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Measuring Phylogenetic Information of Incomplete Sequence Data

2022-04-19T00:00:00Z

Title: Measuring Phylogenetic Information of Incomplete Sequence Data Authors: Seo, Tae-Kun; Gascuel, Olivier; Thorne, Jeffrey L. Abstract: Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the effective sequence length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set of equal size, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification. [Fisher information; gaps; insertion; deletion; indel; model adequacy; goodness-of-fit test; sequence alignment.]

Identification of ventilated and submarine glacial meltwaters in the Amundsen Sea, Antarctica, using noble gases

2022-01-01T00:00:00Z

Title: Identification of ventilated and submarine glacial meltwaters in the Amundsen Sea, Antarctica, using noble gases Authors: 신동엽; 함도식; Kim, Tae-Wan; Rhee, Tae Siek; 이상훈; 박기홍; Park, Jisoo; 권영신; Kim, Mi Seon; 이동섭 Abstract: To delineate the glacial meltwater distribution, we used five noble gases for optimum multiparameter analysis (OMPA) of the water masses in the Dotson-Getz Trough (DGT), Amundsen Sea. The increased number of tracers allowed us to define potential source waters at the surface, which have not been possible with a small set of tracers. The highest submarine meltwater (SMW) fraction (~0.6%) was present at the depth of ~450 m near the Dotson Ice Shelf. The SMW appeared to travel beyond the continental shelf break along an isopycnal layer. Air-equilibrated freshwater (up to 1.5%), presumably ventilated SMW (VMW) and surface melts, was present in the surface layer (<100 m). The distribution of SMW indicates that upwelled SMW, known as an important carrier of iron to the upper layer, amounts for 29% of the SMW in the DGT. The clear separation of VMW from SMW enabled partitioning of meltwater into locally-produced and upstream fractions and estimation of the basal melting of 53 ？ 94 Gt yr-1 for the adjacent ice shelves, assuming that the SMW fractions represent accumulation since the previous Winter Water formation. The Meteoric Water (MET) fractions, consisting of SMW and VMW, comprised 24% of those derived from oxygen isotopes, indicating that the annual input from basal melting is far less than the inventory of meteoric water, represented by MET.

Visible Light Illumination Effects on Instability of MoS2 Thin-Film Transistors for Optical Sensor Application

2022-01-01T00:00:00Z

Title: Visible Light Illumination Effects on Instability of MoS2 Thin-Film Transistors for Optical Sensor Application Authors: Seo, Seung Gi; Ryu, Jae Hyeon; Lee, Won Young; Jin, Sung Hun Abstract: With the advent of the trillion sensor era, molybdenum disulfide (MoS2) offers intriguing future optical device opportunities due to qualities such as its novel optoelectronic properties and preferable form factors. However, while a fundamental understanding of device reliability under illumination is significantly important, most of the previous research has focused on persistent photocurrent (PPC) effects. For this reason, understanding of a clear mechanism remains elusive. Herein the work reported, electrical-bias-dependent device instability and net optical illumination effects of MoS2 thin-film transistors (TFTs) are experimentally evaluated to decouple the origins of device instability coming from either net electrical bias stress or illumination stress. In addition, time-dependent monitoring of relaxation behaviors under illumination at different wavelength hints that excess carrier generation and remnant electrons after annihilation during illumination play a key role in determination of photo-initiated instability of a device. For practical suppression of device instability under ambient light, an operation scheme (using trapping time increase under positive bias) is adroitly utilized to provide reliable device performance. Systematic understanding of device instability of MoS2 TFTs, and of their suppression principles, is potentially beneficial for the design of next-generation devices on the basis of 2D materials.

Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages

2022-01-01T00:00:00Z

Title: Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages Authors: Oh, Han Na; Myeong, Nu Ri; Kim, Taeyune; Min, Gi？Sik; Kim, Sanghee; Sul, Woo Jun Abstract: Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three diferent temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.