bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced prevalence of phage defense systems in
Pseudomonas aeruginosa
strains from cystic fibrosis patients
Authors: van den Berg Daan F. , Brouns Stan J. J. 
Published: February 2025

ABSTRACT

Cystic fibrosis is a genetic disorder that affects mucus clearance, particularly of the lungs. As a result, cystic fibrosis patients often experience infections from bacteria, which contribute to the disease progression.
Pseudomonas aeruginosa
is one of the most common opportunistic pathogens associated with cystic fibrosis. The presence of
P. aeruginosa
complicates the treatment due to its high antibiotic resistance. Thus, research is ongoing to treat these infections with bacterial viruses instead, known as bacteriophages. Notably,
P. aeruginosa
clinical strains possess a variety of phage defense mechanisms that may limit the effectiveness of phage therapy. In this study, we compared the defense system repertoire of
P. aeruginosa
strains isolated from cystic fibrosis patients with those from non-cystic fibrosis patients. Our findings reveal that
P. aeruginosa
strains isolated from cystic fibrosis patients have fewer phage defense mechanisms per strain than from non-cystic fibrosis patients, suggesting altered phage selection pressures in strains colonizing CF patient lungs.

IMPORTANCE

Cystic fibrosis patients often experience chronic
Pseudomonas aeruginosa
lung infections, which are challenging to treat with antibiotics and contribute to disease progression and eventual respiratory failure. Phage therapy is being explored as an alternative treatment strategy for these infections. However, assessing strain susceptibility to phage treatment is essential for ensuring efficacy. To address this, we investigated whether CF-associated clinical
P. aeruginosa
strains have a distinct phage defense repertoire compared with those isolated from other lung patients. We observed that CF-associated
P. aeruginosa
strains have significantly fewer phage defenses, possibly affecting the susceptibility of these strains to phage infection.
Low-dose interleukin 2 therapy halts the progression of post-streptococcal autoimmune complications in a rat model of rheumatic heart disease
Authors: Rafeek Rukshan Ahamed Mohamed , Ketheesan Natkunam , Good Michael F. , Pandey Manisha , Lepletier Ailin 
Published: February 2025

ABSTRACT

Acute rheumatic fever (ARF) is an autoimmune disease triggered by antibodies and T cells targeting the group A
Streptococcus
(GAS, Strep A) bacterium, often leading to rheumatic heart disease (RHD) and Sydenham’s chorea. Long-term monthly penicillin injections are recognized as a cornerstone of public health programs to prevent Strep A reinfection and progression of ARF. However, compliance is poor, and better tools are required to slow disease progression. Preclinical evidence suggests that this can be achieved. Using a rat model that replicates post-streptococcal autoimmune complications, we explored the potential of low-dose interleukin-2 (LD-IL-2) as an immunotherapeutic intervention for ARF/RHD. In this model, injections of recombinant M protein from Strep A type 5 (rM5) to Lewis rats induce cardiac tissue inflammation, conduction abnormalities, and cross-reactive antibodies against cardiac and brain proteins central to disease pathogenesis. In animals injected with rM5 and treated with LD-IL-2, no cardiac functional or histological changes was observed. LD-IL-2 therapy effectively reduced the production of cross-reactive antibodies raised against host proteins and significantly increased regulatory T cells in the mediastinal lymph nodes. These novel findings suggest that LD-IL-2 will be an effective immunotherapeutic agent for treating ARF and has the potential to replace the standard monthly penicillin injections.

IMPORTANCE

Post-streptococcal autoimmune syndromes, including acute rheumatic fever, rheumatic heart disease, and Sydenham’s chorea, represent a significant yet often under-recognized health and economic burden. This is especially true in low-income countries and among Indigenous populations in high-income nations, where the disease burden is most severe. These conditions arise from an autoimmune response to group A
Streptococcus
infections, leading to long-term health complications, disability, and premature death. Despite their widespread impact, no vaccine is currently available to prevent reinfections, and no specific therapy exists to treat the resulting autoimmune process. This study uses a rat model of rheumatic heart disease to evaluate the potential of low-dose interleukin 2 therapy in improving clinical outcomes and reducing the incidence of autoimmune diseases triggered by streptococcal infections.
Draft genome sequence of the
Serratia liquefaciens
strain UNJFSC002, isolated from the soil of a potato field of the Bicentenaria variety
Authors: Rodriguez-Grados Pedro M. , Arbizu Carlos I. , Castillo Gianmarco , Camel Vladimir , Conteras-Liza Sergio 
Published: February 2025

ABSTRACT

In this study, we present the draft genome assembly of the
Serratia liquefaciens
strain UNJFSC002, isolated from the experimental potato field of the Bicentenaria variety at the Universidad Nacional José Faustino Sánchez Carrión, Lima, Peru.
Complete genome sequence of three methicillin-resistant
Staphylococcus aureus
ST630 strains isolated from cattle in Algeria
Authors: Belhout Chahrazed , Fernandez Javier E. , Perreten Vincent 
Published: February 2025

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) sequence type 630 (ST630) is an emerging clone causing infections in humans. We report the complete genomes of three MRSA ST630 from cattle. The 2.8 Mbp genomes contained several antimicrobial resistance and virulence genes and were related to those of previously detected human-associated MRSA ST630.
Complete genome of the mutualistic symbiont “
Candidatus
Carsonella ruddii” from a Japanese island strain of the Asian citrus psyllid
Diaphorina citri
Authors: Mizutani Masaki , Fujikawa Takashi , Fukatsu Takema , Kakizawa Shigeyuki 
Published: February 2025

ABSTRACT

The complete genome, 173,958 bp in size, of “
Candidatus
Carsonella ruddii” DC-OKEB1
,
an obligate bacterial endosymbiont of the Asian citrus psyllid
Diaphorina citri
, was determined. The genome sequence provides valuable information for comparative and evolutionary aspects of the intimate insect–microbe mutualism.
Draft genome sequence of
Streptomyces
sp. Sce081 isolated from the nest of wasp
Sceliphron destillatorium
(Illiger, 1807)
Authors: Pytel-Huta Sofiia , Kachor Anna , Zatushevsky Andriy , Samborskyy Markiyan , Rebets Yuriy 
Published: February 2025

ABSTRACT

Actinobacteria are often involved in ecological interactions with insects.
Streptomyces
sp. Sce081 with notable antifungal activity was isolated from the nest of wasp
Sceliphron destillatorium
(Illiger, 1807). Here, we report the draft sequence and analysis of the
Streptomyces
sp. Sce081 genome.
Estimated size of the total genome and protein space of viruses
Authors: Lu Congyu , Wu Yifan , Zhang Zheng , Mao Longfei , Ge Xingyi , Wu Aiping , Sun Fengzhu , Jiang Yongqiang , Peng Yousong 
Published: February 2025

ABSTRACT

Recent metagenomic studies have identified a vast number of viruses. However, the systematic assessment of the true genetic diversity of the whole virus community on our planet remains to be investigated. Here, we explored the genome and protein space of viruses by simulating the process of virus discovery in viral metagenomic studies. Among multiple functions, the power function was found to best fit the increasing trends of virus diversity and was, therefore, used to predict the genetic space of viruses. The estimate suggests that there are at least 8.23e+08 viral operational taxonomic units and 1.62e+09 viral protein clusters on Earth when assuming the saturation of the virus genetic space, taking into account the balance of costs and the identification of novel viruses. It is noteworthy that less than 3% of the viral genetic diversity has been uncovered thus far, emphasizing the vastness of the unexplored viral landscape. To saturate the genetic space, a total of 3.08e+08 samples would be required. Analysis of viral genetic diversity by ecosystem yielded estimates consistent with those mentioned above. Furthermore, the estimate of the virus genetic space remained robust when accounting for the redundancy of sampling, sampling time, sequencing platform, and parameters used for protein clustering. This study provides a guide for future sequencing efforts in virus discovery and contributes to a better understanding of viral diversity in nature.

IMPORTANCE
Viruses are the most abundant and diverse biological entities on Earth. In recent years, a large number of viruses have been discovered based on sequencing technology. However, it is not clear how many kinds of viruses exist on Earth. This study estimates that there are at least 823 million types of viruses and 1.62 billion types of viral proteins. Remarkably, less than 3% of this large diversity has been uncovered to date. These findings highlight the enormous potential for discovering new viruses and reveal a significant gap in our current understanding of the viral world. This study calls for increased attention and resources to be directed toward viral discovery and metagenomics and provides a guide for future sequencing efforts, enhancing our knowledge of viral diversity in nature for ecology, biology, and public health.
Studies of Composite Protective Coatings of an Ancient Ship from Phanagoria (1st Century BC)
Authors: Greshnikov E. A. , Olkhovskiy S. V. , Chernova O. F. , Kamaev A. V. , Antipin A. M. , Svetogorov R. D. , Mandrykina A. V. , Kondratev O. A. , Tereschenko E. Yu. , Yatsishina E. B. 
Published: February 2025

Abstract
Samples of the internal and external coatings of the hull of a warship that sank in the seaport of Phanagoria (modern Taman Bay) in the 1st century BC are studied. As a result of the application of a complex of complementary natural-science methods (optical microscopy, X-ray diffractometry, scanning electron microscopy with energy dispersive X-ray microanalysis, gas chromatography with mass-selective detection), it is found that the internal wooden part of the ship was treated with a “mastic,” based on clay mixed with wool and down. The outer surface of the ship’s sheathing board was coated by realgar mixed with wax and pine resin. Thus the recipes used for the waterproofing, fireproofing, and bioprotection of warships used by sailors of the Pontic Kingdom more than 2000 years ago are presented.
Glass Imports to Southwestern Crimea in the 13th Century AD Based on Findings from a Hillfort of the Eski-Kermen Plateau
Authors: Khairedinova E. A. , Rumyantseva O. S. , Ismagulov A. M. , Bilida E. Yu. , Shalyavina N. B. , Saifutyarov R. R. , Tereschenko E. Yu. 
Published: February 2025

Abstract
The chemical composition of glass of 19 items (mostly vessels) from the Eski-Kermen plateau in southwestern Crimea has been studied with LA-ICP-MS and SEM-EDX techniques. The findings originate from the destruction layer of the late 13th century AD as well as from two churches and a manor of a noble citizen. The studied samples are made of Eastern Mediterranean plant ash glass, mainly of the Levantine origin, and of glass with high concentrations of boron and lithium, which origin is associated with Western Anatolia. It does not necessarily imply that the vessels themselves originate from these glassmaking regions, because raw glass, at least Eastern Mediterranean (Levantine), was a long-distance trade commodity and could have been imported into Byzantium or elsewhere. Glass of presumably Western Anatolian origin is heterogeneous in composition and likely originate from glassmaking centers that used raw materials from different sources. Most glass of this group features signs of the extensive recycling. The glass with a high B and Li content appears in Esky-Kermen in the 10th century AD at the latest. According to an earlier study of window glass composition from the site, its emergence here before the 13th century remained doubtful. Two early Islamic marvered vessels are made of glass with elevated content of boron and lithium, featuring signs of recycling. Such examples have already been recorded earlier among glassware made in this style from Pergamon and Branichevo in Serbia. This raises the question of possible manufacturing centers for some vessels with marvered décor.
Benchmarking open-source large language models on Portuguese Revalida multiple-choice questions
Authors: Bruneti Severino João Victor , Basei de Paula Pedro Angelo , Berger Matheus Nespolo , Loures Filipe Silveira , Todeschini Solano Amadori , Roeder Eduardo Augusto , Veiga Maria Han , Guedes Murilo , Marques Gustavo Lenci 
Published: February 2025

ObjectiveThe study aimed to evaluate the top large language models (LLMs) in validated medical knowledge tests in Portuguese.MethodsThis study compared 31 LLMs in the context of solving the national Brazilian medical examination test. The research compared the performance of 23 open-source and 8 proprietary models across 399 multiple-choice questions.ResultsAmong the smaller models, Llama 3 8B exhibited the highest success rate, achieving 53.9%, while the medium-sized model Mixtral 8×7B attained a success rate of 63.7%. Conversely, larger models like Llama 3 70B achieved a success rate of 77.5%. Among the proprietary models, GPT-4o and Claude Opus demonstrated superior accuracy, scoring 86.8% and 83.8%, respectively.Conclusions10 out of the 31 LLMs attained better than human level of performance in the Revalida benchmark, with 9 failing to provide coherent answers to the task. Larger models exhibited superior performance overall. However, certain medium-sized LLMs surpassed the performance of some of the larger LLMs.
Thrombus iodine-based perviousness is associated with recanalisation and functional outcomes in endovascular thrombectomy
Authors: Tian Chao , Liu Song , Fu Lejun , Guo Jingjing , Cao Chen , Sun Yu , Ren Tao , Wang Huiying , Wang Sifei , Luo Leilei , Wang Luotong , Wei Ming , Xia Shuang , Jin Song , Han Tong , Hao Nina 
Published: February 2025

BackgroundDual-energy CT (DECT) provides several novel methods to assess thrombus perviousness. We aimed to evaluate whether the novel thrombus perviousness measured with DECT is associated with improved recanalisation and better functional outcomes in acute ischaemic stroke (AIS) patients with endovascular thrombectomy (EVT).Methods108 AIS patients with middle cerebral artery occlusion who underwent DECT angiography on admission and received EVT treatment between April 2020 and September 2023 were retrospectively analysed. Thrombus attenuation increase (TAI) was evaluated on routine CT angiography and non-contrast CT, and DECT quantitative parameters of thrombus, including iodine concentration (IC) and normalised IC (NIC) were measured. Multivariable logistic regression analysis was used to evaluate the association of thrombus characteristics with arterial occlusive lesion scale and 90-day modified Rankin Scale.ResultsNIC was significantly associated with successful recanalisation (OR 1.372 (95% CI 1.194 to 1.625); p<0.001) and good functional outcome (OR 1.252 (95% CI 1.114 to 1.446); p<0.001). NIC yielded higher performance, with area under curve (AUC) of 0.789 and 0.740, in the prediction of recanalisation and functional outcome than TAI (AUCs=0.635 and 0.592). Compared with low-level NIC thrombus, high-level NIC was associated with 11.4 and 15.4 times higher likelihood of successful recanalisation and good functional outcome. Moreover, NIC was a significant indicator to differentiate large artery atherosclerosis from cardioembolism stroke with high specificity and positive predictive value.ConclusionsHigher DECT-derived NIC is associated with increased odds of successful recanalisation and good functional outcome for EVT patients, and it yielded higher prediction performance than TAI.
A comprehensive study of particle dynamics, thermal fluctuations with Barrow entropy, and greybody factors of quantum-improved charged black holes
Authors: Fatima Ghulam , Zhu Tao , Javed Faisal , Waseem Arfa , Mustafa G. 
Published: February 2025

Abstract
This study examines the characteristics and behavior of quantum-improved charged black holes, focusing on the relationships between mass, charge, and the quantum-improved parameter. We explore the consequences of these characteristics on the structure of a black hole’s horizon, particularly investigating the ways that variations in charge and mass modify the horizon radius and size of innermost stable circular orbits. A thorough thermodynamic analysis indicates substantial impacts on corrected energies, including Helmholtz free energy, enthalpy, internal energy, and Gibbs free energy, in the context of Barrow entropy, emphasizing stable and unstable configurations across various quantum correction parameter ranges. Additionally, we analyze wave behavior near the cosmic horizon and its correlation with effective potential, illustrating whether wave frequency influences the gravitational absorption function and the transmission properties of scalar fields near quantum-improved charged black holes. Our findings highlight the complex interaction between black hole dynamics and quantum parameters, facilitating a more profound comprehension of black hole thermodynamics and their significance in curved space-time quantum field theory.
How Computational Theorists Deal with Electrode Potential
Authors: Anderson Alfred B 
Published: February 2025

Abstract
For many years since Gurney introduced quantum mechanics to electrochemistry, models and calculations assumed bonding and other properties at the electrochemical interface may be calculated with adequate accuracy at the potential of zero charge (PZC) and that the effect of potential lies solely in controlling the energy of the electron involved in the transfer, which comes from or goes to an external energy level. The energy of the electron is assigned to the Fermi energy, Ef, of the electrode for the particular potential being modeled. This is done in the Butler-Volmer theory as well as in several quantum mechanical modeling procedures that are introduced here. Though the PZC in fact changes as the identity, amount, and structures of molecules chemically bonded to the electrode are varied during calculations using these models, there is no control of the electrode potential in the calculations. The past two decades have seen the development of computer codes that can incorporate controlled incremental surface charging with polarizable electrolyte models that compensate it, resulting in zero net interface charge. Calculations using these codes provide accurate predictions of the potential-dependent energies of reactants and products, reversible potentials, and electron transfer activation energies.
A Roadmap to Precision Immunotherapy for Early-Stage Non–Small Cell Lung Cancer
Authors: Vaccaro Alessandra , Rahal Zahraa , Kadara Humam , Cascone Tina 
Published: February 2025

Summary:
Immunotherapy has revolutionized the treatment of early-stage non–small cell lung cancer; yet many patients fail to achieve long-lasting benefit, partially because of incomplete or inconsistent biomarker predictions. Integrative multiomics, combining tumor-intrinsic, immune microenvironment, and systemic factors, offer a more comprehensive framework for precision immunotherapy, enabling improved patient stratification, treatment selection and outcomes.
Effect of Early Life Trauma Exposure on Vascular Dysfunction in Black Men and Women
Authors: Spikes Telisa A. , Thorpe Roland J. , Michopoulos Vasiliki , Wharton Whitney , Pelkmans Jordan , Dunbar Sandra B. , Mehta Puja K. , Pemu Priscilla , Taylor Herman , Quyyumi Arshed 
Published: February 2025

Background
Psychosocial stressors such as childhood trauma have been associated with an increased risk of hypertension. The impact of childhood trauma on vascular dysfunction in Black adults remains less clear. We examined the association between childhood trauma and vascular function in Black adults.

Methods and Results

Childhood trauma exposure and vascular function were assessed in a cohort of healthy Black participants without known cardiovascular disease (n=404) from a large metropolitan city. Childhood trauma was assessed using the Early Trauma Inventory Short Form with higher scores indicative of higher traumatic life events assessed before age 18 years. Outcomes of central augmentation index (CAIx) and carotid femoral pulse wave velocity were measured as indices of wave reflections and arterial stiffness using applanation tonometry (Sphygmocor Inc.), and central pulse pressure (CPP) was calculated as the difference between the central aortic systolic and diastolic blood pressures. Relationships between Early Trauma Inventory Short Form and outcomes were assessed using multivariate‐adjusted and sex‐stratified linear regression models. The mean age of the cohort was 53 (SD=10.3), 61% women. Cumulative childhood trauma was not associated with CAIx, central pulse pressure, or carotid femoral pulse wave velocity in the minimal or fully adjusted models for sociodemographic, sex, clinical factors, medical history, health behaviors, and depression. Significant trauma × sex interactions were identified for CAIx (
P
=0.003) and central pulse pressure (
P
=0.025). Childhood trauma was associated with lower CAIx (
β
=−0.55% [95% CI, −1.07 to −0.03] in men, but higher CAIx (
β
=0.35% [95% CI, 0.08–0.63]) and central pulse pressure (
β
=0.23 mm Hg [95% CI, 0.01–0.43]) in women.

Conclusions
Childhood trauma is independently associated with impaired arterial compliance in Black women.