Investigating potential auxiliary anaerobic digestion activity of phage under polyvinyl chloride microplastic stress.

Polyvinyl chloride (PVC) microplastics present in sewage were trapped in sludge, thereby hindering anaerobic digestion performance of waste active sludge (WAS). Phages regulate virocell metabolism by encoding auxiliary metabolic genes (AMGs) related to energy acquisition and material degradation, supporting hosts survive in harsh environments and play a crucial role in biogeochemical cycles. This study investigated the potential effects of phages on the recovery of WAS anaerobic digestion under PVC stress. We observed a significant alteration in the phage community induced by PVC microplastics. Phages encoded AMGs related to anaerobic digestion and cell growth probably alleviate PVC microplastics inhibition on WAS anaerobic digestion, and 54.2 % of hydrolysis-related GHs and 40.8 % of acidification-related AMGs were actively transcribed in the PVC-exposed group. Additionally, the degradation of chitin and peptidoglycan during hydrolysis and the conversion of glucose to pyruvate during acidification were more susceptible to phages. Prediction of phage-host relationship indicated that the phyla Pseudomonadota were predominantly targeted hosts by hydrolysis-related and acidification-related phages, and PVC toxicity had minimal impact on phage-host interaction. Our findings highlight the importance of phages in anaerobic digestion and provide a novel strategy for using phages in the functional recovery of microplastic-exposed sludge.

Clinical, genomic and immune microenvironmental determinants of nivolumab response in head and neck squamous cell carcinoma.

Background: In view of improving biomarkers predicting the efficacy of immunotherapy for head and neck squamous cell carcinoma (R/M HNSCC), this multicenter retrospective study aimed to identify clinical, tumor microenvironmental, and genomic factors that are related to therapeutic response to the anti- Programmed cell death protein 1 (PD-1) antibody, nivolumab, in patients with R/M HNSCC. Methods: The study compared 53 responders and 47 non-responders, analyzing formalin-fixed paraffin-embedded samples using 14-marker multiplex immunohistochemistry and targeted gene sequencing. Results: Of 100 patients included, responders had significantly lower smoking and alcohol index, higher incidence of immune related adverse events, and higher PD-1 ligand (PD-L1) expression in immune cells as well as PD-L1 combined positive score (CPS) than non-responders. The frequency of natural killer cells was associated with nivolumab response in patients with prior cetuximab use, but not in cetuximab-naïve status. Age-stratified analysis showed nivolumab response was linked to high CPS and lymphoid-inflamed profiles in patients aged ≥ 65. In contrast, lower NLR in peripheral blood counts was associated with response in patients aged < 65. Notably, TP53 mutation-positive group had lower CPS and T cell densities, suggesting an immune-excluded microenvironment. Patients with altered tumor suppressor gene pathways, including TP53, CDKN2A, and SMAD4 mutations, had lower CPS, higher smoking index, and were associated with poor responses. Conclusion: Nivolumab treatment efficacy in HNSCC is influenced by a combination of clinical factors, age, prior treatment, immune environmental characteristics, and gene mutation profiles.

Identification of protein biomarkers in wastewater linked to the incidence of COVID-19.

Wastewater-based epidemiological (WBE) surveillance is a viable disease surveillance technique capable of monitoring the spread of infectious disease agents in sewershed communities. In addition to detecting viral genomes in wastewater, WBE surveillance can identify other endogenous biomarkers that are significantly elevated and excreted in the saliva, urine, and/or stool of infected individuals. Human protein biomarkers allow the realization of real-time WBE surveillance using highly sensitive biosensors. In this study, we analyzed endogenous protein biomarkers present in wastewater influent through liquid chromatography-tandem mass spectrophotometry and scaffold data-independent acquisition to identify candidate target protein biomarkers for WBE surveillance of SARS-CoV-2. We found that out of the 1382 proteins observed in the wastewater samples, 44 were human proteins associated with infectious diseases. These included immune response substances such as immunoglobulins, cytokine-chemokines, and complements, as well as proteins belonging to antimicrobial and antiviral groups. A significant correlation was observed between the intensity of human infectious disease-related protein biomarkers in wastewater and COVID-19 case numbers. Real-time WBE surveillance using biosensors targeting immune response proteins, such as antibodies or immunoglobulins, in wastewater holds promise for expediting the implementation of relevant policies for the effective prevention of infectious diseases in the near future.

Clinical benefits of combining oral cytotoxic chemotherapeutic agents with radiotherapy in patients with T2N0 glottic squamous cell carcinoma based on the reports of the Head and Neck Cancer Registry of Japan.

BACKGROUND: T2N0 glottic squamous cell carcinoma (SCC) typically responds well to radiotherapy (RT); however, achieving local control remains challenging. In cases of RT failure, total laryngectomy may be necessary. Improved local control and preservation of the larynx directly enhances patients' quality of life. Our retrospective analysis using the Japan Head and Neck Cancer Registry (JHNCR) aimed to compare the clinical benefits of RT and chemoradiotherapy (CRT) in patients with T2N0 glottic SCC. METHODS: Using data from the JHNCR (2011-2015), we included 1,231 patients with T2N0 glottic SCC. Among them, 346 received curative RT and 425 underwent curative CRT. The CRT group was further divided into the oral CRT (Oral CRT, N=120) and intravenous CRT (DIV CRT, N=305) groups. This study assessed local control rate (LCR), progression-free survival (PFS), and overall survival (OS). A 1:1 propensity score-matching analysis was used to adjust for patient characteristics. RESULTS: After matching, 105 pairs compared RT with Oral CRT, and 224 pairs compared RT with DIV CRT. The variables were well-balanced in the matched populations. In the matched populations, the Oral CRT group had significantly better 5-year LCR and PFS than the RT group (LCR, 89.4 % vs. 80.6 %, P=0.043; and PFS, 85.5 % vs. 72.3 %, P=0.025, respectively), while the DIV RT group had significantly better 5-year PFS than the RT group (80.1 % vs. 68.6 %, P=0.026). CONCLUSIONS: The clinical benefits of better local and disease controls were observed when oral chemotherapy was added to RT in patients with T2N0 glottic SCC. Thus, the significance of adding oral chemotherapeutic agents to RT in the treatment of T2N0 glottic SCC requires further prospective investigation.

Quantitative evaluation of water, sanitation, and hygiene measures on COVID-19 pandemic peak reduction in the Philippines.

New cases of coronavirus disease 2019 (COVID-19) are continually being recorded worldwide, despite global efforts in implementing non-pharmaceutical interventions and establishing vaccination programs. This trend highlights the need to identify the factors associated with the continued spread of COVID-19. The World Health Organization recommends hand washing as a cost-effective intervention for preventing COVID-19, indicating that water, sanitation, and hygiene (WaSH) are central to the prevention of the disease. However, low- and middle-income countries lack adequate access to WaSH, which increases the risk of contracting COVID-19. The aim of this study was to identify the WaSH factors associated with the incidence of COVID-19 and quantitatively estimate the effects of improvements in WaSH on reducing the incidence of COVID-19 during the peak of the pandemic. Lasso regression and extreme gradient boosting models were used to identify the WaSH factors. Distinct estimation models were developed to assess the effect of WaSH in rural regions under two assumptions: increasing regional basic sanitation coverage up to 25 % and 50%. The reduction in the incidence of COVID-19 during the peak of the pandemic was calculated for each rural region. The results of the analyses indicated that basic sanitation is important for reducing the incidence of COVID-19 in rural regions compared to urban regions in the Philippines. In addition, the results suggested that increasing basic sanitation coverage could reduce the incidence of COVID-19 by 2-66 %, alleviating the burden on healthcare facilities. This study indicates that improved basic sanitation infrastructure are needed in rural Philippines. The results of this study emphasise the significance of WaSH as an indicator of COVID-19 incidence, highlighting the need for its enhancement to enable the achievement of sustainable disease prevention and pandemic preparedness goals.

A soft-sensor approach for predicting an indicator virus removal efficiency of a pilot-scale anaerobic membrane bioreactor (AnMBR).

The anaerobic membrane bioreactor (AnMBR) is a promising technology for not only water reclamation but also virus removal; however, the virus removal efficiency of AnMBR has not been fully investigated. Additionally, the removal efficiency estimation requires datasets of virus concentration in influent and effluent, but its monitoring is not easy to perform for practical operation because the virus quantification process is generally time-consuming and requires specialized equipment and trained personnel. Therefore, in this study, we aimed to identify the key, monitorable variables in AnMBR and establish the data-driven models using the selected variables to predict virus removal efficiency. We monitored operational and environmental conditions of AnMBR in Sendai, Japan and measured virus concentration once a week for six months. Spearman's rank correlation analysis revealed that the pH values of influent and mixed liquor suspended solids (MLSS) were strongly correlated with the log reduction value of pepper mild mottle virus, indicating that electrostatic interactions played a dominant role in AnMBR virus removal. Among the candidate models, the random forest model using selected variables including influent and MLSS pH outperformed the others. This study has demonstrated the potential of AnMBR as a viable option for municipal wastewater reclamation with high microbial safety.

Effect of environmental factors on conjugative transfer of antibiotic resistance genes in aquatic settings.

Antimicrobial-resistance genes (ARGs) are spread among bacteria by horizontal gene transfer, however, the effect of environmental factors on the dynamics of the ARG in water environments has not been very well understood. In this systematic review, we employed the regression tree algorithm to identify the environmental factors that facilitate/inhibit the transfer of ARGs via conjugation in planktonic/biofilm-formed bacterial cells based on the results of past relevant research. Escherichia coli strains were the most studied genus for conjugation experiments as donor/recipient in the intra-genera category. Conversely, Pseudomonas spp., Acinetobacter spp., and Salmonella spp. were studied primarily as recipients across inter-genera bacteria. The conjugation efficiency (ce) was found to be highly dependent on the incubation period. Some antibiotics, such as nitrofurantoin (at ≥0.2 µg ml-1) and kanamycin (at ≥9.5 mg l-1) as well as metallic compounds like mercury (II) chloride (HgCl2, ≥3 µmol l-1), and vanadium (III) chloride (VCl3, ≥50 µmol l-1) had enhancing effect on conjugation. The highest ce value (-0.90 log10) was achieved at 15°C-19°C, with linoleic acid concentrations <8 mg l-1, a recognized conjugation inhibitor. Identifying critical environmental factors affecting ARG dissemination in aquatic environments will accelerate strategies to control their proliferation and combat antibiotic resistance.

Identification of environmental, socioeconomic, water, sanitation, and hygiene (WaSH) factors associated with COVID-19 incidence in the Philippines: A nationwide modelling study.

Despite the implementation of non-pharmaceutical interventions, the threat of coronavirus disease 2019 (COVID-19) remains significant on a global scale. Identifying external factors contributing to its spread is crucial, especially given the World Health Organization's recommendation emphasizing access to water, sanitation, and hygiene as essential in curbing COVID-19. There is a notable discrepancy in access to sanitation facilities, particularly evident in low- and middle-income countries. However, there is a lack of quantitative assessments regarding these factors. This study examines various environmental, socioeconomic, water, sanitation, and hygiene factors and their associations with COVID-19 incidence. All regions in the Philippines were categorized into clusters based on socioeconomic factors. A conceptual structural equation model (SEM) was developed using domain knowledge. The best-fitting SEM for each cluster was determined, and associations between factors and COVID-19 incidence were estimated. The correlation analysis revealed that rainfall, minimum temperature, and relative humidity were positively correlated with weekly COVID-19 incidence in urban regions. Maximum temperature, mean temperature, wind speed, and wind direction were negatively correlated with weekly COVID-19 incidence in rural regions, with time lags of 0, 3, and 7 weeks. In urban regions (Cluster 1), factors such as urbanization rate (1.00), area (-0.93), and population (0.54) were found to be associated with weekly COVID-19 incidence. Conversely, in rural regions (Cluster 2), factors including area (0.17), basic sanitation (0.84), and wind direction (0.83) showed associations with weekly COVID-19 incidence. These factors were causally associated with a latent variable reflecting the hidden confounders associated with COVID-19 incidence. It is important to note that sanitation factors were associated only in rural regions. Improving access to sanitation facilities in rural regions of the Philippines is imperative to effectively mitigate disease transmission in future pandemics. Identification of the causal effect of unobserved confounders with COVID-19 incidence is recommended for future research.

Pepper mild mottle virus intended for use as a process indicator for drinking water treatment: Present forms and quantitative relations to norovirus and rotavirus in surface water.

Pepper mild mottle virus (PMMoV) has been proposed as a potential indicator of human enteric viruses in environmental water and for viral removal during drinking water treatment. To investigate the occurrence and present forms of PMMoV and quantitative relations to norovirus GII and rotavirus A (RVA) in surface waters, 147 source water samples were collected from 21 drinking water treatment plants (DWTPs) in Japan between January 2018 and January 2021, and the concentrations of viruses in suspended and dissolved fractions were measured using real-time RT-PCR. PMMoV was detected in 81-100 % of samples in each sample month and observed concentrations ranged from 3.0 to 7.0 log10 copies/L. The concentrations of PMMoV were higher in dissolved fraction compared to suspended fractions, while different partitioning was observed for NoV GII depending on seasons. The concentrations of PMMoV were basically higher than those of norovirus GII (1.9-5.3 log10 copies/L) and RVA (1.9-6.6 log10 copies/L), while in 18 samples, RVA presented higher concentrations than PMMoV. Partial regions of VP7, VP4, and VP6 of the RVA in the 18 samples were amplified using nested PCR, and the genotypes were determined using an amplicon-based next-generation sequencing approach. We found that these source water samples included not only human RVA but also various animal RVA and high genetic diversity due to the existence of animal RVA was associated with a higher RVA concentration than PMMoV. Our findings suggest that PMMoV can be used as an indicator of norovirus GII and human RVA in drinking water sources and that the indicator performance should be evaluated by comparing to zoonotic viruses as well as human viruses.

Genetic diversity of murine norovirus populations less susceptible to chlorine.

High genetic diversity in RNA viruses contributes to their rapid adaptation to environmental stresses, including disinfection. Insufficient disinfection can occur because of the emergence of viruses that are less susceptible to disinfection. However, understanding regarding the mechanisms underlying the alteration of viral susceptibility to disinfectants is limited. Here, we performed an experimental adaptation of murine norovirus (MNV) using chlorine to understand the genetic characteristics of virus populations adapted to chlorine disinfection. Several MNV populations exposed to an initial free chlorine concentration of 50 ppm exhibited reduced susceptibility, particularly after the fifth and tenth passages. A dominant mutation identified using whole-genome sequencing did not explain the reduced susceptibility of the MNV populations to chlorine. Conversely, MNV populations with less susceptibility to chlorine, which appeared under higher chlorine stress, were accompanied by significantly lower synonymous nucleotide diversity (πS) in the major capsid protein (VP1). The nonsynonymous nucleotide diversity (πN) in VP1 in the less-susceptible populations was higher than that in the susceptible populations, although the difference was not significant. Therefore, the ability of MNV populations to adapt to chlorine was associated with the change in nucleotide diversity in VP1, which may lead to viral aggregate formation and reduction in chlorine exposure. Moreover, the appearance of some nonsynonymous mutations can also contribute to the alteration in chlorine susceptibility by influencing the efficiency of viral replication. This study highlights the importance of understanding the genetic characteristics of virus populations under disinfection, which can contribute to the development of effective disinfection strategies and prevent the development of virus populations less susceptible to disinfectants.

Removal of RNA viruses from swine wastewater using anaerobic membrane bioreactor: Performance and mechanisms.

The effective removal of viruses from swine wastewater using anaerobic membrane bioreactor (AnMBR) is vital to ecological safety. However, most studies have focused only on disinfectants, whereas the capabilities of the treatment process have not been investigated. In this study, the performance and mechanism of an AnMBR in the removal of porcine hepatitis E virus (HEV), porcine kobuvirus (PKoV), porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV) are systematically investigated. The results show that the AnMBR effectively removes the four viruses, with average removal efficiencies of 1.62, 3.05, 2.41, and 1.34 log for HEV, PKoV, PEDV and TGEV, respectively. Biomass adsorption contributes primarily to the total virus removal in the initial stage of reactor operation, with contributions to HEV and PKoV removal exceeding 71.7 % and 68.2 %, respectively. When the membrane is fouled, membrane rejection dominated virus removal. The membrane rejection contribution test shows the significant contribution of membrane pore foulants (23-76 %). Correlation analysis shows that the surface characteristics and size differences of the four viruses contribute primarily to their different effects on biomass adsorption and membrane rejection. This study provides technical guidance for viral removal during the treatment of high-concentration swine wastewater using an AnMBR.

Multiple pathogen contamination of water, hands, and fomites in rural Nepal and the effect of WaSH interventions.

Water, Sanitation, and Hygiene (WaSH) interventions are the most effective in reducing diarrheal disease severity and prevalence. However, very few studies have investigated the effectiveness of WaSH intervention in reducing pathogen presence and concentration. In this study, we employed a microfluidic PCR approach to quantify twenty bacterial pathogens in water (n = 360), hands (n = 180), and fomite (n = 540) samples collected in rural households of Nepal to assess the pathogen exposures and the effect of WaSH intervention on contamination and exposure rates. The pathogen load and the exposure pathways for each pathogen in intervention and control villages were compared to understand the effects of WaSH intervention. Pathogens were detected in higher frequency and concentration from fomites samples, toilet handle (21.42%; 5.4,0 95%CI: mean log10 of 4.69, 5.96), utensils (23.5%; 5.47, 95%CI: mean log10 of 4.77, 6.77), and water vessels (22.42%; 5.53, 95%CI: mean log10 of 4.79, 6.60) as compared to cleaning water (14.36%; 5.05, 95%CI: mean log10 of 4.36, 5.89), drinking water (14.26%; 4.37, 85%CI: mean log10 of 4.37, 5.87), and hand rinse samples (16.92%; 5.49, 95%CI: mean log10 of 4.77, 6.39). There was no clear evidence that WaSH intervention reduced overall pathogen contamination in any tested pathway. However, we observed a significant reduction (p < 0.05) in the prevalence, but not concentration, of some target pathogens, including Enterococcus spp. in the intervention village compared to the control village for water and hands rinse samples. Conversely, no significant reduction in target pathogen concentration was observed for water and hand rinse samples. In swab samples, there was a reduction mostly in pathogen concentration rather than pathogen prevalence, highlighting that a reduction in pathogen prevalence was not always accompanied by a reduction in pathogen concentration. This study provides an understanding of WaSH intervention on microbe concentrations. Such data could help with better planning of intervention activities in the future.

Exploring indoor and outdoor dust as a potential tool for detection and monitoring of COVID-19 transmission.

This study investigated the potential of using SARS-CoV-2 viral concentrations in dust as an additional surveillance tool for early detection and monitoring of COVID-19 transmission. Dust samples were collected from 8 public locations in 16 districts of Bangkok, Thailand, from June to August 2021. SARS-CoV-2 RNA concentrations in dust were quantified, and their correlation with community case incidence was assessed. Our findings revealed a positive correlation between viral concentrations detected in dust and the relative risk of COVID-19. The highest risk was observed with no delay (0-day lag), and this risk gradually decreased as the lag time increased. We observed an overall decline in viral concentrations in public places during lockdown, closely associated with reduced human mobility. The effective reproduction number for COVID-19 transmission remained above one throughout the study period, suggesting that transmission may persist in locations beyond public areas even after the lockdown measures were in place.

Risk factors of secondary cancer in laryngeal, oropharyngeal, or hypopharyngeal cancer after definitive therapy.

BACKGROUND: Our previous research showed that a high rate of secondary carcinogenesis is observed during follow-up after transoral surgery in patients with early-stage laryngeal, oropharyngeal, and hypopharyngeal cancers. We speculate that the contributing factors are alcohol drinking, smoking, and aging; however, we could not provide clear evidence. In this study, we aimed to identify the risk factors for secondary carcinogenesis in patients with these cancers, particularly factors associated with drinking and/or smoking. METHODS: The medical records of all-stage laryngeal, oropharyngeal, and hypopharyngeal cancer patients who had undergone definitive treatment were retrospectively analyzed. Assessments included visual and endoscopic observations of the primary site, enhanced cervical CT or US of the primary site and regional lymph nodes, PET-CT, and enhanced whole-body CT. Clinical characteristics were compared in patients with and without secondary carcinogenesis and in patients with hypopharyngeal cancer and patients with other cancers. RESULTS: Hypopharyngeal cancer was an independent risk factor for secondary cancer. The 5-year incidence rate of secondary cancer was 25.5%, 28.6%, and 41.2% in laryngeal, oropharyngeal, and hypopharyngeal cancers, respectively. Radiotherapy was defined as an independent risk factor in hypopharyngeal cancer patients with secondary cancers. No direct correlation was found between secondary carcinogenesis and alcohol consumption, smoking, or aging. CONCLUSIONS: Patients with hypopharyngeal cancer require close follow-up as they are at high risk of developing secondary cancer, possibly because out-of-field radiation exposure may induce systemic secondary carcinogenesis in hypopharyngeal cancer patients with genetic abnormality induced by alcohol consumption.

Sensitivity Evaluation of Enveloped and Non-enveloped Viruses to Ethanol Using Machine Learning: A Systematic Review.

Viral diseases are a severe public health issue worldwide. During the coronavirus pandemic, the use of alcohol-based sanitizers was recommended by WHO. Enveloped viruses are sensitive to ethanol, whereas non-enveloped viruses are considerably less sensitive. However, no quantitative analysis has been conducted to determine virus ethanol sensitivity and the important variables influencing the inactivation of viruses to ethanol. This study aimed to determine viruses' sensitivity to ethanol and the most important variables influencing the inactivation of viruses exposed to ethanol based on machine learning. We examined 37 peer-reviewed articles through a systematic search. Quantitative analysis was employed using a decision tree and random forest algorithms. Based on the decision tree, enveloped viruses required around ≥ 35% ethanol with an average contact time of at least 1 min, which reduced the average viral load by 4 log10. In non-enveloped viruses with and without organic matter, ≥ 77.50% and ≥ 65% ethanol with an extended contact time of ≥ 2 min were required for a 4 log10 viral reduction, respectively. Important variables were assessed using a random forest based on the percentage increases in mean square error (%IncMSE) and node purity (%IncNodePurity). Ethanol concentration was a more important variable with a higher %IncMSE and %IncNodePurity than contact time for the inactivation of enveloped and non-enveloped viruses with the available organic matter. Because specific guidelines for virus inactivation by ethanol are lacking, data analysis using machine learning is essential to gain insight from certain datasets. We provide new knowledge for determining guideline values related to the selection of ethanol concentration and contact time that effectively inactivate viruses.

Transoral robotic surgery (TORS) in Japan: procedures, advantages and current status.

Transoral robotic surgery (TORS), introduced by Weinstein et al. in 2005, has been widely adopted as a minimally invasive procedure, particularly for the treatment of patients with early stage oropharyngeal cancer. TORS is typically performed using the da Vinci Surgical System, similar to robot-assisted surgeries for other malignancies. The main difference between TORS and these other robot-assisted surgeries is that it is performed through the natural orifice of the mouth, which limits the surgical working space, and that it progresses from the lumen of the pharynx to the deeper tissues. The advantages of TORS are mainly due to the benefits of using the da Vinci Surgical System, such as three-dimensional high-definition images, magnification, multiple forceps articulation, tremor-stabilization function and motion scale function. To date, many big data and meta-analyses have shown that TORS is superior to conventional surgeries, such as open surgery, in terms of oncological outcomes, post-operative functionality and quality of life. In Japan, TORS is expected to spread across the country, as it has been covered by health insurance since April 2022. This review highlights the procedures of TORS, its unique aspects, its unparalleled advantages as a minimally invasive surgery for treating laryngeal and pharyngeal cancers, and its current status in Japan.