bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistence of sewage-associated genetic markers in advanced and conventional treated recycled water: implications for microbial source tracking in surface waters
Authors: Lobos Aldo E. , Brandt Amanda M. , Gallard-Góngora Javier F. , Korde Ruchi , Brodrick Eleanor , Harwood Valerie J. 
Published: June 2024

ABSTRACT

Sewage contamination of environmental waters is increasingly assessed by measuring DNA from sewage-associated microorganisms in microbial source tracking (MST) approaches. However, DNA can persist through wastewater treatment and reach surface waters when treated sewage/recycled water is discharged, which may falsely indicate pollution from untreated sewage. Recycled water discharged from an advanced wastewater treatment (AWT) facility into a Florida stream elevated the sewage-associated HF183 marker 1,000-fold, with a minimal increase in cultured
Escherichia coli
. The persistence of sewage-associated microorganisms was compared by qPCR in untreated sewage and recycled water from conventional wastewater treatment (CWT) and AWT facilities.
E. coli
(EC23S857) and sewage-associated markers HF183, H8, and viral crAssphage CPQ_056 were always detected in untreated sewage (6.5–8.7 log
10
GC/100 mL). Multivariate analysis found a significantly greater reduction of microbial variables via AWT vs CWT. Bacterial markers decayed ~4–5 log
10
through CWT, but CPQ_056 was ~100-fold more persistent. In AWT facilities, the log
10
reduction of all variables was ~5. In recycled water, bacterial marker concentrations were significantly correlated (
P
≤ 0.0136; tau ≥ 0.44); however, CPQ_056 was not correlated with any marker, suggesting varying drivers of decay. Concentrations of cultured
E. coli
carrying the H8 marker (EcH8) in untreated sewage were 5.24–6.02 log
10
CFU/100 mL, while no
E. coli
was isolated from recycled water. HF183 and culturable EcH8 were also correlated in contaminated surface waters (odds ratio
β
1
= 1.701). Culturable EcH8 has a strong potential to differentiate positive MST marker signals arising from treated (e.g., recycled water) and untreated sewage discharged into environmental waters.

IMPORTANCE
Genes in sewage-associated microorganisms are widely accepted indicators of sewage pollution in environmental waters. However, DNA persists through wastewater treatment and can reach surface waters when recycled water is discharged, potentially causing false-positive indications of sewage contamination. Previous studies have found that bacterial and viral sewage-associated genes persist through wastewater treatment; however, these studies did not compare different facilities or identify a solution to distinguish sewage from recycled water. In this study, we demonstrated the persistence of bacterial marker genes and the greater persistence of a viral marker gene (CPQ_056 of crAssphage) through varying wastewater treatment facilities. We also aim to provide a tool to confirm sewage contamination in surface waters with recycled water inputs. This work showed that the level of wastewater treatment affects the removal of microorganisms, particularly viruses, and expands our ability to identify sewage in surface waters.
Metagenome-assembled genomes of an acid-tolerant nitrifying bacterial community isolated from a bioreactor used in ammonium scrubbers at animal-rearing facilities
Authors: Manning Viola A. , Moore Phillip A. , Trippe Kristin M. 
Published: June 2024

ABSTRACT

We report 12 metagenome-assembled genomes (MAGS) of a bioreactor community of acid-tolerant nitrifying bacteria. The MAGS include autotrophs in the
Nitrospira
genus and heterotrophs in the Xanthomonadales, Ktedonobacterales, Cytophagales, Burkholderiales, and Hyphomicrobiales. These taxonomic and genomic data provide insights into the core community members required for nitrification at low pH.
Pediatric urinary tract infections caused by poultry-associated
Escherichia coli
Authors: Aziz Maliha , Davis Gregg S. , Park Daniel E. , Idris Azza H. , Sariya Sanjeev , Wang Yashan , Zerbonne Sarah , Nordstrom Lora , Weaver Brett , Statham Sally , Johnson Timothy J. , Campos Joseph , Castro-Nallar Eduardo , Crandall Keith A. , Wu Zhenke , Liu Cindy M. , DeBiasi Roberta L. , Price Lance B. 
Published: June 2024

ABSTRACT

Escherichia coli
is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic
E. coli
, which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic
E. coli
strains.
E. coli
urine isolates were collected from DC residents aged 2 months to 17 years from the Children’s National Medical Center Laboratory, 2013–2014. During the same period,
E. coli
isolates were collected from retail poultry products purchased from 15 sites throughout DC. A total of 52 urine and 56 poultry isolates underwent whole-genome sequencing, core genome phylogenetic analysis, and host-origin prediction by a Bayesian latent class model that incorporated data on the presence of mobile genetic elements (MGEs) among
E. coli
isolates from multiple vertebrate hosts. A total of 56 multilocus sequence types were identified among the isolates. Five sequence types—ST10, ST38, ST69, ST117, and ST131—were observed among both urine and poultry isolates. Using the Bayesian latent class model, we estimated that 19% (10/52) of the clinical
E. coli
isolates in our population were foodborne zoonotic strains. These data suggest that a substantial portion of pediatric UTIs in the Washington DC region may be caused by
E. coli
strains originating in food animals and likely transmitted via contaminated poultry meat.

IMPORTANCE

Escherichia coli
UTIs are a heavy public health burden and can have long-term negative health consequences for pediatric patients.
E. coli
has an extremely broad host range, including humans, chickens, turkeys, pigs, and cattle.
E. coli
derived from food animals is a frequent contaminant of retail meat products, but little is known about the risk these strains pose to pediatric populations. Quantifying the proportion of pediatric UTIs caused by food-animal-derived
E. coli
, characterizing the highest-risk strains, and identifying their primary reservoir species could inform novel intervention strategies to reduce UTI burden in this vulnerable population. Our results suggest that retail poultry meat may be an important vehicle for pediatric exposure to zoonotic
E. coli
strains capable of causing UTIs. Vaccinating poultry against the highest-risk strains could potentially reduce poultry colonization, poultry meat contamination, and downstream pediatric infections.
The nasal microbiota is a potential diagnostic biomarker for sepsis in critical care units
Authors: Tan XiLan , Liu Haiyue , Qiu Wen , Li Zewen , Ge Shuang , Luo Yuemei , Zeng Nianyi , Chen Manjun , Zhou Qiqi , Cai Shumin , Long Jun , Cen Zhongran , Su Jin , Zhou Hongwei , He Xiaolong 
Published: June 2024

ABSTRACT

This study aimed to characterize the composition of intestinal and nasal microbiota in septic patients and identify potential microbial biomarkers for diagnosis. A total of 157 subjects, including 89 with sepsis, were enrolled from the affiliated hospital. Nasal swabs and fecal specimens were collected from septic and non-septic patients in the intensive care unit (ICU) and Department of Respiratory and Critical Care Medicine. DNA was extracted, and the V4 region of the 16S rRNA gene was amplified and sequenced using Illumina technology. Bioinformatics analysis, statistical processing, and machine learning techniques were employed to differentiate between septic and non-septic patients. The nasal microbiota of septic patients exhibited significantly lower community richness (
P
= 0.002) and distinct compositions (
P
= 0.001) compared to non-septic patients.
Corynebacterium
,
Staphylococcus
,
Acinetobacter
, and
Pseudomonas
were identified as enriched genera in the nasal microbiota of septic patients. The constructed machine learning model achieved an area under the curve (AUC) of 89.08, indicating its efficacy in differentiating septic and non-septic patients. Importantly, model validation demonstrated the effectiveness of the nasal microecological diagnosis prediction model with an AUC of 84.79, while the gut microecological diagnosis prediction model had poor predictive performance (AUC = 49.24). The nasal microbiota of ICU patients effectively distinguishes sepsis from non-septic cases and outperforms the gut microbiota. These findings have implications for the development of diagnostic strategies and advancements in critical care medicine.

IMPORTANCE
The important clinical significance of this study is that it compared the intestinal and nasal microbiota of sepsis with non-sepsis patients and determined that the nasal microbiota is more effective than the intestinal microbiota in distinguishing patients with sepsis from those without sepsis, based on the difference in the lines of nasal specimens collected.
Seasonal human coronaviruses OC43, 229E, and NL63 induce cell surface modulation of entry receptors and display host cell-specific viral replication kinetics
Authors: Siragam Vinayakumar , Maltseva Mariam , Castonguay Nicolas , Galipeau Yannick , Srinivasan Mrudhula Madapuji , Soto Justino Hernandez , Dankar Samar , Langlois Marc-André 
Published: June 2024

ABSTRACT

The emergence of the COVID-19 pandemic prompted an increased interest in seasonal human coronaviruses. OC43, 229E, NL63, and HKU1 are endemic seasonal coronaviruses that cause the common cold and are associated with generally mild respiratory symptoms. In this study, we identified cell lines that exhibited cytopathic effects (CPE) upon infection by three of these coronaviruses and characterized their viral replication kinetics and the effect of infection on host surface receptor expression. We found that NL63 produced CPE in LLC-MK2 cells, while OC43 produced CPE in MRC-5, HCT-8, and WI-38 cell lines, while 229E produced CPE in MRC-5 and WI-38 by day 3 post-infection. We observed a sharp increase in nucleocapsid and spike viral RNA (vRNA) from day 3 to day 5 post-infection for all viruses; however, the abundance and the proportion of vRNA copies measured in the supernatants and cell lysates of infected cells varied considerably depending on the virus-host cell pair. Importantly, we observed modulation of coronavirus entry and attachment receptors upon infection. Infection with 229E and OC43 led to a downregulation of CD13 and GD3, respectively. In contrast, infection with NL63 and OC43 leads to an increase in ACE2 expression. Attempts to block entry of NL63 using either soluble ACE2 or anti-ACE2 monoclonal antibodies demonstrated the potential of these strategies to greatly reduce infection. Overall, our results enable a better understanding of seasonal coronaviruses infection kinetics in permissive cell lines and reveal entry receptor modulation that may have implications in facilitating co-infections with multiple coronaviruses in humans.

IMPORTANCE
Seasonal human coronavirus is an important cause of the common cold associated with generally mild upper respiratory tract infections that can result in respiratory complications for some individuals. There are no vaccines available for these viruses, with only limited antiviral therapeutic options to treat the most severe cases. A better understanding of how these viruses interact with host cells is essential to identify new strategies to prevent infection-related complications. By analyzing viral replication kinetics in different permissive cell lines, we find that cell-dependent host factors influence how viral genes are expressed and virus particles released. We also analyzed entry receptor expression on infected cells and found that these can be up- or down-modulated depending on the infecting coronavirus. Our findings raise concerns over the possibility of infection enhancement upon co-infection by some coronaviruses, which may facilitate genetic recombination and the emergence of new variants and strains.
QED-vacuum response and Cherenkov radiated energy in non-linear and Lorentz-symmetry violating scenarios
Authors: Gaete Patricio , Helayël-Neto José Abdalla 
Published: June 2024

AbstractWe explore the physical effects of non-linear electrodynamic coupled to parameters that indicate a violation of Lorentz-symmetry breaking (LSV). To do this, we consider a general non-linear photonic Lagrangian that is coupled to the Carroll–Field–Jackiw’s model (CFJ). Our investigation reveals how the constitutive properties of the vacuum and wave propagation are affected by the interference of the parameters LSV with the specific non-linear electrodynamic model under consideration. We also analyze the refractive indices for this new medium characterized by the coupling between non-linearities and the operators that carry the LSV message. Our results show that the QED-vacuum responds with birefringence and a dispersive propagation of waves. After that, we study the electromagnetic radiation produced by a moving charged particle interacting with this new medium. Our analysis shows that the emitted radiation is similar (resembles) to that of the Cherenkov effect for certain intensities of background magnetic fields. Finally, we compute the static potential profile within the framework of the gauge-invariant, but path-dependent, variables formalism. We find a logarithmic correction to the usual static Coulomb potential stemming from the LSV parameter, and there are also corrections due to the non-linearity. However, the logarithm behavior disappears whenever the LSV parameter is switched off.
Analyzing Russia’s propaganda tactics on Twitter using mixed methods network analysis and natural language processing: a case study of the 2022 invasion of Ukraine
Authors: Alieva Iuliia , Kloo Ian , Carley Kathleen M. 
Published: June 2024

AbstractThis paper examines Russia’s propaganda discourse on Twitter during the 2022 invasion of Ukraine. The study employs network analysis, natural language processing (NLP) techniques, and qualitative analysis to identify key communities and narratives associated with the prevalent and damaging narrative of “fascism/Nazism” in discussions related to the invasion. The paper implements a methodological pipeline to identify the main topics, and influential actors, as well as to examine the most impactful messages in spreading this disinformation narrative. Overall, this research contributes to the understanding of propaganda dissemination on social media platforms and provides insights into the narratives and communities involved in spreading disinformation during the invasion.
Neuron Sensitivity-Guided Test Case Selection
Authors: Huang Dong , Bu Qingwen , Fu Yichao , Qing Yuhao , Xie Xiaofei , Chen Junjie , Cui Heming 
Published: June 2024

Deep neural networks (DNNs) have been widely deployed in software to address various tasks (e.g., autonomous driving, medical diagnosis). However, they can also produce incorrect behaviors that result in financial losses and even threaten human safety. To reveal and repair incorrect behaviors in DNNs, developers often collect rich, unlabeled datasets from the natural world and label them to test DNN models. However, properly labeling a large number of datasets is a highly expensive and time-consuming task.
To address the above-mentioned problem, we propose neuron sensitivity-guided test case selection (NSS), which can reduce the labeling time by selecting valuable test cases from unlabeled datasets. NSS leverages the information of the internal neuron induced by the test cases to select valuable test cases, which have high confidence in causing the model to behave incorrectly. We evaluated NSS with four widely used datasets and four well-designed DNN models compared to the state-of-the-art (SOTA) baseline methods. The results show that NSS performs well in assessing the probability of failure triggering in test cases and in the improvement capabilities of the model. Specifically, compared to the baseline approaches, NSS achieves a higher fault detection rate (e.g., when selecting 5% of the test cases from the unlabeled dataset in the MNIST and LeNet1 experiment, NSS can obtain an 81.8% fault detection rate, which is a 20% increase compared with SOTA baseline strategies).
Tissue-Free Liquid Biopsies Combining Genomic and Methylation Signals for Minimal Residual Disease Detection in Patients with Early Colorectal Cancer from the UK TRACC Part B Study
Authors: Slater Susanna , Bryant Annette , Aresu Maria , Begum Ruwaida , Chen Hsiang-Chi , Peckitt Clare , Lazaro-Alcausi Retchel , Carter Paul , Anandappa Gayathri , Khakoo Shelize , Melcher Lucinda , Potter Vanessa , Marti Francisca M. , Huang Joesph , Branagan Graham , George Nicol , Abulafi Muti , Duff Sarah , Raja Ashraf , Gupta Ashish , West Nicholas , Bucheit Leslie , Rich Thereasa , Chau Ian , Cunningham David , Starling Naureen ,   for the TRACC Part B trial investigators
Published: June 2024

Abstract

Purpose:
The absence of postoperative circulating tumor DNA (ctDNA) identifies patients with resected colorectal cancer (CRC) with low recurrence risk for adjuvant chemotherapy (ACT) de-escalation. Our study presents the largest resected CRC cohort to date with tissue-free minimal residual disease (MRD) detection.

Experimental Design:
TRACC (tracking mutations in cell-free tumor DNA to predict relapse in early colorectal cancer) included patients with stage I to III resectable CRC. Prospective longitudinal plasma collection for ctDNA occurred pre- and postsurgery, post-ACT, every 3 months for year 1 and every 6 months in years 2 and 3 with imaging annually. The Guardant Reveal assay evaluated genomic and methylation signals. The primary endpoint was 2-year recurrence-free survival (RFS) by postoperative ctDNA detection (NCT04050345).

Results:
Between December 2016 and August 2022, 1,203 were patients enrolled. Plasma samples (n = 997) from 214 patients were analyzed. One hundred forty-three patients were evaluable for the primary endpoint; 92 (64.3%) colon, 51 (35.7%) rectal; two (1.4%) stage I, 64 (44.8%) stage II, and 77 (53.8%) stage III. Median follow-up was 30.3 months (95% CI, 29.5–31.3). Two-year RFS was 91.1% in patients with ctDNA not detected postoperatively and 50.4% in those with ctDNA detected [HR, 6.5 (2.96–14.5); P &lt; 0.0001]. Landmark negative predictive value (NPV) was 91.2% (95% CI, 83.9–95.9). Longitudinal sensitivity and specificity were 62.1% (95% CI, 42.2–79.3) and 85.9% (95% CI, 78.9–91.3), respectively. The median lead time from ctDNA detection to radiological recurrence was 7.3 months (IQR, 3.3–12.5; n = 9).

Conclusions:
Tissue-free MRD detection with longitudinal sampling predicts recurrence in patients with stage I to III CRC without the need for tissue sequencing. The UK TRACC Part C study is currently investigating the potential for ACT de-escalation in patients with undetectable postoperative ctDNA, given the high NPV indicating a low likelihood of residual disease.
A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier
Authors: Song Yi , Boerner Thomas , Drill Esther , Shin Paul , Kumar Sandeep , Sigel Carlie , Cercek Andrea , Kemeny Nancy , Abou-Alfa Ghassan , Iacobuzio-Donahue Christine , Cowzer Darren , Schultz Nikolaus , Walch Henry , Balachandran Vinod , Groot Koerkamp Bas , Kingham Peter , Soares Kevin , Wei Alice , D’Angelica Michael , Drebin Jeffrey , Chandwani Rohit , Harding James J. , Jarnagin William 
Published: June 2024

Abstract

Purpose:
Intrahepatic cholangiocarcinoma (IHC) is a heterogeneous tumor. The hidden-genome classifier, a supervised machine learning–based algorithm, was used to quantify tumor heterogeneity and improve classification.

Experimental Design:
A retrospective review of 1,370 patients with IHC, extrahepatic cholangiocarcinoma (EHC), gallbladder cancer (GBC), hepatocellular carcinoma (HCC), or biphenotypic tumors was conducted. A hidden-genome model classified 527 IHC based on genetic similarity to EHC/GBC or HCC. Genetic, histologic, and clinical data were correlated.

Results:
In this study, 410 IHC (78%) had &gt;50% genetic homology with EHC/GBC; 122 (23%) had &gt;90% homology (“biliary class”), characterized by alterations of KRAS, SMAD4, and CDKN2A loss; 117 IHC (22%) had &gt;50% genetic homology with HCC; and 30 (5.7%) had &gt;90% homology (“HCC class”), characterized by TERT alterations. Patients with biliary- versus non-biliary-class IHC had median overall survival (OS) of 1 year (95% CI, 0.77, 1.5) versus 1.8 years (95% CI, 1.6, 2.0) for unresectable disease and 2.4 years (95% CI, 2.1, NR) versus 5.1 years (95% CI, 4.8, 6.9) for resectable disease. Large-duct IHC (n = 28) was more common in the biliary class (n = 27); the HCC class was composed mostly of small-duct IHC (64%, P = 0.02). The hidden genomic classifier predicted OS independent of FGFR2 and IDH1 alterations. By contrast, the histology subtype did not predict OS.

Conclusions:
IHC genetics form a spectrum with worse OS for tumors genetically aligned with EHC/GBC. The classifier proved superior to histologic subtypes for predicting OS independent of FGFR2 and IDH1 alterations. These results may explain the differential treatment responses seen in IHC and may direct therapy by helping stratify patients in future clinical trials.
Alcohol Intake and Risk of Hypertension: A Systematic Review and Dose-Response Meta-Analysis of Nonexperimental Cohort Studies
Authors: Cecchini Marta , Filippini Tommaso , Whelton Paul K. , Iamandii Inga , Di Federico Silvia , Boriani Giuseppe , Vinceti Marco 
Published: June 2024

BACKGROUND:
Alcohol consumption has been associated with higher blood pressure and an increased risk of hypertension. However, the possible exposure thresholds and effect-modifiers are uncertain.

METHODS:
We assessed the dose-response relationship between usual alcohol intake and hypertension incidence in nonexperimental cohort studies. After performing a systematic literature search through February 20, 2024, we retrieved 23 eligible studies. We computed risk ratios and 95% CI of hypertension incidence using a nonlinear meta-analytic model based on restricted cubic splines, to assess the dose-response association with alcohol consumption.

RESULTS:
We observed a positive and almost linear association between alcohol intake and hypertension risk with risk ratios of 0.89 (0.84–0.94), 1.11 (1.07–1.15), 1.22 (1.14–1.30), and 1.33 (1.18–1.49) for 0, 24, 36 and 48 g/d, respectively, using 12 g alcohol/d as the reference value. In sex-specific analyses, the association was almost linear in men over the entire range of exposure but only observed above 12 g/d in women, although with a steeper association at high levels of consumption compared with men. The increased risk of hypertension above 12 to 24 g alcohol/d was similar in Western and Asian populations and considerably greater in White than in Black populations, mainly due to the positive association in women at moderate-to-high intake.

CONCLUSIONS:
Overall, our results lend support to a causal association between alcohol consumption and risk of hypertension, especially above an alcohol intake of 12 g/d, and are consistent with recommendations to avoid or limit alcohol intake. Sex and ethnicity appear to be major effect-modifiers of such association.