Genome assembly and population genomic data of a pulmonate snail Ellobium chinense.

Ellobium chinense is an airbreathing, pulmonate gastropod species that inhabits saltmarshes in estuaries of the northwestern Pacific. Due to a rapid population decline and their unique ecological niche in estuarine ecosystems, this species has attracted special attention regarding their conservation and the genomic basis of adaptation to frequently changing environments. Here we report a draft genome assembly of E. chinense with a total size of 949.470 Mb and a scaffold N50 of 1.465 Mb. Comparative genomic analysis revealed that the GO terms enriched among four gastropod species are related to signal transduction involved in maintaining electrochemical gradients across the cell membrane. Population genomic analysis using the MSMC model for 14 re-sequenced individuals revealed a drastic decline in Korean and Japanese populations during the last glacial period, while the southern Chinese population retained a much larger effective population size (Ne). These contrasting demographic changes might be attributed to multiple environmental factors during the glacial-interglacial cycles. This study provides valuable genomic resources for understanding adaptation and historical demographic responses to climate change.

Compression Performance Analysis of Experimental Holographic Data Coding Systems.

It is challenging to find a proper way to compress computer-generated holography (CGH) data owing to their huge data requirements and characteristics. This study proposes CGH data coding systems with high-efficiency video coding (HEVC), three-dimensional extensions of HEVC (3D-HEVC), and video-based point cloud compression (V-PCC) codecs. In the proposed system, we implemented a procedure for codec usage and format conversion and evaluated the objective and subjective results to analyze the performance of the three coding systems. We discuss the relative advantages and disadvantages of the three coding systems with respect to their coding efficiency and reconstruction results. Our analysis concluded that 3D-HEVC and V-PCC are potential solutions for compressing red, green, blue, and depth (RGBD)-sourced CGH data.

Morphological and molecular analysis of the tropical hermit crab Calcinus vachoni (Decapoda, Diogenidae) and its potential association with colonial anemone.

Calcinus is the colorful hermit crab genus belonging to the family Diogenidae and is often found in coral reefs of the tropical Indo-West Pacific region, including southern Honshu, Japan, which is the northern limit of their occurrence. In the present study, we found C. vachoni for the first time in the intertidal zone of Jeju Island-the southernmost island of South Korea. We examined their morphology and provided a diagnosis of their morphological details with illustrations. In addition, the Korean Calcinus population was genetically characterized using mtDNA cox1 sequences and by placing them into three previously reported regional haplogroups. The phylogenetic tree from maximum likelihood analysis revealed that Korean C. vachoni is assigned to the C. vachoni haplogroups exclusively, one of the three well-supported mitochondrial haplogroups with distinct geographic ranges (i.e., C. vachoni, C. aff. vachoni Cooks, and C. aff. vachoni Mascarenes). This result provides new information on the species distribution of C.vachoni, extending their geographic range further north into the southern coast of Korea. In this study, we also first report the potential association of C. vachoni with their co-occurring colonial anemone species Palythoa aff. mutuki and dead coral head of Pocillopora species based on our on-site observation and a public coral collection database of Calcinus species. However, their ecological association with co-occurring coral species is putatively assumed for now and therefore has to be validated by compelling evidence from further field observation and experimental studies (i.e., whether the presence/absence of colonial anemones affects the behavior and survival of the hermit crabs).

In-line and off-axis polarization-selective holographic lenses recorded in azopolymer thin films via polarization holography and polarization multiplexing.

Polarization-selective diffractive in-line and off-axis lenses are recorded in azopolymer thin films using polarization holography. A simple, yet efficient, and to the best of our knowledge, new method is used to suppress the surface relief grating formation and to improve the polarization properties of the lenses. The in-line lenses are converging for right circularly polarized (RCP) light and diverging for left circularly polarized (LCP) light. Bifocal off-axis lenses are recorded by polarization multiplexing. By rotating the sample at 90° between the exposures, the two focal points of these lenses are located in orthogonal directions O x and O y, so we can refer to these novel lenses as 2D bifocal polarization holographic lenses. The light intensity in their focuses depends on the reconstructing light polarization. According to the recording scheme, they can either reach maximum intensities simultaneously (for LCP or RCP), or alternatively, one of them can be at maximum for LCP, while the other for RCP. These lenses may be used as polarization controllable optical switches, in the field of self-interference incoherent digital holography or for other photonics applications.

Noise analysis in outdoor dynamic speckle measurement.

The dynamic speckle method (DSM) is an effective tool for the estimation of speed of processes. The speed distribution is encoded in a map built by statistical pointwise processing of time-correlated speckle patterns. For industrial inspection, the outdoor noisy measurement is required. The paper analyzes the efficiency of the DSM in the presence of environmental noise as phase fluctuations due to the lack of vibration isolation and shot noise due to ambient light. The usage of normalized estimates for the case of non-uniform laser illumination is studied. The feasibility of the outdoor measurement has been proven by numerical simulations of noisy image capture and real experiments with test objects. Good agreement has been demonstrated in both the simulation and experiment between the ground truth map and the maps extracted from noisy data.

Effective Size Reduction of the Metallic Waveguide Bandpass Filter with Metamaterial Resonators and Its 3D-Printed Version.

In this paper, a novel method is proposed to effectively reduce the size of a waveguide bandpass filter (BPF). Because the metallic cavities make the conventional waveguide end up with a large geometry, especially for high-order BPFs, very compact waveguide-type resonators having metamaterial zeroth-order resonance (WG ZOR) are designed on the cross section of the waveguide and substituted for the cavities. While the cavities are half-wavelength resonators, the WG ZOR is shorter than one-eighth of a wavelength. A substantial reduction in the size and weight of the waveguide filter is observed as the resonators are cascaded in series through coupling elements in the X-band that is much longer than that in K- or Ka-bands. The proposed metamaterial filter is realized as a 3D-printed structure to be lighter and thus more suitable for low earth orbit (LEO) satellites. An X-band of 7.25-7.75 GHz is chosen to verify the method as the passband with an attenuation of 40 dB at 7.00 GHz and 8.00 GHz as the roll-off in the stopband. The BPF is manufactured in two ways, namely the CNC-milling technique and metal coating-added 3D printing. The design is carried out with a geometrical parameter of not 10-2 mm but rather 10-1 mm, which is good for manufacturers but challenging for component designers. The measurement of the manufactured metal waveguide filters reveals that the passband has about ≤1 dB and ≤-15 dB as the insertion loss and the reflection coefficient, respectively, and the stopband has an attenuation of ≤-40 dB, which are in good agreement with the results of the circuit and the simulation. The proposed filter has a length of 14 cm as the eighth-order BPF, but the conventional waveguide is 20 cm as the seventh-order BPF for the same area of the cross section.

Wide-viewing holographic stereogram based on self-interference incoherent digital holography.

We propose a holographic stereogram synthesis method which uses holograms that are optically captured by self-interference incoherent digital holography (SIDH) based on a geometric phase lens. SIDH is a promising solution for hologram acquisition under low-coherence lighting condition. A mechanical scanning system is constructed to acquire multiple perspective holograms. Numerical simulations and experimental analyses conducted using high-resolution diffractive optical element demonstrate that the proposed method can produce a wide-viewing hologram which can realize realistic 3D scenarios with depth cues such as accommodation and motion parallax. The future objectives include the implementation of a multiple-camera system for holographic videos.

Complete mitochondrial genome of Conuslischkeanus Weinkauff, 1875 (Neogastropoda, Conidae) and phylogenetic implications of the evolutionary diversification of dietary types of Conus species.

The family Conidae, commonly known as cone snails, is one of the most intriguing gastropod groups owing to their diverse array of feeding behaviors (diets) and toxin peptides (conotoxins). Conuslischkeanus Weinkauff, 1875 is a worm-hunting species widely distributed from Africa to the Northwest Pacific. In this study, we report the mitochondrial genome sequence of C.lischkeanus and inferred its phylogenetic relationship with other Conus species. Its mitochondrial genome is a circular DNA molecule (16,120 bp in size) composed of 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. Phylogenetic analyses of concatenated nucleotide sequences of 13 PCGs and two ribosomal RNA genes showed that C.lischkeanus belongs to the subgenus Lividoconus group, which is grouped with species of the subgenus Virgiconus, and a member of the largest assemblage of worm-hunting (vermivorous) species at the most basal position in this group. Mitochondrial genome phylogeny supports the previous hypothesis that the ancestral diet of cone snails was worm-hunting, and that other dietary types (molluscivous or piscivorous) have secondarily evolved multiple times from different origins. This new, complete mitochondrial genome information provides valuable insights into the mitochondrial genome diversity and molecular phylogeny of Conus species.

Reversible supramolecular chiral structures induced in azopolymers by elliptically polarized light: influence of the irradiation wavelength and intensity.

Photoinduced supramolecular chiral structures in azo materials have been extensively studied for the development of all-optical switches and because of their influence on the properties of certain types of polarization holographic gratings. Here, we investigate chiral structures induced by irradiation with elliptically polarized light in thin films of four azopolymers denoted as PAZO, P1, P1-2, which are amorphous, and P2, which is liquid crystalline. Their formation is characterized in real time by the kinetics of azimuth rotation. The influence of the irradiation wavelength and intensity is also analyzed. The largest azimuth rotation per unit thickness is achieved in PAZO (33°/µm) and P1-2 (25°/µm). Reversibility of the chiral structures is demonstrated by a tenfold change in the direction of rotation. Our results also indicate that chiral structures formation occurs significantly faster than the induction of linear birefringence.

Intensity-based dynamic speckle method using JPEG and JPEG2000 compression.

Statistical processing of speckle data enables observation of the speed of processes. In intensity-based pointwise dynamic speckle analysis, a map related to speed's spatial distribution is extracted from a sequence of speckle patterns formed on an object under coherent light. Monitoring of time evolution of a process needs storage, transfer, and processing of a large number of images. We have proposed lossy compression of these images using JPEG and JPEG2000 formats. We have compared the maps computed from noncompressed and decompressed synthetic and experimental images, and we have proven that both compression formats can be applied in the dynamic speckle analysis.

Morphological and molecular analyses of parasitic barnacles (Crustacea: Cirripedia: Rhizocephala) in Korea: preliminary data for the taxonomy and host ranges of Korean species.

Morphological and molecular analyses of Korean rhizocephalan barnacle species were performed to examine their host ranges and taxonomy. Morphological examination and molecular analysis of mtDNA cox1, 16S, and nuclear 18S rRNA sequences revealed nine rhizocephalan species from three genera of the two families, Sacculinidae and Polyascidae. Phylogenetic analysis of molecular sequences revealed two new species candidates in the genus Parasacculina, and three Sacculina species (S. pilosella, S. pinnotherae, and S. imberbis) were transferred to the genus Parasacculina. Examination of host ranges revealed higher host specificity and lower infestation rates in Korean rhizocephalan species than rhizocephalans from other geographic regions. This is the first report of the taxonomy, species diversity, and host ranges of Korean parasitic rhizocephalan barnacles based on their morphological and molecular analyses. More information from extensive sampling of parasitic barnacles from a wide range of crustacean host species is necessary to fully understand their taxonomy, prevalence on decapod hosts, and phylogenetic relationships among major rhizocephalan taxa.

Out-of-core GPU 2D-shift-FFT algorithm for ultra-high-resolution hologram generation.

We propose a novel out-of-core GPU algorithm for 2D-Shift-FFT (i.e., 2D-FFT with FFT-shift) to generate ultra-high-resolution holograms. Generating an ultra-high-resolution hologram requires a large complex matrix (e.g., 100K2) with a size that typically exceeds GPU memory. To handle such a large-scale hologram plane with limited GPU memory, we employ a 1D-FFT based 2D-FFT computation method. We transpose the column data to have a continuous memory layout to improve the column-wise 1D-FFT stage performance in both the data communication and GPU computation. We also combine the FFT-shift and transposition steps to reduce and hide the workload. To maximize the GPU utilization efficiency, we exploit the concurrent execution ability of recent heterogeneous computing systems. We also further optimize our method's performance with our cache-friendly chunk generation algorithm and pinned-memory buffer approach. We tested our method on three computing systems having different GPUs and various sizes of complex matrices. Compared to the conventional implementation based on the state-of-the-art GPU FFT library (i.e., cuFFT), our method achieved up to 3.24 and 3.06 times higher performance for a large-scale complex matrix in single- and double-precision cases, respectively. To assess the benefits offered by the proposed approach in an actual application, we applied our method to the layer-based CGH process. As a result, it reduced the time required to generate an ultra-high-resolution hologram (e.g., 100K2) up to 28% compared to the use of the conventional algorithm. These results demonstrate the efficiency and usefulness of our method.

Quantization of dynamic speckle patterns with spatially varying statistics.

Raw data compression is mandatory for monitoring of processes by dynamic speckle analysis when two-dimensional activity maps are built by pointwise statistical processing of correlated speckle patterns formed on the surface of diffusely reflecting objects under laser illumination. Coarse quantization of speckle patterns enables storage and transfer of a huge amount of images, but it may be inefficient at spatially varying speckle statistics, such as for patterns recorded at non-uniform illumination or reflectivity. We prove efficacy of coarse quantization of the raw speckle data with varying statistics for a normalized algorithm by simulation and a polymer drop drying experiment. Both uniform and non-uniform quantization are proposed for treating such data. Decreasing the bit depth from 8 to 3 is possible without worsening the quality of the activity map.

Phylogeography of Mytilisepta virgata (Mytilidae: Bivalvia) in the northwestern Pacific: Cryptic mitochondrial lineages and mito-nuclear discordance.

The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout nearly their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas due to sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. In contrast to mtDNA sequences, a clear lineage split between the two mitochondrial lineages was not found in ITS1 sequences, which showed a star-like structure composed of a mixture of southern and northern mitochondrial lineages. Possible reasons for this type of mito-nuclear discordance include stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Cryptic speciation cannot be ruled out from these results, and future work using genomic analyses is required to address whether the thermal physiology of these mussels corresponds to the deep divergence of their mitochondrial genes and to test for the existence of morphologically indistinguishable but genetically separate cryptic species.

Life-history features and oceanography drive phylogeographic patterns of the chiton Acanthochitona cf. rubrolineata (Lischke, 1873) in the northwestern Pacific.

Chitons are a group of marine mollusks (class Polyplacophora) characterized by having eight articulating shell plates on their dorsal body surface. They represent suitable materials for studying the spatiotemporal processes that underlie population differentiation and speciation in ocean environments. Here we performed population genetic analyses on the northwestern Pacific chiton Acanthochitona cf. rubrolineata (Lischke, 1873) using two mitochondrial gene fragments (COI and 16S) from 180 individuals sampled from 11 populations among the coastal waters of Korea, Japan, and China. The phylogenetic network uncovered a reticulated relationship with several sub-haplogroups for all A. cf. rubrolineata haplotypes. SAMOVA analyses suggested the best grouping occurred at three groups (ΦCT = 0.151, P < 0.0001), which geographically corresponds to hydrographic discontinuity among the coastal regions of Korea, Japan, and China. The assumed limited dispersal ability of A. cf. rubrolineata, coupled with northeasterly flowing, trifurcate warm currents, might have contributed to the genetic differentiation among the three groups. Meanwhile, a high level of within-group genetic homogeneity was detected, indicating extensive coastal currents might facilitate gene flow among the populations within each group. Bayesian skyline plots demonstrated significant population expansion after the Last Glacial Period (110-25 thousand years ago) for all studied populations except the Japan group. Together these results suggest that the present-day phylogeographic patterns of A. cf. rubrolineata are strongly affected by the interplay of historical and/or contemporary oceanography and species-specific life-history features.

The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda).

The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.

Michelson-interferometric-configuration-based incoherent digital holography with a geometric phase shifter.

The phase-shifting method is a simple and efficient approach to extract complex hologram information free of bias and twin-image noise. In this study, the geometric phase-shifting method is utilized for a self-interference incoherent digital holographic recording system based on the Michelson-type interferometer. The phase-shifting module consists of a horizontal polarizer, and two achromatic quarter-wave plates are employed inside the interferometer, replacing conventional phase-shifting devices, such as the piezo-actuated mirror. Since the phase-shifting amount of the introduced method herein is theoretical, regardless of the input wavelength, the simultaneous recording of step-wise phase-shifted interferograms for different color channels is available. Therefore, the multi-color hologram recording is achieved with fewer numbers of exposures. The demonstration of multi-color hologram recording and reconstruction are presented to validate the proposed idea.

Dynamic speckle analysis with coarse quantization of the raw data.

Analysis of dynamic speckle formed on the surface of diffusely reflecting objects under laser illumination is a non-contact method for inspection of speed of processes. The paper deals with intensity-based implementation of the method that relies on statistical processing of correlated in time sequences of speckle images. A two-dimensional activity map is built for each sequence to visualize regions of different speed on the object surface at a given instant. A great number of images is required to track a process in time. We propose data compression by coarse quantization of the raw speckle data. Efficacy of quantization is analyzed by simulation and experiment for low- and high-contrast speckle patterns with bell-shaped and long-tailed distributions of intensity, respectively. Non-uniform quantization is proposed for long-tailed speckle intensity distributions. Decreasing the bit depth from 8 to 4 causes no change in the probability density function of the activity estimate.

A mitochondrial genome phylogeny of Mytilidae (Bivalvia: Mytilida).

The family Mytilidae is a family of bivalve mussels that are distributed worldwide in diverse marine habitats. Within the family, classification systems and phylogenetic relationships among subfamilies remain not yet fully resolved. In this study, we newly determined 9 mitochondrial genome sequences from 7 subfamilies: Bathymodiolus thermophilus (Bathymodiolinae), Modiolus nipponicus (Modiolinae), Lithophaga curta (the first representative of Lithophaginae), Brachidontes mutabilis (Brachidontinae), Mytilisepta virgata (Brachidontinae), Mytilisepta keenae (Brachidontinae), Crenomytilus grayanus (Mytilinae), Gregariella coralliophaga (Crenellinae), and Septifer bilocularis (the first representative of Septiferinae). Phylogenetic trees using maximum likelihood and Bayesian inference methods for 28 mitochondrial genomes (including 19 previously published sequences) showed two major clades with high support values: Clade 1 ((Bathymodiolinae + Modiolinae) + (Lithophaginae + Limnoperninae)) and Clade 2 (((Mytilinae + Crenellinae) + Septiferinae) + Brachidontinae). The position of the genus Lithophaga (representing Lithophaginae) differed from a previously published molecular phylogeny. Divergence time analysis with a molecular clock indicated that lineage splitting among the major subfamilies of Mytilidae (including the habitat transition from marine to freshwater environments by ancestral Limnoperninae) occurred in the Mesozoic period, coinciding with high diversification rates of marine fauna during that time. This is the first mitochondrial genome-based phylogenetic study of the Mytilidae that covers nearly all subfamily members, excluding the subfamily Dacrydiinae.

Evidence that alternative transcriptional initiation is largely nonadaptive.

Alternative transcriptional initiation (ATI) refers to the frequent observation that one gene has multiple transcription start sites (TSSs). Although this phenomenon is thought to be adaptive, the specific advantage is rarely known. Here, we propose that each gene has one optimal TSS and that ATI arises primarily from imprecise transcriptional initiation that could be deleterious. This error hypothesis predicts that (i) the TSS diversity of a gene reduces with its expression level; (ii) the fractional use of the major TSS increases, but that of each minor TSS decreases, with the gene expression level; and (iii) cis-elements for major TSSs are selectively constrained, while those for minor TSSs are not. By contrast, the adaptive hypothesis does not make these predictions a priori. Our analysis of human and mouse transcriptomes confirms each of the three predictions. These and other findings strongly suggest that ATI predominantly results from molecular errors, requiring a major revision of our understanding of the precision and regulation of transcription.