• Title/Summary/Keyword: Gram positive

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Genomic insights of S. aureus associated with bovine mastitis in a high livestock activity region of Mexico

  • Jose Roberto Aguirre-Sanchez;Nohemi Castro-del Campo;José Andres Medrano-Felix;Alex Omar Martínez-Torres;Cristobal Chaidez;Jordi Querol-Audi;Nohelia Castro-del Campo
    • Journal of Veterinary Science
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    • v.25 no.4
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    • pp.42.1-42.12
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    • 2024
  • Importance: Bovine mastitis, predominantly associated with gram-positive Staphylococcus aureus, poses a significant threat to dairy cows, leading to a decline in milk quality and volume with substantial economic implications. Objective: This study investigated the incidence, virulence, and antibiotic resistance of S. aureus associated with mastitis in dairy cows. Methods: Fifty milk-productive cows underwent a subclinical mastitis diagnosis, and the S. aureus strains were isolated. Genomic DNA extraction, sequencing, and bioinformatic analysis were performed, supplemented by including 124 S. aureus genomes from cows with subclinical mastitis to enhance the overall analysis. Results: The results revealed a 42% prevalence of subclinical mastitis among the cows tested. Genomic analysis identified 26 sequence types (STs) for all isolates, with Mexican STs belonging primarily to CC1 and CC97. The analyzed genomes exhibited multidrug resistance to phenicol, fluoroquinolone, tetracycline, and cephalosporine, which are commonly used as the first line of treatment. Furthermore, a similar genomic virulence repertoire was observed across the genomes, encompassing the genes related to invasion, survival, pathogenesis, and iron uptake. In particular, the toxic shock syndrome toxin (tss-1) was found predominantly in the genomes isolated in this study, posing potential health risks, particularly in children. Conclusion and Relevance: These findings underscore the broad capacity for antibiotic resistance and pathogenicity by S. aureus, compromising the integrity of milk and dairy products. The study emphasizes the need to evaluate the effectiveness of antibiotics in combating S. aureus infections.

KNU Korean Sentiment Lexicon: Bi-LSTM-based Method for Building a Korean Sentiment Lexicon (Bi-LSTM 기반의 한국어 감성사전 구축 방안)

  • Park, Sang-Min;Na, Chul-Won;Choi, Min-Seong;Lee, Da-Hee;On, Byung-Won
    • Journal of Intelligence and Information Systems
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    • v.24 no.4
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    • pp.219-240
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    • 2018
  • Sentiment analysis, which is one of the text mining techniques, is a method for extracting subjective content embedded in text documents. Recently, the sentiment analysis methods have been widely used in many fields. As good examples, data-driven surveys are based on analyzing the subjectivity of text data posted by users and market researches are conducted by analyzing users' review posts to quantify users' reputation on a target product. The basic method of sentiment analysis is to use sentiment dictionary (or lexicon), a list of sentiment vocabularies with positive, neutral, or negative semantics. In general, the meaning of many sentiment words is likely to be different across domains. For example, a sentiment word, 'sad' indicates negative meaning in many fields but a movie. In order to perform accurate sentiment analysis, we need to build the sentiment dictionary for a given domain. However, such a method of building the sentiment lexicon is time-consuming and various sentiment vocabularies are not included without the use of general-purpose sentiment lexicon. In order to address this problem, several studies have been carried out to construct the sentiment lexicon suitable for a specific domain based on 'OPEN HANGUL' and 'SentiWordNet', which are general-purpose sentiment lexicons. However, OPEN HANGUL is no longer being serviced and SentiWordNet does not work well because of language difference in the process of converting Korean word into English word. There are restrictions on the use of such general-purpose sentiment lexicons as seed data for building the sentiment lexicon for a specific domain. In this article, we construct 'KNU Korean Sentiment Lexicon (KNU-KSL)', a new general-purpose Korean sentiment dictionary that is more advanced than existing general-purpose lexicons. The proposed dictionary, which is a list of domain-independent sentiment words such as 'thank you', 'worthy', and 'impressed', is built to quickly construct the sentiment dictionary for a target domain. Especially, it constructs sentiment vocabularies by analyzing the glosses contained in Standard Korean Language Dictionary (SKLD) by the following procedures: First, we propose a sentiment classification model based on Bidirectional Long Short-Term Memory (Bi-LSTM). Second, the proposed deep learning model automatically classifies each of glosses to either positive or negative meaning. Third, positive words and phrases are extracted from the glosses classified as positive meaning, while negative words and phrases are extracted from the glosses classified as negative meaning. Our experimental results show that the average accuracy of the proposed sentiment classification model is up to 89.45%. In addition, the sentiment dictionary is more extended using various external sources including SentiWordNet, SenticNet, Emotional Verbs, and Sentiment Lexicon 0603. Furthermore, we add sentiment information about frequently used coined words and emoticons that are used mainly on the Web. The KNU-KSL contains a total of 14,843 sentiment vocabularies, each of which is one of 1-grams, 2-grams, phrases, and sentence patterns. Unlike existing sentiment dictionaries, it is composed of words that are not affected by particular domains. The recent trend on sentiment analysis is to use deep learning technique without sentiment dictionaries. The importance of developing sentiment dictionaries is declined gradually. However, one of recent studies shows that the words in the sentiment dictionary can be used as features of deep learning models, resulting in the sentiment analysis performed with higher accuracy (Teng, Z., 2016). This result indicates that the sentiment dictionary is used not only for sentiment analysis but also as features of deep learning models for improving accuracy. The proposed dictionary can be used as a basic data for constructing the sentiment lexicon of a particular domain and as features of deep learning models. It is also useful to automatically and quickly build large training sets for deep learning models.

Physiological and Ecological Characteristics of Indigenous Soybean Rhizobia Distributed in Korea -II. Studies on Some Physiological Characteristics and Nitrogen Fixation Activity Under Free-Living Conditions of Indigenous Rhizobia (우리나라 토착대두근류균(土着大豆根瘤菌)의 분포상태(分布狀態)와 생리(生理) 및 생태학적(生態學的) 특성(特性) -제(第)II보(報) : 토착근류균(土着根瘤菌)의 질소고정력(窒素固定力)과 생리적특성(生理的特性)에 관(關)한 연구(硏究))

  • Ryu, Jin-Chang;Lee, Seong-Jae;Suh, Jang-Sun;Cho, Moo-Je
    • Korean Journal of Soil Science and Fertilizer
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    • v.19 no.2
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    • pp.157-165
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    • 1986
  • This experiment was conducted to find out the some physiological characteristics and nitrogen fixation activities under free-living conditions of indigenous rhizobia isolated from soybean-cultivated (30 fields) and un-cultivated (30 fields) soil. The results were summerized as follows: 1. In free-living condition, only 12.8% and 6.4% of the indigenous rhizobia isolated from soybean cultivated (133 strains) and un-cultivated (125 strains) soils were nitrogenase positive as more than 4 n mole $C_2H_4$ per tube per hour by acetylene reduction assay. 2. The acid-producing rhizobia on litmus milk test was observed to be 20% of the total 160 strains isolated from soybean cultivated soil but about 34% of 166 strains isolated from un-cultivated soil. And the serum zone positive strains were higher in the soybean un-cultivated soil than cultivated soil. 3. The population ratio of fast-to slow-growing indigenous rhizobia based on growth pattern of AMA medium was 35.6% to 64.4% of the total 346 strains. 4. The population of indigenous Rhizobium japonicum counted by MPN method was ranged from $9.2{\times}10^2$ cells per gram of soil in soybean un-cultivated soil to $2.3{\times}10^4$ cells per gram of soil soybean cultivated soil. The number of indigenous R. japonicum in 0-10cm depth of surface layer was higher than low layer.

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Antimicrobial Effects against Food-Borne Pathogens and Antioxidant Activity of Rhododendron brachycarpum Extract (만병초 추출물의 식중독 유발균에 대한 항균효과 및 항산화활성)

  • Choi, Moo-Young;Rhim, Tae-Jin
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.40 no.10
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    • pp.1353-1360
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    • 2011
  • This study was performed to investigate the antimicrobial effects against food-borne pathogens and antioxidant activity of Rhododendron brachycarpum ethanol-extract. The antimicrobial activity of the extract was determined using a paper disc-diffusion method, and the diameter of the clear zone was measured. The diameter of the clear zone in the presence of 10 mg of extract was maximal against Bacillus cereus among the three tested Gram-positive bacteria and against Escherichia coli O157:H7 among the five tested Gram-negative bacteria. Analysis of the minimum inhibitory concentration (MIC) showed that the extract exhibited a similar efficacy as that of sorbic acid, a well-known chemical preservative. The growth inhibitory effects of the extract at concentrations of 250, 500, 1,000, and 2,000 mg/L on food-borne pathogens were determined against Staphylococcus aureus, Listeria monocytogenes, Salmonella Typhimurium, and Escherichia coli O157:H7. Growth of the microorganisms was not affected by the extract at concentrations up to 250 mg/L, but it was significantly (p<0.05) inhibited by the extract at concentrations higher than 1,000 mg/L. The antioxidant effects of the extract were examined via measurement of DPPH radical scavenging activity, inhibition of reactive oxygen species (ROS) generation using fluorescent dichlorofluorescien (DCF) assay, and prevention of peroxyl radical- and hydroxyl radical-induced supercoiled DNA breakage. The $IC_{50}$ of the extract for DPPH radical scavenging activity was about half that of ${\alpha}$-tocopherol, which was used as a positive control. DCF fluorescence intensity decreased as the concentration of the extract increased, demonstrating that ROS generation was inhibited in a concentration-dependent manner. The ROS inhibitory effect of the extract was higher than that of ascorbic acid. The extract prevented supercoiled DNA strand breakage induced by peroxyl radical and hydroxyl radical. Thus, the results of the present study demonstrate that the extract exhibits antimicrobial effects against food-borne pathogens as well as potent antioxidant capacity, suggesting that R. brachycarpum could be used as a natural antibacterial agent and effective antioxidant in food.

Antibacterial Effect of Cinnamon (Cinnamomum cassia) Bark Extract against Fish Pathogenic Bacteria (계피 추출물의 어류 질병 세균에 대한 항균 효과)

  • MOK Jong-Soo;SONG Ki-Cheol;CHOI Nack-Joong;YANG Ho-Shik
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.34 no.5
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    • pp.545-549
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    • 2001
  • To develop a natural antibacterial agent for fish bacterial diseases, antibacterial activity, minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and bactericidal effect of cinnamon bark extract were examined against fish pathogenic bacteria. The antimicrobial effect of the extract to the fish diet was also estimated, Cinnamon bark extract showed the broad spectrum of antibacterial activity against fish pathogenic bacteria, especially, it had strong activity against Streptococcus iniae, Edwardsiella tarda and Listonella anguillarum. Its MIC was $75.8\sim189.6{\mu}g/mL$ against Cram positive bacteria, and $75.8\sim113.8{\mu}g/mL$ against Gram negative bacteria in liquid medium, It was found to show stronger bactericidal action against Gram negative bacteria than Cram positive bacteria. According to increasing concentrations of the extract, it resulted in a proportional reduction of viable cell counts of both S. iniae and L. anguillarum. The former was not detected by addition of $189.6{\mu}g/mL$ after 12 hours incubation and the latter by addition of $151.6{\mu}g/mL$ after 24 hours incubation, respectively. It was reasonable that fish diet was soaked in cinnamon bark extract for ten minutes. The relationship formula between the weight of fish diet and the extract absorbed to fish diet was Y=7.2726X+4.5083 ($R^2=0.9998$). The fish diet soaked in the extract inhibited the growth of all strains used in this study. Its antibacterial activity was stable at the range from $10^{\circ}C\;to\;35^{\circ}C$ during the storage period of 28 days. When the diet soaked in the extract was incubated in liquid medium at $35^{\circ}C$, it inhibited the growth of microorganisms inhabited in the diet.

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Pathogens and Prognotic Factors for Early Onset Sepsis in Very Low Birth Weight Infants (극소 저체중 출생아에서 조기 패혈증의 원인균과 예후인자)

  • Kim, Yi-Sun;Kim, Jin-Kyu;Yoo, Hye-Soo;Ahn, So-Yoon;Seo, Hyun-Ju;Choi, Seo-Heui;Park, Soo-Kyung;Jung, Yu-Jin;Kim, Myo-Jing;Jeon, Ga-Won;Koo, Soo-Hyun;Lee, Kyung-Hoon;Chang, Yun-Sil;Park, Won-Soon
    • Neonatal Medicine
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    • v.16 no.2
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    • pp.163-171
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    • 2009
  • Purpose: This study was conducted to determine the incidence, causative pathogens, risk factors and mortality for early onset sepsis in the first three days in very low birth weight infants. Methods: The medical records of 1,124 very low birth weight infants admitted to the neonatal intensive care unit of Samsung Medical Center between November 1994 and December 2008 were retrospectively reviewed. The incidence, causative pathogens, risk factors, and mortality for early onset sepsis in the first 3 days of life in very low birth weight infants were evaluated. Results: Early onset sepsis, as confirmed by positive blood cultures, was present in 17 of 1,124 infants (1.5%). Sixty-four percent of the isolated pathogens were gram-positive bacteria and 35% of the isolated pathogens were gram-negative bacteria. The dominant pathogens of early onset sepsis included Staphylococcus aureus (23.5%), Esherichia coli (23.5%), and Enterococcus (17.6%). Vaginal delivery (adjusted odds ratio [OR], 3.7; 95% confidence interval [CI], 1.3-10.3; P=0.01) was associated with early onset sepsis. The overall mortality (adjusted hazard ratio, 3.0; 95% CI, 1.4-6.5; adjusted P=0.0039) and mortality within 72 hours of life (adjusted hazard ratio, 6.5; 95% CI, 2.2-18.9; adjusted P=0.0005) of infants with early onset sepsis were higher than that of uninfected infants. Conclusion: Early onset sepsis remains an uncommon, but potentially lethal problem among very low birth weight infants. Knowledge of the likely causative organisms and risk factors for early onset sepsis can aid in instituting prompt and appropriate therapy, in order to minimize mortality.

The Changes of Intestinal Normal Flora in Neonates for Seven Days Postnatally (정상 신생아의 대변에서 생후 1주일 동안 장내세균총의 변화)

  • Sung, Nam-ju;Lee, Seung Gue;Kim, Me Jin;Kim, Young Ho;Yang, Seung;Hwang, Il Tae;Jung, Ji A;Lee, Hae Ran;Kim, Jae-Seok
    • Pediatric Gastroenterology, Hepatology & Nutrition
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    • v.9 no.2
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    • pp.162-168
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    • 2006
  • Purpose: Microbial colonization of the intestine begins just after birth and development of the normal flora is a gradual process. The first bacteria colonizing the intestine in newborns are Staphylococcus, Enterobacteriaceae and Streptococcus. For several days after birth, the number of Bifidobacterium spp. increase. The aim of this study was to investigate the changes of microflora for seven days postnatally in neonatal stool. Methods: Fifteen neonates (breast : formula : mixed feeding 1 : 8 : 6, vaginal delivery : cesarean section 3 : 12) who were born at the Kangdong Sacred Heart Hospital, Hallym University were enrolled. First meconium and stools of postnatal 1-, 3-, and 7-day were innoculated. Blood agar plates for total aerobes, trypton bile X-glucuronide agar for E. coli, phenylethyl alcohol agar for gram positive anaerobes, MRS agar for Lactobacillus spp., bifidobacterium selective agar for Bifidobacterium spp. and cefoxitin-cycloserine-fructose agar for Clostridium difficile were used in the general incubator ($CO_2$ free incubator), $CO_2$ incubator or the anaerobic chamber for 48 or 72 hours at $37^{\circ}C$ and then colony forming units were counted. Results: No microflora was identified in the first meconium. Total aerobes, E. coli, and gram positive anaerobes were significantly increased with advancing postnatal days. In only one baby, Lactobacillus acidophilus was detected $2{\times}10^5CFU/g$ in the seven-day stool. Bifidobacterium spp. was detected in two babies. Clostridium difficile was not detected during the seven days. There were no significant differences in the bowel flora depending on the delivery pattern and feeding method. Conclusion: This study shows many changes in the intestinal normal flora in neonatal stool during seven days postnatally. If these findings are confirmed with larger studies, the data may be preliminary findings to support use of probiotics in neonates.

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Antimicrobial Activity of Niaouli (Melaleuca quinquenervia) Leaf Extracts against Skin Flora (피부 상재균에 대한 니아울리 잎 추출물의 항균활성)

  • Jang, Ha Na;Park, Soo Nam
    • Journal of the Society of Cosmetic Scientists of Korea
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    • v.40 no.3
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    • pp.313-320
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    • 2014
  • In this study, the antimicrobial activity of niaouli leaf extracts was evaluated against skin flora. The skin flora used for experiments were three gram-positive bacteria such as Bacillus subtilis (B. subtilis), Staphylococcus aureus (S. aureus), Propionibacterium acnes (P. acnes), and two gram-negative, Escherichia coli (E. coli), Pseudomonas aeruginosa( P. aeruginosa), and the yeast, Plasmodium ovale (P. ovale). The bioassay applied for determining the antimicrobial effects of niouli leaf extracts or fraction included the disc diffusion assay and broth dilution assay. Minimum inhibitory concentration (MIC) values of 50% ethanol extract on B. subtilis, S. aureus, P. acnes, E. coli and P. aeruginosa were 0.25%, 0.50%, 1.00%, 0.13% and 0.25% respectively and the MIC values of water fraction were 0.25%, 0.25%, 4,00%, 0.25% and 0.25%. P. ovale did not show antimicrobial activities. The MIC values of methyl paraben used as positive control indicated 0.25%, 0.25%, 0.25%, 0.13% and 0.50%. Also, Minimum bactericidal concentration (MBC) values of 50% ethanol extract were 2.00%, 2.00%, 1.00%, 0.50% and 2.00% individually and the MBC values of water fraction were 0.50%, 0.25%, 4.00%, 0.50% and 1.00%. The MBC values of methyl paraben indicated 1.00%, 0.500%, 0.50%, 0.50% and 1.00%. These results showed that water fraction was as good as methyl paraben except for P. acnes. The 50% ethanol extract also showed activity similar with it. Thus, it is concluded that the 50% ethanol extract/fraction of niaouli could be applicable to cosmetics as a natural preservatives effective in antimicrobial activity against skin flora.

A Study on the Necessity Verification of Convex Probe Disinfection (Convex Probe 소독 필요성 검증에 관한 연구)

  • Choi, Kwan-Yong;Yoo, Se-jong;Lee, Jun-ho;Hong, Sung-Yong
    • Journal of the Korean Society of Radiology
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    • v.13 no.2
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    • pp.193-200
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    • 2019
  • The study was conducted surveying ultrasound room workers on hospital infection awareness in Daejeon and Choong-chunng region. The contamination of ultrasonic probes used in clinical trials was measured using ATP, and the results were verified after using 70% alcohol sterilization. It was measured on the group's general characteristics and the specific categories such as academic background, job type, having professional certificate and infection education. After the examination, the gel removal and method, disinfection status of the probe and variable correlation analysis were performed to analyze the recognition of the ultrasonic probe disinfection. After examination in ultrasound room, it was found that towels were used the most for cleaning, and the gel container was not replaced for more than three months. After 70% alcohol disinfection, ATP contamination was reduced from $1055.4{\pm}944.2$ to $133.5{\pm}93.2$ and the result was analyzed to be statistically significant.(${\rho}<0.01$) The found bacteria were CNS, Gram positive bacillus, and Micrococcus specs. In order to solve this problem, 70% alcohol sterilization was applied and the bacteria were not detected after the treatment. The research shows that regular training on infection control and efforts to prevent infection are necessary, and that 70% alcohol is effective in disinfect the bacteria. Therefore, the medical institution should provide active hospital infection control education to improve the awareness of hospital infection among workers and contribute to the prevention of patient infection. It is also understood that proper use of the results of this study will help prevent infection by means of ultrasonic probes.

Isolation of Bacillus amyloliquefaciens ATC6 Producing Acidic Cellulase (산성 Cellulase를 분비하는 Bacillus amyloliquefaciens ATC6의 분리)

  • Lee, Se-Hyung;Chae, Jong-Pyo;Kim, Min-Jeong;Kang, Dae-Kyung
    • Journal of Animal Science and Technology
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    • v.52 no.1
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    • pp.65-70
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    • 2010
  • A bacterium producing acidic cellulase was isolated from pig feces. The isolate, ATC6 strain, was found to be Gram-positive, non-motile, catalase-positive, and spore-forming stain. Under an electron microscope, the cells were observed to be rod-shaped. The isolate was identified as Bacillus amyloliquefaciens ATC6 on the basis of morphological and biochemical properties as well as 16S rRNA gene sequences. Optimum pH and temperature for the cellulase activity of the culture supernatant of B. amyloliquefaciens ATC6 were found to be pH 4.5 and $55^{\circ}C$, respectively. More than 80% of its maximum activity was maintained at pH 4.0. The cellulase activity was maintained at temperatures ranging from 35 to $55^{\circ}C$ after 2 h incubation at pH 4.5, whereas it's activity decreased rapidly at $65^{\circ}C$.