Development of machine learning models for the surveillance of colon surgical site infections

BACKGROUND

Conventional surgical site infection (SSI) surveillance is labour-intensive. We aimed to develop machine learning (ML) models for the surveillance of SSIs for colon surgery and to assess whether the ML could improve surveillance process efficiency.

METHODS

This study included cases who underwent colon surgery at a tertiary center between 2013 and 2014. Logistic regression and four ML algorithms including random forest (RF), gradient boosting (GB), and neural networks (NNs) with or without recursive feature elimination (RFE) were first trained on the entire cohort, and then re-trained on cases selected based on a previous rule-based algorithm. We assessed model performance based on the area under the curve (AUC), sensitivity, and positive predictive value (PPV). The estimated proportion of reduction in workload for chart review based on the ML models was evaluated and compared with the conventional method.

RESULTS

At a sensitivity of 95%, the NN with RFE using 29 variables had the best performance with an AUC of 0.963 and PPV of 21.1%. When combining both the rule-based algorithm and ML algorithms, the NN with RFE using 19 variables had a higher PPV (28.9%) than with the ML algorithm alone, which could decrease the number of cases requiring chart review by 83.9% compared with the conventional method.

CONCLUSION

We demonstrated that ML can improve the efficiency of SSI surveillance for colon surgery by decreasing the burden of chart review while providing high sensitivity. In particular, the hybrid approach of ML with a rule-based algorithm showed the best performance in terms of PPV.

Management of newborns and healthcare workers exposed to isoniazid-resistant congenital tuberculosis in the neonatal intensive care unit

BACKGROUND

Management of newborns and healthcare workers (HCWs) exposed to congenital tuberculosis (TB) in the neonatal intensive care unit (NICU) has been reported rarely.

AIM

To outline a contact investigation process for individuals exposed to congenital TB in the NICU and investigate nosocomial transmission. Additionally, to assess the efficacy and safety of window prophylaxis in exposed newborns.

METHODS

A baby, born at a gestational age of 28 + 1 weeks, was diagnosed with isoniazid-resistant congenital TB on the 39th day of admission to the level IV NICU. Newborns and HCWs exposed cumulatively for ≥8 h underwent contact investigation and follow-up for a year.

FINDINGS

Eighty-two newborns underwent contact investigation. All newborns displayed normal chest X-rays, and 42 hospitalized newborns tested negative for acid-fast bacilli stain and Xpert® MTB/RIF assay in their endotracheal sputum or gastric juices. Eighty received window prophylaxis: six of 75 on rifampin experienced mild adverse events, and none of the five on levofloxacin. After 12 weeks, five (6.1%) had a positive tuberculin skin test, all of whom had already received the Bacillus Calmette-Guérin vaccine and tested negative on TB interferon-gamma releasing assay. Of 119 exposed HCWs, three (2.5%) were diagnosed with latent TB infection and completed a four-month rifampin therapy. There was no active TB disease among exposed newborns and HCWs during a one-year follow-up.

CONCLUSION

Timely diagnosis of congenital TB is crucial for minimizing transmission among exposed neonates and HCWs in the NICU setting. In cases of isoniazid-resistant index patients, even premature newborns may consider the use of rifampin or levofloxacin for window prophylaxis.

Dietary Bacillus spp. supplementation to both sow and progenies improved post-weaning growth rate, gut function, and reduce the pro-inflammatory cytokine production in weaners challenged with Escherichia coli K88

BACKGROUND

The use of probiotics (PRO) in late gestation sow and their impact on progenies' performance during the post-weaning stage has received more attention from the researchers recently. This study aimed to analyze the effect of probiotic mixture (Bacillus subtilis and Bacillus licheniformis) on both sow and offspring's performance.

METHODS

First experiment (Exp.1) was conducted from the 100th day of gestation through to post-weaning. A total of twenty sows and their litters were assigned to one of two dietary treatments, Control (CON) based diet and PRO- CON+ 0.05% probiotic mixture. Dietary treatments were arranged in a split-plot pattern with sow and weaner treatment (CON and PRO diet) as the main and sub plot. Exp.2. E. coli challenge study was carried out two weeks after weaning with 40 piglets. Dietary treatments remained same while all pigs were orally administered with a 1.5 ml suspension of 1010 CFU of K88 strain of E. coli per ml.

RESULT

PRO group sow showed significantly decreased backfat thickness difference and body weight difference after farrowing and at the end of weaning d21. The nutrient digestibility of PRO group sows was significantly higher at the end of weaning. Moreover, piglets born from PRO group sow showed higher weaning weight and tend to increase average daily gain at the end of d21. The addition of mixed probiotic in sow and weaner diet had suppressed the production of TNF-α and interleukin-6 in E. coli challenged pigs. The phyla Firmicutes and Bacteroidetes in E. coli -challenged pigs were highly abundant while, the relative abundance of clostridium_sensu_stricto_1 at genus level was significantly reduced by the inclusion of probiotic in both the sow and weaner diet. Also, taxonomic distribution analysis showed significantly lower prevalence of Clostridium and Brachyspira and higher prevalence of Lactobacilli in E. coli-challenged pigs that were born from PRO group sow and fed CON and PRO weaner diet.

CONCLUSION

This study reveals that the inclusion of 0.05% mixed probiotics (Bacillus spp.) to both sow and their progenies diet would be more beneficial to enhance the post-weaning growth rate, gut health, and immune status of E. coli challenged pigs.

"Primer shot" fractionation with an early treatment break is theoretically superior to consecutive weekday fractionation schemes for early-stage non-small cell lung cancer

PURPOSE

Radiotherapy is traditionally given in equally spaced weekday fractions. We hypothesize that heterogeneous interfraction intervals can increase radiosensitivity via reoxygenation. Through modeling, we investigate whether this minimizes local failures and toxicity for early-stage non-small cell lung cancer (NSCLC).

METHODS

Previously, a tumor dose-response model based on resource competition and cell-cycle-dependent radiosensitivity accurately predicted local failure rates for early-stage NSCLC cohorts. Here, the model mathematically determined non-uniform inter-fraction intervals minimizing local failures at similar normal tissue toxicity risk, i.e., iso-BED3 (iso-NTCP) for fractionation schemes 18Gyx3, 12Gyx4, 10Gyx5, 7.5Gyx8, 5Gyx12, 4Gyx15. Next, we used these optimized schedules to reduce toxicity risk (BED3) while maintaining stable local failures (TCP).

RESULTS

Optimal schedules consistently favored a "primer shot" fraction followed by a 2-week break, allowing tumor reoxygenation. Increasing or decreasing the assumed baseline hypoxia extended or shortened this optimal break by up to one week. Fraction sizes of 7.5 Gy and up required a single primer shot, while smaller fractions needed one or two extra fractions for full reoxygenation. The optimized schedules, versus consecutive weekday fractionation, predicted absolute LF reductions of 4.6%-7.4%, except for the already optimal LF rate seen for 18Gyx3. Primer shot schedules could also reduce BED3 at iso-TCP with the biggest improvements for the shortest schedules (94.6Gy reduction for 18Gyx3).

CONCLUSION

A validated simulation model clearly supports non-standard "primer shot" fractionation, reducing the impact of hypoxia-induced radioresistance. A limitation of this study is that primer-shot fractionation is outside prior clinical experience and therefore will require clinical studies for definitive testing.

Alterations in gastric and gut microbiota following sleeve gastrectomy in high-fat diet-induced obese rats

Obesity is considered a high-risk disease and a global epidemic, and the number of obese patients is rising at an alarming rate worldwide. High-fat diet-induced dysbiosis of the intestinal microbiota is considered an essential factor related to obesity. Bariatric surgery induces a sharp decrease in fat content and effectively improves the metabolism of obese individuals. Herein, we aimed to investigate the effects of a high-fat diet-induced obesity and the alterations in gastric and intestinal microbiota resulting from sleeve gastrectomy on clinical outcomes. We performed 16S sequencing of gastric and fecal samples obtained from rats in three treatment groups: normal chow diet, high-fat diet (HFD), and sleeve gastrectomy after HDF for 14 weeks. The area under the curve of fasting glucose and the levels of leptin and low-density lipoproteins were significantly different between groups. Microbial taxa that were highly correlated with several clinical parameters were identified for each group. Glyoxylate and dicarboxylate, taurine and hypotaurine, butanoate, nitrogen, and pyrimidine metabolism and aminoacyl-transfer ribonucleic acid biosynthesis were affected by bariatric surgery and were significantly associated with changes in the composition of gastric and fecal microbiomes. Connectivity and co-occurrence were higher in fecal samples than in gastric tissues. Our results elucidated the positive effects of sleeve gastrectomy in obesity and shed light on changes in the microbiomes of gastric and fecal samples.

Comparison of microbial molecular diagnosis efficiency within unstable template metagenomic DNA samples between qRT-PCR and chip-based digital PCR platforms

Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.

Multi-Enzyme Supplementation to Diets Containing 2 Protein Levels Affects Intramuscular Fat Content in Muscle and Modulates Cecal Microflora Without Affecting the Growth Performance of Finishing Pigs

We investigated the effects of crude protein (CP) levels and exogenous enzymes on growth performance, meat quality, toxic gas emissions, and colonic microbiota community in 200 finishing pigs. Four groups corresponded to 4 diets: 16.74% CP (high-protein level, HP) and 14.73% CP (medium protein level, MP) diet supplemented with or without 1-g/kg multi-enzymes (ENZs, including 1000-U/kg protease, 2500-U/kg α-amylase, and 10,000-U/kg β-glucanase), using a 2 × 2 factorial arrangement. After 7 weeks of trial, ENZs supplementation increased (P < 0.05) the average daily gain (ADG) of finishing pigs during weeks 4 to 7 and in the overall period and improved gross energy utilization. Dietary HP improved (P < 0.05) ADG during the overall period. The MP diet-treated pigs had higher intramuscular fat (IMF) content in the longissimus dorsi muscle (P < 0.01). ENZs supplementation to the MP diets lowered muscle IMF content (P < 0.01). Additionally, pigs fed the HP diet released (P < 0.05) more NH3 and H2S in excrement. The HP diet enhanced (P < 0.05) intestinal microbial richness, represented by higher observed_ amplicon sequence variants and Chao1. Administration of ENZs to the HP diet increased (P < 0.05) the Shannon and Pielou's evenness. Dietary MP promoted Firmicutes proliferation. Supplementary HP diet increased the relative abundances of Spirochaetota, Verrucomicrobiota, Desulfobacterota, and Fibrobacterota (P < 0.05). Supplemental ENZ elevated (P < 0.05) Actinobacteriota and Desulfobacterota abundances. ENZ supplementation to the HP diet increased the abundances of Bacteroidota, Desulfobacterota, and Proteobacteria but lowered their abundances in the MP diet. Taken together, the HP diet or ENZs' supplements improved growth performance. Although the interaction between CP levels and ENZs had no effect on growth performance, it modulated colonic flora and muscle IMF content.

Effective microbial molecular diagnosis of periodontitis-related pathogen Porphyromonas gingivalis from salivary samples using rgpA gene

Importance of accurate molecular diagnosis and quantification of particular disease-related pathogenic microorganisms is highlighted as an introductory step to prevent and care for diseases. In this study, we designed a primer/probe set for quantitative real-time polymerase chain reaction (qRT-PCR) targeting rgpA gene, known as the specific virulence factor of periodontitis-related pathogenic bacteria ‘Porphyromonas gingivalis’, and evaluated its diagnostic efficiency by detecting and quantifying relative bacterial load of P. gingivalis within saliva samples collected from clinical subjects. As a result of qRT-PCR, we confirmed that relative bacterial load of P. gingivalis was detected and quantified within all samples of positive control and periodontitis groups. On the contrary, negative results were confirmed in both negative control and healthy groups. Additionally, as a result of comparison with next-generation sequencing (NGS)–based 16S metagenome profiling data, we confirmed relative bacterial load of P. gingivalis, which was not identified on bacterial classification table created through 16S microbiome analysis, in qRT-PCR results. It showed that an approach to quantifying specific microorganisms by applying qRT-PCR method could solve microbial misclassification issues at species level of an NGS-based 16S microbiome study. In this respect, we suggest that P. gingivalis–specific primer/probe set introduced in present study has efficient applicability in various oral healthcare industries, including periodontitis-related microbial molecular diagnosis field.

Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans

Oral microbial ecosystem could influence intestinal diseases, but there have been insufficient studies demonstrating the association of microbial composition between the oral cavity and the intestinal system. Thus, we aimed to investigate the compositional network within the oral microbiome related to gut enterotype from saliva and stool samples collected from 112 healthy Korean subjects. Here, we performed bacterial 16S amplicon sequencing from clinical samples. Then, we determined oral microbiome type related to individual's gut enterotype for healthy Korean. The co-occurrence analysis was performed to interactivity prediction of microbiome within saliva samples. As a result, it could be classified into two Korean oral microbiome types (KO) and four oral-gut-associated microbiome types (KOGA) according to distribution and significant differences of oral microflora. The co-occurrence analysis showed various bacterial compositional networks linked around Streptococcus and Haemophilus within healthy subjects. The present study was first approach in healthy Koreans to identify the oral microbiome types related to the gut microbiome and investigate their characteristics. Hence, we suggest that our results could be potential healthy control data for identifying differences in microbial composition between healthy people and oral disease patients and studying microbial association with the gut microbial environment (oral-gut microbiome axis).

Nourishing neonatal piglets with synthetic milk and Lactobacillus sp. at birth highly modifies the gut microbial communities at the post-weaning stage

The importance of probiotics in pig production is widely recognized. However, the precise role of probiotics in regulating the gut microbiota of piglets has not been assessed extensively. Therefore, we intend to examine whether suckling pigs ingesting with synthetic milk (SM) and probiotics along with mother milk has a carryover effect on its growth and gut health at the post-weaning stage. A total of 40 [Duroc× (Yorkshire× Landrace)] neonates with an initial BW of 1.49 ± 0.28 kg were assigned to one of two treatments groups: control (CON) and treatment (TRT). Control group piglets were nourished with synthetic milk, while TRT group piglets were nourished SM with (1 × 109 CFU/g) Lactobacillus sp. probiotics. The treatment group piglets showed higher (p < 0.05) body weight and daily gain at week 3 than the CON group piglets. 16S metagenome sequencing showed average demultiplexed reads and denoised reads counts of 157,399 and 74,945, respectively. The total ASV taxonomy number classified with a confidence threshold > 70% (default) on sequence alignment with the SILVA v138 reference database was 4,474. During week 1, Escherichia-Shigella, Clostridium sensu stricto 1, and Bacteroides were confirmed as the major dominant bacterial genera in both the groups at the genus level. However, during week 2, the relative proportion of Escherichia-Shigella, Clostridium sensu stricto 1, and Proteobacteria was decreased, while that of Lactobacillus and Bacteroidota was increased in pigs receiving the probiotic supplement. During weeks 2 and 3, Firmicutes, Proteobacteria, and Bacteroidota phyla were dominant in both groups. During week 6, the relative proportion of Proteobacteria was slightly increased in both groups. Furthermore, Prevotella was confirmed as the major dominant bacterial genus in both groups during weeks 3 and 6. This study suggests that nourishing neonatal piglets with synthetic milk and Lactobacillus sp. probiotics from birth to 21 days would be beneficial to enhance the gut health of piglets and to overcome post-weaning mortality.

Late ventricular potential for risk prediction of sudden cardiac death risk: a valuable tool or an unnecessary step?

Background/Introduction

Signal-averaged electrocardiography (SA-ECG) is a high-resolution electrocardiography that can detect late ventricular potential, which known to be a noninvasive tool for risk stratification of sudden cardiac death (SCD) by predicting reentrant ventricular tachyarrhythmia. There is a paucity of data with SA-ECG on SCD survivors without structural heart disease, whereas majority of previous studies had been focused on post myocardial infarction survivors.

Purpose

This study assessed the clinical utility of SA-ECG as a risk stratification modality for lethal arrhythmic event in patients at risk of SCD without definite structural heart disease.

Methods

Total 629 patients who experienced or had potential risk of SCD were studied with SA-ECG. Among them, 48 patients who were found to have significant structural heart disease were excluded, except arrhythmogenic right ventricular cardiomyopathy. Major arrhythmic event (MAE) was defined as composite of all-cause death, aborted SCD, and sustained VT during any time either before visit of clinic or during follow up period. Syncope and non-sustained VT was defined as non-major arrhythmic event. SA-ECG was defined positive when fulfilling three or more criterion: (1) unfiltered QRS duration ≥114ms, (2) filtered QRS duration ≥114ms, (3) duration of terminal QRS &lt;40uV exceeding 40ms, and (4) root mean square voltage in the terminal 40ms of ≤20ms.

Results

Among total 581 patients, 145 patients with positive SA-ECG showed higher incidence of MAE compared to patients with negative SA-ECG (21.4% vs. 6.7%, OR 3.816 [95% CI 2.208–6.597], p&lt;0.001, Table). As the number of positive SA-ECG criteria increases, incidence of MAE tended to increase sequentially, which was markedly noted from 2 positive to 3 positive criteria (10.7% to 20.8%, p&lt;0.001, Figure). In particular, patient with inherited arrhythmia showed higher rate of positive late potential compared to those with non-inherited arrhythmia (51.0% vs. 19.3%, p&lt;0.001).

Conclusion

This study showed that at least 3 out of 4 diagnostic criteria in SA-ECG can independently predict lethal arrhythmic events and the positive late potential was associated with lethal arrhythmic event that leads to SCD, suggesting risk prediction for SCD using SA-ECG in patients even without structural heart disease including inherited arrhythmias.

Funding Acknowledgement

Type of funding sources: None.

Clinical role of genetic testing for overlapping between Brugada syndrome and arrhythmogenic right ventricular cardiomyopathy

Background/Introduction

Brugada syndrome (BrS) and arrhythmogenic right ventricular cardiomyopathy (ARVC) are inherited arrhythmias that may predispose to sudden cardiac arrest. Although its pathogenetic mechanisms differ, overlapping features between BrS and ARVC have been demonstrated previously. However, it remains to be determined whether genetic testing for ARVC-related gene is needed in patients with BrS.

Purpose

This study is aimed to analyze genetic profiles of BrS patients using next generation sequencing (NGS) based multigene panel including ARVC related genes.

Methods

Patients who were confirmed as BrS or clinically suspected as BrS with type 2 or 3 Brugada pattern electrocardiography were studied. Genetic testing using NGS panels (Illumina Inc., San Diego, CA, USA) included 30 genetic variants associated with inherited arrhythmia and genetic cardiomyopathy.

Results

Among the total 119 patients from BrS registry, 63 patients were confirmed as BrS and 56 patients were clinically suspected as BrS without fulfilling diagnostic criteria. One-hundred-fourteen patients (95.8%) were male, and mean age of onset was 43.6 year-old. Genetic variants were identified in 25 of 42 patients who received genetic testing. Six out of 25 patients (24.0%) showed ARVC-related genotypes (2 PKP2, 1 DSG2, 1 TMEM43, 1 JUP, and 1 DSP) (Figure 1 and Table 1). None of the patients showed structural or electrocardiographic features that fulfill diagnostic criteria of ARVC. It is notable that ARVC-related genotypes were mostly frequently accounted for BrS patients, following SCN5A and SCN10A.

Conclusion

In the clinic setting, ARVC-related genetic variants were identified in significant proportion of BrS patients, supporting that genetic testing of ARVC-overlapping is needed. This study suggests that follow-up including imaging study should be considered in BrS patients with ARVC-related genotypes to monitor disease progression as ARVC.

Funding Acknowledgement

Type of funding sources: None.

Extended DeepILST for Various Thermodynamic States and Applications in Coarse-Graining

Molecular dynamics (MD) simulations are widely used to obtain the microscopic properties of atomistic systems when the interatomic potential or the coarse-grained potential is known. In many practical situations, however, it is necessary to predict the interatomic or coarse-grained potential, which is a tremendous challenge. Many approaches have been developed to predict the potential parameters based on various techniques, including the relative entropy method, integral equation theory, etc., but these methods lack transferability and are limited to a specific range of thermodynamic states. Recently, data-driven and machine learning approaches have been developed to overcome such limitations. In this study, we expand the range of thermodynamic states used to train deep inverse liquid-state theory (DeepILST)¹, a deep learning framework for solving the inverse problem of liquid-state theory. We also assess the performance of DeepILST in coarse-graining various multiatom molecules and identify the molecular characteristics that affect the coarse-graining performance of DeepILST.

A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.

Radiolucent Pure Matrix Stones on Computed Tomography Scan, Arising in Patient with Type I Diabetes and Chronic Kidney Disease: A Case Report

Kidney matrix stones are a rare form of calculi, which are challenging to diagnose. Matrix stones consist of a proteinaceous material which has a radiolucent appearance that might be overlooked on imaging. Recently, endourological intervention has been the standard treatment method for matrix stones. We report a case of urinary matrix stones in a patient with type 1 diabetes mellitus and chronic kidney disease, in whom the stones formed into a pure matrix and were not visualized in the computed tomography scan. The stones were found after additional work-up, and they were managed using a transureteral stone basket, not through endourological intervention.

Comparison of the oral microbial composition between healthy individuals and periodontitis patients in different oral sampling sites using 16S metagenome profiling

Purpose

The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples.

Methods

In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis.

Results

When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples.

Conclusions

In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

Comparative analysis of human facial skin microbiome between topical sites compared to entire face

BACKGROUND

Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling.

OBJECTIVE

Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis.

METHODS

Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests.

RESULTS

We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R² value > 0.93) with the entire face, while the forehead sites were negatively correlated (R² value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face.

CONCLUSION

Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.

Fate and transport in environmental quality

Changes in pollutant concentrations in environmental media occur both from pollutant transport in water or air and from local processes, such as adsorption, degradation, precipitation, straining, and so on. The terms "fate and transport" and "transport and fate" reflect the coupling of moving with the carrier media and biogeochemical processes describing local transformations or interactions. The Journal of Environmental Quality (JEQ) was one of the first to publish papers on fate and transport (F&T). This paper is a minireview written to commemorate the 50th anniversary of JEQ and show how the research interests, methodology, and public attention have been reflected in fate and transport publications in JEQ during the last 40 years. We report the statistics showing how the representation of different pollutant groups in papers changed with time. Major focus areas have included the effect of solution composition on F&T and concurrent F&T, the role of organic matter, and the relative role of different F&T pathways. The role of temporal and spatial heterogeneity has been studied at different scales. The value of long-term F&T studies and developments in modeling as the F&T research approach was amply demonstrated. Fate and transport studies have been an essential part of conservation measure evaluation and comparison and ecological risk assessment. For 50 years, JEQ has delivered new insights, methods, and applications related to F&T science. The importance of its service to society is recognized, and we look forward to new generations of F&T researchers presenting their contributions in JEQ.

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.

97 Function of species-specific OCT4 reporter system during porcine embryo development

The present study examined the activity and function of pig OCT4 (POU5F1) enhancer in porcine early embryo development. OCT4 is one of the master regulators for the pluripotency of early mammalian embryonic development and embryonic stem cells. It has two regulatory elements: distal enhancer (DE) and proximal enhancer (PE) in the upstream regulatory region. They are activated under different conditions such as naïve and primed. It is known that two enhancers are activated to produce OCT4 simultaneously or sequentially depending on the state of pluripotency. Many porcine OCT4 upstream region-based reporter systems have been reported because this is a necessary part of studying porcine-specific pluripotency. However, the porcine-specific OCT4 reporter system has never been transfected and functionally tested during porcine early embryo development. We performed functional tests of the previously established porcine-specific OCT4 reporter system in the early embryo development stage. Porcine embryos were micro-injected with the pOCT4-ΔPE-eGFP (DE-GFP) containing a distal enhancer and core promoter and pOCT4-ΔDE-DsRed2 (PE-RFP) containing a proximal enhancer and core promoter. They were cultured in PZM-3 at 39°C in a humidified atmosphere, 5% CO2, and 5% O2 for 168h. Fifty of the 100 embryos were injected with OCT4 reporter system as treatment groups and the other 50 were not injected (control groups). We analysed mRNA and protein expression of GFP and RFP using quantitative real-time PCR and confocal microscopy by developmental stages. The introduced reporter system could function beginning with the 4-cell stage. The expression of GFP and RFP was observed simultaneously in the early embryonic development stage up to blastocyst, indicating that porcine OCT4 was produced by distal and proximal enhancers, unlike mouse Oct4 expression, which was only controlled by the distal enhancer during early embryo development. Therefore, the mechanisms and functions of distal and proximal enhancers of porcine OCT4 were different from those of the mouse. This is similar to results of the previous experiment using porcine-induced pluripotent stem cells, which suggest that porcine OCT4 is expressed by two enhancers and in a stage-specific manner during reprogramming and that pigs do not use only one enhancer in pluripotent states, but two enhancers at the same time, and there is only a difference in degree. This work showed that the porcine OCT4 reporter system enables non-destructive analysis during early embryo development and it could be applied to study species-specific pluripotency and to help the establishment of naïve embryonic stem cells in the pig. This work was supported by the BK21 Plus Program, the National Research Foundation of Korea (NRF) grant funded by the Korea government (NRF-2019R1C1C1004514), the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through the Development of High Value-Added Food Technology Program funded by the Ministry of Agriculture, Food, and Rural Affairs (MAFRA; 118042-03-3-HD020).

42 Disruption of endogenous SOX2 during porcine embryo development using the CRIPSR/Cas9 system

The lineage specification of the pre-implantation embryo is important to understand the developmental process, but it remains unclear because the expression of lineage-specific genes is distinct among species. Pigs have genetic and physiological traits similar to humans; however, there are differences in gene expression during the pre-implantation stage. To select a candidate gene that affects the formation of the inner cell mass (ICM) in porcine embryo, we conducted preliminary experiments. First, we measured the expression level of candidate genes for lineage specification in parthenogenetic-activated embryos. The expression of pluripotent genes peaked on Day 3 and thereafter decreased gradually. Next, we conducted immunocytochemistry. OCT4 was expressed in all cells in morula and Day 5 blastocyst, but some Day 7 blastocysts expressed OCT4 in both ICM and trophectoderm (TE), whereas others expressed OCT4 only in ICM. NANOG was not observed in the morula stage, whereas SOX2 was located in a restricted area. To examine the effect of SOX2 in ICM formation, we injected plasmid expressing Cas9 and guide (g)RNA using Lipofectamine for efficient transgene expression at the 2-cell stage to increase viability by inducing mosaicism. The expression of enhanced green fluorescent protein (EGFP) contained in the plasmid confirmed that the plasmid was operating normally. In SOX2-knockout (KO) early blastocysts, the numbers of total cells and SOX2- and NANOG-positive cells were greatly decreased, while OCT4 was expressed in most cells. As in early blastocysts, SOX2-KO late blastocysts had fewer cells expressing SOX2, NANOG, and SOX17 than control. To identify the transcriptional consequences of SOX2 reduction, we performed quantitative PCR analysis on non-injected and PX458-gRNA injected blastocysts. Injection of PX458-gRNA resulted in downregulation of NANOG, SOX17, and SMAD7, but not SOX2 and OCT4. Furthermore, proliferation-associated genes were downregulated in injected blastocysts. In conclusion, SOX2-targeted porcine embryos showed blastocoel formation, the inner cell mass formed poorly, and embryos have inefficient cells. Also, the depletion of SOX2 in porcine blastocysts downregulated pluripotent genes and proliferation genes. This work was supported by the BK21 Plus Program, the National Research Foundation of Korea (NRF) grant funded by the Korea government (NRF-2019R1C1C1004514), the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through the Development of High Value-Added Food Technology Program funded by the Ministry of Agriculture, Food, and Rural Affairs (MAFRA; 118042-03-3-HD020).

Performance comparison of fecal preservative and stock solutions for gut microbiome storage at room temperature

The gut microbiome, which is symbiotic within the human body, assists in human digestion. It plays significant roles in identifying intestinal disease as well as in maintaining a healthy body with functional immune and metabolic activities. To confirm the consistency of fecal intestinal microbial research, it is necessary to study the changes in intestinal microbial flora according to the fecal collection solution and storage period. We collected fecal samples from three healthy Korean adults. To examine the efficacy of fecal collection solution, we used NBgene-Gut, OMNIgene-Gut, 70% ethanol (Ethanol-70%), and RNAlater. The samples were stored for up to two months at room temperature using three different methods, and we observed changes in microbial communities over time. We analyzed clusters of changes in the microbial flora by observing fecal stock solutions and metagenome sequencing performed over time. In particular, we confirmed the profiling of alpha and beta diversity and microbial classification according to the differences in intestinal environment among individuals. We also confirmed that the microbial profile remained stable for two months and that the microbial profile did not change significantly over time. In addition, our results suggest the possibility of verifying microbial profiling even for long-term storage of a single sample. In conclusion, collecting fecal samples using a stock solution rather than freezing feces seems to be relatively reproducible and stable for GUT metagenome analysis. Therefore, stock solution tubes in intestinal microbial research can be used without problems.

Measurement of the Lund Jet Plane Using Charged Particles in 13 TeV Proton-Proton Collisions with the ATLAS Detector

The prevalence of hadronic jets at the LHC requires that a deep understanding of jet formation and structure is achieved in order to reach the highest levels of experimental and theoretical precision. There have been many measurements of jet substructure at the LHC and previous colliders, but the targeted observables mix physical effects from various origins. Based on a recent proposal to factorize physical effects, this Letter presents a double-differential cross-section measurement of the Lund jet plane using 139  fb^{-1} of sqrt[s]=13  TeV proton-proton collision data collected with the ATLAS detector using jets with transverse momentum above 675 GeV. The measurement uses charged particles to achieve a fine angular resolution and is corrected for acceptance and detector effects. Several parton shower Monte Carlo models are compared with the data. No single model is found to be in agreement with the measured data across the entire plane.

Measurement of Azimuthal Anisotropy of Muons from Charm and Bottom Hadrons in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

The elliptic flow of muons from the decay of charm and bottom hadrons is measured in pp collisions at sqrt[s]=13  TeV using a data sample with an integrated luminosity of 150  pb^{-1} recorded by the ATLAS detector at the LHC. The muons from heavy-flavor decay are separated from light-hadron decay muons using momentum imbalance between the tracking and muon spectrometers. The heavy-flavor decay muons are further separated into those from charm decay and those from bottom decay using the distance-of-closest-approach to the collision vertex. The measurement is performed for muons in the transverse momentum range 4-7 GeV and pseudorapidity range |η|<2.4. A significant nonzero elliptic anisotropy coefficient v_{2} is observed for muons from charm decays, while the v_{2} value for muons from bottom decays is consistent with zero within uncertainties.

Prospective randomized comparison of cerebrospinal fluid aspiration and conventional popping methods using 27-gauge spinal needles in patients undergoing spinal anaesthesia

Background

Performing spinal anaesthesia using the conventional popping method with a 27-gauge (27G) spinal needle is technically difficult. In this study, we compared the aspiration and conventional popping method for spinal anaesthesia using 27G Quincke-type needles.

Methods

This prospective, randomized study enrolled 90 patients, aged 19 to 65 years, with American Society of Anesthesiologists physical status I-III, who were undergoing spinal anaesthesia. Patients were randomly assigned to one of two groups using a computer-generated random number table: patients receiving spinal anaesthesia using the aspiration method, in which the needle is advanced with continuous aspiration, or the conventional popping method. The primary outcome measure was the success rate of the first attempt to perform dural puncture. Number of attempts and passages, withdrawal cases, successful attempt time, total procedure time, and actual depth of dural puncture were recorded.

Results

Eighty-eight patients were included in the study. In the aspiration group, the success rate of first attempt for dural puncture was 93.3%, compared with 72.1% in the popping group (P = 0.019). Success involving needle withdrawal was recorded in 4 (8.9%) patients in the aspiration group and 13 (30.2%) in the popping group (P = 0.024). In the popping group, the number of attempts was significantly higher (P = 0.044), and total procedure time was significantly longer (P = 0.023). Actual depths of dural puncture were deeper in the popping group than in the aspiration group (P = 0.019).

Conclusions

The aspiration method using a 27G Quincke-type needle offers clinical benefits for dural puncture compared with the conventional popping method for spinal anaesthesia.

Trial registration

Clinical research information service number: KCT0002815, registered 21/Apr/2018. Retrospectively registered.

Search for Magnetic Monopoles and Stable High-Electric-Charge Objects in 13 Tev Proton-Proton Collisions with the ATLAS Detector

A search for magnetic monopoles and high-electric-charge objects is presented using 34.4  fb^{-1} of 13 TeV pp collision data collected by the ATLAS detector at the LHC during 2015 and 2016. The considered signature is based upon high ionization in the transition radiation tracker of the inner detector associated with a pencil-shape energy deposit in the electromagnetic calorimeter. The data were collected by a dedicated trigger based on the tracker high-threshold hit capability. The results are interpreted in models of Drell-Yan pair production of stable particles with two spin hypotheses (0 and 1/2) and masses ranging from 200 to 4000 GeV. The search improves by approximately a factor of 5 the constraints on the direct production of magnetic monopoles carrying one or two Dirac magnetic charges and stable objects with electric charge in the range 20≤|z|≤60 and extends the charge range to 60<|z|≤100.