Habitat use of loggerhead (Caretta caretta) and green (Chelonia mydas) turtles at the northern limit of their distribution range of the Northwest Pacific Ocean.

Verifying habitats, including the foraging and nesting areas for sea turtles, enables an understanding of their spatial ecology and successful planning of their conservation and management strategies. Recently, the observation frequency and bycatch of loggerhead (Caretta caretta) and green (Chelonia mydas) turtles have increased in the northern limit of their distribution range, in the northern part of the East China Sea and East (Japan) Sea. We conducted satellite tracking to investigate the habitat use of seven loggerhead and eight green turtles from June 2016 to August 2022 in this area, where little is known about their spatial ecology. We applied a 50 percent volume contour method to determine their main foraging areas and analyzed 6 environmental variables to characterize their habitats. Loggerhead turtles mainly stayed in and used the East China Sea as a foraging area during the tracking period, while two individuals among them also used the East Sea as a seasonal foraging area. Most green turtles also used the East China Sea as a foraging area, near South Korea and Japan, with one individual among them using the lower area of the East Sea as a seasonal foraging area. Notably, one green turtle traveled to Hainan Island in the South China Sea, a historical nesting area. Our results showed that the two sea turtle species included the East Sea as a seasonal foraging area, possibly owing to the abundance of food sources available, despite its relatively lower sea temperature. Considering that loggerhead and green sea turtles were observed using the northern part of the East China Sea and East Sea more frequently than previously known and that the sea temperature gradually increases due to climate change, conservation and management activities are required for sea turtles in these areas.

Cellular abundance-based prognostic model associated with deregulated gene expression of leukemic stem cells in acute myeloid leukemia.

Background: Previous studies have reported that genes highly expressed in leukemic stem cells (LSC) may dictate the survival probability of patients and expression-based cellular deconvolution may be informative in forecasting prognosis. However, whether the prognosis of acute myeloid leukemia (AML) can be predicted using gene expression and deconvoluted cellular abundances is debatable. Methods: Nine different cell-type abundances of a training set composed of the AML samples of 422 patients, were used to build a model for predicting prognosis by least absolute shrinkage and selection operator Cox regression. This model was validated in two different validation sets, TCGA-LAML and Beat AML (n = 179 and 451, respectively). Results: We introduce a new prognosis predicting model for AML called the LSC activity (LSCA) score, which incorporates the abundance of 5 cell types, granulocyte-monocyte progenitors, common myeloid progenitors, CD45RA + cells, megakaryocyte-erythrocyte progenitors, and multipotent progenitors. Overall survival probabilities between the high and low LSCA score groups were significantly different in TCGA-LAML and Beat AML cohorts (log-rank p-value = 3.3×10-4 and 4.3×10-3, respectively). Also, multivariate Cox regression analysis on these two validation sets shows that LSCA score is independent prognostic factor when considering age, sex, and cytogenetic risk (hazard ratio, HR = 2.17; 95% CI 1.40-3.34; p < 0.001 and HR = 1.20; 95% CI 1.02-1.43; p < 0.03, respectively). The performance of the LSCA score was comparable to other prognostic models, LSC17, APS, and CTC scores, as indicated by the area under the curve. Gene set variation analysis with six LSC-related functional gene sets indicated that high and low LSCA scores are associated with upregulated and downregulated genes in LSCs. Conclusion: We have developed a new prognosis prediction scoring system for AML patients, the LSCA score, which uses deconvoluted cell-type abundance only.

Whole-Genome Sequencing Reveals Mutational Signatures Related to Radiation-Induced Sarcomas and DNA-Damage-Repair Pathways.

Radiation-induced sarcoma (RIS) is a rare but serious late complication arising from radiotherapy. Despite unfavorable clinical outcomes, the genomic footprints of ionizing radiation in RIS development remain largely unknown. Hence, this study aimed to characterize RIS genomes and the genomic alterations in them. We analyzed whole-genome sequencing in 11 RIS genomes matched with normal genomes to identify somatic alterations potentially associated with RIS development. Furthermore, the abundance of mutations, mutation signatures, and structural variants in RIS were compared with those in radiation-naïve spontaneous sarcomas. The mutation abundance in RIS genomes, including one hypermutated genome, was variable. Cancer-related genes might show different types of genomic alterations. For instance, NF1, NF2, NOTCH1, NOTCH2, PIK3CA, RB1, and TP53 showed singleton somatic mutations; MYC, CDKN2A, RB1, and NF1 showed recurrent copy number alterations; and NF2, ARID1B, and RAD51B showed recurrent structural variations. The genomic footprints of nonhomologous end joining are prevalent at indels of RIS genomes compared with those in spontaneous sarcoma genomes, representing the genomic hallmark of RIS genomes. In addition, frequent chromothripsis was identified along with predisposing germline variants in the DNA-damage-repair pathways in RIS genomes. The characterization of RIS genomes on a whole-genome sequencing scale highlighted that the nonhomologous end joining pathway was associated with tumorigenesis, and it might pave the way for the development of advanced diagnostic and therapeutic strategies for RIS.

Movement Patterns of Juvenile Loggerhead Turtles (Caretta caretta L. 1758) and Green Turtles (Chelonia mydas L. 1758) Hatched in Captivity and Released in the Korean Waters.

With most sea turtle populations declining, activities to conserve their habitat and nesting grounds and restore their populations are being implemented worldwide. To preserve the Northwestern Pacific populations, the National Marine Biodiversity Institute of Korea has been releasing artificially propagated sea turtles, but whether these individuals join the wild population remains unknown. The present study aimed to determine the movement patterns of artificially propagated juvenile loggerhead (Caretta caretta) and green (Chelonia mydas) turtles fitted with satellite transmitters on their carapaces and released in the waters of Jeju or Yeosu, Republic of Korea, between August 2018 and April 2022. Loggerheads traveled northward to the East Sea, whereas green turtles moved west or southwest. Two 36-month-old and two 48-month-old loggerheads moved toward their potential nursery grounds and toward their feeding grounds, respectively. Three green turtles with a curved carapace length (CCL) of <40 cm moved toward their nursery or feeding grounds, while three individuals (CCL > 45 cm) moved toward their inshore foraging areas. The travel paths were closely related to the direction of local sea currents. Our results implied that releasing artificially propagated sea turtles, considering their age and CCL, can positively contribute to the conservation of Northwestern Pacific populations.

Distinct Patterns of HBV Integration and TERT Alterations between in Tumor and Non-Tumor Tissue in Patients with Hepatocellular Carcinoma.

Although hepatitis B virus (HBV) integration into the cellular genome is well known in HCC (hepatocellular carcinoma) patients, its biological role still remains uncertain. This study investigated the patterns of HBV integration and correlated them with TERT (telomerase reverse transcriptase) alterations in paired tumor and non-tumor tissues. Compared to those in non-tumors, tumoral integrations occurred less frequently but with higher read counts and were more preferentially observed in genic regions with significant enrichment of integration into promoters. In HBV-related tumors, TERT promoter was identified as the most frequent site (38.5% (10/26)) of HBV integration. TERT promoter mutation was observed only in tumors (24.2% (8/33)), but not in non-tumors. Only 3.00% (34/1133) of HBV integration sites were shared between tumors and non-tumors. Within the HBV genome, HBV breakpoints were distributed preferentially in the 3' end of HBx, with more tumoral integrations detected in the preS/S region. The major genes that were recurrently affected by HBV integration included TERT and MLL4 for tumors and FN1 for non-tumors. Functional enrichment analysis of tumoral genes with integrations showed enrichment of cancer-associated genes. The patterns and functions of HBV integration are distinct between tumors and non-tumors. Tumoral integration is often enriched into both human-virus regions with oncogenic regulatory function. The characteristic genomic features of HBV integration together with TERT alteration may dysregulate the affected gene function, thereby contributing to hepatocarcinogenesis.

Tomographic Structural Changes of the Inner Retina after Internal Limiting Membrane Peeling for Idiopathic Epiretinal Membrane.

PURPOSE: To investigate the tomographic structural changes in the retinal layers after internal limiting membrane (ILM) peeling for idiopathic epiretinal membrane (ERM). METHODS: Sixty-nine eyes treated with vitrectomy and ILM peeling for idiopathic ERM were analyzed. Parafoveal retinal thickness was measured at baseline and 6 months after surgery. RESULTS: Total retinal thickness decreased significantly in the nasal and temporal subfields after surgery (p < 0.001), whereas the inner nuclear layer and outer nuclear layer showed nasal thickening (all, p < 0.001). The postoperative temporal/nasal subfield thickness ratio of each layer was significantly lower than that of fellow eyes. Eyes with larger ILM peeling showed a significantly lower temporal/nasal subfield thickness ratio (p = 0.033) than those with smaller sizes. CONCLUSIONS: The retinal thickness of each layer showed anatomical changes from ILM peeling and ERM removal. Nasal parafoveal thickening and temporal thinning occurred in the inner retinal architecture, which might be affected by ILM peeling size.

All-solid-state flexible supercapacitor based on nanotube-reinforced polypyrrole hollowed structures.

Supercapacitors are strong future candidates for energy storage devices owing to their high power density, fast charge-discharge rate, and long cycle stability. Here, a flexible supercapacitor with a large specific capacitance of 443 F g-1 at a scan rate of 2 mV s-1 is demonstrated using nanotube-reinforced polypyrrole nanowires with hollowed cavities grown vertically on a nanotube/graphene based film. Using these electrodes, we obtain improved capacitance, rate capability, and cycle stability for over 3000 cycles. The assembled all-solid-state supercapacitor exhibits excellent mechanical flexibility, with the capacity to endure a 180° bending angle along with a maximum specific and volumetric energy density of 7 W h kg-1 (8.2 mW h cm-3) at a power density of 75 W kg-1 (0.087 W cm-3), and it showed an energy density of 4.13 W h kg-1 (4.82 mW h cm-3) even at a high power density of 3.8 kW kg-1 (4.4 W cm-3). Also, it demonstrates a high cycling stability of 94.3% after 10 000 charge/discharge cycles at a current density of 10 A g-1. Finally, a foldable all-solid-state supercapacitor is demonstrated, which confirms the applicability of the reported supercapacitor for use in energy storage devices for future portable, foldable, or wearable electronics.

PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine.

Despite the growing attention given to Traditional Medicine (TM) worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM) database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound), disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software) and BioMart (a data federation framework) for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.