Transcriptional Changes in Damask Rose Suspension Cell Culture Revealed by RNA Sequencing.

Damask roses (Rosa x damascena) are widely used in cosmetics and pharmaceutics. Here, we established an in vitro suspension cell culture for calli derived from damask rose petals. We analyzed rose suspension cell transcriptomes obtained at two different time points by RNA sequencing to reveal transcriptional changes during rose suspension cell culture. Of the 580 coding RNAs (1.3%) highly expressed in the suspension rose cells, 68 encoded cell wall-associated proteins. However, most RNAs encoded by the chloroplasts and mitochondria are not expressed. Many highly expressed coding RNAs are involved in translation, catalyzing peptide synthesis in ribosomes. Moreover, the amide metabolic process producing naturally occurring alkaloids was the most abundant metabolic process during the propagation of rose suspension cells. During rose cell propagation, coding RNAs involved in the stress response were upregulated at an early stage, while coding RNAs associated with detoxification and transmembrane transport were upregulated at the late stage. We used transcriptome analyses to reveal important biological processes and molecular mechanisms during rose suspension cell culture. Most non-coding (nc) RNAs were not expressed in the rose suspension cells, but a few ncRNAs with unknown functions were highly expressed. The expression of ncRNAs and their target coding RNAs was highly correlated. Taken together, we revealed significant biological processes and molecular mechanisms occurring during rose suspension cell culture using transcriptome analyses.

Association of Body Mass Index and Waist Circumference with Osteoarthritis among Korean Adults: A Nationwide Study.

Background: Evidence on the association between obesity parameters, including body mass index (BMI) and waist circumference (WC), and osteoarthritis is limited. This study aimed to investigate these associations in Korean adults. Methods: This nationwide cross-sectional study used data from 24,101 adults aged ≥19 years who participated in the Korea National Health and Nutrition Examination Survey 2016-2020. Odds ratios (ORs) and 95% confidence intervals (CIs) for osteoarthritis according to BMI and WC were analyzed using multivariable logistic regression analyses. Results: The prevalence of osteoarthritis was higher in individuals with general (10.0%) and abdominal obesity (12.8%) compared with those without. Greater BMI and WC were associated with a higher prevalence (P<0.001) and risk of osteoarthritis (Model 3, P for trend <0.001). Individuals with general and abdominal obesity were associated with a 1.50-fold (OR, 1.50; 95% CI, 1.35-1.67) and 1.64-fold (OR, 1.64; 95% CI, 1.47-1.84) increased risk of osteoarthritis, compared with those without. Similar associations were observed in subgroups according to age, sex, smoking status, and presence of diabetes mellitus. The odds of osteoarthritis 1.73-fold increased (OR, 1.73; 95% CI, 1.53-1.95) in individuals with both general and abdominal obesity compared with those without any of them. Conclusion: Greater BMI, WC, and general and abdominal obesity were associated with an increased risk of osteoarthritis in Korean adults. Appropriate management of abdominal and general obesity may be important to reduce the risk of osteoarthritis.

Skin-Whitening Effect of a Callus Extract of Nelumbo nucifera Isolate Haman.

The sacred lotus (Nelumbo nucifera Gaertn. Isolate Haman, in the family Nelumbonaceae) used in this study originated from the Haman region of Korea, and lotus seeds dating back to the Goryeo Dynasty (650-760 years ago) were accidentally discovered. Lotus is known to possess antioxidant, anti-inflammatory, and soothing properties. Instead of using the lotus alone, we obtained extracts using Haman region lotus-derived callus (HLC), which allowed for a controlled, quantitative, and infinite supply. Based on the reported effects of the lotus, we formulated a hypothesis to investigate the skin-whitening effect of the HLC extract (HLCE). The HLCE was first obtained by extraction with distilled water and using 5% propanediol as a solvent and subsequently verified for the whitening effect (melanin content tests) using mammalian cells in vitro. Its efficacy at the molecular level was confirmed through real-time polymerase chain reaction (PCR) using melanin-related genes. Furthermore, clinical trials with 21 volunteers confirmed the significant whitening effect of cosmetics containing the HLCE. In conclusion, we found that the HLCE not only has anti-inflammatory, antioxidant, and skin-soothing properties but also plays an essential role in skin whitening. Therefore, we propose that the HLCE has the potential to become a new raw material for the cosmetic industry.

Therapeutic role of 2-stearoxyphenethyl phosphocholine targeting microtubule dynamics and Wnt/ß-catenin/EMT signaling in human colorectal cancer cells.

The inhibition of cell death, perturbation of microtubule dynamics, and acceleration of Wnt/ß-catenin/epithelial-mesenchymal transition (EMT) signaling are fundamental processes in the progression and metastasis of colorectal cancer (CRC). To explore the role of 2-stearoxyphenethyl phosphocholine (stPEPC), an alkylphospholipid-based compound, in CRC, we conducted an MTT assay, cell cycle analysis, western blot analysis, immunoprecipitation, immunofluorescence staining, Annexin V/propidium iodide double staining, small interfering RNA gene silencing, a wound-healing assay, an invasion assay, and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay in the human CRC cell lines HT29 and HCT116. stPEPC showed anti-proliferative properties and mitotic cell accumulation via upregulated phosphorylation of BUBR1 and an association between mitotic arrest deficiency 2 (MAD2) and cell division cycle protein 20 homolog (CDC20). These results suggest that activation of the mitotic checkpoint complex and tubulin polymerization occurred, resulting in mitotic catastrophe in HT29 and HCT116 cells. In addition, stPEPC attenuated cell migration and invasion by regulating proteins mediated by EMT, such as E-cadherin and occludin. stPEPC altered the protein expression of Wnt3a and phosphorylation of low-density lipoprotein receptor-related protein 6 (LRP6), glycogen synthase kinase 3ß (GSK3ß), and ß-catenin as well as their target genes, including cMyc and cyclin D1, in CRC cells. Thus, stPEPC may be useful for developing new drugs to treat human CRC.

A Lesson from a Measles Outbreak among Healthcare Workers in a Single Hospital in South Korea: The Importance of Knowing the Prevalence of Susceptibility.

BACKGROUND: Despite the high vaccination coverage rate, in-hospital transmission of measles continues to occur in South Korea. We present a measles outbreak in which two healthcare workers (HCWs) with presumptive evidence of measles immunity were infected by a patient with typical measles at a single hospital in South Korea. This facilitated the evaluation of measles seroprevalence in all HCWs. METHODS: In 2018, suspected patients and contacts exposed during a measles outbreak were investigated based on their medical histories and vaccination status. Cases were confirmed by the detection of measles-specific immunoglobulin M or RNA. After the measles outbreak in 2018, measles IgG testing was conducted on a total of 972 HCWs for point-prevalence, including those exposed to the measles. In addition, we have routinely performed measles IgG tests on newly employed HCWs within one week of their hire date since 2019. The measles vaccine was administered to HCWs who tested negative or equivocally negative for IgG antibodies. RESULTS: An index patient who returned from China with fever and rash was diagnosed with measles at a hospital in Korea. Two additional HCWs were revealed as measles cases: one was vaccinated with the two-dose measles-mumps-rubella (MMR) vaccine, and the other, who was born in 1967, was presumed to have immunity from natural infection in South Korea. All three patients harbored the same D8 genotype. No additional measles cases were identified among the 964 contacts of secondary patients. A total of 2310 HCWs, including those tested during the 2018 outbreak, underwent measles IgG tests. The average age at the time of the test was 32.6 years, and 74.3% were female. The overall seropositivity of measles was 88.9% (95% confidence interval, 87.5-90.1). Although the birth cohorts between 1985 and 1994 were presumed to have received the measles-rubella (MR) catch-up vaccination in 2001, 175 (89.3%) HCWs were born after 1985 among the 195 seronegative cases. CONCLUSION: Despite high population immunity, imported measles transmission occurred among HCWs with presumed immunity. This report underscores the importance of understanding the prevalence of measles susceptibility among newly employed HCWs. This is important for policymaking regarding hospital-wide vaccinations to prevent the spread of vaccine-preventable diseases.

Comparative Analysis of Water Extracts from Roselle (Hibiscus sabdariffa L.) Plants and Callus Cells: Constituents, Effects on Human Skin Cells, and Transcriptome Profiles.

Roselle (Hibiscus sabdariffa L.) is a plant that has traditionally been used in various food and beverage products. Here, we investigated the potential of water extracts derived from Roselle leaves and callus cells for cosmetic and pharmaceutical purposes. We generated calluses from Roselle leaves and produced two different water extracts through heat extraction, which we named Hibiscus sabdariffa plant extract (HSPE) and Hibiscus sabdariffa callus extract (HSCE). HPLC analysis showed that the two extracts have different components, with nucleic acids and metabolites such as phenylalanine and tryptophan being the most common components in both extracts. In vitro assays demonstrated that HSCE has strong anti-melanogenic effects and functions for skin barrier and antioxidant activity. Transcriptome profiling of human skin cells treated with HSPE and HSCE showed significant differences, with HSPE having more effects on human skin cells. Up-regulated genes by HSPE function in angiogenesis, the oxidation-reduction process, and glycolysis, while up-regulated genes by HSCE encode ribosome proteins and IFI6, functioning in the healing of radiation-injured skin cells. Therefore, we suggest that the two extracts from Roselle should be applied differently for cosmetics and pharmaceutical purposes. Our findings demonstrate the potential of Roselle extracts as a natural source for skincare products.

The D-Dimer to Troponin Ratio Is a Novel Marker for the Differential Diagnosis of Thoracic Acute Aortic Syndrome from Non-ST Elevation Myocardial Infarction.

BACKGROUND: Thoracic acute aortic syndrome (AAS) and non-ST elevation myocardial infarction (NSTEMI) have similar clinical presentations, making them difficult to differentiate. This study aimed to identify useful biomarkers for the differential diagnosis of thoracic AAS and NSTEMI. METHODS: This was a retrospective observational study. PARTICIPANTS: consecutive adult patients who visited the emergency department for acute chest pain between January 2015 and December 2021 diagnosed with thoracic AAS or NSTEMI. Clinical variables, including D-dimer (µg/mL) and high-sensitivity troponin T (ng/mL, hs-TnT) levels, were compared between the groups. RESULTS: A total of 52 (30.1%) and 121 (69.9%) patients were enrolled in the thoracic AAS and NSTEMI groups, respectively. Logistic regression analysis revealed that the D-dimer to hs-TnT (D/T) ratio (odds ratio (OR), 1.038; 95% confidence interval (CI), 1.020-1.056; p < 0.001) and the thrombolysis in myocardial infarction (TIMI) score (OR, 0.184; 95% CI, 0.054-0.621; p = 0.006) were associated with thoracic AAS. The D/T ratio had an area under the receiver operating characteristic curve (AUC) of 0.973 (95% CI, 0.930-0.998), and the optimal cutoff value was 81.3 with 91.4% sensitivity and 96.2% specificity. The TIMI score had an AUC of 0.769 (95% CI, 0.644-0.812), and the optimal cutoff value was 1.5 with 96.7% sensitivity and 38.5% specificity. CONCLUSION: the D/T ratio may be a simple and useful parameter for differentiating thoracic AAS from NSTEMI.

Comparative Transcriptome Profiles of Human HaCaT Cells in Response to Gynostemma pentaphyllum Extracts Obtained Using Three Independent Methods by RNA Sequencing.

Gynostemma pentaphyllum (GP) is widely used in herbal medicine. In this study, we developed a method for the large-scale production of GP cells using plant tissue culture techniques combined with bioreactors. Six metabolites (uridine, adenosine, guanosine, tyrosine, phenylalanine, and tryptophan) were identified in GP extracts. Transcriptome analyses of HaCaT cells treated with GP extracts using three independent methods were conducted. Most differentially expressed genes (DEGs) from the GP-all condition (combination of three GP extracts) showed similar gene expression on treatment with the three individual GP extracts. The most significantly upregulated gene was LTBP1. Additionally, 125 and 51 genes were upregulated and downregulated, respectively, in response to the GP extracts. The upregulated genes were associated with the response to growth factors and heart development. Some of these genes encode components of elastic fibers and the extracellular matrix and are associated with many cancers. Genes related to folate biosynthesis and vitamin D metabolism were also upregulated. In contrast, many downregulated genes were associated with cell adhesion. Moreover, many DEGs were targeted to the synaptic and neuronal projections. Our study has revealed the functional mechanisms of GP extracts' anti-aging and photoprotective effects on the skin using RNA sequencing.

Anti-Pollutant Activity of Porphyra yezoensis Water Extract and Its Active Compound, Porphyra 334, against Urban Particulate Matter-Induced Keratinocyte Cell Damage.

Urban particulate matter (UPM) causes skin aging and inflammatory reactions by influencing skin cells through the aryl hydrocarbon receptor (AhR) signaling pathway. Porphyra yezoensis (also known as Pyropia yezoensis), a red alga belonging to the Bangiaceae family, is an edible red seaweed. Here, we examined the anti-pollutant effect of P. yezoensis water extract. While UPM treatment induced xenobiotic response element (XRE) promoter luciferase activity, P. yezoensis water extract reduced UPM-induced XRE activity. Next, we isolated an active compound from P. yezoensis and identified it as porphyra 334. Similar to the P. yezoensis water extract, porphyra 334 attenuated UPM-induced XRE activity. Moreover, although UPM augmented AhR nuclear translocation, which led to an increase in cytochrome P450 1A1 (CYP1A1) mRNA levels, these effects were reduced by porphyra 334. Moreover, UPM induced the production of reactive oxygen species (ROS) and reduced cell proliferation. These effects were attenuated in response to porphyra 334 treatment. Furthermore, our results revealed that the increased ROS levels induced by UPM treatment induced transient receptor potential vanilloid 1 (TRPV1) activity, which is related to skin aging and inflammatory responses. However, porphyra 334 treatment reduced this reaction by inhibiting ROS production induced by CYP1A1 activation. This indicates that porphyra 334, an active compound of P. yezoensis, attenuates UP-induced cell damage by inhibiting AhR-induced ROS production, which results in a reduction in TRPV1 activation, leading to cell proliferation. This also suggests that porphyra 334 could protect the epidermis from harmful pollutants.

Viromes of 15 Pepper (Capsicum annuum L.) Cultivars.

Pepper (Capsicum annuum L.) plants produce berry fruits that are used as spices. Here, we examined the viromes of 15 pepper cultivars through RNA sequencing. We obtained 1,325 virus-associated contigs derived from 8 virus species. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, followed by potato virus Y, bell pepper endornavirus, and hot pepper endornavirus. The proportion of viral reads in each transcriptome ranged from 0.04% to 24.5%. BBWV2 was the dominant virus in seven cultivars, whereas CMV was dominant in five cultivars. All the bell pepper cultivars showed severe viral disease symptoms, whereas the commercially developed hot pepper cultivars were asymptomatic or had mild symptoms. In addition, 111 complete viral segments were obtained from 7 viruses. Based on the obtained viral genomes, the genetic relationship between the identified viruses and quasispecies of BBWV2 and CMV in each pepper plant was determined. Newly designed primers for nine viruses confirmed the results of RNA sequencing. Taken together, this study, for the first time, provides a comprehensive overview of viromes in 15 major pepper cultivars through RNA sequencing.

Anti-Colitic Effect of an Exopolysaccharide Fraction from Pediococcus pentosaceus KFT-18 on Dextran Sulfate Sodium-Induced Colitis through Suppression of Inflammatory Mediators.

We previously reported the immunostimulatory effect of an exopolysaccharide fraction from Pediococcus pentosaceus KFT18 (PE-EPS), a lactic acid bacterium, in macrophages and primary splenocytes, as well as in cyclophosphamide-induced immunosuppressed mice. In this study, the anti-colitic activity of PE-EPS was investigated in a dextran sulfate sodium (DSS)-induced colitis animal model. PE-EPS relieved DSS-induced colitis symptoms, such as stool blood, decreased colon length, crypt disruption, and mucus layer edema. Regarding the molecular mechanism, PE-EPS reduced the enhanced expression of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), and pro-inflammatory cytokines (TNF-α, IL-6, and IL-1) in the colon tissue of colitis-induced mice. Additionally, PE-EPS protected against DSS-induced phosphorylation of p65 and signal transducer and activator of transcription 1 (STAT1). These findings suggested that the exopolysaccharide fraction from Ped. pentosaceus KFT18 can be used to treat inflammatory bowel disease by alleviating colonic inflammation.

Identification of highly selective type II kinase inhibitors with chiral peptidomimetic tails.

Identification of highly selective type II kinase inhibitors is described. Two different chiral peptidomimetic scaffolds were introduced on the tail region of non-selective type II kinase inhibitor GNF-7 to enhance the selectivity. Kinome-wide selectivity profiling analysis showed that type II kinase inhibitor 7a potently inhibited Lck kinase with great selectivity (IC50 of 23.0 nM). It was found that 7a and its derivatives possessed high selectivity for Lck over even structurally conserved all Src family kinases. We also observed that 7a inhibited Lck activation in Jurkat T cells. Moreover, 7a was found to alleviate clinical symptoms in DSS-induced colitis mice. This study provides a novel insight into the design of selective type II kinase inhibitors by adopting chiral peptidomimetic moieties on the tail region.

Age-Adjusted D-Dimer in Ruling Out Acute Aortic Syndrome.

BACKGROUND: Recently, D-dimer has been suggested as a biomarker to rule out acute aortic syndrome (AAS). Since it increases with age, this study was conducted to reveal whether an age-adjusted D-dimer can increase diagnostic accuracy in ruling out AAS. METHOD: A retrospective observational study design was used. Consecutive adult patients who visited an emergency room between January 2015 and September 2020 and who underwent a D-dimer test and computed tomography angiography for suspected AAS were enrolled. We calculated the diagnostic accuracy of both the conventional (0.5 µg/ml) and age-adjusted (age × 0.01 in patients >50 years) D-dimer cut-offs. RESULT: D-dimer was higher in the AAS group (n = 82) than in the non-AAS group (n = 122) (10.85 (3.61-33.12) vs. 0.40 (0.23-1.07), OR: 1.139 (CI: 1.085 - 1.195), p < 0.001). The D-dimer plasma level had an area under the ROC curve of 0.915 (CI: 0.873-0.956) with AAS. At the age-adjusted cutoff point compared to a 0.5 µg/ml cutoff, the sensitivity of 97.6% and the NLR of 0.04 did not change, but the specificity increased by 5.7% to 65.6%, the PPV increased by 3.6% to 65.6%, and the NPV slightly increased by 0.2% to 97.6%. CONCLUSION: Compared with a conventional method, the age-adjusted D-dimer cutoff may have higher specificity and PPV while maintaining high sensitivity for ruling out AAS.

Prehospital Factors Associated with Refractory Traumatic Arrest.

OBJECTIVE: Identification of the prehospital factors associated with a poor prognosis of immediate traumatic arrest should help reduce unwarranted treatment. We aim to reveal the clinical factors related to death after traumatic arrest on the scene. METHODS: We performed a multicenter (4 tertiary hospitals in urban areas of South Korea) retrospective study on consecutive adult patients with trauma arrest on scene who were transferred by fire ambulance from January 2016 to December 2018. Patients with death on arrival in the emergency room (ER) were excluded. Prehospital data were collected from first aid records, and information on each patient's survival outcome in the ER was collected from an electronic database. Patients were divided into ER death and ER survival groups, and variables associated with prehospital trauma were compared. RESULTS: A total of 145 (84.3%) and 27 (15.7%) patients were enrolled in the ER death and survival groups, respectively. Logistic regression analysis revealed that asystole (OR 4.033, 95% CI 1.342-12.115, p = 0.013) was related to ER death and that ROSC in the prehospital phase (OR 0.100, 95% CI 0.012-0.839, p = 0.034) was inversely related to ER death. In subgroup analysis of those who suffered fall injuries, greater height of fall was associated with ER death (15.0 (5.5-25.0) vs. 4.0 (2.0-7.5) meters, p = 0.001); the optimal height cutoff for prediction of ER death was 10 meters, with 66.1% sensitivity and 100% specificity. CONCLUSIONS: In cases of traumatic arrest, asystole, no prehospital ROSC, and falls from a greater height were associated with trauma death in the ER. Termination of resuscitation in traumatic arrest cases should be done on the basis of comprehensive clinical factors.

Regulation of ROS-Dependent JNK Pathway by 2'-Hydroxycinnamaldehyde Inducing Apoptosis in Human Promyelocytic HL-60 Leukemia Cells.

The present study demonstrated that 2'-hydroxycinnamaldehyde (2'-HCA) induced apoptosis in human promyelocytic leukemia HL-60 cells through the activation of mitochondrial pathways including (1) translocation of Bim and Bax from the cytosol to mitochondria, (2) downregulation of Bcl-2 protein expression, (3) cytochrome c release into the cytosol, (4) loss of mitochondrial membrane potential (ΔΨm), and (5) caspase activation. 2'-HCA also induced the activation of c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase1/2 (ERK1/2) in HL-60 cells. The pharmacological and genetic inhibition of JNK effectively prevented 2'-HCA-induced apoptosis and activator protein-1 (AP-1)-DNA binding. In addition, 2'-HCA resulted in the accumulation of reactive oxygen species (ROS) and depletion of intracellular glutathione (GSH) and protein thiols (PSH) in HL-60 cells. NAC treatment abrogated 2'-HCA-induced JNK phosphorylation, AP-1-DNA binding, and Bim mitochondrial translocation, suggesting that oxidative stress may be required for 2'-HCA-induced intrinsic apoptosis. Xenograft mice inoculated with HL-60 leukemia cells demonstrated that the intraperitoneal administration of 2'-HCA inhibited tumor growth by increasing of TUNEL staining, the expression levels of nitrotyrosine and pro-apoptotic proteins, but reducing of PCNA protein expression. Taken together, our findings suggest that 2'-HCA induces apoptosis via the ROS-dependent JNK pathway and could be considered as a potential therapeutic agent for leukemia.

AKF-D52, a Synthetic Phenoxypyrimidine-Urea Derivative, Triggers Extrinsic/Intrinsic Apoptosis and Cytoprotective Autophagy in Human Non-Small Cell Lung Cancer Cells.

Previously, we discovered that 1-(3,5-dimethoxyphenyl)-3-(4-(3-methoxyphenoxy)-2-((4-morpholinophenyl)amino)pyrimidin-5-yl)urea (AKF-D52), a synthetic phenoxypyrimidine urea derivative, acts as a growth inhibitor of various cancer cell types. In this study, we elucidated the antiproliferative properties of AFK-D52 and underlying mechanisms in non-small cell lung cancer (NSCLC) cells and an A549 xenograft animal model. AKF-D52 was found to induce both caspase-dependent and -independent apoptotic cell death. Furthermore, the mitochondrial component of the AKF-D52-induced apoptosis mechanism involves a reduction in mitochondrial membrane potential and regulation in B cell lymphoma-2 family protein expression. Moreover, AKF-D52 activates the extrinsic pathway through up-regulated expression of death receptor 3 and Fas and then the formation of a death-inducing signaling complex. AKF-D52 also induced autophagy by increasing acidic vesicular organelle formation and microtubule-associated protein 1A/1B-light chain 3-II levels and reducing p62 levels. Notably, pretreatment with autophagy inhibitors enhanced AKF-D52-induced cell death, indicating that the induced autophagy is cytoprotective. AKF-D52 treatment also triggered reactive oxygen species (ROS) production in NSCLC cells, whereas the antioxidant α-tocopherol abolished AKF-D52-induced cell death. In a xenograft lung cancer mouse model, AKF-D52 administration attenuated tumor growth by inducing apoptosis and autophagy in tumor tissues. Collectively, our data indicate that AKF-D52-induced ROS production plays a role in mediating apoptosis and cytoprotective autophagy in NSCLC.

Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits.

Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.

Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes.

Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.

Medical X-band linear accelerator for high-precision radiotherapy.

PURPOSE: Recently, high-precision radiotherapy systems have been developed by integrating computerized tomography or magnetic resonance imaging to enhance the precision of radiotherapy. For integration with additional imaging systems in a limited space, miniaturization and weight reduction of the linear accelerator (linac) system have become important. The aim of this work is to develop a compact medical linac based on 9.3 GHz X-band RF technology instead of the S-band RF technology typically used in the radiotherapy field. METHODS: The accelerating tube was designed by 3D finite-difference time-domain and particle-in-cell simulations because the frequency variation resulting from the structural parameters and processing errors is relatively sensitive to the operating performance of the X-band linac. Through the 3D simulation of the electric field distribution and beam dynamics process, we designed an accelerating tube to efficiently accelerate the electron beam and used a magnetron as the RF source to miniaturize the entire linac. In addition, a side-coupled structure was adopted to design a compact linac to reduce the RF power loss. To verify the performance of the linac, we developed a beam diagnostic system to analyze the electron beam characteristics and a quality assurance (QA) experimental environment including 3D lateral water phantoms to analyze the primary performance parameters (energy, dose rate, flatness, symmetry, and penumbra) The QA process was based on the standard protocols AAPM TG-51, 106, 142 and IAEA TRS-398. RESULTS: The X-band linac has high shunt impedance and electric field strength. Therefore, even though the length of the accelerating tube is 37 cm, the linac could accelerate an electron beam to more than 6 MeV and produce a beam current of more than 90 mA. The transmission ratio is measured to be approximately 30% ~ 40% when the electron gun operates in the constant emission region. The percent depth dose ratio at the measured depths of 10 and 20 cm was approximately 0.572, so we verified that the photon beam energy was matched to approximately 6 MV. The maximum dose rate was measured as 820 cGy/min when the source-to-skin distance was 80 cm. The symmetry was smaller than the QA standard and the flatness had a higher than standard value due to the flattening filter-free beam characteristics. In the case of the penumbra, it was not sufficiently steep compared to commercial equipment, but it could be compensated by improving additional devices such as multileaf collimator and jaw. CONCLUSIONS: A 9.3 GHz X-band medical linac was developed for high-precision radiotherapy. Since a more precise design and machining process are required for X-band RF technology, this linac was developed by performing a 3D simulation and ultraprecision machining. The X-band linac has a short length and a compact volume, but it can generate a validated therapeutic beam. Therefore, it has more flexibility to be coupled with imaging systems such as CT or MRI and can reduce the bore size of the gantry. In addition, the weight reduction can improve the mechanical stiffness of the unit and reduce the mechanical load.

End-Tidal Carbon Dioxide Monitoring for Spontaneous Pneumothorax.

BACKGROUND: Spontaneous pneumothorax should be classified as primary spontaneous pneumothorax (PSP) or secondary spontaneous pneumothorax (SSP) because treatment strategies may differ depending on underlying lung conditions and clinical course. The pulmonary dysfunction can lead to changes in end-tidal carbon dioxide (ETCO2). The aim of this study was to investigate the difference in ETCO2 between PSP and SSP. METHODS: This retrospective observational study included adult patients diagnosed with spontaneous pneumothorax in the emergency room from April 2019 to September 2020. We divided patients into PSP and SSP groups and compared ETCO2 variables between the two groups. RESULTS: There were 33 (66%) patients in the PSP group and 17 (34%) patients in the SSP group. Initial ETCO2 was lower in the SSP group than in the PSP group (30 (23-33) vs. 35 (33-38) mmHg, p=0.002). Multivariate analysis revealed that respiratory gas associated with SSP was initial ETCO2 (OR: 0.824; 95% CI: 0.697-0.974, p=0.023). The optimal cutoff for initial ETCO2 to detection of SSP was 32 mmHg (area under curve, 0.754), with 76.5% sensitivity and 72.7% specificity. CONCLUSION: ETCO2 monitoring is a reliable noninvasive indicator of differentiating between PSP and SSP. Initial ETCO2 lower than 32 mmHg is a predictor of SSP.