Difference of Microbial Community in the Stream Adjacent to the Mixed Antibiotic Effluent Source.

Released antibiotics from source to stream can influence bacterial communities and potentially alter the ecosystem. This research provides a comprehensive examination of the sources, distribution, and bacterial community dynamics associated with varied antibiotic release sources adjacent to the stream. The residual of antibiotics from different sources was determined, and the bacterial community structure was examined to reveal the differences in the bacteria community in the stream. The residual of antibiotics was quantified with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the Illumina MiSeq platform was utilized to sequence bacterial 16S rRNA genes, providing comprehensive insights into the bacterial community structure in the sediment across five different sites. Results indicated that the presence and distribution of antibiotics were significantly influenced by released sources. In the case of the bacterial community, the Proteobacteria and Firmicutes were the most dominant phyla in the sediment, and especially, the Firmicutes showed higher abundance in sites mostly affected by livestock sources. Additionally, livestock gut bacteria such as Clostridium saudiense, Proteiniclasticum ruminis, and Turicibacter sanguinis were prevalent in antibiotic-contaminated sites adjacent to livestock facilities. Overall, this study provides critical insights into the effect of antibiotic contamination by verifying the relationship between the occurrence of antibiotic residuals and the alteration in the bacterial community in the stream.

Bioaccumulation and Mass Balance Analysis of Veterinary Antibiotics in an Agricultural Environment.

Veterinary antibiotics (VAs) released into the environment are a concern because of the possibility for increasing antibiotic-resistance genes. The concentrations of six VAs, chlortetracycline, oxytetracycline, tetracycline, sulfamethazine, sulfamethoxazole, and sulfathiazole, in manure-based compost, soil, and crops were measured using liquid chromatography-tandem mass spectrometry. Mass balance analysis was conducted based on the measured antibiotic concentration, cultivation area, and amount of manure-based compost applied. The result showed that the detected mean concentration of VAs ranges was 3.52~234.19 µg/kg, 0.52~13.08 µg/kg, and 1.05~39.57 µg/kg in manure-based compost, soil, and crops, respectively, and the substance of VAs detected in different media was also varied. Mass balance analysis showed that the VAs released from the manure-based compost can remain in soil (at rates of 26% to 100%), be taken up by crops (at rates of 0.4% to 3.7%), or dissipated (at rates of 9% to 73%) during the cultivation period. Among the six VAs, chlortetracycline and oxytetracycline mainly remained in the soil, whereas sulfamethoxazole and sulfathiazole were mainly dissipated. Although we did not verify the exact mechanism of the fate and distribution of VAs in this study, our results showed that these can vary depending on the different characteristics of VAs and the soil properties.

Constraints on Scalar Field Dark Matter from Colocated Michelson Interferometers.

Low-mass (sub-eV) scalar field dark matter may induce apparent oscillations of fundamental constants, resulting in corresponding oscillations of the size and the index of refraction of solids. Laser interferometers are highly sensitive to changes in the size and index of refraction of the main beam splitter. Using cross-correlated data of the Fermilab Holometer instrument, which consists of twin colocated 40-m arm length power-recycled interferometers, we investigate the possible existence of scalar field dark matter candidates in the mass range between 1.6×10^{-12} eV and 1.0×10^{-7} eV. We set new upper limits for the coupling parameters of scalar field dark matter, improving on limits from previous direct searches by up to 3 orders of magnitude.

Graphene Oxide-Supported Microwell Grids for Preparing Cryo-EM Samples with Controlled Ice Thickness.

Cryogenic-electron microscopy (cryo-EM) is the preferred method to determine 3D structures of proteins and to study diverse material systems that intrinsically have radiation or air sensitivity. Current cryo-EM sample preparation methods provide limited control over the sample quality, which limits the efficiency and high throughput of 3D structure analysis. This is partly because it is difficult to control the thickness of the vitreous ice that embeds specimens, in the range of nanoscale, depending on the size and type of materials of interest. Thus, there is a need for fine regulation of the thickness of vitreous ice to deliver consistent high signal-to-noise ratios for low-contrast biological specimens. Herein, an advanced silicon-chip-based device is developed which has a regular array of micropatterned holes with a graphene oxide (GO) window on freestanding silicon nitride (Six Ny ). Accurately regulated depths of micropatterned holes enable precise control of vitreous ice thickness. Furthermore, GO window with affinity for biomolecules can facilitate concentration of the sample molecules at a higher level. Incorporation of micropatterned chips with a GO window enhances cryo-EM imaging for various nanoscale biological samples including human immunodeficiency viral particles, groEL tetradecamers, apoferritin octahedral, aldolase homotetramer complexes, and tau filaments, as well as inorganic materials.

Interferometric Constraints on Spacelike Coherent Rotational Fluctuations.

Precision measurements are reported of the cross-spectrum of rotationally induced differential position displacements in a pair of colocated 39 m long, high-power Michelson interferometers. One arm of each interferometer is bent 90° near its midpoint to obtain sensitivity to rotations about an axis normal to the plane of the instrument. The instrument achieves quantum-limited sensing of spatially correlated signals in a broad frequency band extending beyond the 3.9-MHz inverse light travel time of the apparatus. For stationary signals with bandwidth Δf>10 kHz, the sensitivity to rotation-induced strain h of classical or exotic origin surpasses CSD_{δh}

Sex difference of mortality by age and body mass index in gastric cancer.

Mortality difference by age, sex, body mass index (BMI) in gastric cancer (GC) has been controversial. We evaluated sex-specific mortality by age and BMI. A total of 5961 patients diagnosed with GC from 2005 to 2013 in a single tertiary center were included and were followed until December 2017. The plot in goodness-of-fit-test by sex was crossed, so we performed sex-specific analysis. Overall mortality was lower in women than in men (adjusted hazard ratio [aHR], 0.72). Favor outcomes in women compared to men were observed among patients older than 60 yr (aHR, 0.64; 95% CI, 0.56-0.74), a BMI less than 25 kg/m2 (aHR, 0.69; 95% CI, 0.61-0.79), and stage I (aHR, 0.46; 95% CI, 0.38-0.56). In sex-specific analysis, mortality increased in age older than 60 yr in men, whereas it increased in both extreme ages (<40 yr and ≥ 70 yr) in women. Mortality by BMI was lowest at BMI of 25-29.9 kg/m2 and gradually increased according to decrease of BMI in men; aHR, 1.24 (23-24.9 kg/m2), 1.44 (18.5-22.9 kg/m2), and 2.54 (BMI<18.5 kg/m2). However, mortality decreased in patients with BMI ≥ 30 kg/m2 (aHR, 0.46) in women. The sex discrepancies in GC mortality by age and BMI suggest the need for sex-specific approaches to prognostic prediction.

Double staining method for array tomography using scanning electron microscopy.

Scanning electron microscopy (SEM) plays a central role in analyzing structures by imaging a large area of brain tissue at nanometer scales. A vast amount of data in the large area are required to study structural changes of cellular organelles in a specific cell, such as neurons, astrocytes, oligodendrocytes, and microglia among brain tissue, at sufficient resolution. Array tomography is a useful method for large-area imaging, and the osmium-thiocarbohydrazide-osmium (OTO) and ferrocyanide-reduced osmium methods are commonly used to enhance membrane contrast.Because many samples prepared using the conventional technique without en bloc staining are considered inadequate for array tomography, we suggested an alternative technique using post-staining conventional samples and compared the advantages.

Clinical significance and prognostic role of hypoxia-induced microRNA 382 in gastric adenocarcinoma.

Hypoxia and angiogenesis are critical components in the progression of solid cancer, including gastric cancers (GCs). miR-382 has been identified as a hypoxia-induced miR (hypoxamiR), but the clinical significance in GCs has not been identified yet. To explore the clinical and prognostic importance of miR-382 in GCs, the surgical specimens of 398 patients with GCs in KNU hospital in Korea, the total of 183 patients was randomly selected using simple sampling methods and big data with 446 GCs and 45 normal tissues from the data portal (https://portal.gdc.cancer.gov/) were analysed. Expression of miR-382 as well as miR-210, as a positive control hypoxamiR by qRT-PCR in histologically malignant region of GCs showed significantly positive correlation (R = 0.516, p<0.001). High miR-210 and miR-382 expression was significantly correlated with unfavorable prognosis including advanced GCs (AGC), higher T category, N category, pathologic TNM stage, lymphovascular invasion, venous invasion, and perinueral invasion, respectively (all p<0.05). In univariate analysis, high miR-210 expression was significantly associated with worse overall survival (OS) (p = 0.036) but not high miR-382. In paired 60 gastric normal and cancer tissues, miR-382 expression in cancer tissues was significantly higher than normal counterpart (p = 0.003), but not miR-210 expression. However, by increasing the patient number from the big data analysis, miR-210 as well as miR-382 expression in tumor tissues was significantly higher than the normal tissues. Our results suggest that miR-382, as novel hypoxamiR, can be a prognostic marker for advanced GCs and might be correlated with metastatic potential. miR-382 might play important roles in the aggressiveness, progression and prognosis of GCs. In addition, miR-382 give a predictive marker for progression of GCs compared to the normal or preneoplastic lesion.

Evaluation of Coronary Artery Calcium Progression in Asymptomatic Individuals with an Initial Score of Zero.

BACKGROUND AND OBJECTIVES: Coronary artery calcium (CAC) scoring in the asymptomatic population can improve cardiovascular risk prediction. We aimed to assess CAC progression and the impact of coronary risk factors on the CAC progression rate in asymptomatic Korean individuals with a baseline CAC score of zero. METHODS: The study population was derived from the Korea Initiatives on Coronary Artery Calcification (KOICA) registry: a retrospective, single ethnicity, multicenter registry of asymptomatic individuals who underwent CAC scoring as a part of a health checkup. Individuals with at least two CAC scores and an initial score of zero were included. CAC progression was defined as [√CAC score (follow-up) - √CAC score (baseline)] ≥2.5. The 10-year atherosclerotic cardiovascular disease (ASCVD) risk was calculated. RESULTS: Among 6,268 participants (mean age, 48.0±7.1 years; male, 80.5%), 719 (11.5%) experienced CAC progression during follow-up (median, 109 months; interquartile range, 78-208 months). The CAC progression rate was 0.3%, 1.9%, 4.3%, 8.6%, and 16.7% in years 1-5, respectively. The chance of CAC progression at 5 years was 13.1%, 22.0%, and 27.9% for individuals with a 10-year ASCVD risk of <5%, ≥5% but <7.5%, and ≥7.5%, respectively. A multivariable analysis revealed age, male sex, waist circumference, diabetes, and low-density lipoprotein cholesterol level as independently associated with annualized CAC progression (p<0.001, p=0.017, p=0.025, p=0.032, and p=0.003, respectively). CONCLUSIONS: The probability of CAC progression is very low in Korean individuals with a CAC score of zero. However, the risk of CAC progression increases nonlinearly over time, and increases as the 10-year ASCVD risk increases.

Occurrence of microplastics in municipal sewage treatment plants: a review.

Municipal sewage treatment plants (STPs) are thought to be important point sources of microplastics in freshwater systems and many peer-reviewed articles have been published on this issue since mid-2010s. In this review, we summarize existing literature on the occurrence of microplastics in STPs and experimental methods used for isolation and identification of microplastics. The number concentrations of microplastics in STP influents were 15.1-640 L-1 , whereas those in the STP effluents were highly variable and ranged from not detectable to 65 L-1 . For most of cases, conventional STPs are removing microplastics very effectively. Fragments and fibers are dominant shapes of microplastics. Thermoplastics (polyethylene and polypropylene) and polyester are the predominant materials recovered. Although further research is needed, size distribution of microplastics in STPs is likely to follow a power law, implying that different studies using different size cutoffs may be compared after establishing a power law relationship.

First Measurements of High Frequency Cross-Spectra from a Pair of Large Michelson Interferometers.

Measurements are reported of the cross-correlation of spectra of differential position signals from the Fermilab Holometer, a pair of colocated 39 m long, high power Michelson interferometers with flat broadband frequency response in the MHz range. The instrument obtains sensitivity to high frequency correlated signals far exceeding any previous measurement in a broad frequency band extending beyond the 3.8 MHz inverse light-crossing time of the apparatus. The dominant but uncorrelated shot noise is averaged down over 2×10^{8} independent spectral measurements with 381 Hz frequency resolution to obtain 2.1×10^{-20}m/sqrt[Hz] sensitivity to stationary signals. For signal bandwidths Δf>11 kHz, the sensitivity to strain h or shear power spectral density of classical or exotic origin surpasses a milestone PSD_{δh}

Drug susceptibility to etravirine and darunavir among Human Immunodeficiency Virus Type 1-derived pseudoviruses in treatment-experienced patients with HIV/AIDS in South Korea.

BACKGROUND: In South Korea, about 20 types of antiretroviral drugs are used in the treatment of patients with human immunodeficiency virus/acquired immune deficiency syndrome. Since 2010, raltegravir, etravirine, and darunavir have been spotlighted as new drugs for highly active antiretroviral therapy (HAART)-experienced adults with resistant HIV-1 in South Korea. In this study, we investigated potential susceptibility of pseudoviruses derived from treatment-experienced Korean patients to etravirine vs efavirenz and to darunavir vs amprenavir and indinavir using a modified single-round assay. METHODS: Pseudoviruses derived from nine treatment-experienced patients infected with HIV-1 were investigated by comparison with the wild-type strain pNL4-3. The 50% inhibitory concentration (IC50) values were calculated and drug susceptibility was compared. The intensity of genotypic drug resistance was classified based on the 'SIR' interpretation of the Stanford data base. RESULTS: Drug susceptibility was generally higher for etravirine and darunavir compared with efavirenz, amprenavir, and indinavir in pseudoviruses derived from treatment-experienced patients. Pseudoviruses derived from patients KRB4025 and KRB8014, who exhibited long-term use of protease inhibitors, showed an outside of tested drug concentration, especially for amprenavir and indinavir. However, they exhibited a lower fold-change in resistance to darunavir. CONCLUSIONS: Etravirine and darunavir have been used in HAART since 2010 in South Korea. Therefore, these antiretroviral drugs together with other newly introduced antiretroviral drugs are interesting for the optimal treatment of patients with treatment failure. This study may help to find a more effective HAART in the case of HIV-1 infected patients that have difficulty being treated.

The prevalence of antiretroviral multidrug resistance in highly active antiretroviral therapy-treated patients with HIV/AIDS between 2004 and 2009 in South Korea.

BACKGROUND: Highly active antiretroviral therapy (HAART) including protease inhibitors (PIs) has been used in South Korea since 1997. Currently, more than 20 types of antiretroviral drugs are used in the treatment of human immunodeficiency virus-infected/acquired immune deficiency syndrome patients in South Korea. Despite the rapid development of various antiretroviral drugs, many drug-resistant variants have been reported after initiating HAART, and the efficiency of HAART is limited by these variants. OBJECTIVES: To investigate and estimate the annual antiretroviral drug resistance and prevalence of antiretroviral multi-class drug resistance in Korean patients with experience of treatment. STUDY DESIGN: The amplified HIV-1 pol gene in 535 patients requested for genotypic drug resistance testing from 2004 to 2009 by the Korea Centers for Disease Control and Prevention was sequenced and analyzed annually and totally. The prevalence of antiretroviral drug resistance was estimated based on "SIR" interpretation of the Stanford sequence database. RESULTS: Of viruses derived from 787 specimens, 380 samples (48.3%) showed at least one drug class-related resistance. Predicted NRTI drug resistance was highest at 41.9%. NNRTI showed 27.2% resistance with 23.3% for PI. The percent of annual drug resistance showed similar pattern and slightly declined except 2004 and 2005. The prevalence of multi-class drug resistance against each drug class was: NRTI/NNRTI/PI, 9.8%; NRTI/PI, 21.9%; NNRTI/PI, 10.4%; and NRTI/NNRTI, 21.5%. CONCLUSIONS: About 50% and less than 10% of patients infected with HIV-1 have multidrug and multiclass resistance linked to 16 antiretroviral drugs, respectively. The significance of this study lies in its larger-scale examination of the prevalence of drug-resistant variants and multidrug resistance in HAART-experienced patients in South Korea.

Pilot study of adjuvant chemotherapy with 3-week combination of S-1 and cisplatin for patients with stage II-IV (M0) gastric cancer.

PURPOSE: The feasibility of a 3-week combination of S-1 and cisplatin as an adjuvant chemotherapy for patients with curatively resected gastric cancer was investigated. EXPERIMENTAL DESIGN: Korean patients with stage II-IV (M0) gastric adenocarcinoma who underwent a gastrectomy with D2 lymph node resection were enrolled. The S-1 was administered orally at 80 mg/m(2) divided into two daily doses for 14 days, while the cisplatin was administered at 60 mg/m(2) intravenously over 2 h every 21 days. The patients received a maximum of six cycles. RESULTS: From January 2006 to July 2010, 74 patients were included in this study. The median patient age was 56 years (range, 22-71), and 51.4% (38/74) of the patients had a performance status of 0. The median number of chemotherapy cycles administered was 6 (range, 1-6). The median relative dose intensity was 86.4% for S-1 and 80.0% for cisplatin. With a median follow-up duration of 13.9 months, the median relapse-free survival (RFS) and overall survival (OS) have not yet been reached. Fifteen relapses (20.3%) were documented. Plus, the estimated RFS rate was 60.5% at 3 years. The treatments were generally well tolerated. The most frequently observed grade 3-4 hematological toxicity was neutropenia (35.1%), and only 1 cycle of neutropenic fever occurred. The most frequently observed grade 3-4 non-hematological toxicities were nausea (4.1%) and asthenia (4.1%), and all the other grade 3-4 non-hematological toxicities were observed in less than 3% of the patients. CONCLUSIONS: Postoperative adjuvant S-1 plus cisplatin for 18 weeks was found to be feasible for patients with stage II-IV (M0) gastric adenocarcinoma following complete surgical resection.

Three-dimensional reconstruction of serial mouse brain sections: solution for flattening high-resolution large-scale mosaics.

Recent advances in high-throughput technology facilitate massive data collection and sharing, enabling neuroscientists to explore the brain across a large range of spatial scales. One such form of high-throughput data collection is the construction of large-scale mosaic volumes using light microscopy (Chow et al., 2006; Price et al., 2006). With this technology, researchers can collect and analyze high-resolution digitized volumes of whole brain sections down to 0.2 µm. However, until recently, scientists lacked the tools to easily handle these large high-resolution datasets. Furthermore, artifacts resulting from specimen preparation limited volume reconstruction using this technique to only a single tissue section. In this paper, we carefully describe the steps we used to digitally reconstruct a series of consecutive mouse brain sections labeled with three stains, a stain for blood vessels (DiI), a nuclear stain (TO-PRO-3), and a myelin stain (FluoroMyelin). These stains label important neuroanatomical landmarks that are used for stacking the serial sections during reconstruction. In addition, we show that the use of two software applications, ir-Tweak and Mogrifier, in conjunction with a volume flattening procedure enable scientists to adeptly work with digitized volumes despite tears and thickness variations within tissue sections. These applications make processing large-scale brain mosaics more efficient. When used in combination with new database resources, these brain maps should allow researchers to extend the lifetime of their specimens indefinitely by preserving them in digital form, making them available for future analyses as our knowledge in the field of neuroscience continues to expand.

Drug susceptibility of human immunodeficiency virus type 1-derived pseudoviruses from treatment-experienced patients to protease inhibitors and reverse transcriptase inhibitors, using a modified single-round assay.

BACKGROUND: Genotypic drug resistance assay has been the only method available to provide information related to drug resistance in South Korea since 1999. Phenotypic assay is also a useful method to predict a patient's state related to antiretroviral drug resistance. However, commercial systems and methods for phenotyping have not been introduced into South Korea. OBJECTIVES: To establish and apply modified phenotypic drug susceptibility assay using treatment-experienced patients' derived HIV-1 in South Korea. STUDY DESIGN: The genotypic drug resistance and phenotypic drug susceptibility of two different methods, Stanford HIV Drug Resistance Database (Stanford DB) and modified phenotypic drug susceptibility assay were compared especially focused on the HIV-1 protease (PR) and reverse transcriptase (RT) sequences. RESULTS: There was some discordance in comparing drug susceptibility results (a modified drug susceptibility assay) with the predicted genotypic drug resistance (Stanford DB). Phenotypic drug resistance showed the following order for pseudoviruses from treatment-experienced patients infected with HIV/AIDS: Efavirenz (EFV, 21 to 1,319-fold change), Lamivudine (3TC, 31 to >189-fold change), Indinavir sulfate (IDV, 26 to 63-fold change), Amprenavir (APV, 4 to 35-fold change) and Zidovudine (AZT, 20 to 634-fold change). For patient KRC3221, the AZT-related phenotypic drug resistance was the greatest, with 634-fold change compared with the wild type. CONCLUSIONS: Application of this modified phenotypic drug susceptibility assay is expected to help in predicting drug resistance as a guideline for clinicians to obtain a combined interpretation among genotyping, phenotyping and effective clinical treatments.

Infectivity of Homologous Recombinant HIV-1 Pseudo-virus with Reverse Transcriptase Inhibitor-related Mutations from Highly Active Antiretroviral Therapy Experienced Patients.

OBJECTIVES: In this study, the viral fitness of pseudo-viruses with a drug-resistant site in the reverse transcriptase (RT) region of the genome was investigated. The pseudo-viruses were derived from highly active antiretroviral therapy (HAART)-experienced HIV/AIDS patients. METHODS: HIV-1 RNA was extracted from the plasma of HAART-experienced (KRB9149, KRB7021, KRC1097) and HAART-naïve (KRC5180, KRC5123) HIV-1 patients. The RT gene from the extracted viral RNA was amplified and the polymerase chain reaction product was cloned from the pHXB2Δ2-261 RT vector. C8166 and TZM-bl cell lines were used as the HIV-1 replication capacity measurement system. To quantify the infectivity of homologous recombinant HIV-1, the infectivity derived from each pseudo-virus was compared with the infectivity of the reference strain HXB2. RESULTS: Patient-derived HIV-1 was cotransfected into C8166 cells and the expression level of the p24 antigen was measured. The expression was high in the HIV-1 isolates from patients KRC5180 and KRB9149 and low in patients KRB7021, KRC5123, and KRC1097, when compared with the reference strain. The infectivity of the pseudo-virus measured in TZM-bl cells decreased in the order, reference strain HXB2 > KRC5180 > KRC5123 > KRB9149 > KRB7021 > KRC1097. CONCLUSION: In this study, HIV-1 infectivity of the drug-resistant strain isolated from HAART-experienced patients with HIV/AIDS was found to be lower than the infectivity of the reference strain HXB2. This study provides useful data for the phenotypic susceptibility assay in HAART-experienced patients infected with HIV-1.

Evaluation of the NucliSens EasyQ HIV-1 v1.1 and RealTime HIV-1 kits for quantitation of HIV-1 RNA in plasma.

Human immunodeficiency virus type-1 (HIV-1) RNA viral load is an important biomarker to evaluate the therapeutic efficacy of antiretroviral drugs and to monitor disease progression in HIV-infected individuals. We compared HIV-1 RNA quantitation between two different kits, the NucliSens EasyQ HIV-1 v1.1 (EasyQ, bioMérieux) and RealTime HIV-1 (RealTime, Abbott), using HIV-1 RNA quality control (QC) materials, cell-cultivated viruses, and the plasma samples of 104 patients with HIV. Correlation between the two kits for HIV RNA-1 quantitation with clinical samples was high (R=0.91). Based on results obtained with quality control standards, the reproducibility of the RealTime kit was higher than the EasyQ kit: the viral load value and coefficient of variation of each kit was 4.11+/-0.136 and 3.3% for EasyQ and 3.55+/-0.042 and 1.2% for RealTime, respectively (P<0.002). This is the first comparative analysis of the detection limit and reproducibility of two different quantitation kits using clinical plasma samples from Korean HIV-1-infected patients. It will serve a useful reference to determine correction values for each HIV-1 RNA quantitation kits and to choose an appropriate assay kit for each laboratory.