Stereotactic body radiation therapy (SBRT) for the treatment of primary breast cancer in patients not undergoing surgery.

PURPOSE: The purpose was to explore the role of stereotactic body radiation therapy (SBRT) in providing local control (LC) for primary breast cancer in patients unable to undergo surgery. MATERIALS/METHODS: Between 2015 and 2019, 13 non-surgical candidates with 14 lesions were treated with SBRT for primary breast cancer. In 4 cases, SBRT was used after whole breast radiation therapy (WBRT; 40-50 Gy/20-25 fractions). SBRT dose was 30-40 â€‹Gy in 5 fractions for patients treated with SBRT alone and 25-32 â€‹Gy in 4-5 fractions for those treated with SBRT â€‹+ â€‹WBRT. LC and overall survival (OS) were estimated using Kaplan-Meier curves. Response was also assessed using RECIST guidelines. RESULTS: Median follow-up was 32 (range: 3.4-70.4) months. Imaging at median 2.2 (0.6-8.1) months post-SBRT showed median 43.2 â€‹% (range: 2-100 â€‹%) decrease in the largest diameter and median 68.7 â€‹% (range: 27.9-100 â€‹%) SUV reduction. There were 3 cases of local progression at 8.7-10.6 months. Estimated LC was 100 â€‹% at 6 months and 71.6 â€‹% at 12, 24 and 36 months. Estimated median OS was 100 â€‹% at 6 months, 76.9 â€‹% at 12 months, and 61.5 â€‹% at 24 and 36 months. Acute toxicity (n â€‹= â€‹13; 92.9 â€‹%) included grade (G)1 (n â€‹= â€‹8), G2 (n â€‹= â€‹4), and G4 (necrosis; n â€‹= â€‹1). Late toxicity included G2 edema (n â€‹= â€‹1) and G4 necrosis (n â€‹= â€‹2, including 1 consequential late effect). Only patients treated with SBRT â€‹+ â€‹WBRT experienced acute/late G4 toxicity, managed with resection or steroids. CONCLUSIONS: SBRT to primary breast cancer resulted in good LC in non-surgical/metastatic patients. Although necrosis (n â€‹= â€‹2) occurred in the SBRT â€‹+ â€‹WBRT group, it was successfully salvaged.

Comparative ontogeny and phylogenetic relationships of eight lizardfish species (Synodontidae) from the Northwest Pacific, with a focus on Trachinocephalus monophyly.

Lizardfish (Aulopiforms: Synodontidae), distributed broadly in temperate to tropical waters, are represented globally by 83 species across four genera, with 10 species in Korea. Despite these numbers, few studies have been conducted on the early life history of lizardfishes compared to their adult counterparts. Thus, we conducted molecular identification of 123 Synodontidae larvae collected from the Northwest Pacific (Korea Strait, Yellow Sea, East China Sea, and East Sea) between June 2017 and July 2021, using mitochondrial DNA COI and 16S rRNA sequences. Significant morphological differences were observed in the larvae and juvenile, including variation in melanophore, count, morphometric characteristics, and body shape. The morphological traits of eight species (Harpadon nehereus, Saurida macrolepis, Saurida wanieso, Saurida sp., Synodus hoshinonis, Synodus kaianus, Synodus macrops, and Trachinocephalus trachinus) served as vital data for interpreting the phylogenetic relationships within the Northwest Pacific Synodontidae. Ultimately, the identification key revealed by this study will enable accurate identification of Synodontid larvae and juveniles, and further facilitate our understanding of the phylogenetic relationships within this family.

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean.

Chub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first chromosome-level genome assembly of chub mackerel (fScoJap1) using the Vertebrate Genomes Project assembly pipeline with PacBio HiFi genomic sequencing and Arima Hi-C chromosome contact data. The final assembly is 828.68 Mb with 24 chromosomes, nearly all containing telomeric repeats at their ends. We annotated 31,656 genes and discovered that approximately 2.19% of the genome contained DNA transposon elements repressed within duplicated genes. Analyzing 5-methylcytosine (5mC) modifications using HiFi reads, we observed open/close chromatin patterns at gene promoters, including the FADS2 gene involved in Omega-3 production. This chromosome-level reference genome provides unprecedented opportunities for advancing our knowledge of chub mackerels in biology, industry, and conservation.

The study on the complete mitochondrial genome of Acanthopsetta nadeshnyi and its phylogenetic position.

Pleuronectidae is a well-studied familyin the order Pleuronectiformes. In contrast, genetic research on the flatfish Acanthopsetta nadeshnyi of the Pleuronectidae family is limited. This study reports the complete mitogenome of A. nadeshnyi. The mitogenome was 17,206 bases long and included 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a putative control region. Phylogenetic analysis based on the nucleotide sequences of the 13 PCGs confirmed that A. nadeshnyi belongs to the Pleuronectidae family.

Isolation and characterization of single domain antibodies from banded houndshark (Triakis scyllium) targeting SARS-CoV-2 spike RBD protein.

The COVID-19 pandemic has significantly impacted human health for three years. To mitigate the spread of SARS-CoV-2, the development of neutralizing antibodies has been accelerated, including the exploration of alternative antibody formats such as single-domain antibodies. In this study, we identified variable new antigen receptors (VNARs) specific for the receptor binding domain (RBD) of SARS-CoV-2 by immunizing a banded houndshark (Triakis scyllium) with recombinant wild-type RBD. Notably, the CoV2NAR-1 clone showed high binding affinities in the nanomolar range to various RBDs and demonstrated neutralizing activity against SARS-CoV-2 pseudoviruses. These results highlight the potential of the banded houndshark as an animal model for the development of VNAR-based therapeutics or diagnostics against future pandemics.

Analysis of the complete mitochondrial genome sequence of Japanese butterflyfish, Chaetodon nippon (Chaetodontiformes, Chaetodontidae).

Japanese butterflyfish (Chaetodon nippon) belong to the family Chaetodontidae and order Chaetodontiformes. It has circular mitochondrial genome of 16,507 bp in length with 55.4% of A + T content and has 37 genes, including 22 tRNA, 2 rRNA, and 13 protein-coding genes, in addition to a control region. The results of phylogenetic analysis indicated that the C. nippon, C. wiebeli, C. auripes, C. auriga, C. octofasciatus, C. speculum, and C. modestus are closely related to each other. The findings of this study will provide useful genetic information for further phylogenetic and taxonomic classifications of Chaetodontidae.

Characteristics and phylogenetic analysis of the complete mitochondrial genome of Microstomus achne.

Microstomus achne (Jordan and Starks, 1904) is an economically valuable flatfish belonging to the family Pleuronectidae and the only flatfish that inhabits Korea. Here, we report on the complete mitochondrial genome of M. achne and the phylogenetic relationship between close species. The mitogenome is 16,971 bp long and encodes 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The phylogenetic analysis showed that M. achne clustered with Glyptocephalus stelleri, which supports the conclusion that M. achne belongs to the family Pleuronectidae. The results of this study provide a better understanding of M. achne.

Complete mitochondrial genome of brown-banded butterflyfish Chaetodon modestus (Chaetodontiformes, Chaetodontidae) and phylogenetic analysis.

The complete mitochondrial genome of the Chaetodon modestus (Temminck and Schlegel, 1844) was first determined in this study, which is 16,490 bp in length, containing 13 protein-coding genes, two rRNA genes, and 22 tRNA. Out of 37 mitochondrial genes, except for ND6 and eight tRNA (Pro, Glu, Ser, Tyr, Cys, Asn, Ala, Gln) genes were encoded on the L-strand, the others were encoded on the H-strand. The overall base composition includes A (28.0%), T (28.7%), G (16.7%), ad C (26.6%). The phylogenetic tree was built using the maximum-likelihood approach to provide a relationship within Chaetodontidae, which might be valuable for species management.

The complete mitochondrial genome of threadfin butterflyfish, Chaetodon auriga (Chaetodontiformes: Chaetodontidae) and phylogenetic analysis.

Chaetodon auriga (Forsskal, 1775) belongs to the family Chaetodontidae and the order Chaetodontiformes. Here, we report the complete mitochondrial genome of C. auriga assembled using the Illumina MiSeq platform. The circular mitochondrial genome of C. auriga is 16,527 bp long, has an A + T content of 54.53%, and contains 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes), and a non-coding region. The overall nucleotide composition was A: 28.19%, T: 26.34%, G: 16.27%, and C: 29.20%. The mitochondrial genome of C. auriga contributes to revealing the phylogenetic relationships among species of the Chaetodontidae family.

New descriptions of four larval lanternfish species and cryptic diversity of Benthosema pterotum (Pisces: Myctophidae) from the Northwest Pacific.

Although there have been many studies on the taxonomy of lanternfishes, morphological similarities during larval and juvenile stages make it difficult to identify species and understand their early life histories. During an ichthyoplankton survey in the Northwest Pacific (East Sea, East China Sea) between 2017 and 2020, a research vessel from the National Institute of Fisheries Science collected larvae and juveniles that belonged to the family Myctophidae using a bongo net. To accurately identify species, mtDNA sequences encoding cytochrome c oxidase subunit I and 16S ribosomal RNA were obtained and compared with those of adult voucher specimens. These comparisons led to the identification of four previously unknown larval lanternfish species (Diaphus chrysorhynchus, Diaphus suborbitalis, Diaphus watasei and Lampanyctus fernae), which are described here for the first time. The authors also describe the cryptic diversity of Benthosema pterotum and provide identification keys for 10 species of larval lanternfish, in accordance with their developmental stages.

Shallow population structure of southern bluefin tuna, Thunnus maccoyii (Castelnau, 1872) between Indian and Atlantic Oceans inferred from mitochondrial DNA sequences.

Southern bluefin tuna (Thunnus maccoyii Castelnau, 1872) is distributed across most of the southern temperate ocean and migrates extensively between 30°S and 50°S. Since T. maccoyii has been continually and heavily exploited, it is necessary to investigate the genetic diversity, population structure and demographic history of T. maccoyii for effective management and conservation. Thirty-seven gonad tissues of T. maccoyii were sampled from two locations, which were in the eastern Indian Ocean and the eastern Atlantic Ocean, by scientific observers onboard Korean T. maccoyii longline vessels in 2015. We compared 1240-bp sequences of combined mitochondrial DNA (mtDNA) from the cytochrome c oxidase subunit I (COI, 504-bp) and control region (CR, 736-bp) sequences. The pairwise fixation index (F ST) and maximum-likelihood tree showed that two clades (A and B) were formed regardless of locations. Clade A occurred more commonly than clade B in both localities: the occurrence ratio of clade A was 69% in the Indian Ocean, and 79% in the Atlantic Ocean, respectively. Our findings suggest that a historic differentiation event may have occurred in T. maccoyii, but recently the connectivity between the two oceans may be possible in T. maccoyii populations.

Molecular and morphological comparison of larvae and juveniles of five species of callionymids, with ontogenetic evidence on the monophyly of Repomucenus (Callionymidae).

Dragonet fishes (Callionymidae) are benthic inhabitants of shallow waters, even in tidal pools, down to depths below 900 m in all subtropical, tropical and temperate oceans. The family comprises 200 species in 20 genera worldwide, of which 18 species in 6 genera occur in Korea. Classification within the family Callionymidae has been controversial because of the differing proposals of Fricke and Nakabo (Fishes of Japan with pictorial keys to the species, 1983). For example, Fricke suggested genus Repomucenus and Bathycallionymus, whose genera contains most callionymid species in Korean waters, as junior synonym of genus Callionymus while Nakabo (Fishes of Japan with pictorial keys to the species, 1983) suggested as valid. In such cases, when classifications of adults have taxonomic contention, examination of larval characters may prove informative. Therefore, in this study, the authors conducted comprehensive molecular and morphological analyses on larvae and juveniles of five species in the genus Repomucenus and discussed their taxonomic status within the family Callionymidae. Larval and juvenile callionymids show high morphological similarities during their ontogenetic development. Nonetheless, the following morphological differences were observed in melanophore distribution and preopercular spine development: (a) stellate or punctate melanophores in Bathycallionymus kaianus vs. branched melanophores in genus Repomucenus, (b) melanophores on the abdominal cavity gradually disappearing in B. kaianus vs. gradually becoming prominent in Repomucenus and (c) preopercular spine development giving rise to one perpendicular spine in B. kaianus vs. two or three spines in Repomucenus. Molecular analysis based on 16S ribosomal RNA showed similar results to the morphological analysis. Genera Bathycallionymus and Repomucenus showed significant genetic distance (d = 0.113-0.120); moreover, genus Callionymus, which was suggested as a senior synonym of genus Bathycallionymus and Repomucenus by Fricke (Journal of Natural History, 2014, 48, 2419-2448), also showed considerable difference (d = 0.226-0.246). In the present study, the monophyly of genus Repomucenus seemed well supported by the results of morphological and molecular analyses of larval stage Callionymidae.

AUTOMATIC BRAIN ORGAN SEGMENTATION WITH 3D FULLY CONVOLUTIONAL NEURAL NETWORK FOR RADIATION THERAPY TREATMENT PLANNING.

3D organ contouring is an essential step in radiation therapy treatment planning for organ dose estimation as well as for optimizing plans to reduce organs-at-risk doses. Manual contouring is time-consuming and its inter-clinician variability adversely affects the outcomes study. Such organs also vary dramatically on sizes - up to two orders of magnitude difference in volumes. In this paper, we present BrainSegNet, a novel 3D fully convolutional neural network (FCNN) based approach for automatic segmentation of brain organs. BrainSegNet takes a multiple resolution paths approach and uses a weighted loss function to solve the major challenge of the large variability in organ sizes. We evaluated our approach with a dataset of 46 Brain CT image volumes with corresponding expert organ contours as reference. Compared with those of LiviaNet and V-Net, BrainSegNet has a superior performance in segmenting tiny or thin organs, such as chiasm, optic nerves, and cochlea, and outperforms these methods in segmenting large organs as well. BrainSegNet can reduce the manual contouring time of a volume from an hour to less than two minutes, and holds high potential to improve the efficiency of radiation therapy workflow.

A new perspective on biogeographic barrier in the flathead grey mullet (Pisces: Mugilidae) from the northwest Pacific.

BACKGROUND: The flathead grey mullet, Mugil cephalus has a global distribution in tropical, subtropical and temperate seas worldwide. Previous studies proposed that globally distributed M. cephalus comprises at least 14 different lineages, and divided into two or three groups in the northwest Pacific. Therefore, we hypothesized that there may exist at least two lineages in Korea. OBJECTIVE: The aim of this study was to determine the number of lineages of flathead grey mullet in Korea, and detail their biogeographic boundaries, and taxonomic implications using various molecular markers. METHODS: Two partial mitochondrial DNA (mtDNA) gene sequences (COI and 16S rRNA) and nine microsatellite loci were analyzed in 260 individuals from ten locations. RESULTS: Phylogenetic trees from two partial mtDNA gene sequences revealed two distinct lineages of flathead grey mullet (P distance = 0.016-0.021). Lineage 1 (L1) consisted of mullets from all locations except for the Pacific coasts of Japan, while lineage 2 (L2) consisted of mullets from the Jeju Island, Shanghai, and the Pacific coasts of Japan. The STRUCTURE analyses of msat data also revealed two distinct groups. CONCLUSION: This study was the first to reveal the coexistence of two lineages of flathead grey mullet in Korea. L2 was confined to the Jeju Island in Korea, implying a biogeographic boundary between the two lineages. The allopatric distribution and genetic heterogeneity between lineages may be affected by an ancient geographic isolation during the glacial period and maintained due to adaptation to oceanic characteristics. Collectively, the two lineages may be comprised of distinct species.

A new species of hagfish, Eptatretus wandoensis sp. nov. (Agnatha, Myxinidae), from the southwestern Sea of Korea.

Four specimens of the five-gilled white mid-dorsal line hagfish, Eptatretus wandoensis sp. nov. were recently collected from the southwestern Sea of Korea (Wando). This new species has five pairs of gill apertures, 14-18 prebranchial slime pores, 4 branchial slime pores, a dark brown back with a white mid-dorsal line and a white belly. These hagfish are similar to Eptatretus burgeri and Eptatretus minor in having a white mid-dorsal line, but can be readily distinguished by the numbers of gill apertures (5 vs. 6-7), gill pouches (5 vs. 6), and prebranchial slime pores (14-18 vs. > 18), as well as the body color (dark brown back vs. gray or brown pale). In terms of genetic differences, Eptatretus wandoensis could be clearly distinguished from E. burgeri (0.9% in 16S rRNA and 8.5% in cytochrome c oxidase subunit I sequences) and E. minor (4.5% and 13.9%).

Experimental and Numerical Sensitivity Assessment of Viscoelasticity for Polymer Composite Materials.

Viscoelastic polymer composites are widely used for vibration control in different fields of engineering like aerospace, mechanical, and structural engineering. The viscoelastic properties of these materials are strain rate-dependent and are highly related to frequency. Yet to date, less attention has been paid to quantifying the effects of these parameters and their interactions on damping properties and providing an approximation method for further applications. In the present research, a series of experimental tests was conducted on a viscoelastic material and the experimental data were numerically analyzed in detail. Sensitivity analyses are usually applied to quantify uncertainty using sampling techniques. However, in this study a method was proposed to derive a closed-form solution using the response surface function and a derivative-based global sensitivity analysis to evaluate the output contribution of each parameter. These effects were quantified and several approximation statistics were provided for future engineering implementations. The computational evaluation conducted in this study gives a detailed insight into the mechanical behavior of viscoelastic materials.

Cryptic diversity in the inshore hagfish, Eptatretus burgeri (Myxinidae, Pisces) from the northwest Pacific.

The fishery of inshore hagfish (Eptatretus burgeri) is particularly important from the perspective of the eel-skin leather industry in the northwest Pacific. In order to reveal the genetic diversity and population structure of E. burgeri in the northwest Pacific, we analyzed partial nucleotide sequences of three mitochondrial DNA regions (523 bp in COI, 712 bp in ND4 and 617 bp in Cytb) based on specimens collected from six locations in Korea and Japan. The genetic diversities of E. burgeri were higher in Korean locations compared to Japanese ones. AMOVA showed that E. burgeri was completely separated into two groups (group A: southern coast of Korea and western coast of Japan vs. group B: eastern coast of Japan). Furthermore, groups A and B were divided into each two lineages (lineage I: west southern coast of Korea, lineage II: east southern coast of Korea and western coast of Japan, lineage III and IV: eastern coast of Japan). Our molecular results suggest that these two groups and lineages of E. burgeri may be different evolutionary significant unit and management unit, respectively.

Molecular systematics of Pampus (Perciformes: Stromateidae) based on thousands of nuclear loci using target-gene enrichment.

Pomfret fishes of the genus Pampus are commercially important in the Indo-Pacific region, yet the phylogenetic relationships and taxonomy of Pampus remain contentious. Here, we sampled 151 specimens, representing all known species of the genus, as well as two outgroup species (two families). We collected sequences from 17,292 single-copy nuclear coding loci using target-gene enrichment and Illumina sequencing for a subset samples of P. echinogaster, P. argenteus, P. cinereus, P. liuorum, P. chinensis, P. minor, and P. punctatissimus, which were carefully examined according to their species descriptions. Concatenated gene tree and species tree analyses resulted in identical and highly supported phylogenies, in which P. argenteus was sister to P. minor in one clade and P. cinereus sister to P. chinensis and P. punctatissimus in the other clade. Phylogenetic reconstruction using sequences of cytochrome c oxidase subunit I (COI) collected by us and those retrieved from NCBI suggests extensive misidentification of Pampus species in the NCBI database. We also measured morphological characters of each species as well as observed their osteological structure using micro-CT. Both molecular and morphological results suggest that P. echinogaster is a synonym of P. argenteus, and P. liuorum is a synonym of P. cinereus. Pampus cinereus from China, Bangladesh and an uncertain origin were grouped into three clades according to their sampling localities, but we could not find decisive morphological characters to describe the "cryptic species" of P. cinereus. Finally, based on the results of the molecular analyses and morphological reexamination, we created an identification key for the genus of Pampus.

The complete mitochondrial genome of Cynoglossus interruptus and its novel rearrangement (Pleuronectiformes: Cynoglossidae).

The complete mitochondrial genome was determined for the Cynoglossus interruptus belonging to the family Cynoglossidae. The length of the complete mitochondrial genome is 17,262 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. The gene rearrangement related to tRNAGln and a control region gene were found, forming the gene order of CR-Ile-Gln-Met. Phylogenetic analysis using mitochondrial genomes of 12 species showed that C. interruptus formed a well-supported monophyletic group with other Cynoglossus species.

Gene rearrangements in the mitochondrial genome of robust tonguefish, Cynoglossus robustus (Pleuronectiformes: Cynoglossidae) and a comparative analysis with other Cynoglossus fishes.

The complete mitochondrial genome was determined for the Robust tonguefish Cynoglossus robustus belonging to the family Cynoglossidae. The length of the complete mitochondrial genome is 16,720 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Rearrangements of the tRNAGln and a control region gene were found and tRNAGln is translocated from the light to the heavy strand. Phylogenetic analysis using mitochondrial genomes of 12 species showed that C. robustus formed a well-supported monophyletic group with other Cynoglossus species.