bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective analysis of antimicrobial resistance associated with bovine respiratory disease
Authors: Kos Daniel , Jelinski Murray , Ruzzini Antonio 
Published: February 2025

ABSTRACT

The administration and utility of antibiotics to control and treat bovine respiratory disease (BRD) in beef cattle feedlots is a growing concern. Antimicrobial resistance (AMR) among BRD-associated bacterial pathogens has been the subject of cultivation-dependent and cultivation-independent surveillance. Bacterial genome sequencing and metagenomic approaches facilitate the characterization of AMR in the beef industry; however, the current collection of cattle-associated AMR research programs lack connections to each other. A more integrated view of how antimicrobial use (AMU) is related to resistance at a gene level is needed. We sought to establish a catalog of commonly observed AMR genes (ARGs) in opportunistic bacterial pathogens that contribute to BRD using publicly available data sets that were generated by the scientific community with and without AMU in mind. The presence of these clinically relevant ARGs appeared to differ by geography. Greater sampling in North America facilitated the generation of a list of ARGs often encoded by
Mannheimia haemolytica
and
Pasteurella multocida
. Detection of clinically relevant ARGs in shotgun metagenomes of cattle-associated and accessible feedlot samples such as water, soil, and feces was possible but limited by relative sequence read abundance. An exception was the tylosin esterase-encoding gene
estT
, which is among the most frequently observed ARGs in
M. haemolytica
and feedlot-related metagenomic data sets. Finally, by re-evaluating studies on the impact of AMU on AMR in beef production systems, we show that conventional practices, including in-feed antibiotic use, increase the relative abundance of ARGs in animal-derived samples.

IMPORTANCE
This retrospective analysis delivers a list of ARGs found in opportunistic pathogens that contribute to BRD. The high incidence of BRD in North America is linked to the origin and implementation of metaphylaxis to mitigate detrimental animal losses at feedlots. Notably, ARGs commonly observed in these pathogens isolated in North America were not conserved across the globe, underscoring the relationship between regional AMU and AMR. A positive relationship was also observed between the relative abundance of ARGs in cattle-associated metagenomes with greater exposure to antibiotics. Overall, this analysis should help to guide future surveillance efforts and experimental designs to more directly evaluate the impacts of feedlot practices on AMR.
Polysulfides promote protein disulfide bond formation in microorganisms growing under anaerobic conditions
Authors: Xin Yuping , Wang Qingda , Yang Jianming , Wu Xiaohua , Xia Yongzhen , Xun Luying , Liu Huaiwei 
Published: February 2025

ABSTRACT

Polysulfides commonly occur in anaerobic, microbial active environments, where they play key roles in sulfur cycling and redox transformations. Anaerobic survival of microorganisms requires the formation of protein disulfide bond (DSB). The relationship between polysulfides and anaerobic DSB formation has not been studied so far. Herein, we discovered that polysulfides can efficiently mediate protein DSB formation of microorganisms under anaerobic conditions. We used polysulfides to treat proteins, including roGFP2, Trx1, and DsbA, under anaerobic conditions and found that all three proteins formed intramolecular DSB
in vitro
. Under anaerobic conditions,
Escherichia coli
Δ
dsbB
displayed reduced growth and decreased intracellular protein DSB levels, but polysulfide treatment restored both growth and DSB content. Similarly, polysulfide treatment of
E. coli
Δ
dsbA
promoted periplasmic roGFP2 DSB formation and recovered growth under anaerobic conditions. Furthermore, treating
Schizosaccharomyces pombe
and
Cupriavidus pinatubonensis
JMP134 with polysulfides increased their intracellular protein DSB content. Collectively, these findings demonstrate that polysulfides can promote DSB formation independently of known enzymatic DSB-mediated systems and the presence of oxygen, thereby benefiting the survival of microorganisms in anaerobic habitats.

IMPORTANCE

How polysulfides enhance the adaption of microorganisms to anaerobic environments remains unclear. Our study reveals that polysulfides efficiently facilitate protein DSB formation under anaerobic conditions. Polysulfides contain zero-valent sulfur atoms (S
0
), which can be transferred to the thiol group of cysteine residue. This S
0
atom then accepts two electrons from two cysteine residues and is reduced to H
2
S, leaving the two cysteines linked by a disulfide bond. Anaerobic growth of microorganisms benefits from the formation of DSB. These findings pave the way for a deeper understanding of the intricate relationship between polysulfides and microorganisms in various environmental contexts.
Hands-on learning for probiotic quality assessment: enhancing microbiology education through applied microbial counting techniques
Authors: Mangieri Nicola , Arioli Stefania , Russo Pasquale , Mora Diego 
Published: February 2025

ABSTRACT

The microbial plate count continues to be an essential technique in food microbiology research and quality control. In food science education, this technique is often taught through traditional fact-based methods, requiring students to follow pre-established protocols. This approach may not fully engage students or enhance their problem-solving skills. Eighty-two final-year Food Science and Technology bachelor’s students at the University of Milan were asked to combine their knowledge on general microbiology and microbial physiology for quality assessment of different probiotic products, including freeze-dried cells, fermented milk, and bacterial spore suspension. They were required to select the appropriate culture media, incubation conditions, and treatments based on flow cytometry cell quantification to optimize microbial plate counts and selectively count the different microbial species present in the probiotic formulations. The project aimed to bridge theoretical knowledge with practical applications, emphasizing the most appropriate procedure for viable and cultivable cell quantification, particularly relevant in probiotic formulation. Survey feedback indicated high satisfaction and relevance to future careers, with the majority finding the activity challenging yet engaging. The project demonstrated the effectiveness of combining different microbiological techniques in education, fostering a deeper understanding of the cultivability of probiotics and the role of selective agents.
Thioridazine Induces Increase in Expression of the Pyruvate Transporter MPC1 Associated with Immune Infiltration in Malignant Tumors
Authors: Bogomolova E. A. , Murashko M. M. , Stasevich E. M. , Uvarova A. N. , Zheremyan E. A. , Korneev K. V. , Kuprash D. V. , Demin D. E. 
Published: February 2025

Abstract
The MPC1 gene is involved in the transport of pyruvate into mitochondria, playing an important role in metabolic processes. Recently, it has been reported that higher MPC1 expression correlates with an increased number of immune cells in human cervical and lung cancers, indicating an enhanced antitumor immune response. Reduced MPC1 levels in gastric tumors are associated with a more severe disease course. Correlational analysis of the MPC1 gene in human lung, hippocampus and frontal cortex tissue samples based on data from the GTEx database revealed associations of this gene with schizophrenia, non-small cell lung cancer, and immune diseases. Our experiments showed that the mRNA level of the MPC1 gene in the non-small cell lung cancer cell line A549 increases 5-fold under the influence of the schizophrenia neuroleptic thioridazine. The observed elevation of MPC1 level may cause tumor infiltration by immune cells, complementing the previously reported data indicating the ability of thioridazine to slow cell growth, induce apoptosis and reduce the ability of cells to migrate.
Evaluating the implementation of a digital coordination centre in an Australian hospital setting: a mixed method study protocol
Authors: Freeman Sam , Malone Colin , Black Wynona , Capurro Daniel , Chapman Wendy W , Fazio Timothy N , Gazarek Jana , Layton Meredith J , Lyons Kayley , Pumo Laura , Plumb Samantha , Astbury Brad 
Published: February 2025

IntroductionThis protocol outlines a mixed methods study evaluating a new Digital Coordination Centre (DCC) at the Royal Melbourne Hospital (RMH), Melbourne, Australia. While coordination centres show potential for impact, evidence on effective implementation in the Australian context remains scarce. This study aims to address this gap.Methods and analysisThe evaluation involves a two-stage approach: a process evaluation to clarify DCC design and identify implementation factors, and an initial outcome evaluation to assess short and medium term outcomes. A developmental approach will support continuous improvement, and implementation science theories applied to unpack change processes. Data sources will include interviews, project documentation and observations, with qualitative and quantitative analyses targeting metrics like emergency department boarding and length of stay.Ethics and disseminationThis study has been approved by the RMH Human Research Ethics Committee (QA2023089). Findings will be shared through peer-reviewed publications and conference presentations.
Comparison of syndromic surveillance and hospital discharge data for unintentional drowning in metropolitan Houston, Texas, USA
Authors: Peoples Nicholas , Jones Jennifer L , Camp Elizabeth A , Levine Ned Norman , Shenoi Rohit P 
Published: February 2025

Background
Syndromic surveillance, which provides real-time data, may provide timely drowning surveillance compared with hospital discharge data where the release of data may be delayed. We compared data on hospital visits for unintentional drowning identified in hospital discharge and syndromic surveillance data sets for accuracy and completeness.

Methods

We compared data for hospital visits for unintentional drowning identified in the Texas Health Care Information Collection hospital discharge and syndromic surveillance data sets for metropolitan Houston, Texas, USA from 2019 to 2021. Hospital visits included emergency department-only visits and hospital admissions. We compared time-series visualisation of hospital visits between data sets. Injury burden, demographics and intercounty distribution of drowning patients were compared using the Pearson correlation coefficient for continuous data and the Pearson χ
2
goodness-of-fit test for categorical data.

Results
We identified 860 hospital discharge visits and 929 syndromic surveillance visits (quarterly median (IQR): 64.0 (26.8–117.5); 54.5 (28.0–132.3), respectively) for unintentional drowning. Time-series visualisation showed a high correlation between syndromic surveillance and hospital discharge visits (correlation coefficient: 0.93 (95% CI: 0.77 to 0.98)). There were small differences by race, ethnicity and county for all ages and for paediatrics and large differences by sex for all ages in the number of unintentional drowning hospital visits identified within the data sets.

Conclusions
Regional unintentional drowning burden and trends are highly correlated between syndromic surveillance and hospital discharge data. Small differences by race, ethnicity and county and large differences by sex in the number of unintentional drowning hospital visits were identified between data sets. Syndromic surveillance is useful for real-time surveillance of unintentional drowning.
Pembrolizumab hybrid dosing is non-inferior to flat dosing in advanced non-small cell lung cancer: a real-world, retrospective bicenter cohort study
Authors: Smeenk Michiel M , van der Noort Vincent , Hendrikx Jeroen M A , Abedian Kalkhoran Hanieh , Smit Egbert F , Theelen Willemijn S M E 
Published: February 2025

BackgroundImmune checkpoint inhibitors (ICIs) have revolutionized cancer treatment but come with high costs. Alternative ICI dosing strategies could reduce costs without losing efficacy. However, clinical efficacy data are lacking.MethodsIn this retrospective cohort trial, consecutive patients with advanced non-small cell lung cancer (NSCLC) who received ≥1 cycle pembrolizumab±chemotherapy at two tertiary institutions were included. Hybrid dosed patients received either 100, 150 or 200 mg pembrolizumab every 3 weeks or double every 6 weeks depending on their weight: <65 kg, 65–90 kg or >90 kg, respectively. Standard-of-care flat dosed patients received 200 mg every 3 weeks or 400 mg every 6 weeks. Overall survival (OS) and progression-free survival (PFS) were assessed by Kaplan-Meier estimation, compared by log-rank test and HRs were calculated with the Cox proportional hazards model in both unweighted and inverse probability of treatment weighted (IPTW) cohorts. Non-inferiority margin was set at an HR of 1.15.ResultsIn total, 375 patients and 391 patients were included and median follow-up was 43.1 and 61.0 months in the hybrid and flat dose cohort, respectively. OS was non-inferior in the hybrid dose cohort compared with the flat dose cohort: median 17.7 months (95% CI 14.9 to 20.9) vs 11.8 months (95% CI 9.3 to 13.8, HR 0.76, 95% CI 0.65 to 0.90, p<0.0001 for non-inferiority). After correcting for confounders by IPTW, OS remained non-inferior (HR 0.76, 95% CI 0.63 to 0.91, p<0.0001 for non-inferiority). PFS in the hybrid cohort was also non-inferior to the flat dose cohort with a median of 6.4 months (95% CI 5.7 to 7.7) vs 4.6 months (95% CI 3.9 to 5.5, HR 0.82, 95% CI 0.70 to 0.96, p<0.0001 for non-inferiority). In total, 26.2% (or 52.5 mg per cycle, p<0.0001) pembrolizumab was saved in the hybrid dose cohort accounting to US$36 331.36 per patient.ConclusionsIn this retrospective analysis of a large cohort of advanced NSCLC patients treated with pembrolizumab±chemotherapy, OS of hybrid dosed patients was non-inferior to flat dosed patients. OS remained non-inferior after correcting for possible confounding factors. This hybrid regimen resulted in significant savings of pembrolizumab and costs.
Complete metabolic response as early predictor of long-term efficacy after adoptive T cell therapy using tumor-infiltrating lymphocytes
Authors: Borch Troels Holz , Andersen Rikke , Hendel Helle Westergren , Madsen Kasper , Ellebaek Eva , Marie Svane Inge 
Published: February 2025

Introduction:Adoptive cell therapy using tumor-infiltrating lymphocytes (TILs) has proved to be an effective treatment for metastatic melanoma, even in patients failing anti-PD-1 blockade. Nevertheless, progression is observed in a substantial subgroup of patients following an initial objective response to treatment with TILs. These patients might benefit from additional consolidating treatment before clinical progression, but thus far, it is not possible to identify this subgroup of patients prone to progress. In this study the predictive value of early metabolic response after TIL therapy is explored.Materials and methods:60 patients treated with TIL therapy in 4 different clinical trials and with available [18F]2-fluoro-2-deoxy-d-glucose positron emission tomography-CT (FDG-PET/CT) scans at baseline and at least one follow-up scan 6–8 weeks and/or 12–16 weeks post-TIL infusion were included.Results:Obtaining complete metabolic response (CMR) was associated with significantly superior median overall survival (mOS) compared with not obtaining CMR (p<0.0001). Of particular interest, metabolic response divided RECIST partial responders (22 patients) into two groups with significantly different clinical outcomes. Neither mOS (range 32.2–149.8+) nor median progression-free survival (mPFS; range 20.7–123.4+) were reached for patients with partial response (PR)/CMR (10 patients), whereas patients with PR/non-CMR (12 patients) had a mOS of 28.7 months (p=0.0016) and a mPFS of 7.8 months (p<0.0001).Overall, not achieving a CMR was associated with a short mPFS of 3.2 months, and 97.9% (47/48) of all patients in this group progressed within 12 months.Conclusion:In conclusion, early CMR is a strong predictor of long-term survival after TIL therapy in metastatic melanoma patients. Furthermore, FDG-PET/CT scans appear superior to CT scans for providing early prognostic information after TIL therapy in melanoma and can be used to tailor patient-specific management and follow-up strategies.
Role of spinal Barrier-to-Autointegration Factor (BAF) in the epigenetic silencing of the mu-opioid receptor gene in neuropathic pain
Authors: Hsieh Ming-Chun , Lai Cheng-Yuan , Lin Tzer-Bin , Wang Hsueh-Hsiao , Cheng Jen-Kun , Yang Po-Sheng , Hsu Chieh-Chien , Chou Dylan , Peng Hsien-Yu 
Published: February 2025

BackgroundNeuropathic pain presents a significant clinical challenge, with spinal cord epigenetic mechanisms playing a critical role in its development. This study investigated the impact of nerve injury on the Barrier-to-Autointegration Factor (BAF) in the rat spinal dorsal horn.MethodsAdult Sprague-Dawley rats underwent spinal nerve ligation (SNL) to model neuropathic pain. Pain behaviors were assessed using von Frey and burrow tests. Biochemical analyses measured mRNA and protein expression in the dorsal horn.ResultsSNL elevated BAF levels, which interacts with LEM domain–containing protein 2 (LEMD2), activating the histone-modifying enzyme EZH2. This enzyme adds a gene-silencing mark, H3K27me3, to the promoter region of theOprm1gene, which encodes the mu-opioid receptor. Consequently, the expression of the mu-opioid receptor is decreased, potentially contributing to neuropathic pain. Using gene knockdown techniques to reduce BAF expression, we reversed the changes in LEMD2, EZH2, and mu-opioid receptor expressions induced by SNL and attenuated mechanical allodynia. Additionally, knocking down LEMD2 disrupted the binding of BAF to theOprm1promoter, without affecting BAF levels. Inhibiting EZH2 also reversed the signaling without altering BAF and LEMD2 levels. Glutamate activated BAF pathways via pNR2B receptors, and NR2B receptor blockade reversed this effect.ConclusionThese findings suggest that spinal pNR2B receptors may activate BAF, which interacts with LEMD2 to enhance EZH2-mediated H3K27me3 at the mu-opioid receptor promoter after nerve injury. Targeting this pathway may offer novel strategies to inhibit neuropathic pain.
Simulating toponium formation signals at the LHC
Authors: Fuks Benjamin , Hagiwara Kaoru , Ma Kai , Zheng Ya-Juan 
Published: February 2025

Abstract
We present a method to simulate toponium formation events at the LHC using the Green’s function of non-relativistic QCD in the Coulomb gauge, which governs the momentum distribution of top quarks in the presence of the QCD potential. This Green’s function can be employed to re-weight any matrix elements relevant for

$$t{\bar{t}}$$

t

t

¯

production and decay processes where a colour-singlet top–antitop pair is produced in the S-wave at threshold. As an example, we study the formation of

$$\eta _t$$

η
t

toponium states in the gluon fusion channel at the LHC, combining the re-weighted matrix elements with parton showering.
Star shearing season: transient signals in wave-like dark matter experiments from black hole formation
Authors: de Giorgi Arturo , Jaeckel Joerg 
Published: February 2025

Abstract
Ordinary matter coupled to light weakly interacting bosons can lead to the formation of a macroscopic bosonic field in the vicinity of large matter concentrations such as ordinary or neutron stars. When these objects are turned into black holes due to a supernova or a binary merger this “hair” could be “shorn” off. Part of the field configuration would then be released leading to an outgoing field wave. For small masses this field transient remains rather compact and can induce a transient signal in experiments, in particular those that look for wave-like dark matter. This signal can be correlated with the corresponding astrophysical signal of the event. In this note, we consider a variety of couplings and the associated signals and estimate the corresponding sensitivities.
Correlated systematic uncertainties and errors-on-errors in measurement combinations with an application to the 7–8 TeV ATLAS–CMS top quark mass combination
Authors: Canonero Enzo , Cowan Glen 
Published: February 2025

Abstract
The Gamma Variance Model is a statistical model that incorporates uncertainties in the assignment of systematic errors (informally called errors-on-errors). The model is of particular use in analyses that combine the results of several measurements. In the past, combinations have been carried out using two alternative approaches: the Best Linear Unbiased Estimator (BLUE) method or what we will call the nuisance-parameter method. In this paper, we obtain a general relation between the BLUE and nuisance-parameter methods when the correlations induced by systematic uncertainties are non-trivial (i.e., not

$$\pm 1$$

±
1

or 0), and we then generalise the nuisance-parameter approach to include errors-on-errors. We then present analytical formulas for estimating central values, confidence intervals, and goodness-of-fit when errors-on-errors are incorporated into the statistical model. To illustrate the properties of the Gamma Variance Model, we apply it to the 7–8 TeV ATLAS–CMS top quark mass combination. We also explore a hypothetical scenario by artificially adding a fictitious measurement as an outlier to the combination, illustrating a key feature of the Gamma Variance Model – its sensitivity to the internal consistency of the input data – which could become relevant for future combinations.
Research on Efficient Algorithms of Deep Learning in Visible and Infrared Light Image Fusion
Authors: Xiao Zeliang , Ye Jiafa 
Published: February 2025

Image fusion plays a vital method that integrates data from infrared (IR) and visible light images, to improve visual data quality for specific applications, like, surveillance and object detection. This research investigates efficient algorithms for deep learning (DL)-based image fusion, in the concept of architectures that utilize the complementary characteristics of IR and visible light images. It employs data comprising IR and visible light images captured under varying environmental conditions, ensuring a diverse representation of scenarios. The images perform pre-processing methods such as noise reduction and histogram equalization to optimize the fusion quality. Multi-scale feature extraction is used for feature extraction. This research presents a novel approach leveraging a synergistic fibroblast fine-tuned efficient convolutional neural network (SF-ECNN) for fusion. The SF-ECNN model is analyzed using various metrics and evaluations. Evaluation metrics reveal an EN value of 7.2368, VIF of 0.8124, SD of 95.3515, SF of 19.5314, and AG of 7.3571. Thus, the outcomes exhibit significant improvements in comparison to current advanced fusion techniques, underscoring the efficacy and efficiency of the methodology in producing fused images of superior quality.
7. Analytical Models
Authors: Lee M. A. , Preene M. 
Published: February 2025

Analytical models can be powerful tools which aid the assessment and quantification of groundwater behaviour in engineering projects. Analytical models are simplified representations of reality that typically take the form of empirical, closed form mathematical or numerical solutions. A sound conceptual understanding, based on comprehensive observed data, is fundamental to successfully using analytical models to improve understanding and inform engineering design decisions.
This chapter includes examples of commonly used analytical models and sets out how to select an appropriate model as part of the development of a considered modelling strategy. It also sets out how to select appropriate boundary conditions and material property inputs, and how to assess the degree of confidence that can be placed on model outputs. Potential limitations and commonly encountered constraints in the use of analytical models are presented and the effective communication of model results, including residual uncertainty and risk, is discussed.