Prognostic nomograms for young breast cancer: A retrospective study based on the SEER and METABRIC databases.

Background: Young breast cancer (YBC) is a subset of breast cancer that is often more aggressive, but less is known about its prognosis. In this study, we aimed to generate nomograms to predict the overall survival (OS) and breast cancer-specific survival (BCSS) of YBC patients. Methods: Data of women diagnosed with YBC between 2010 and 2020 were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. The patients were randomly allocated into a training cohort (n = 15,227) and internal validation cohort (n = 6,526) at a 7:3 ratio. With the Cox regression models, significant prognostic factors were identified and used to construct 3-, 5-, and 10-year nomograms of OS and BCSS. Data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) database were used as an external validation cohort (n = 90). Results: We constructed nomograms incorporating 10 prognostic factors for OS and BCSS. These nomograms demonstrated strong predictive accuracy for OS and BCSS in the training cohort, with C-indexes of 0.806 and 0.813, respectively. The calibration curves verified that the nomograms have good prediction accuracy. Decision curve analysis demonstrated their practical clinical value for predicting YBC patient survival rates. Additionally, we provided dynamic nomograms to improve the operability of the results. The risk stratification ability assessment also showed that the OS and BCSS rates of the low-risk group were significantly better than those of the high-risk group. Conclusions: Here, we generated and validated more comprehensive and accurate OS and BCSS nomograms than models previously developed for YBC. These nomograms can help clinicians evaluate patient prognosis and make clinical decisions.

Wastewater surveillance provides 10-days forecasting of COVID-19 hospitalizations superior to cases and test positivity: A prediction study.

Background: The public health response to COVID-19 has shifted to reducing deaths and hospitalizations to prevent overwhelming health systems. The amount of SARS-CoV-2 RNA fragments in wastewater are known to correlate with clinical data including cases and hospital admissions for COVID-19. We developed and tested a predictive model for incident COVID-19 hospital admissions in New York State using wastewater data. Methods: Using county-level COVID-19 hospital admissions and wastewater surveillance covering 13.8 million people across 56 counties, we fit a generalized linear mixed model predicting new hospital admissions from wastewater concentrations of SARS-CoV-2 RNA from April 29, 2020 to June 30, 2022. We included covariates such as COVID-19 vaccine coverage in the county, comorbidities, demographic variables, and holiday gatherings. Findings: Wastewater concentrations of SARS-CoV-2 RNA correlated with new hospital admissions per 100,000 up to ten days prior to admission. Models that included wastewater had higher predictive power than models that included clinical cases only, increasing the accuracy of the model by 15%. Predicted hospital admissions correlated highly with observed admissions (r = 0.77) with an average difference of 0.013 hospitalizations per 100,000 (95% CI = [0.002, 0.025]). Interpretation: Using wastewater to predict future hospital admissions from COVID-19 is accurate and effective with superior results to using case data alone. The lead time of ten days could alert the public to take precautions and improve resource allocation for seasonal surges.

Electro-Fenton and Induced Electro-Fenton as Versatile Wastewater Treatment Processes for Decontamination and Nutrient Removal without Byproduct Formation.

It is a long-pursued goal to develop electrified water treatment technology that can remove contaminants without byproduct formation. This study unveiled the overlooked multifunctionality of electro-Fenton (EF) and induced EF (I-EF) processes to remove organics, pathogens, and phosphate in one step without halogenated byproduct formation. The EF and I-EF processes used a sacrificial anode or an induced electrode to generate Fe2+ to activate H2O2 produced from a gas diffusion cathode fed by naturally diffused air. We used experimental and kinetic modeling approaches to illustrate that the •OH generation and radical speciation during EF were not impacted by chloride. More importantly, reactive chlorine species were quenched by H2O2, which eliminated the formation of halogenated byproducts. When applied in treating septic wastewater, the EF process removed >80% COD, >50% carbamazepine (as representative trace organics), and >99% phosphate at a low energy consumption of 0.37 Wh/L. The EF process also demonstrated broad-spectrum disinfection activities in removing and inactivating Escherichia coli, Enterococcus durans, and model viruses MS2 and Phi6. In contrast to electrochemical oxidation (EO) that yielded mg/L level byproducts to achieve the same degree of treatment, EF did not generate byproducts (chlorate, perchlorate, trihalomethanes, and haloacetic acids). The I-EF carried over all the advantages of EF and exhibited even faster kinetics in disinfection and carbamazepine removal with 50-80% less sludge production. Last, using septic wastewater treatment as a technical niche, we demonstrated that iron sludge formation is predictable and manageable, clearing roadblocks toward on-site water treatment applications.

Robust Performance of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method.

The sequencing of human virus genomes from wastewater samples is an efficient method for tracking viral transmission and evolution at the community level. However, this requires the recovery of viral nucleic acids of high quality. We developed a reusable tangential-flow filtration system to concentrate and purify viruses from wastewater for genome sequencing. A pilot study was conducted with 94 wastewater samples from four local sewersheds, from which viral nucleic acids were extracted, and the whole genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was sequenced using the ARTIC V4.0 primers. Our method yielded a high probability (0.9) of recovering complete or near-complete SARS-CoV-2 genomes (>90% coverage at 10× depth) from wastewater when the COVID-19 incidence rate exceeded 33 cases per 100 000 people. The relative abundances of sequenced SARS-CoV-2 variants followed the trends observed from patient-derived samples. We also identified SARS-CoV-2 lineages in wastewater that were underrepresented or not present in the clinical whole-genome sequencing data. The developed tangential-flow filtration system can be easily adopted for the sequencing of other viruses in wastewater, particularly those at low concentrations.

Reactivity of Viral Nucleic Acids with Chlorine and the Impact of Virus Encapsidation.

Free chlorine disinfection is widely applied to inactivate viruses by reacting with their biomolecules, which include nucleic acids, proteins, and lipids. Knowing the reactivities of viral genomes with free chlorine and the protection that encapsidation provides would ultimately help predict virus susceptibility to the disinfectant. The relative reactivities of different viral genome types and the impact of viral higher order structure with free chlorine are poorly characterized. Here, we studied the reactivity of viral genomes representing four genome types from virus particles with diverse structures, namely, (+)ssRNA (MS2), dsRNA (φ6), ssDNA (φX174), and dsDNA (T3) with free chlorine. We compared the reactivities of these viral nucleic acids when they were suspended in phosphate buffer solutions (naked forms) and when they were in the native virus particles (encapsidated forms). The reactivities of nucleic acids were tracked by polymerase chain reaction (PCR)-based assays. The naked dsDNA of T3 was the least reactive with free chlorine, with an average second order rate constant normalized by the number of bases in the measured regions (in M-1 s-1 b-1) that was 34×, 65×, and 189× lower than those of the dsRNA of φ6, ssRNA of MS2, and ssDNA of φX174, respectively. Moreover, different regions in the ssRNA genome of MS2 and the dsRNA genome of φ6 exhibited statistically different reaction kinetics. The genomes within virus particles reacted slower than the naked genomes overall, but the extent of these differences varied among the four viruses. The results on viral nucleic acid reactivity help explain different susceptibilities of viruses to inactivation by free chlorine and also provide a valuable comparison of the susceptibilities of different nucleic acids to oxidants.

Central versus ambulatory blood pressure for predicting mortality and cardiovascular events in hemodialysis patients: a multicenter cohort study.

OBJECTIVE: Studies in the general population suggest that central blood pressure (BP) may be superior to peripheral BP in risk assessment. Although ambulatory brachial BP is recognized as the most reliable BP measurement in the dialysis population, there is no comparison of office central BP with ambulatory BP regarding risk stratification in these patients. METHODS: In a multicenter prospective study of dialysis patients, central BP was measured noninvasively on a midweek nondialysis day, with interdialytic ambulatory BP and predialysis BP also collected. The primary outcomes were a composite of major adverse cardiovascular events (MACE) and all-cause mortality. Agreement between central and ambulatory BP was assessed using Cohen's Kappa index and Bland--Altman plot. Linear and nonlinear Cox regression models were used to determine the association of BP parameters with outcomes. RESULTS: A total of 368 patients were recruited and 366 underwent central BP measurement. Central BP had a moderate agreement with ambulatory BP in defining hypertension (κ = 0.42) with wide limits of agreement in Bland--Altman analysis. After a median follow-up of 51.5 months, central pulse pressure, ambulatory SBP and ambulatory pulse pressure were associated with all-cause mortality, whereas all BP parameters, except for predialysis DBP, were significant predictors of MACE. However, whenever evaluated in a stepwise variable selection Cox model, only ambulatory pulse pressure, but not any central BP, was determined as the best candidate for prediction of both all-cause mortality and MACE. Nonlinear Cox models revealed no significant nonlinear trend of the association between central BP and outcomes. CONCLUSION: Central BP is predictive of all-cause mortality and cardiovascular events in dialysis patients but its prognostic value does not outperform ambulatory peripheral BP. Our data support the superiority of ambulatory BP in the dialysis population.

Opportunistic pathogens exhibit distinct growth dynamics in rainwater and tap water storage systems.

Opportunistic pathogens (OPs) are emerging microbial contaminants in engineered water systems, yet their growth potential in rainwater systems has not been evaluated. The purpose of this study was to compare the growth dynamics of bacterial OPs and related genera (Pseudomonas aeruginosa, Legionella spp., L. pneumophila, Mycobacterium spp., and M. avium), two amoebal hosts (Acanthamoeba spp. and Vermamoeba vermiformis), and the fecal indicator Escherichia coli in simulated rainwater and tap water storage systems (SWSSs). Quantitative polymerase chain reaction (q-PCR) analysis of target microorganisms in SWSS influents and effluents demonstrated that P. aeruginosa and Legionella thrived in rainwater, but not in tap water. V. vermiformis proliferated in both rainwater and tap water polyvinyl chloride (PVC) SWSSs, while mycobacteria were largely absent in rainwater SWSSs. Tank materials exerted stronger influence on target microorganisms in rainwater SWSSs relative to tap water SWSSs, with species-specific responses noted in bulk water and biofilm. For instance, P. aeruginosa and V. vermiformis had the highest gene copy numbers in PVC rainwater SWSS effluents and biofilm, while Legionella peaked in stainless steel rainwater SWSS effluents and PVC rainwater SWSS biofilm. These results highlighted the OP contamination risks in rainwater storage systems and provided insights into rainwater system design and operation in terms of OP control.

Pyruvate kinase M2 mediates fibroblast proliferation to promote tubular epithelial cell survival in acute kidney injury.

Acute kidney injury (AKI) is a devastating condition with high morbidity and mortality rates. The pathological features of AKI are tubular injury, infiltration of inflammatory cells, and impaired vascular integrity. Pyruvate kinase is the final rate-limiting enzyme in the glycolysis pathway. We previously showed that pyruvate kinase M2 (PKM2) plays an important role in regulating the glycolytic reprogramming of fibroblasts in renal interstitial fibrosis. The present study aimed to determine the role of PKM2 in fibroblast activation during the pathogenesis of AKI. We found increased numbers of S100A4 positive cells expressing PKM2 in renal tissues from mice with AKI induced via folic acid or ischemia/reperfusion (I/R). The loss of PKM2 in fibroblasts impaired fibroblast proliferation and promoted tubular epithelial cell death including apoptosis, necroptosis, and ferroptosis. Mechanistically, fibroblasts produced less hepatocyte growth factor (HGF) in response to a loss of PKM2. Moreover, in two AKI mouse models, fibroblast-specific deletion of PKM2 blocked HGF signal activation and aggravated AKI after it was induced in mice via ischemia or folic acid. Fibroblast proliferation mediated by PKM2 elicits pro-survival signals that repress tubular cell death and may help to prevent AKI progression. Fibroblast activation mediated by PKM2 in AKI suggests that targeting PKM2 expression could be a novel strategy for treating AKI.

A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer.

Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.

Effect of Flow Configuration on Nitrifiers in Biological Activated Carbon Filters for Potable Water Production.

Up-flow biological activated carbon (BAC) filters have been empirically employed in drinking water treatment plants (DWTPs) to address the challenges of its down-flow counterparts (e.g., high head loss and insufficient use of BAC beds), yet their performances and mechanisms toward ammonia removal are not fully evaluated. This study characterized the occurrence, distribution, and diversities of nitrifiers in up-flow and down-flow BAC filters by investigating 18 full-scale drinking water treatment trains in different geographic locations. Quantitative polymerase chain reaction analysis of gene markers of target microorganisms demonstrated higher numbers of total bacteria, ammonia-oxidizing bacteria (AOB), and Nitrospira in the up-flow filters relative to the down-flow filters (P < 0.05), implying enhanced biological activities and nitrification potential within up-flow filters. The dominance of ammonia-oxidizing archaea (AOA) over AOB (i.e., 1.3-4.0 log10 gene copies higher) in 17 BAC filters illustrated the critical role of AOA in drinking water nitrification. Stratification of biomass was mainly found in the down-flow filters rather than the up-flow filters, suggesting better mixing of filter media across up-flow filter beds. Analysis of similarity results revealed that the AOA and Nitrospira community compositions were mainly affected by water sources and locations (P < 0.05) but not flow configurations. These results provide insight into nitrification mechanisms in BAC filters with different flow configurations in real-world DWTPs.

A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni.

The symptoms of infectious diarrheal disease are mediated by a combination of a pathogen's virulence factors and the host immune system. Campylobacter jejuni is the leading bacterial cause of diarrhea worldwide due to its near-ubiquitous zoonotic association with poultry. One of the outstanding questions is to what extent the bacteria are responsible for the diarrheal symptoms via intestinal cell necrosis versus immune cell initiated tissue damage. To determine the stepwise process of inflammation that leads to diarrhea, we used a piglet ligated intestinal loop model to study the intestinal response to C. jejuni. Pigs were chosen due to the anatomical similarity between the porcine and the human intestine. We found that the abundance of neutrophil related proteins increased in the intestinal lumen during C. jejuni infection, including proteins related to neutrophil migration (neutrophil elastase and MMP9), actin reorganization (Arp2/3), and antimicrobial proteins (lipocalin-2, myeloperoxidase, S100A8, and S100A9). The appearance of neutrophil proteins also corresponded with increases of the inflammatory cytokines IL-8 and TNF-α. Compared to infection with the C. jejuni wild-type strain, infection with the noninvasive C. jejuni ∆ciaD mutant resulted in a blunted inflammatory response, with less inflammatory cytokines and neutrophil markers. These findings indicate that intestinal inflammation is driven by C. jejuni virulence and that neutrophils are the predominant cell type responding to C. jejuni infection. We propose that this model can be used as a platform to study the early immune events during infection with intestinal pathogens.

Aloperine suppresses LPS-induced macrophage activation through inhibiting the TLR4/NF-κB pathway.

OBJECTIVE: The currently available anti-inflammatory drugs often cause diverse side effects with long-term use. Exploring anti-inflammatory drugs with better efficacy and lower toxicity presents an ongoing challenge. Aloperine is an alkaloid extracted from the leaves and seeds of Sophora alopecuroides L. However, the anti-inflammatory effects of Aloperine have not been fully elucidated. This study aimed to investigate whether Aloperine suppresses lipopolysaccharide (LPS)-induced inflammatory responses in RAW264.7 macrophages. METHODS: RAW264.7 macrophages were stimulated with LPS (1 µg/mL) in the presence or absence of Aloperine (50 and 100 µM). mRNA expression was measured by real-time PCR, and protein expression was assessed by western blot analysis. The secretion of pro-inflammatory cytokines was measured by ELISA. The levels of nitric oxide (NO) and reactive oxygen species (ROS) were measured by staining. The transcriptional activity of NF-κB was assayed by a luciferase activity assay. RESULTS: The results proved that Aloperine inhibited the expression of LPS-induced pro-inflammatory cytokines [tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and interleukin-17A (IL-17A)] in macrophages. Treatment with Aloperine inhibited NO production through suppressing inducible nitric oxide synthase (iNOS) expression and the secretion of prostaglandin E2 (PGE2) by inhibiting cyclooxygenase 2 (COX-2) expression. Aloperine prevented LPS-induced oxidative stress by reducing the generation of ROS. Furthermore, aloperine significantly reduced Toll-like receptor 4 (TLR4) and myeloid differentiation factor (Myd-88) levels and prevented the nuclear translocation of nuclear factor-κB (NF-κB) in LPS-treated macrophages. CONCLUSION: Taken together, our findings show that Aloperine could suppress LPS-induced macrophage activation by inhibiting the TLR4/Myd-88/NF-κB pathway.

Tubule-derived lactate is required for fibroblast activation in acute kidney injury.

Acute kidney injury (AKI) is a highly prevalent medical syndrome associated with high mortality and morbidity. Several types of cells, including epithelial cells, vascular endothelial cells, pericytes, and macrophages, participate in the development of AKI. Recently, renal fibroblasts were found to play an important role in the regulation of tubular injury, repair, and recovery after AKI. However, the mechanisms underlying fibroblast activation and proliferation during the progression of AKI remain unclear. In the present study, we found many activated myofibroblasts located in the renal interstitium with an abundance of extracellular matrix deposition following folic acid-induced AKI. The proliferative pattern of tubular epithelial cells and interstitial cells following acute injury was different, indicating that the proliferation of fibroblasts followed the proliferation of tubular epithelial cells. Furthermore, we observed that proliferative tubular epithelial cells preferred aerobic glycolysis as the dominating metabolic pathway in the progression of AKI. Lactate generated from injured tubules was taken up by interstitial fibroblasts in the later stages of AKI, which induced fibroblast activation and proliferation in vitro. Early inhibition of lactate production in tubules by glycolytic inhibitors suppressed fibroblast activation after folic acid-induced injury. Collectively, these results support the important role of fibroblasts in the development of AKI and suggest that lactate produced by glycolysis in tubular epithelial cells is a novel regulator of fibroblast activation and proliferation.

Nucleic Acid Photolysis by UV254 and the Impact of Virus Encapsidation.

Determining the influence of higher order structure on UVC photolysis will help inform predictions of nucleic acid fate and microorganism inactivation. We measured the direct UV254 photolysis kinetics of four model viral genomes composed of single-stranded and double-stranded RNA (ssRNA and dsRNA, respectively), as well as single-stranded and double-stranded DNA (ssDNA and dsDNA, respectively), in ultrapure water, in phosphate buffered saline (PBS), and encapsidated in their native virus particles. The photolysis rate constants of naked nucleic acids measured by qPCR (RT-qPCR for RNA) and normalized by the number of bases measured in a particular sequence exhibited the following trend: ssDNA > ssRNA ≈ dsDNA > dsRNA. In PBS, naked ssRNA bases reacted, on average, 24× faster than the dsRNA bases, whereas naked ssDNA bases reacted 4.3× faster than dsDNA bases. Endogenous indirect photolysis involving 1O2 and ·OH was ruled out as a major contributing factor in the reactions. A comparison of our measured rate constants with rate constants reported in the literature shows a general agreement among the nucleic acid UV254 direct photolysis kinetics. Our results underscore the high resistance of dsRNA to UVC photolysis and demonstrate the role that nucleic acid structure and solution chemistry play in photoreactivity.

Reactivity of Enveloped Virus Genome, Proteins, and Lipids with Free Chlorine and UV254.

The survivability of viruses in natural and engineered systems impacts public health. Inactivation mechanisms in the environment have been described for nonenveloped viruses, but it remains unclear how the membrane layer of enveloped viruses influences inactivation. We applied molecular tools and high-resolution mass spectrometry to measure reactions in the genome, proteins, and lipids of enveloped Pseudomonas phage Phi6 during inactivation by free chlorine and UV254. Free chlorine readily penetrated the lipid membrane to react with proteins in the nucleocapsid and polymerase complex. The most reactive Phi6 peptides were approximately 150 times more reactive with free chlorine than the most reactive peptides reported in nonenveloped coliphage MS2. The inactivation kinetics of Phi6 by UV254 was comparable with those of nonenveloped adenovirus and coliphage MS2 and were driven by UV254 reactions with viral genomes. Our research identifies molecular features of an enveloped virus that are susceptible to chemical oxidants or UV radiation. Finally, the framework developed in the manuscript for studying molecular reactivities of Phi6 can be adopted to investigate enveloped virus survivability under various environmental conditions.

Survivability, Partitioning, and Recovery of Enveloped Viruses in Untreated Municipal Wastewater.

Many of the devastating pandemics and outbreaks of the 20th and 21st centuries have involved enveloped viruses, including influenza, HIV, SARS, MERS, and Ebola. However, little is known about the presence and fate of enveloped viruses in municipal wastewater. Here, we compared the survival and partitioning behavior of two model enveloped viruses (MHV and ϕ6) and two nonenveloped bacteriophages (MS2 and T3) in raw wastewater samples. We showed that MHV and ϕ6 remained infective on the time scale of days. Up to 26% of the two enveloped viruses adsorbed to the solid fraction of wastewater compared to 6% of the two nonenveloped viruses. Based on this partitioning behavior, we assessed and optimized methods for recovering enveloped viruses from wastewater. Our optimized ultrafiltration method resulted in mean recoveries (±SD) of 25.1% (±3.6%) and 18.2% (±9.5%) for the enveloped MHV and ϕ6, respectively, and mean recoveries of 55.6% (±16.7%) and 85.5% (±24.5%) for the nonenveloped MS2 and T3, respectively. A maximum of 3.7% of MHV and 2% of MS2 could be recovered from the solids. These results shed light on the environmental fate of an important group of viruses and the presented methods will enable future research on enveloped viruses in water environments.