting from the reaction of NO3 with isoprene and stable trace gases formed as products was measured directly using a flow tube reactor coupled to a cavity ring-down spectrometer (FT-CRDS). The experiments were carried out in both dry and humid air with variation of the initial mixing ratios of ozone (50–100 ppbv), isoprene (3–22 ppbv) and NO2 (5–30 ppbv). kNO3 was in excellent agreement with values calculated from the isoprene mixing ratio and the rate coefficient for the reaction of NO3 with isoprene. This result serves to confirm that the FT-CRDS returns accurate values of kNO3 even at elevated NO2 concentrations and to show that reactions of NO3 with stable reaction products like non-radical organic nitrates do not contribute significantly to NO3 reactivity during the oxidation of isoprene. A comparison of kNO3 with NO3 reactivities calculated from NO3 mixing ratios and NO3 production rates suggests that organic peroxy radicals and HO2 account for ∼50 % of NO3 losses. This contradicts predictions based on numerical simulations using the Master Chemical Mechanism (MCM version 3.3.1) unless the rate coefficient for reaction between NO3 and isoprene-derived RO2 is roughly doubled to ∼5×10-12 cm3 molecule−1 s−1.

Published
2020
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5. Importance of isomerization reactions for OH radical regeneration from the photo-oxidation of isoprene investigated in the atmospheric simulation chamber SAPHIR

Author

A. Novelli, L. Vereecken, B. Bohn, H.-P. Dorn, G. I. Gkatzelis, A. Hofzumahaus, F. Holland, D. Reimer, F. Rohrer, S. Rosanka, D. Taraborrelli, R. Tillmann, R. Wegener, Z. Yu, A. Kiendler-Scharr, A. Wahner, and H. Fuchs

Subjects
Physics, QC1-999, Chemistry, QD1-999
Abstract

Theoretical, laboratory, and chamber studies have shown fast regeneration of the hydroxyl radical (OH) in the photochemistry of isoprene, largely due to unimolecular reactions which were previously thought not to be important under atmospheric conditions. Based on early field measurements, nearly complete regeneration was hypothesized for a wide range of tropospheric conditions, including areas such as the rainforest where slow regeneration of OH radicals is expected due to low concentrations of nitric oxide (NO). In this work the OH regeneration in isoprene oxidation is directly quantified for the first time through experiments covering a wide range of atmospherically relevant NO levels (between 0.15 and 2 ppbv – parts per billion by volume) in the atmospheric simulation chamber SAPHIR. These conditions cover remote areas partially influenced by anthropogenic NO emissions, giving a regeneration efficiency of OH close to 1, and areas like the Amazonian rainforest with very low NO, resulting in a surprisingly high regeneration efficiency of 0.5, i.e. a factor of 2 to 3 higher than explainable in the absence of unimolecular reactions. The measured radical concentrations were compared to model calculations, and the best agreement was observed when at least 50 % of the total loss of isoprene peroxy radicals conformers (weighted by their abundance) occurs via isomerization reactions for NO lower than 0.2 ppbv. For these levels of NO, up to 50 % of the OH radicals are regenerated from the products of the 1,6 α-hydroxy-hydrogen shift (1,6-H shift) of Z-δ-RO2 radicals through the photolysis of an unsaturated hydroperoxy aldehyde (HPALD) and/or through the fast aldehydic hydrogen shift (rate constant ∼10 s−1 at 300 K) in di-hydroperoxy carbonyl peroxy radicals (di-HPCARP-RO2), depending on their relative yield. The agreement between all measured and modelled trace gases (hydroxyl, hydroperoxy, and organic peroxy radicals, carbon monoxide, and the sum of methyl vinyl ketone, methacrolein, and hydroxyl hydroperoxides) is nearly independent of the adopted yield of HPALD and di-HPCARP-RO2 as both degrade relatively fast ( h), forming the OH radical and CO among other products. Taking into consideration this and earlier isoprene studies, considerable uncertainties remain on the distribution of oxygenated products, which affect radical levels and organic aerosol downwind of unpolluted isoprene-dominated regions.

Published
2020
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6. Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry

Author

Jitendra PS. Sawhney, Veerappa A. Kothiwale, Vikas Bisne, Rajashekhar Durgaprasad, Praveen Jadhav, Manoj Chopda, Velam Vanajakshamma, Ramdhan Meena, Govindan Vijayaraghavan, Kamaldeep Chawla, Jagan Allu, Karen S. Pieper, A. John Camm, Ajay K. Kakkar, Jean-Pierre Bassand, David A. Fitzmaurice, Samuel Z. Goldhaber, Shinya Goto, Sylvia Haas, Werner Hacke, Lorenzo G. Mantovani, Frank Misselwitz, Alexander G.G. Turpie, Martin van Eickels, Freek W.A. Verheugt, Gloria Kayani, Keith A.A. Fox, Bernard J. Gersh, Hector Lucas Luciardi, Harry Gibbs, Marianne Brodmann, Frank Cools, Antonio Carlos Pereira Barretto, Stuart J. Connolly, Alex Spyropoulos, John Eikelboom, Ramon Corbalan, Dayi Hu, Petr Jansky, Jørn Dalsgaard Nielsen, Hany Ragy, Pekka Raatikainen, Jean-Yves Le Heuzey, Harald Darius, Matyas Keltai, Sanjay Kakkar, Jitendra Pal Singh Sawhney, Giancarlo Agnelli, Giuseppe Ambrosio, Yukihiro Koretsune, Carlos Jerjes Sánchez Díaz, Hugo Ten Cate, Dan Atar, Janina Stepinska, Elizaveta Panchenko, Toon Wei Lim, Barry Jacobson, Seil Oh, Xavier Viñolas, Marten Rosenqvist, Jan Steffel, Pantep Angchaisuksiri, Ali Oto, Alex Parkhomenko, Wael Al Mahmeed, David Fitzmaurice, D.Y. Hu, K.N. Chen, Y.S. Zhao, H.Q. Zhang, J.Z. Chen, S.P. Cao, D.W. Wang, Y.J. Yang, W.H. Li, Y.H. Yin, G.Z. Tao, P. Yang, Y.M. Chen, S.H. He, Ying Wang, Yong Wang, G.S. Fu, X. Li, T.G. Wu, X.S. Cheng, X.W. Yan, R.P. Zhao, M.S. Chen, L.G. Xiong, P. Chen, Y. Jiao, Y. Guo, L. Xue, F.Z. Wang, H. Li, Z.M. Yang, C.L. Bai, J. Chen, J.Y. Chen, X. Chen, S. Feng, Q.H. Fu, X.J. Gao, W.N. Guo, R.H. He, X.A. He, X.S. Hu, X.F. Huang, B. Li, J. Li, L. Li, Y.H. Li, T.T. Liu, W.L. Liu, Y.Y. Liu, Z.C. Lu, X.L. Luo, T.Y. Ma, J.Q. Peng, X. Sheng, X.J. Shi, Y.H. Sun, G. Tian, K. Wang, L. Wang, R.N. Wu, Q. Xie, R.Y. Xu, J.S. Yang, L.L. Yang, Q. Yang, Y. Ye, H.Y. Yu, J.H. Yu, T. Yu, H. Zhai, Q. Zhan, G.S. Zhang, Q. Zhang, R. Zhang, Y. Zhang, W.Y. Zheng, B. Zhou, Z.H. Zhou, X.Y. Zhu, S. Kakkar, J.P.S. Sawhney, P. Jadhav, R. Durgaprasad, A.G. Ravi Shankar, R.K. Rajput, K. Bhargava, R. Sarma, A. Srinivas, D. Roy, U.M. Nagamalesh, M. Chopda, R. Kishore, G. Kulkarni, P. Chandwani, R.A. Pothiwala, M. Padinhare Purayil, S. Shah, K. Chawla, V.A. Kothiwale, B. Raghuraman, G. Vijayaraghavan, V.M. Vijan, G. Bantwal, V. Bisne, A. Khan, J.B. Gupta, S. Kumar, D. Jain, S. Abraham, D. Adak, A. Barai, H. Begum, P. Bhattacharjee, M. Dargude, D. Davies, B. Deshpande, P. Dhakrao, V. Dhyani, S. Duhan, M. Earath, A. Ganatra, S. Giradkar, V. Jain, R. Karthikeyan, L. Kasala, S. Kaur, S. Krishnappa, A. Lawande, B. Lokesh, N. Madarkar, R. Meena, P. More, D. Naik, K. Prashanth, M. Rao, N.M. Rao, N. Sadhu, D. Shah, M. Sharma, P. Shiva, S. Singhal, S. Suresh, V. Vanajakshamma, S.G. Panse, Y. Koretsune, S. Kanamori, K. Yamamoto, K. Kumagai, Y. Katsuda, K. Sadamatsu, F. Toyota, Y. Mizuno, I. Misumi, H. Noguchi, S. Ando, T. Suetsugu, M. Minamoto, Hiroshi Oda, K. Shiraishi, S. Adachi, K. Chiba, H. Norita, M. Tsuruta, T. Koyanagi, H. Ando, T. Higashi, K. Okada, S. Azakami, S. Komaki, K. Kumeda, T. Murayama, J. Matsumura, Y. Oba, R. Sonoda, K. Goto, K. Minoda, Y. Haraguchi, H. Suefuji, H. Miyagi, H. Kato, Tadashi Nakamura, Tsugihiro Nakamura, H. Nandate, R. Zaitsu, Yoshihisa Fujiura, A. Yoshimura, H. Numata, J. Ogawa, H. Tatematsu, Y. Kamogawa, K. Murakami, Y. Wakasa, M. Yamasawa, H. Maekawa, S. Abe, H. Kihara, S. Tsunoda, Katsumi Saito, Kazuyuki Saito, T. Fudo, K. Obunai, H. Tachibana, I. Oba, T. Kuwahata, S. Higa, M. Gushiken, T. Eto, H. Yoshida, D. Ikeda, Yoshitake Fujiura, M. Ishizawa, M. Nakatsuka, K. Murata, C. Ogurusu, M. Shimoyama, M. Akutsu, I. Takamura, F. Hoshino, N. Yokota, T. Iwao, K. Tsuchida, M. Takeuchi, Y. Hatori, Y. Kitami, Yoichi Nakamura, R. Oyama, M. Ageta, Hiroyuki Oda, Y. Go, K. Mishima, T. Unoki, S. Morii, Yuhei Shiga, H. Sumi, T. Nagatomo, K. Sanno, K. Fujisawa, Y. Atsuchi, T. Nagoshi, T. Seto, T. Tabuchi, M. Kameko, K. Nii, K. Oshiro, H. Takezawa, S. Nagano, N. Miyamoto, M. Iwaki, Yuichiro Nakamura, M. Fujii, M. Okawa, Masahiko Abe, Masatake Abe, Mitsunori Abe, T. Saito, T. Mito, K. Nagao, J. Minami, T. Mita, I. Sakuma, T. Taguchi, S. Marusaki, H. Doi, M. Tanaka, T. Fujito, M. Matsuta, T. Kusumoto, S. Kakinoki, K. Ashida, N. Yoshizawa, J. Agata, O. Arasaki, M. Manita, M. Ikemura, S. Fukuoka, H. Murakami, S. Matsukawa, Y. Hata, T. Taniguchi, T. Ko, H. Kubo, M. Imamaki, M. Akiyama, M. Inagaki, H. Odakura, T. Ueda, Y. Katsube, A. Nakata, H. Watanabe, M. Techigawara, M. Igarashi, K. Taga, T. Kimura, S. Tomimoto, M. Shibuya, M. Nakano, K. Ito, T. Seo, S. Hiramitsu, H. Hosokawa, M. Hoshiai, M. Hibino, K. Miyagawa, Hajime Horie, N. Sugishita, Yukio Shiga, A. Soma, K. Neya, Tetsuro Yoshida, Tomoki Yoshida, M. Mizuguchi, M. Ishiguro, T. Minagawa, M. Wada, H. Mukawa, F. Okuda, S. Nagasaka, Y. Abe, Sen Adachi, Susumu Adachi, T. Adachi, K. Akahane, T. Amano, K. Aoki, T. Aoyama, H. Arai, S. Arima, T. Arino, H. Asano, T. Asano, J. Azuma, T. Baba, T. Betsuyaku, H. Chibana, H. Date, J. Doiuchi, Y. Emura, M. Endo, Y. Fujii, R. Fujiki, A. Fujisawa, Y. Fujisawa, T. Fukuda, T. Fukui, N. Furukawa, T. Furukawa, W. Furumoto, T. Goto, M. Hamaoka, N. Hanazono, K. Hasegawa, T. Hatsuno, Y. Hayashi, K. Higuchi, K. Hirasawa, H. Hirayama, M. Hirose, S. Hirota, M. Honda, Hideki Horie, T. Ido, O. Iiji, H. Ikeda, K. Ikeda, K. Ikeoka, M. Imaizumi, H. Inaba, T. Inoue, F. Iseki, A. Ishihara, N. Ishioka, N. Ito, T. Iwase, H. Kakuda, J. Kamata, H. Kanai, H. Kanda, M. Kaneko, H. Kano, T. Kasai, T. Kato, Y. Kato, Y. Kawada, K. Kawai, K. Kawakami, S. Kawakami, T. Kawamoto, S. Kawano, J. Kim, T. Kira, H. Kitazawa, H. Kitazumi, T. Kito, T. Kobayashi, T. Koeda, J. Kojima, H. Komatsu, I. Komatsu, Y. Koshibu, T. Kotani, T. Kozuka, Y. Kumai, T. Kumazaki, I. Maeda, K. Maeda, Y. Maruyama, S. Matsui, K. Matsushita, Y. Matsuura, K. Mineoi, H. Mitsuhashi, N. Miura, S. Miyaguchi, S. Miyajima, H. Miyamoto, A. Miyashita, S. Miyata, I. Mizuguchi, A. Mizuno, T. Mori, O. Moriai, K. Morishita, O. Murai, Sho Nagai, Shunichi Nagai, E. Nagata, H. Nagata, A. Nakagomi, S. Nakahara, M. Nakamura, R. Nakamura, N. Nakanishi, T. Nakayama, R. Nakazato, T. Nanke, J. Nariyama, Y. Niijima, H. Niinuma, Y. Nishida, Y. Nishihata, K. Nishino, H. Nishioka, K. Nishizawa, I. Niwa, K. Nomura, S. Nomura, M. Nozoe, T. Ogawa, N. Ohara, M. Okada, K. Okamoto, H. Okita, M. Okuyama, H. Ono, T. Ono, Y. Onuki Pearce, S. Oriso, A. Ota, E. Otaki, Y. Saito, H. Sakai, N. Sakamoto, Y. Sakamoto, Y. Samejima, Y. Sasagawa, H. Sasaguri, A. Sasaki, T. Sasaki, Kazuki Sato, Kiyoharu Sato, M. Sawano, S. Seki, Y. Sekine, Y. Seta, K. Sezaki, N. Shibata, Y. Shiina, H. Shimono, Y. Shimoyama, T. Shindo, H. Shinohara, R. Shinohe, T. Shinozuka, T. Shirai, T. Shiraiwa, Y. Shozawa, T. Suga, C. Sugimoto, Kazuo Suzuki, Keita Suzuki, Shu Suzuki, Shunji Suzuki, Susumu Suzuki, Y. Suzuki, M. Tada, A. Taguchi, T. Takagi, Y. Takagi, K. Takahashi, S. Takahashi, H. Takai, C. Takanaka, S. Take, H. Takeda, K. Takei, K. Takenaka, T. Tana, G. Tanabe, K. Taya, H. Teragawa, S. Tohyo, S. Toru, Y. Tsuchiya, T. Tsuji, K. Tsuzaki, H. Uchiyama, O. Ueda, Y. Ueyama, N. Wakaki, T. Wakiyama, T. Washizuka, M. Watanabe, T. Yamada, T. Yamagishi, H. Yamaguchi, Kenichi Yamamoto, Kentaro Yamamoto, Kunihiko Yamamoto, T. Yamamoto, M. Yamaura, M. Yamazoe, K. Yasui, Y. Yokoyama, K. Yoshida, T.W. Lim, C.K. Ching, C.G. Foo, J.H. Chow, D.D. Chen, F.R. Jaufeerally, Y.M. Lee, G. Lim, W.T. Lim, S. Thng, S.Y. Yap, C. Yeo, S. Oh, H.N. Pak, J.-B. Kim, J.H. Kim, S.-W. Jang, D.H. Kim, D.R. Ryu, S.W. Park, D.-K. Kim, D.J. Choi, Y.S. Oh, M.-C. Cho, S.-H. Kim, H.-K. Jeon, D.-G. Shin, J.S. Park, H.K. Park, S.-J. Han, J.H. Sung, J.-G. Cho, G.-B. Nam, Y.K. On, H.E. Lim, J.J. Kwak, T.-J. Cha, T.J. Hong, S.H. Park, J.H. Yoon, N.-H. Kim, K.-S. Kim, B.C. Jung, G.-S. Hwang, C.-J. Kim, D.B. Kim, J.J. Ahn, H.J. An, H. Bae, A.L. Baek, W.J. Chi, E.A. Choi, E.H. Choi, H.K. Choi, H.S. Choi, S. Han, E.S. Heo, K.O. Her, S.W. Hwang, E.M. Jang, H.-S. Jang, S. Jang, H.-G. Jeon, S.R. Jeon, Y.R. Jeon, H.K. Jeong, I.-A. Jung, Hyeon Jeong Kim, Hyun Ju Kim, Ji Seon Kim, Jung Sook Kim, J.A. Kim, K.T. Kim, M.S. Kim, Sang Hee Kim, Sang Hyun Kim, Y.-I. Kim, C.S. Lee, E.H. Lee, G.H. Lee, H.Y. Lee, H.-Y. Lee, K.H. Lee, K.R. Lee, M.S. Lee, M.-Y. Lee, R.W. Lee, S.E. Lee, S.H. Lee, S. Lee, W.Y. Lee, I.K. Noh, A.R. Park, B.R. Park, H.N. Park, J.H. Park, M. Park, Y. Park, S.-Y. Seo, J. Shim, J.H. Sim, Y.M. Sohn, W.S. Son, Y.S. Son, H.J. Song, H.K. Wi, J.J. Woo, S. Ye, K.H. Yim, K.M. Yoo, E.J. Yoon, S.Y. Yun, P. Angchaisuksiri, S. Chawanadelert, P. Mongkolwongroj, K. Kanokphatcharakun, S. Cheewatanakornkul, T. Laksomya, S. Pattanaprichakul, T. Chantrarat, S. Rungaramsin, S. Silaruks, W. Wongcharoen, K. Siriwattana, K. Likittanasombat, P. Katekangplu, W. Boonyapisit, D. Cholsaringkarl, B. Chatlaong, P. Chattranukulchai, Y. Santanakorn, P. Hutayanon, P. Khunrong, T. Bunyapipat, S. Jai-Aue, P. Kaewsuwanna, P. Bamungpong, S. Gunaparn, S. Hongsuppinyo, R. Inphontan, R. Khattaroek, K. Khunkong, U. Kitmapawanont, C. Kongsin, B. Naratreekoon, S. Ninwaranon, J. Phangyota, A. Phrommintikul, P. Phunpinyosak, K. Pongmorakot, S. Poomiphol, N. Pornnimitthum, S. Pumprueg, S. Ratchasikaew, K. Sanit, K. Sawanyawisuth, B. Silaruks, R. Sirichai, A. Sriwichian, W. Suebjaksing, P. Sukklad, T. Suttana, A. Tangsirira, O. Thangpet, W. Tiyanon, Y. Vorasettakarnkij, T. Wisaratapong, W. Wongtheptien, A. Wutthimanop, S. Yawila, A. Oto, A. Altun, I. Ozdogru, K. Ozdemir, O. Yilmaz, A. Aydinlar, M.B. Yilmaz, E. Yeter, Z. Ongen, M. Cayli, H. Pekdemir, M. Ozdemir, M. Sucu, T. Sayin, M. Demir, H. 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Sterry, T. Wong, M. Boon, R. Bunney, R. Haria-Shah, R.T. Baron, S. Davies, T. Schatzberger, N. Hargreaves, T. Stephenson, H. Choi, R. Batson, L. Lucraft, T. Myhill, S. Estifano, D. Geatch, J. Wilkinson, R. Veale, K. Forshaw, T. Davies, K. Zaman, P. Vinson, C. Liley, M. Bandrapalli, P. McGinty, R. Wastling, P. McEleny, A. Beattie, P. Cooke, M. Wong, J. Gunasegaram, M. Pugsley, S. Ahmad, C. A'Court, J. Ayers, J. Bennett, S. Cartwright, S. Dobson, C. Dooldeniya, A. Flynn, R. Fox, J. Goram, A. Halpin, A. Hay, P. Jacobs, L. Jeffers, L. Lomax, I. Munro, R. Muvva, M. Nadaph, K. Powell, S. Randfield, D. Redpath, R. Reed, M. Rickenbach, G. Rogers, P.B. Saunders, C. Seamark, J. Shewring, P. Simmons, H. Simper, H. Stoddart, A. Sword, N. Thomas, A. Thomson, H. Gibbs, A. Blenkhorn, B. Singh, W. Van Gaal, W. Abhayaratna, R. Lehman, P. Roberts-Thomson, J. Kilian, D. Coulshed, A. Catanchin, D. Colquhoun, H. Kiat, D. Eccleston, J. French, L. Zimmett, B. Ayres, T. Phan, P. Blombery, D. Crimmins, D. 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Vorster, A. Waldman, L. Wallis, E. Wilford, K. Wong, S.J. Connolly, A. Spyropoulos, J. Eikelboom, R. Luton, M. Gupta, A.S. Pandey, S. Cheung, R. Leader, P. Beaudry, F. Ayala-Paredes, J. Berlingieri, J. Heath, G. Poirier, M. Du Preez, R. Nadeau, G. Dresser, R. Dhillon, T. Hruczkowski, B. Schweitzer, B. Coutu, P. Angaran, P. MacDonald, S. Vizel, S. Fikry, R. Parkash, A. Lavoie, J. Cha, B. Ramjattan, J. Bonet, K. Ahmad, L. Aro, T. Aves, K. Beaudry, C. Bergeron, J. Bigcanoe, N. Bignell, L. Breakwell, E. Burke, L. Carroll, B. Clarke, T. Cleveland, S. Daheb, P. Dehghani, I. Denis, Z. Djaidani, P. Dorian, S. Douglass, J. Dunnigan, A. Ewert, D. Farquhar, A. Fearon, L. Ferleyko, D. Fournier, B. Fox, M.-C. Grenier, W. Gulliver, K. Haveman, C. Hines, K. Hines, A.M. Jackson, C. Jean, G. Jethoo, R. Kahlon, S. Kelly, R. Kim, V. Korley, J. Kornder, L. Kwan, J. Largy, C. Lewis, S. Lewis, I. Mangat, R. Moor, J. Navratil, I. Neas, J. Otis, R. Otis, M. Pandey, F. Petrie, A. Pinter, M. Raines, P. 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Nathani, M. Ibrahim, E.M. Esheiba, R. Singh, A. Naguib, M. Abu-Mahfouz, M. Al Omairi, A. Al Naeemi, R. Maruthanayagam, N. Bazargani, A. Wassef, R. Gupta, M. Khan, B. Subbaraman, A. Abdul, A. Al Mulla, S. El Bardisy, P. Haridas, S. Jadhav, K. Magdaluyo, M. Makdad, I. Maqsood, R. Mohamed, N. Sharma, R. Sharma, M. Thanzeel, S.Z. Goldhaber, R. Canosa, P. Rama, E. Blumberg, J. Garcia, P. Mullen, V. Wilson, A. Quick, K. Ferrick, W.M. Kutayli, M. Cox, M. Franco, S. Falkowski, R. Mendelson, M. Williams, S. Miller, S. Beach, A. Alfieri, T. Gutowski, I. Haque, R. Reddy, W. Ahmed, P. Delafontaine, D. Diercks, D. Theodoro, K. Remmel, M. Alberts, R. Ison, H. Noveck, P. Duffy, S. Pitta, D. Nishijima, C. Treasure, N. Asafu-Adjaye, K. Ball, M. Bartlett, M. Bentley, S. Bowers, A. Brown, A. Browne, J. Cameron-Watts, M. Canova, D. Cassidy, K. Cervellione, S. Congal, J. DePauw, A. Dickerson, M. Eley, L. Evans, S. Felpel, K. Ferdinand, D. Fielder, P. Gentry, A. Haideri, F. Hakimi, T. Harbour, E. Hartranft, B. Hawkins, M. Headlee, L. Henson, C. Herrick, T. Hicks, S. Jasinski, A. Jones, L. Jones, P. Jones, S. Karl, M. Keeling, J. Kerr, P. Knowles, J. Langdon, M. Lay, J.A. Lee, T. Lincoln, E. Malone, A. Merliss, D. Merritt, J. Minardo, B. Mooso, C. Orosco, V. Palumbo, M. Parker, T. Parrott, S. Paserchia, G. Pearl, J. Peterson, N. Pickelsimer, T. Purcell, J. Raynor, S. Raziano, C. Richard, T. Richardson, C. Robertson, A. Sage, T. Sanghera, P. Shaw, J. Shoemaker, K. Smith, B. Stephanie, A. Thatcher, H. Theobald, N. Thompson, L. Treasure, T. Tripti, C. Verdi, and V. Worthy

Subjects
Surgery, RD1-811, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: The Global Anticoagulant Registry in the FIELD–Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. Methods and results: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012–2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P

Published
2018
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7. Investigation of the oxidation of methyl vinyl ketone (MVK) by OH radicals in the atmospheric simulation chamber SAPHIR

Author

H. Fuchs, S. Albrecht, I. Acir, B. Bohn, M. Breitenlechner, H.-P. Dorn, G. I. Gkatzelis, A. Hofzumahaus, F. Holland, M. Kaminski, F. N. Keutsch, A. Novelli, D. Reimer, F. Rohrer, R. Tillmann, L. Vereecken, R. Wegener, A. Zaytsev, A. Kiendler-Scharr, and A. Wahner

Subjects
Physics, QC1-999, Chemistry, QD1-999
Abstract

The photooxidation of methyl vinyl ketone (MVK) was investigated in the atmospheric simulation chamber SAPHIR for conditions at which organic peroxy radicals (RO2) mainly reacted with NO (high NO case) and for conditions at which other reaction channels could compete (low NO case). Measurements of trace gas concentrations were compared to calculated concentration time series applying the Master Chemical Mechanism (MCM version 3.3.1). Product yields of methylglyoxal and glycolaldehyde were determined from measurements. For the high NO case, the methylglyoxal yield was (19 ± 3) % and the glycolaldehyde yield was (65 ± 14) %, consistent with recent literature studies. For the low NO case, the methylglyoxal yield reduced to (5 ± 2) % because other RO2 reaction channels that do not form methylglyoxal became important. Consistent with literature data, the glycolaldehyde yield of (37 ± 9) % determined in the experiment was not reduced as much as implemented in the MCM, suggesting additional reaction channels producing glycolaldehyde. At the same time, direct quantification of OH radicals in the experiments shows the need for an enhanced OH radical production at low NO conditions similar to previous studies investigating the oxidation of the parent VOC isoprene and methacrolein, the second major oxidation product of isoprene. For MVK the model–measurement discrepancy was up to a factor of 2. Product yields and OH observations were consistent with assumptions of additional RO2 plus HO2 reaction channels as proposed in literature for the major RO2 species formed from the reaction of MVK with OH. However, this study shows that also HO2 radical concentrations are underestimated by the model, suggesting that additional OH is not directly produced from RO2 radical reactions, but indirectly via increased HO2. Quantum chemical calculations show that HO2 could be produced from a fast 1,4-H shift of the second most important MVK derived RO2 species (reaction rate constant 0.003 s−1). However, additional HO2 from this reaction was not sufficiently large to bring modelled HO2 radical concentrations into agreement with measurements due to the small yield of this RO2 species. An additional reaction channel of the major RO2 species with a reaction rate constant of (0.006 ± 0.004) s−1 would be required that produces concurrently HO2 radicals and glycolaldehyde to achieve model–measurement agreement. A unimolecular reaction similar to the 1,5-H shift reaction that was proposed in literature for RO2 radicals from MVK would not explain product yields for conditions of experiments in this study. A set of H-migration reactions for the main RO2 radicals were investigated by quantum chemical and theoretical kinetic methodologies, but did not reveal a contributing route to HO2 radicals or glycolaldehyde.

Published
2018
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8. Nesometra integra, a New Species of Feather Star (Echinodermata: Crinoidea: Comatulida: Antedonidae) from Southern Japan and Western Australia

Author

Gregorius A. Pratama, Riccardo Virgili, James D. Reimer, and Toshihiko Fujita

Subjects
antedonidae, nesometra, new species, japan, australia, coral reef, Zoology, QL1-991
Abstract

A new species of the genus Nesometra Virgili, Poliseno, Fujita, Pratama, Fernández-Silva, and Reimer, 2023 is described based on the specimens collected from the Amami Islands and Ogasawara Islands, Japan and Cunningham Island, Australia. Nesometra integra n. sp. is distinguished from its single congener, N. sesokonis (Obuchi, Kogo, and Fujita, 2009), by having complete proximal pinnulation and cirri with reduced medial constriction on its distal part.

Published
2024
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9. Preliminary genetic assessment of three goatfish species in the Mediterranean Sea

Author

Taha Soliman, Joseph D. DiBattista, Reda M. Fahim, and James D. Reimer

Subjects
Dispersal, Egypt, Life history, mtDNA, Mullidae, Lessepsian migrant, Aquaculture. Fisheries. Angling, SH1-691, Environmental sciences, GE1-350
Abstract

We examined the genetic diversity and connectivity of two indigenous Mediterranean goatfish species (Mullus barbatus and M. surmuletus), and a Lessepsian migrant species (Upeneus moluccensis), across the Nile Delta outflow using two mitochondrial DNA markers (COI and cyt b). Genetic diversity was high for the two Mediterranean species but relatively lower for the migrant species, suggesting founder effects after invasion from the Red Sea. Confirmation of this hypothesis, however, would require comparison with populations of origin in the Red Sea and the broader Indo-West Pacific. AMOVA and network analyses revealed no genetic partitioning for all species, indicating that the Nile outflow does not currently, and may not have historically, posed a significant barrier to larval dispersal in these goatfish, despite a present-day temperature and salinity gradient along the Mediterranean coastline of Egypt.

Published
2024
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10. Trait networks: Assessing marine community resilience and extinction recovery

Author

Charlotte G. Clay, Alexander M. Dunhill, James D. Reimer, and Maria Beger

Subjects
Paleontology, Ecology, Paleobiology, Science
Abstract

Summary: Extensive global habitat degradation and the climate crisis are tipping the biosphere toward a “sixth” mass extinction and marine communities will not be spared from this catastrophic loss of biodiversity. The resilience of marine communities following large-scale disturbances or extinction events is mediated by the life-history traits of species and their interplay within communities. The presence and abundance of traits in communities provide proxies of function, but whether the breakdown of their associations with species loss can delineate functional loss remains unclear. Here, we propose that relationships between traits within trait networks provide unique perspectives on the importance of specific traits, trait combinations, and their role in supporting the stability of communities, while exploring the vulnerability of both past deep time and present-day marine communities.

Published
2024
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11. Tracing Geographic and Molecular Footprints of Copepod Crustaceans Causing Multifocal Purple Spots Syndrome in the Caribbean Sea Fan Gorgonia ventalina

Author

Oksana A. Korzhavina, Mikhail A. Nikitin, Bert W. Hoeksema, Maickel Armenteros, James D. Reimer, and Viatcheslav N. Ivanenko

Subjects
parasites, gorgonian octocorals, integrative taxonomic approach, phylogenetic analysis, Caribbean region, copepod crustaceans, Biology (General), QH301-705.5
Abstract

The recent rise in ocean temperatures, accompanied by other environmental changes, has notably increased the occurrence and spread of diseases in Octocorallia, many species of which are integral to shallow tropical and subtropical coral reef ecosystems. This study focuses on the understanding of these diseases, which has been largely limited to symptomatic descriptions, with clear etiological factors identified in only a fraction of cases. A key example is the multifocal purple spots syndrome (MFPS) affecting the common Caribbean octocoral sea fan Gorgonia ventalina, linked to the gall-forming copepods of the genus Sphaerippe, a member of the widespread family, Lamippidae. The specialized nature of these copepods as endoparasites in octocorals suggests the potential for the discovery of similar diseases across this host spectrum. Our investigation employed four molecular markers to study disease hotspots in Saint Eustatius, Curaçao, northwest and southwest Cuba, and Bonaire. This led to the discovery of a group of copepod species in these varied Caribbean locations. Importantly, these species are morphologically indistinguishable through traditional methods, challenging established taxonomic approaches. The observed diversity of symbionts, despite the host species’ genetic uniformity, is likely due to variations in larval dispersal mechanisms. Our phylogenetic analyses confirmed that the Lamippidae copepods belong to the order, Poecilostomatoida (Copepoda), and revealed their sister group relationship with the Anchimolgidae, Rhynchomolgidae, and Xarifiidae clades, known for their symbiotic relationships with scleractinian corals. These results add to our understanding of the evolutionary and ecological interactions of copepods and their hosts, and the diseases that they cause, and are important data in a changing climate.

Published
2024
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12. Expanding walls and shrinking beaches: loss of natural coastline in Okinawa Island, Japan

Author

Giovanni Diego Masucci and James D. Reimer

Subjects
Habitat loss, Habitat fragmentation, Land reclamation, Coastal armoring, Coral reefs, Okinawa Island, Medicine, Biology (General), QH301-705.5
Abstract

Okinawa is the largest and most populated island of the Ryukyu Archipelago in southern Japan and is renowned for its natural resources and beauty. Similar as to what has been happening in the rest of the country, Okinawa Island has been affected by an increasing amount of development and construction work. The trend has been particularly acute after reversion to Japanese sovereignty in 1972, following 27 years of post-war American administration. A coastline once characterized by extended sandy beaches surrounded by coral reefs now includes tracts delimited by seawalls, revetments, and other human-made hardening structures. Additionally, part of coastal Okinawa Island was obtained by land-filling shallow ocean areas (land reclamation). Nevertheless, the current extension of the artificial coastline, as well as the level of fragmentation of the natural coastline are unclear, due to the lack of both published studies and easily accessible and updated datasets. The aims of this research were to quantify the extension of coastline alterations in Okinawa Island, including the amount of land-filling performed over the last 41 years, and to describe the coastlines that have been altered the most as well as those that are still relatively pristine. The analyses were performed using a reference map of Okinawa Island based on GIS vector data extracted from the OpenStreetMap (OSM) coastline dataset (average node distance for Okinawa Island = 24 m), in addition to satellite and aerial photography from multiple providers. We measured 431.8 km of altered coastline, equal to about 63% of the total length of coastline in Okinawa Island. Habitat fragmentation is also an issue as the remaining natural coastline was broken into 239 distinct tracts (mean length = 1.05 km). Finally, 21.03 km2 of the island’s surface were of land reclaimed over the last 41 years. The west coast has been altered the most, while the east coast is in relatively more natural conditions, particularly the northern part, which has the largest amount of uninterrupted natural coastline. Given the importance of the ecosystem services that coastal and marine ecosystems provide to local populations of subtropical islands, including significant economic income from tourism, conservation of remaining natural coastlines should be given high priority.

Published
2019
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15. Temperate functional niche availability not resident-invader competition shapes tropicalisation in reef fishes

Author

Mark G. R. Miller, James D. Reimer, Brigitte Sommer, Katie M. Cook, John M. Pandolfi, Masami Obuchi, and Maria Beger

Subjects
Multidisciplinary, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract

Temperate reefs are at the forefront of warming-induced community alterations resulting from poleward range shifts. This tropicalisation is exemplified and amplified by tropical species’ invasions of temperate herbivory functions. However, whether other temperate ecosystem functions are similarly invaded by tropical species, and by what drivers, remains unclear. We examine tropicalisation footprints in nine reef fish functional groups using trait-based analyses and biomass of 550 fish species across tropical to temperate gradients in Japan and Australia. We discover that functional niches in transitional communities are asynchronously invaded by tropical species, but with congruent invasion schedules for functional groups across the two hemispheres. These differences in functional group tropicalisation point to habitat availability as a key determinant of multi-species range shifts, as in the majority of functional groups tropical and temperate species share functional niche space in suitable habitat. Competition among species from different thermal guilds played little part in limiting tropicalisation, rather available functional space occupied by temperate species indicates that tropical species can invade. Characterising these drivers of reef tropicalisation is pivotal to understanding, predicting, and managing marine community transformation.

Published
2023
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16. Diversity of Feeding in Anthozoa (Cnidaria): A Systematic Review

Author

Thaís Barbosa Santos, James D. Reimer, Fabián H. Acuña, and Sérgio N. Stampar

Subjects
feeding behavior, feeding habits, physiology, Hexacorallia, Octocorallia, Ceriantharia, Biology (General), QH301-705.5
Abstract

In this study, we performed a bibliographical review examining the scientific literature on “feeding in Anthozoa” for the period from 1890 to 2019, using the scientific database Google Scholar, supplemented with additional literature. This study categorized published scientific papers on this topic by decade of publication, target taxa, variability of species studied in each order and main themes studied. As a result, 153 studies were found, and based on their content, it was observed that within Anthozoa, there has been a concentration of feeding studies on species in the orders Actiniaria (Hexacorallia), Scleractinia (Hexacorallia), and Alcyonacea (Octocorallia). This indicates that the other remaining orders of the group have been comparatively neglected with regards to their feeding aspects. Therefore, as data on feeding in some groups of Anthozoa are scarce, studies need to be carried out to fill the gaps that permeate this important benthic group, in order to better understand their ecology.

Published
2020
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17. Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

Author

Joseph D. DiBattista, James D. Reimer, Michael Stat, Giovanni D. Masucci, Piera Biondi, Maarten De Brauwer, and Michael Bunce

Subjects
18S rRNA, Community structure, Demospongiae, Anthozoa, Porifera, Environmental DNA, Medicine, Biology (General), QH301-705.5
Abstract

Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

Published
2019
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18. Widespread Occurrence of a Rarely Known Association between the Hydrocorals Stylaster roseus and Millepora alcicornis at Bonaire, Southern Caribbean

Author

Simone Montano, James D. Reimer, Viatcheslav N. Ivanenko, Jaaziel E. García-Hernández, Godfried W.N.M. van Moorsel, Paolo Galli, and Bert W. Hoeksema

Subjects
Caribbean Netherlands, fire corals, Hydrozoa, pseudo-auto-epizoism, stony corals, substrate, Biology (General), QH301-705.5
Abstract

Among symbiotic associations, cases of pseudo-auto-epizoism, in which a species uses a resembling but not directly related species as substrate, are poorly documented in coral reef ecosystems. In the present study, we assessed the distribution of an association between the hydrocorals Stylaster roseus and Millepora alcicornis on about 50% of coral reef sites studied in Bonaire, southern Caribbean. Although previously thought to be uncommon, associations between the lace coral S. roseus and the fire coral M. alcicornis were observed at both the windward and leeward sides of Bonaire, mainly between 15 and 25 m depth, reaching a maximum occupation of 47 S. roseus colonies on a single M. alcicornis colony. Both species’ tissues did not show any signs of injuries, while an in-depth inspection of the contact points of their skeletons revealed that both partners can partially overgrow each other. How it is possible that S. roseus is able to settle on the stinging tissue of Millepora as well as how, by contrast, the latter may facilitate the lace coral by offering a certain degree of protection are questions that deserve further investigations.

Published
2020
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19. Speciation among sympatric lineages in the genus Palythoa (Cnidaria: Anthozoa: Zoantharia) revealed by morphological comparison, phylogenetic analyses and investigation of spawning period

Author

Masaru Mizuyama, Giovanni D. Masucci, and James D. Reimer

Subjects
Zoantharia, Palythoa spp., Incomplete lineage sorting, Reproductive isolation, Sympatric speciation, Medicine, Biology (General), QH301-705.5
Abstract

Zoantharians are sessile marine invertebrates and colonial organisms possessing sexual and asexual reproductive ability. The zooxanthellate zoantharian genus Palythoa is widely distributed in coral reef ecosystems. In the Ryukyu Archipelago, Japan, sympatric Palythoa tuberculosa and P. mutuki are the dominant species of this genus in the intertidal zone. Previous phylogenetic analyses have shown that these two species are closely related, and additionally revealed a putative sympatric hybrid species (designated as Palythoa sp. yoron). In this study, we attempted to delineate Palythoa species boundaries and to clarify the relationships among these three groups plus another additional putative sympatric species (P. aff. mutuki) by multiple independent criteria. The morphology of these four lineages was clearly different; for example the number of tentacles was significantly different for each species group in all pairwise comparisons. From observations of gonadal development conducted in 2010 and 2011, P. sp. yoron and P. aff. mutuki appear to be reproductively isolated from P. tuberculosa. In the phylogenetic tree resulting from maximum likelihood analyses of the ITS-rDNA sequence alignment, P. tuberculosa and P. sp. yoron formed a very well supported monophyletic clade (NJ = 100%, ML = 95%, Bayes = 0.99). This study demonstrates that despite clear morphological and/or reproductive differences, P. tuberculosa and P. sp. yoron are phylogenetically entangled and closely related to each other, as are P. mutuki and P. aff. mutuki. Additionally, no single molecular marker was able to divide these four lineages into monophyletic clades by themselves, and a marker that has enough resolution to solve this molecular phylogenetic species complex is required. In summary, the morphological and reproductive results suggest these lineages are four separate species, and that incomplete genetic lineage sorting may prevent the accurate phylogenetic detection of distinct species with the DNA markers utilized in this study, demonstrating the value of morphological and reproductive data when examining closely related lineages.

Published
2018
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20. Battle of the bands: systematics and phylogeny of the white Goniobranchus nudibranchs with marginal bands (Nudibranchia, Chromodorididae)

Author

Giun Yee Soong, Lynn J. Bonomo, James D. Reimer, and Terrence M. Gosliner

Subjects
Philippines, Gastropoda, Chromodorididae, Goniobranchus, Chromodoridinae, Ringipleura, Papua New Guinea, Japan, Systematics, Nudipleura, Euthyneura, Madagascar, Animalia, Nudibranchia, Ecology, Evolution, Behavior and Systematics, Phylogeny, Taxonomy, mtDNA, Doridoidei, Malaysia, Biodiversity, Biota, Doridina, species delimitation, QL1-991, Mollusca, Heterobranchia, Chromodoridoidea, Animal Science and Zoology, coral reefs, Zoology, Research Article
Abstract

Species identities of Goniobranchus nudibranchs with white bodies and various marginal bands have long been problematic. In this study, specimens of these Goniobranchus nudibranchs from the Philippines, Peninsular Malaysia, Japan, Papua New Guinea, and Madagascar were analyzed and molecular data were obtained in order to re-examine the relationships between species within this “white Goniobranchus with marginal bands” group. The analyses clearly recovered six species groups corresponding to the described species Goniobranchus albonares, G. preciosus, G. rubrocornutus, G. sinensis, and G. verrieri as well as one new species, G. fabulus Soong & Gosliner, sp. nov. Notably, G. preciosus, G. sinensis, G. rubrocornutus, G. verrieri, and G. fabulus Soong & Gosliner, sp. nov. exhibit color variation and polymorphism, suggesting that some aspects of color patterns (e.g., presence or absence of dorsal spots) may not always be useful in the identification of species in the “white Goniobranchus with marginal bands” group, whereas other features such as gill and rhinophore colors and the arrangement and colors of the mantle marginal bands are more diagnostic for each species.

Published
2022

22. Shifting communities after­­ typhoon damage on an upper mesophotic reef in Okinawa, Japan

Author

Kristine N. White, David K. Weinstein, Taku Ohara, Vianney Denis, Javier Montenegro, and James D. Reimer

Subjects
Mesophotic, Succession, Coral reef, Pachyseris, Japan, Typhoon recovery, Medicine, Biology (General), QH301-705.5
Abstract

Very few studies have been conducted on the long-term effects of typhoon damage on mesophotic coral reefs. This study investigates the long-term community dynamics of damage from Typhoon 17 (Jelawat) in 2012 on the coral community of the upper mesophotic Ryugu Reef in Okinawa, Japan. A shift from foliose to bushy coral morphologies between December 2012 and August 2015 was documented, especially on the area of the reef that was previously recorded to be poor in scleractinian genera diversity and dominated by foliose corals. Comparatively, an area with higher diversity of scleractinian coral genera was observed to be less affected by typhoon damage with more stable community structure due to less change in dominant coral morphologies. Despite some changes in the composition of dominant genera, the generally high coverage of the mesophotic coral community is facilitating the recovery of Ryugu Reef after typhoon damage.

Published
2017
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23. Transient amplification enhances the persistence of tropicalising coral assemblages in marginal high latitude environments

Author

James Cant, Katie M. Cook, James D. Reimer, Takuma Mezaki, Masako Nakamura, Cliodhna O'Flaherty, Roberto Salguero‐Gómez, Maria Beger, and University of St Andrews. School of Biology

Subjects
Transient life table response experiment, QH301, QH301 Biology, MCP, Amplification, Subtropical, DAS, Acropora spp, Integral projection model (IPM), Ecology, Evolution, Behavior and Systematics, Kitagawa and Keyfitz decomposition
Abstract

JC was awarded a Natural Environment Research Council (NERC) Doctoral Training Programme Scholarship. Grants were made by the British Ecological Society, UK; the Winifred Violet Scott Estate, Australia; and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie grant agreement TRIM‐DLV‐747102 to MB. ORCHIDS project funding from the University of the Ryukyus was made to JDR. Recruitment surveys were supported by JSPS KAKENHI grant no. 16K07527 to MN. RS‐G was supported by a NERC Independent Research Grant (no. NE/M018458/1). Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long-term population performance, here we illustrate that short-term (i.e. transient) demographic characteristics, including measures of resistance, recovery and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher latitudes. Through the annual census of subtropical and temperate Acropora spp. colonies in Japan between 2017 and 2019, we show how enhanced transient amplification (i.e. short-term increases in population growth following disturbance) supports the persistence of coral assemblages within more variable high-latitude environments. The transient dynamics of both the subtropical and temperate assemblages were strongly influenced by their corresponding recruitment patterns. However, we demonstrate that variation in colony survival and fragmentation patterns between the two assemblages determines their relative capacities for transient amplification. This latitudinal variation in the transient dynamics of Acropora spp. assemblages emphasizes that coral populations can possess the demographic plasticity necessary for exploiting more variable, marginal conditions. Publisher PDF

Published
2022
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24. Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

Author

Taha Soliman, Okuto Takama, Iria Fernandez-Silva, and James D. Reimer

Subjects
Sea cucumber, Stichopus chloronotus, Okinawa Island, mtDNA, 16S ribosomal DNA, Medicine, Biology (General), QH301-705.5
Abstract

The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.

Published
2016
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26. Evolution and phylogeny of glass-sponge-associated zoantharians, with a description of two new genera and three new species

Author

Hiroki, Kise, Javier, Montenegro, Maria E A, Santos, Bert W, Hoeksema, Merrick, Ekins, Yuji, Ise, Takuo, Higashiji, Iria, Fernandez-Silva, James D, Reimer, Hiroki, Kise, Javier, Montenegro, Maria E A, Santos, Bert W, Hoeksema, Merrick, Ekins, Yuji, Ise, Takuo, Higashiji, Iria, Fernandez-Silva, and James D, Reimer

Abstract

Hexactinellid sponges are important members of deep-sea benthic ecosystems because they provide available hard substrate habitats for filter-feeding invertebrates. However, symbioses between hexactinellid sponges and their symbionts are poorly known. Zoantharians associated with hexactinellid sponges have been reported widely from deep-sea marine ecosystems, either on the bodies or stalks of hexactinellid sponges. Despite these records, there has been a lack of research on their diversity and phylogenetic relationships. In this study, 20 specimens associated with amphidiscophoran and hexasterophoran sponges were collected from the waters of Australia and Japan in the Pacific, and from Curaçao in the southern Caribbean, and these were examined in addition to museum specimens. Based on molecular phylogenetic analyses and morphological observations, we formally describe two new genera and three new species of Zoantharia and report several previously described species. The results suggest at least two independent origins for the symbioses between hexactinellid sponges and zoantharians. Our results demonstrate that the diversity of hexactinellid sponge-associated zoantharians is much higher than has been previously thought. The new taxa described in this work further reconfirm that the deep-sea harbours high levels of undescribed zoantharian diversity., source:https://doi.org/10.1093/zoolinnean/zlab068

Published
2022

27. A Comparison of Size, Shape, and Fractal Diversity Between Coral Rubble Sampled From Natural and Artificial Coastlines Around Okinawa Island, Japan

Author

Giovanni D. Masucci, Piera Biondi, and James D. Reimer

Subjects
coastal development, Aspect ratio, Science, Ocean Engineering, Soil science, spatial complexity, Aquatic Science, engineering.material, QH1-199.5, Oceanography, Fractal dimension, Box counting, Fractal, Japan, Water Science and Technology, Global and Planetary Change, Rubble, General. Including nature conservation, geographical distribution, Roundness (object), Okinawa, breakwaters, Benthic zone, Breakwater, fractals, engineering, Geology
Abstract

Substrate surface area and fractal complexity have been reported to influence the abundance and diversity of mobile cryptic animal communities. Surfaces with higher fractal dimensions not only offer additional space for colonization, but bias space availability toward smaller size ranges, increasing the number of available niches. Conversely, smaller surface areas tend to be associated with a decrease in abundances while reduced fractal complexities may support less diversity in the benthic community. In this study, we compared morphological parameters between rubble sampled from rubble mounds accumulated at the seaward side of artificial breakwaters and rubble sampled from a nearby location with no breakwaters (=control site). The purpose of this work was to establish a methodology for comparing the surface area and fractal complexity of coral rubble fragments using easily available equipment that could be efficiently utilized during field work. Rubble fragments were individually weighed and photographed in controlled light conditions. Each photograph was then analyzed using ImageJ software. Rubble pieces from each photograph went through segmentation, the separation of sample outlines from the picture background, before being measured and analyzed for surface area, width, and length (size estimators), and circularity, aspect ratio, roundness, solidity, and Feret properties (shape estimators). Surface fractal complexity was also measured, using the box counting method on segmented rubble surfaces. We observed lowered surface areas, weight, and fractal complexity for rubble fragments sampled at the breakwater. We demonstrate how this method could be used to compare coral rubble from a variety of environmental conditions, thus becoming a useful aid in environmental monitoring, in addition to adding important information to the collection and analyses of biological data.

Published
2021
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29. Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

Author

Christian R. Voolstra, Kate M. Quigley, Sarah W. Davies, John Everett Parkinson, Raquel S. Peixoto, Manuel Aranda, Andrew C. Baker, Adam R. Barno, Daniel J. Barshis, Francesca Benzoni, Victor Bonito, David G. Bourne, Carol Buitrago-López, Tom C. L. Bridge, Cheong Xin Chan, David J. Combosch, Jamie Craggs, Jörg C. Frommlet, Santiago Herrera, Andrea M. Quattrini, Till Röthig, James D. Reimer, Esther Rubio-Portillo, David J. Suggett, Helena Villela, Maren Ziegler, Michael Sweet, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, and Publica

Subjects
0106 biological sciences, 0301 basic medicine, symbiodiniaceae, Science, Library science, Ocean Engineering, QH1-199.5, Aquatic Science, Genome sequencing, Microbiología, Oceanography, 010603 evolutionary biology, 01 natural sciences, prokaryotes, 03 medical and health sciences, Scleractinia, Symbiodiniaceae, Political science, ddc:570, Prokaryotes, Taxonomy, Water Science and Technology, Global and Planetary Change, 0405 Oceanography, 0602 Ecology, Coral holobiont, General. Including nature conservation, geographical distribution, Coral reef, Genomics, Voucher, Holobiont, genome sequencing, 030104 developmental biology, coral reef, coral holobiont, scleractinia, coral reef, coral holobiont, scleractinia, symbiodiniaceae, prokaryotes, genome sequencing, taxonomy, genomics
Abstract

Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will adhere to as part of the Aquatic Symbiosis Genomics Project sub-hub focused on coral symbioses, will be useful to a broader community and their implementation will facilitate cross- and meta-data comparisons and analyses. CV acknowledges funding from the German Research Foundation (DFG), grants 433042944 and 458901010. Open Access publication fees are covered by an institutional agreement of the University of Konstanz.

Published
2021

30. Typhoon damage on a shallow mesophotic reef in Okinawa, Japan

Author

Kristine N. White, Taku Ohara, Takuma Fujii, Iori Kawamura, Masaru Mizuyama, Javier Montenegro, Haruka Shikiba, Tohru Naruse, TY McClelland, Vianney Denis, and James D. Reimer

Subjects
Coral reef, Mesophotic, Typhoon damage, Succession, Japan, Medicine, Biology (General), QH301-705.5
Abstract

Little is known about effects of large storm systems on mesophotic reefs. This study reports on how Typhoon 17 (Jelawat) affected Ryugu Reef on Okinawa-jima, Japan in September 2012. Benthic communities were surveyed before and after the typhoon using line intercept transect method. Comparison of the benthic assemblages showed highly significant differences in coral coverage at depths of 25–32 m before and after Typhoon 17. A large deep stand of Pachyseris foliosa was apparently less resistant to the storm than the shallower high diversity area of this reef. Contradictory to common perception, this research shows that large foliose corals at deeper depths are just as susceptible to typhoon damage as shallower branching corals. However, descriptive functional group analyses resulted in only minor changes after the disturbance, suggesting the high likelihood of recovery and the high resilience capacity of this mesophotic reef.

Published
2013
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32. Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time

Author

Andrea M, Quattrini, Estefanía, Rodríguez, Brant C, Faircloth, Peter F, Cowman, Mercer R, Brugler, Gabriela A, Farfan, Michael E, Hellberg, Marcelo V, Kitahara, Cheryl L, Morrison, David A, Paz-García, James D, Reimer, and Catherine S, McFadden

Subjects
Oceans and Seas, Animals, Seawater, Hydrogen-Ion Concentration, Anthozoa, Skeleton
Abstract

Identifying how past environmental conditions shaped the evolution of corals and their skeletal traits provides a framework for predicting their persistence and that of their non-calcifying relatives under impending global warming and ocean acidification. Here we show that ocean geochemistry, particularly aragonite-calcite seas, drives patterns of morphological evolution in anthozoans (corals, sea anemones) by examining skeletal traits in the context of a robust, time-calibrated phylogeny. The lability of skeletal composition among octocorals suggests a greater ability to adapt to changes in ocean chemistry compared with the homogeneity of the aragonitic skeleton of scleractinian corals. Pulses of diversification in anthozoans follow mass extinctions and reef crises, with sea anemones and proteinaceous corals filling empty niches as tropical reef builders went extinct. Changing environmental conditions will likely diminish aragonitic reef-building scleractinians, but the evolutionary history of the Anthozoa suggests other groups will persist and diversify in their wake.

Published
2020

34. The Origin of the Subtropical Coral Alveopora japonica (Scleractinia: Acroporidae) in High-Latitude Environments

Author

Ji Hyoun Kang, Ji Eun Jang, Jae Hwan Kim, Sangil Kim, Shashank Keshavmurthy, Sylvain Agostini, James D. Reimer, Chaolun Allen Chen, Kwang-Sik Choi, Sang Rul Park, and Hyuk Je Lee

Subjects
0106 biological sciences, 0301 basic medicine, Species complex, Biodiversity, lcsh:Evolution, Scleractinia, Subtropics, 010603 evolutionary biology, 01 natural sciences, northward migration, Acroporidae, 03 medical and health sciences, hidden diversity, lcsh:QH540-549.5, phylogenetic concordance, lcsh:QH359-425, Internal transcribed spacer, Clade, Ecology, Evolution, Behavior and Systematics, Ecology, biology, Phylogenetic tree, biology.organism_classification, Jeju Island, 030104 developmental biology, climate change, subtropical corals, lcsh:Ecology
Abstract

Marine ecosystems in temperate regions have been significantly affected by rising seawater temperatures due to climate change. Alveopora japonica, a small zooxanthellate scleractinian coral, occurs in the northwestern Pacific including Taiwan, Japan, and Jeju Island in Korea. The northern populations around Jeju Island have recently undergone rapid growth in numbers, with negative impacts on local biodiversity. However, it is unclear whether these Korean populations occurred historically and where they originate from. In this study, we investigated the phylogenetic relationships of A. japonica along with its endosymbiont Symbiodiniaceae across five geographic regions, including Jeju Island in Korea, Taiwan, and Japan. Nuclear internal transcribed spacer (ITS) sequences revealed unexpected species-level divergence among three distinct phylogenetic clusters (Korea, Taiwan, and Japan) with no sharing of haplotypes among lineages, suggesting these may each represent cryptic species in Alveopora. 23S ribosomal DNA of Symbiodiniaceae showed two well-separated phylogenetic clusters, in which Korean and Japanese symbionts shared the same clade and Taiwanese ones formed a distinct clade. Given the deep phylogenetic divergences among the lineages for both corals and Symbiodiniaceae, the Korean populations appear to have existed for a long evolutionary time period rather than representing a poleward migration from subtropical environments following recent climate change. Our study highlights cryptic species diversity in Alveopora at high-latitude environments.

Published
2020
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35. Methods for generating hypotheses in human enteric illness outbreak investigations: a scoping review of the evidence

Author

Mariola Mascarenhas, T. Kershaw, J. M. Cheng, D. Reimer, Lisa Waddell, C. Ickert, Judy Greig, and A. Hexemer

Subjects
medicine.medical_specialty, Enteric illness, Epidemiology, business.industry, hypothesis generation methods, Gastrointestinal Diseases, Outbreak, Grey literature, Review, Descriptive epidemiology, Disease Outbreaks, Infectious Diseases, Environmental health, outbreaks, Communicable Disease Control, medicine, Humans, scoping review, business, Epidemiologic Methods
Abstract

Enteric illness outbreaks are complex events, therefore, outbreak investigators use many different hypothesis generation methods depending on the situation. This scoping review was conducted to describe methods used to generate a hypothesis during enteric illness outbreak investigations. The search included five databases and grey literature for articles published between 1 January 2000 and 2 May 2015. Relevance screening and article characterisation were conducted by two independent reviewers using pretested forms. There were 903 outbreaks that described hypothesis generation methods and 33 papers which focused on the evaluation of hypothesis generation methods. Common hypothesis generation methods described are analytic studies (64.8%), descriptive epidemiology (33.7%), food or environmental sampling (32.8%) and facility inspections (27.9%). The least common methods included the use of a single interviewer (0.4%) and investigation of outliers (0.4%). Most studies reported using two or more methods to generate hypotheses (81.2%), with 29.2% of studies reporting using four or more. The use of multiple different hypothesis generation methods both within and between outbreaks highlights the complexity of enteric illness outbreak investigations. Future research should examine the effectiveness of each method and the contexts for which each is most effective in efficiently leading to source identification.

Published
2019

36. Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan

Author

Taha Soliman, James D. Reimer, Sung-Yin Yang, Alejandro Villar-Briones, Michael C. Roy, and Holger Jenke-Kodama

Subjects
0301 basic medicine, Microbiology (medical), archaea, 030106 microbiology, lcsh:QR1-502, chemodiversity, Microbiology, lcsh:Microbiology, 03 medical and health sciences, eukaryotes, Peninsula, Marine ecosystem, Ecosystem, bacteria, Relative species abundance, Original Research, metagenomics, geography, geography.geographical_feature_category, Ecology, Sediment, 030104 developmental biology, Microbial population biology, Metagenomics, NGS, Causeway, Geology
Abstract

Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan “Kaichu-Doro” Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (

Published
2017
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39. Intra- and postoperative catumaxomab in patients with epithelial ovarian cancer: safety and two-year efficacy results from a multicentre, single-arm, phase II study

Author

D Reimer, Lukas Angleitner-Boubenizek, W. Stummvoll, Radoslav Chekerov, Jalid Sehouli, Alexander Reinthaller, Toralf Reimer, Burkhard Brandt, and Christian Marth

Subjects
Adult, safety, epithelial ovarian cancer, Oncology, Cancer Research, medicine.medical_specialty, efficacy, MEDLINE, Catumaxomab, Phases of clinical research, Carcinoma, Ovarian Epithelial, Internal medicine, Antibodies, Bispecific, medicine, Carcinoma, Humans, postoperative, Epithelial ovarian cancer, In patient, Neoplasms, Glandular and Epithelial, Aged, Ovarian Neoplasms, Postoperative Care, Intraoperative Care, business.industry, Middle Aged, medicine.disease, Surgery, Clinical trial, Multicenter study, Clinical Study, catumaxomab, Female, intraoperative, business, medicine.drug
Abstract

Background: This is the first study investigating the safety and efficacy of the trifunctional antibody catumaxomab administered i.p. at the end of cytoreductive surgery and postoperatively prior to standard chemotherapy in patients with primary epithelial ovarian cancer (EOC). Methods: Patients received i.p. catumaxomab 10 μg intraoperatively and 10, 20, 50 and 150 μg on days 7, 10, 13 and 16, respectively, postoperatively. After the study, patients received standard chemotherapy and were followed for 23 months. The primary endpoint was the rate of postoperative complications. Results: Forty-one patients entered the study and were evaluable for safety and 34 were alive at 24 months. Complete tumour resection rate was 68%. Postoperative complications were observed in 51%, the most common anastomotic leakage (7%) and wound infections (5%). The most common catumaxomab-related adverse events were abdominal pain, nausea, vomiting and pyrexia. Thirty-nine percent discontinued catumaxomab therapy, and 98% received chemotherapy post study. Kaplan–Meier estimates of disease-free and overall survival after 24 months were 56% and 85%, respectively. Conclusions: Intra- and close postoperative catumaxomab seems feasible, but efficacy and safety were limited by postsurgical complications. In the future prospective trials are needed to investigate the best schedule of integration of catumaxomab into current treatment strategies for EOC.

Published
2014
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40. Urban coral reefs: Degradation and resilience of hard coral assemblages in coastal cities of East and Southeast Asia

Author

Eliza C.Heery, Bert W. Hoeksema, Nicola K. Browne, James D. Reimer, Put O. Ang, Danwei Huang, Daniel A. Friess, Chou, Loke Ming, Lynette H.L. Loke, Poonam Saksena-Taylor, Nadia Alsagoff, Thamasak Yeemin, Makamas Sutthacheep, Si Tuan Vo, Arthur R. Bos, Girley S. Gumanao, Muhammad Ali Syed Hussein, David J.W. Lane, Ofri Johan, Andreas Kunzmann, Jamaluddin Jompa, Suharsono, Daisuke Taira, Andrew G. Bauman, Peter A. Todd, Eliza C.Heery, Bert W. Hoeksema, Nicola K. Browne, James D. Reimer, Put O. Ang, Danwei Huang, Daniel A. Friess, Chou, Loke Ming, Lynette H.L. Loke, Poonam Saksena-Taylor, Nadia Alsagoff, Thamasak Yeemin, Makamas Sutthacheep, Si Tuan Vo, Arthur R. Bos, Girley S. Gumanao, Muhammad Ali Syed Hussein, David J.W. Lane, Ofri Johan, Andreas Kunzmann, Jamaluddin Jompa, Suharsono, Daisuke Taira, Andrew G. Bauman, and Peter A. Todd

Abstract

Given predicted increases in urbanization in tropical and subtropical regions, understanding the processes shaping urban coral reefs may be essential for anticipating future conservation challenges. We used a case study approach to identify unifying patterns of urban coral reefs and clarify the effects of urbanization on hard coral assemblages. Data were compiled from 11 cities throughout East and Southeast Asia, with particular focus on Singapore, Jakarta, Hong Kong, and Naha (Okinawa). Our review highlights several key characteristics of urban coral reefs, including “reef compression” (a decline in bathymetric range with increasing turbidity and decreasing water clarity over time and relative to shore), dominance by domed coral growth forms and low reef complexity, variable city-specific inshore-offshore gradients, early declines in coral cover with recent fluctuating periods of acute impacts and rapid recovery, and colonization of urban infrastructure by hard corals. We present hypotheses for urban reef community dynamics and discuss potential of ecological engineering for corals in urban areas.

Published
2018

42. Determining Knowledge and Behaviour Change: After Nutrition Screening Among Older Adults

Author

Holly D. Reimer, Heather H. Keller, and Katherine M. Southgate

Subjects
Male, Gerontology, Health Knowledge, Attitudes, Practice, Nutrition and Dietetics, Risk behaviour, Behaviour change, business.industry, Significant difference, Psychological intervention, Medicine (miscellaneous), General Medicine, medicine.disease, Group B, Treatment and control groups, Malnutrition, Nutrition Assessment, Risk-Taking, Surveys and Questionnaires, Intervention (counseling), Humans, Medicine, Female, business, Health Education, Aged
Abstract

Two education interventions involving personalized messages after nutrition screening in older adults were compared to determine changes in nutrition knowledge and risk behaviour. Of 150 older adults randomly selected from a local seniors’ centre, 61 completed baseline screening and a demographic and nutrition knowledge questionnaire and were randomized to one of two groups. Group A received personalized letters plus an educational booklet, and Group B received personalized letters only. All materials were sent through the mail. Forty-four participants completed post-test questionnaires to determine change in knowledge and risk behaviour. Both groups had reduced nutrition risk scores and increased knowledge scores at post-test. After the intervention, a significant difference was observed in knowledge change by treatment group. Group A participants experienced greater gains in knowledge, with a mean gain of 5.43 points, than did those in Group B, who had a mean gain of 1.36 points (p=0.018). Screening and education with print materials have the potential to change risk behaviour and nutrition knowledge in older adults. A specially designed booklet on older adults’ nutrition risk factors plus a personalized letter provide an effective education strategy for older adults after screening.

Published
2010
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43. IDENTIFICATION OF THE ESSENTIAL AMINO ACIDS OF THE FRESHWATER SHRIMP, Macrobrachium ohione1

Author

Lester S. Miyajima, Glen A. Broderick, and Rollin D. Reimer

Subjects
chemistry.chemical_classification, Macrobrachium, Methionine, biology, Complete protein, Aquatic Science, biology.organism_classification, Macrobrachium ohione, Amino acid, chemistry.chemical_compound, Biochemistry, chemistry, Valine, Essential nutrient, Agronomy and Crop Science, Amino acid synthesis
Abstract

The essential amino acids of the freshwater shrimp, Macrobrachium ohione were identified by radioactive assay using U−14C glucose. Those amino acids which incorporated little or no 14C were arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tyrosine, and valine. It was inferred that Macrobrachium ohione could not synthesize these amino acids and thus, has a dietary requirement for them.

Published
2009
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44. THE USE OF HEATED EFFLUENTS FROM POWER PLANTS FOR THE WINTER PRODUCTION OF SOFT SHELL CRABS1

Author

Rollin D. Reimer and Kirk Strawn

Subjects
body regions, Fishery, animal structures, Stocking, food and beverages, Environmental science, Aquatic Science, Soft-shell crab, Agronomy and Crop Science, Effluent, Bay
Abstract

This research was conducted July, 1969 through February, 1970 at the P. H. Robinson Generating Station on Galveston Bay, Texas and deals with the potential of using heated water from an electric generating station for a soft shell, blue crab (Callinectessapidus) industry. In cost per kg the soft shell crab is one of the more valuable resources being fished along the Atlantic Coast and Gulf of Mexico. The lack of competition from a wild winter stock of soft shell blue crabs would add value to a winter fisheries. The presence of a large wild stock of hard shell blue crabs throughout the year could provide the industry with an inexpensive stocking source. Molting in the intake and discharge canals occured at temperatures between 15 and 35C; the majority of molting crabs were taken in the intake from July to the middle of October and from the discharge from the middle of October through February. Ten percent of the crabs taken after the initial drop below 15 C in the intake canal were soft while 24% of the crabs taken in the discharge canal during the same period of time were soft. The use of the intake canal waters during the warmest months, when discharge temperatures are too high for holding crabs, could make this a year round industry. Holding tanks for maintaining hard and peeler crabs could be moved from one canal to the other as water temperatures demanded.

Published
2009
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45. Strategies to support engagement and continuity of activity during mealtimes for families living with dementia; a qualitative study

Author

Rebecca Genoe, Lori Schindel Martin, Sherry L. Dupuis, Holly D. Reimer, and Heather H. Keller

Subjects
Adult, Male, Further education, Gerontology, Activities of daily living, Care partners, Grounded theory, Quality of life (healthcare), Activities of Daily Living, medicine, Humans, Dementia, Family, Longitudinal Studies, Meals, Qualitative Research, Aged, Aged, 80 and over, Ontario, Mealtimes, business.industry, Middle Aged, Social engagement, medicine.disease, Quality of Life, Female, Geriatrics and Gerontology, Qualitative, business, Research Article, Dyad, Qualitative research
Abstract

Background Mealtimes are an essential part of living and quality of life for everyone, including persons living with dementia. A longitudinal qualitative study provided understanding of the meaning of mealtimes for persons with dementia and their family care partners. Strategies were specifically described by families to support meaningful mealtimes. The purpose of this manuscript is to describe the strategies devised and used by these families living with dementia. Methods A longitudinal qualitative study was undertaken to explore the meaning and experience of mealtimes for families living with dementia over a three-year period. 27 families [older person with dementia and at least one family care partner] were originally recruited from the community of South-Western Ontario. Individual and dyad interviews were conducted each year. Digitally recorded transcripts were analyzed using grounded theory methodology. Strategies were identified and categorized. Results Strategies to support quality mealtimes were devised by families as they adapted to their evolving lives. General strategies such as living in the moment, as well as strategies specific to maintaining social engagement and continuity of mealtime activities were reported. Conclusions In addition to nutritional benefit, family mealtimes provide important opportunities for persons with dementia and their family care partners to socially engage and continue meaningful roles. Strategies identified by participants provide a basis for further education and support to families living with dementia.

Published
2015
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46. Interaction of process parameters in the laser deposition of YBa2Cu3O7 films

Author

K.-O. Subke, D. Reimer, Asta Richter, Meinhard Schilling, and J.-K. Heinsohn

Subjects
Superconductivity, Materials science, Yield (engineering), Excimer laser, medicine.medical_treatment, Analytical chemistry, Energy Engineering and Power Technology, Process variable, Condensed Matter Physics, Laser, Electronic, Optical and Magnetic Materials, law.invention, law, Electrical resistivity and conductivity, medicine, Deposition (phase transition), Electrical and Electronic Engineering, Thin film
Abstract

The electrical and morphological properties of YBa 2 Cu 3 O 7 films grown on SrTiO 3 (100) substrates in a laser deposition process using a pulsed KrF excimer laser are investigated. For the first time, a quantitative order of importance of the relevant deposition parameters and their interactions that determine the quality of such films can be given. This is achieved by using statistical methods such as analysis of variance and multiple regression analysis for the design and evaluation of the experiments. The films prepared under optimum conditions grow c -axis oriented with low outgrowth densities and reveal transition temperatures T c ≅89 K, resistivities ρ (100 K )≤60 μ Ω cm, and resistance ratios R (300 K)/ R (100 K)≅3. The surface of the targets used for the deposition turned out to be crucial. Fresh targets yield significantly better electrical properties with a much lower spread of the data. Thus, a region in the process parameter space of YBa 2 Cu 3 O 7 film deposition has been identified where electrical and morphological properties are at optimum, simultaneously. This is prerequisite for the preparation of multilayer devices.

Published
1998
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47. Integrated YBa2Cu3O7 magnetometers for biomagnetic applications

Author

Bernd David, Meinhard Schilling, D. Reimer, S. Krey, K.-O. Subke, and R. Scharnweber

Subjects
Physics, Josephson effect, business.industry, Magnetometer, General Engineering, General Physics and Astronomy, Flux, White noise, Noise (electronics), law.invention, Magnetic field, Inductance, Nuclear magnetic resonance, law, Shielded cable, Optoelectronics, business
Abstract

Three concepts of integrated magnetometers intended for biomagnetic multichannel systems are investigated: The Ketchen-type magnetometer, the multiloop magnetometer and the magnetometer with integrated multiloop pickup coil (IMPUC). The devices are fabricated from YBa 2 Cu 3 O 7 -SrTiO 3 -YBa 2 Cu 3 O 7 thin-film multilayers, and step-edge grain-boundary Josephson junctions as well as ramp-edge junctions with PrBa 2 Cu 3 O 7 barriers are employed. The magnetometers are compared regarding their effective flux collecting area, inductance and noise performance. With an optimized layout for the multiloop device, we achieve an effective flux collecting area of 2.3 mm 2 at an inductance of 145 pH. At 77 K we measure a magnetic flux density noise down to √ S B =60 fT/√Hz at 1 Hz and of 17 fT/√Hz in the white noise regime. Due to the low noise levels of the magnetometers high quality magnetocardiograms were recorded inside a magnetically shielded room without signal averaging. The noise performance of the magnetometers is also analyzed in unshielded environment and in static magnetic fields.

Published
1997
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48. Sediment yield and seasonal soil erodibility for semiarid cropland in western Canada

Author

B.G. McConkey, W. Nicholaichuk, C. D. Reimer, and H. Steppuhn

Subjects
Sediment yield, Hydrology, geography, geography.geographical_feature_category, Soil Science, Soil science, Crop rotation, Current (stream), Universal Soil Loss Equation, Spring (hydrology), Erosion, Environmental science, Cropping system, Surface runoff
Abstract

Despite its importance to the degradation of the land resource, few estimates of soil loss or soil erodibility for water erosion from cropland have been made for the semiarid Brown soil zone of western Canada. To estimate these, we calibrated the event-based Modified Universal Soil Loss Equation with measured sediment yield for three 5-ha fields near Swift Current, Saskatchewan. The calibration used predetermined C, LS, P, and warm-season K factors with all erositivities and the K factors for other seasons optimized. Using this calibrated equation with 31 yr of measured runoff data, mean annual sediment yield for a conventional-tillage spring wheat-fallow cropping system on an undulating landscape (0 to 5% slopes) was estimated to be 0.8 Mg ha−1 yr−1. Estimated erosion from fallow land from 16 March to 15 April constituted 86% of the mean annual sediment yield. Erosion occurring during rainfall-runoff were relatively unimportant, accounting for about 4% of the estimated total sediment yield. An exceptionally severe rainstorm was predicted to have caused erosion of many Mg ha−1but the frequency of such events on a given field is too low to greatly affect mean annual erosion. Apparent field-scale soil erodibility was least in the winter (November to 15 March) when the soil would typically be frozen to the surface and was greatest in April when the soil would typically be partially frozen. Apparent erodibility in the summer and in late March was intermediate between those values. Key words: Erosion, runoff, snow, Universal Soil Loss Equation

Published
1997
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49. Temperature dependence of noise properties of directly coupled YBa2Cu3O7 magnetometers with PrBa2Cu3O7 ramp-type Josephson junctions

Author

D. Reimer, A. Lewalter, F. Ludwig, and Meinhard Schilling

Subjects
Physics, Josephson effect, Condensed matter physics, Quantum noise, Shot noise, Energy Engineering and Power Technology, Y-factor, Condensed Matter Physics, Electronic, Optical and Magnetic Materials, Pi Josephson junction, Nuclear magnetic resonance, Noise generator, Condensed Matter::Superconductivity, Flicker noise, Electrical and Electronic Engineering, Noise (radio)
Abstract

Josephson junctions in ramp-type geometry with artificial PrBa 2 Cu 3 O 7 barriers are applied in directly coupled magnetometers. We investigate the noise properties of the magnetometers to optimize for low flux noise. By applying a bias current reversal technique in flux-locked loop noise measurements one can distinguish between flux noise contributions from the Josephson junctions and from the superconducting films. The temperature dependence of the flux noise reveals that critical current fluctuations are the most important noise source at frequencies between 1 Hz and 100 Hz. We reach a level of flux noise of √S Ф (1 Hz - 26μФ 0 /√ Hz at 81 K .

Published
1996
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