The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement

<p>Abstract</p> <p>Background</p> <p>The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of <it>Hox </it>expression. The mitochondrial genome of a sea spider, <it>Nymphon gracile </it>(Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, <it>N. gracile </it>appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.</p> <p>Results</p> <p>The complete mitochondrial genome (15,474 bp) of a sea spider (<it>Achelia bituberculata</it>) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the <it>trnQ </it>gene between the <it>rrnS </it>gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (<it>A. bituberculata </it>and <it>N. gracile</it>) may be closely related to the clade of Acari and Araneae.</p> <p>Conclusion</p> <p>The complete mitochondrial genome sequence of <it>A. bituberculata </it>(Family Ammotheidae) and the previously-reported partial sequence of <it>Endeis spinosa </it>show the gene arrangement patterns typical of arthropods (<it>Limulus</it>-like), but they differ markedly from that of <it>N. gracile</it>. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata <it>sensu lato</it>, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory – that the pycnogonids are a sister group of all other arthropods – should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.</p

Knowledge-Augmented Language Model Verification

Recent Language Models (LMs) have shown impressive capabilities in generating texts with the knowledge internalized in parameters. Yet, LMs often generate the factually incorrect responses to the given queries, since their knowledge may be inaccurate, incomplete, and outdated. To address this problem, previous works propose to augment LMs with the knowledge retrieved from an external knowledge source. However, such approaches often show suboptimal text generation performance due to two reasons: 1) the model may fail to retrieve the knowledge relevant to the given query, or 2) the model may not faithfully reflect the retrieved knowledge in the generated text. To overcome these, we propose to verify the output and the knowledge of the knowledge-augmented LMs with a separate verifier, which is a small LM that is trained to detect those two types of errors through instruction-finetuning. Then, when the verifier recognizes an error, we can rectify it by either retrieving new knowledge or generating new text. Further, we use an ensemble of the outputs from different instructions with a single verifier to enhance the reliability of the verification processes. We validate the effectiveness of the proposed verification steps on multiple question answering benchmarks, whose results show that the proposed verifier effectively identifies retrieval and generation errors, allowing LMs to provide more factually correct outputs. Our code is available at https://github.com/JinheonBaek/KALMV.Comment: EMNLP 202

Unusual transport characteristics of nitrogen-doped single-walled carbon nanotubes

Electrical transport characteristics of nitrogen-doped single-walled carbon nanotubes (N-SWCNTs), in which the nitrogen dopant is believed to form a pyridinelike bonding configuration, are studied with the field effect transistor operations. Contrary to the expectation that the nitrogen atoms may induce a n -type doping, the electrical transports through our N-SWCNTs are either ambipolar in vacuum or p -type in air. Through the first-principles electronic structure calculations, we show that the nitrogen dopant indeed favors the pyridinelike configuration and the Fermi level of the pyridinelike N-SWCNT is almost at the intrinsic level.open01

1000 nm tunable acousto-optic filter based on photonic crystal fiber

Author name used in this publication: W. JinAuthor name used in this publication: J. Ju2007-2008 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Nonlinear oscillations of a sessile drop on a hydrophobic surface induced by ac electrowetting

We examine the nature of ac electrowetting (EW)-driven axisymmetric oscillations of a sessile water drop on a dielectric substrate. In ac EW, small-amplitude oscillations of a drop differ from the Rayleigh linear modes of freely oscillating drops. In this paper, we demonstrate that changes in the time-averaged contact angle of the sessile drop attributed to the presence of an electric field and a solid substrate mainly caused this discrepancy. We combine the domain perturbation method with the Lindsted-Poincare method to derive an asymptotic formula for resonant frequency. Theoretical analysis shows that the resonant frequency is a function of the time-averaged contact angle. Each mode of the resonance frequency is a linear function of epsilon(1), which is the magnitude of the cosine of the time-averaged contact angle. The most dominant mode in this study, that is, the fundamental mode n = 2, decreases linearly with epsilon(1). The results of the theoretical model are compared with those of both the experiments and numerical simulations. The average resonant frequency deviation between the perturbation solutions and numerical simulations is 4.3%, whereas that between the perturbation solutions and the experiments is 1.8%.X1121sciescopu