bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tailless and filamentous prophages are predominant in marine Vibrio
Authors: Steensen Kerrin , Séneca Joana , Bartlau Nina , Yu Xiaoqian A , Hussain Fatima A , Polz Martin F 
Published: October 2024

Abstract
Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.
Resource sharing of an infant gut microbiota synthetic community in combinations of human milk oligosaccharides
Authors: Ioannou Athanasia , Berkhout Maryse D , Scott William T , Blijenberg Bernadet , Boeren Sjef , Mank Marko , Knol Jan , Belzer Clara 
Published: October 2024

Abstract
Quickly after birth, the gut microbiota is shaped via species acquisition and resource pressure. Breastmilk, and more specifically, human milk oligosaccharides are a determining factor in the formation of microbial communities and the interactions between bacteria. Prominent human milk oligosaccharide degraders have been rigorously characterized, but it is not known how the gut microbiota is shaped as a complex community. Here, we designed BIG-Syc, a synthetic community of 13 strains from the gut of vaginally born, breastfed infants. BIG-Syc replicated key compositional, metabolic, and proteomic characteristics of the gut microbiota of infants. Upon fermentation of a four and five human milk oligosaccharide mix, BIG-Syc demonstrated different compositional and proteomic profiles, with Bifidobacterium infantis and Bifidobacterium bifidum suppressing one another. The mix of five human milk oligosaccharides resulted in a more diverse composition with dominance of B. bifidum, whereas that with four human milk oligosaccharides supported the dominance of B. infantis, in four of six replicates. Reintroduction of bifidobacteria to BIG-Syc led to their engraftment and establishment of their niche. Based on proteomics and genome-scale metabolic models, we reconstructed the carbon source utilization and metabolite and gas production per strain. BIG-Syc demonstrated teamwork as cross-feeders utilized simpler carbohydrates, organic acids, and gases released from human milk oligosaccharide degraders. Collectively, our results showed that human milk oligosaccharides prompt resource-sharing for their complete degradation while leading to a different compositional and functional profile in the community. At the same time, BIG-Syc proved to be an accurate model for the representation of intra-microbe interactions.
Genomic characterization of MRSA recovered from people with cystic fibrosis during two Spanish multicentre studies (2013 and 2021)
Authors: Maruri-Aransolo Ainhize , Hernandez-García Marta , Barbero Raquel , Michelena Malkoa , Pastor-Vivero María Dolores , Mondejar-Lopez Pedro , Solé Amparo , Cantón Rafael , Caballero-Pérez Juan de Dios ,   GEIFQ study group, Maruri-Aransolo Ainhize , de Dios-Caballero Juan , Cantón Rafael , Michelena-González Malkoa , Máiz Luis , Vicente Saioa , Quintana Esther , Pastor-Vivero María Dolores , Álvarez Antonio , Alarcón Rosa Girón, Teresa , Luna-Paredes Carmen , de Valbuena Marta Ruiz , Prados María Concepción , Castillo-Corullón Silvia , Selma María José , Solé Amparo , Cols-Roig Maria , Mondéjar-López Pedro , Ruiz Estela Pérez , Olveira Casilda , Aguilera Pilar Caro , Ruiz Pilar Bermúdez , Causapé Carla López , Figuerola Joan , Oliver Antonio , Asensio Oscar 
Published: October 2024

Abstract

Background
Chronic bronchopulmonary infection due to MRSA in people with cystic fibrosis (pwCF) has been associated with accelerated decline in lung function, increased hospitalizations and increased mortality.

Material and methods
We studied microbiological and genomic characteristics of MRSA isolates recovered from pwCF in two Spanish multicentre studies (2013, 2021). Antimicrobial susceptibility was performed. WGS was carried out to determine population structure [MLST, spa-typing, staphylococcal cassette chromosome mec (SCCmec)], resistome and virulome. Clinical charts of MRSA-infected and MRSA-non-infected pwCF were also reviewed.

Results
MRSA infection prevalence decreased between 2013 (29/341, 8.5%) and 2021 (21/326, 6.4%) (P = 0.378). Differences in lung function were observed between infected and non-infected patients (P &lt; 0.005). A higher prevalence of hospital-acquired (HA) clones was found compared with community-acquired (CA) clones (2013: 67% versus 33%; and 2021: 71% versus 29%). Overall, we noted clustering of isolates based on year of sampling, type of acquisition and clonal complex (CC). HA-MRSA population was dominated by CC5, with ST125-MRSA-IVc-t067 the most prevalent lineage (37%). A higher clonal diversity was detected among CA-MRSA. One Panton–Valentine leucocidin (PVL)-positive strain (ST8-MRSA-IV) and three strains of porcine origin (two ST398-MRSA-V-t011, one ST398-MRSA-V-t8567) were found. Additionally, acquired resistance genes (n = 24) were detected, including the cfr gene conferring linezolid resistance. A higher gentamicin resistance was found in 2021 (42%) compared with 2013 (7%) (P = 0.046), associated with the aac(6′)-aph(2″) gene.

Conclusions
Despite a decrease in MRSA prevalence, we showed its potential impact on CF severity and progression. Moreover, we observed great genotypic and phenotypic diversity in MRSA isolates from pwCF as well as an MDR trait.
Asaia spp. accelerate development of the yellow fever mosquito, Aedes aegypti, via interactions with the vertically transmitted larval microbiome
Authors: Roman Alessandro , Koenraadt Constantianus Johanna Maria , Raymond Ben 
Published: October 2024

Abstract

Aims
A wide range of vector control programmes rely on the efficient production and release of male mosquito. Asaia bacteria are described as potential symbionts of several mosquito species but their relationship with Aedes aegypti has never been rigorously tested. Here, we aimed to quantify the benefits of three Asaia species on host development in Ae. aegypti, and the ability of these bacteria to form a stable symbiotic association with growing larvae.

Methods and results
In order to disentangle direct and indirect effects of Asaia inoculation on host development, experiments used insects with an intact microbiome and those reared in near-aseptic conditions, while we characterized bacterial communities and Asaia densities with culture dependent and independent methods (16S rRNA amplicon sequencing). Neonate larvae were inoculated with Asaia spp. for 24 h, or left as uninoculated controls, all were reared on sterile food. Aseptic larvae were produced by surface sterilization of eggs. Although all Asaia were transient members of the gut community, two species accelerated larval development relative to controls. The two mutualistic species had lasting impacts on the larval microbiome, largely by altering the relative abundance of dominant bacteria, namely Klebsiella and Pseudomonas. Axenic larvae were dominated by Asaia when inoculated with this species but showed slower development than conventionally reared insects, indicating that Asaia alone could not restore normal development.

Conclusions
Our results reveal Asaia as a poor mutualist for Ae. aegypti, but with a species-specific positive effect on improving host performance mediated by interactions with other bacteria.
Biofilms and microbiome profiles in chronic wounds: links to antibiotic use and wound severity in a Sri Lankan cohort
Authors: Dilhari Ayomi , Campbell Paul M , Munasinghe Anuradha , Brown Hannah , Kaluarachchi Thilini D J , Gunasekara Chinthika , Pathirage Sujatha , Fernando Neluka , Weerasekara Deepaka , Humphreys Gavin J , McBain Andrew J , Weerasekera Manjula 
Published: October 2024

Abstract

Aims
We have characterized the microbiome of infected chronic diabetic wounds (CDWs), exploring associations with antibiotic use and wound severity in a Sri Lankan cohort.

Methods and results
Fifty CDW patients were enrolled, 38 of whom received antibiotics. Tissue biopsies were analysed by microbiome profiling, and wounds were graded using the University of Texas Wound Grading System. Biofilm presence was assessed in 20 wounds. The microbiome was largely dominated by Enterobacteriaceae, Pseudomonadaceae, Streptococcaceae, and Corynebacteriaceae. Proteobacteria levels were significantly higher in antibiotic-treated wounds (P = .019), with increased Pseudomonas abundance. Wounds were categorized as grade 1 (10), grade 2 (29), and grade 3 (11). Alpha diversity varied by wound grade (P = .015), with grade 2 wounds showing the highest diversity and grade 3 the lowest. All 20 tested wounds were biofilm-positive, and community composition varied more in antibiotic-treated wounds (P = .004).

Conclusions
CDW microbiomes were dominated by Enterobacteriaceae and Pseudomonadaceae, with elevated Proteobacteria in antibiotic-treated wounds. Alpha diversity correlated with wound severity, peaking in grade 2 wounds. The high prevalence of biofilms in wounds underscores the need for management of CDWs that address microbial complexity.
Resistance to carbapenems in the urban soil isolate Cupriavidus taiwanensis S2-1-W is associated with OXA-1206, a newly discovered carbapenemase
Authors: Lopez Nicolas V , Ruiz Cristian 
Published: October 2024

Abstract

Aims
Cupriavidus isolates are found in environmental and clinical samples and are often resistant to carbapenems, which are last-resort antibiotics. However, their carbapenem-resistance molecular mechanisms remain unknown. This study aimed to (i) characterize and sequence the carbapenem-resistant soil isolate Cupriavidus taiwanensis S2-1-W to uncover its antibiotic resistance determinants; and (ii) clone and characterize a putative novel carbapenemase gene identified in this isolate.

Methods and results
Antibiotic susceptibility testing of C. taiwanensis S2-1-W revealed that it was resistant to most carbapenems, other β-lactams, and aminoglycosides tested. Genome sequencing of this isolate revealed a complex chromosomal resistome that included multidrug efflux pump genes, one aminoglycoside transferase gene, and three β-lactamase genes. Among them, we identified a novel putative class D β-lactamase gene (blaOXA-1206) that is highly conserved among other sequenced C. taiwanensis isolates. Cloning and characterization of blaOXA-1206 confirmed that it encodes for a newly discovered carbapenemase (OXA-1206) that confers resistance to carbapenems and other β-lactams.

Conclusion
Carbapenem-resistance in C. taiwanensis S2-1-W is associated with a newly discovered carbapenemase, OXA-1206.
CALIFRAME: a proposed method of calibrating reporting guidelines with FAIR principles to foster reproducibility of AI research in medicine
Authors: Shiferaw Kirubel Biruk , Balaur Irina , Welter Danielle , Waltemath Dagmar , Zeleke Atinkut Alamirrew 
Published: October 2024

Abstract

Background
Procedural and reporting guidelines are crucial in framing scientific practices and communications among researchers and the broader community. These guidelines aim to ensure transparency, reproducibility, and reliability in scientific research. Despite several methodological frameworks proposed by various initiatives to foster reproducibility, challenges such as data leakage and reproducibility remain prevalent. Recent studies have highlighted the transformative potential of incorporating the FAIR (Findable, Accessible, Interoperable, and Reusable) principles into workflows, particularly in contexts like software and machine learning model development, to promote open science.

Objective
This study aims to introduce a comprehensive framework, designed to calibrate existing reporting guidelines against the FAIR principles. The goal is to enhance reproducibility and promote open science by integrating these principles into the scientific reporting process.

Methods
We employed the “Best fit” framework synthesis approach which involves systematically reviewing and synthesizing existing frameworks and guidelines to identify best practices and gaps. We then proposed a series of defined workflows to align reporting guidelines with FAIR principles. A use case was developed to demonstrate the practical application of the framework.

Results
The integration of FAIR principles with established reporting guidelines through the framework effectively bridges the gap between FAIR metrics and traditional reporting standards. The framework provides a structured approach to enhance the findability, accessibility, interoperability, and reusability of scientific data and outputs. The use case demonstrated the practical benefits of the framework, showing improved data management and reporting practices.

Discussion
The framework addresses critical challenges in scientific research, such as data leakage and reproducibility issues. By embedding FAIR principles into reporting guidelines, the framework ensures that scientific outputs are more transparent, reliable, and reusable. This integration not only benefits researchers by improving data management practices but also enhances the overall scientific process by promoting open science and collaboration.

Conclusion
The proposed framework successfully combines FAIR principles with reporting guidelines, offering a robust solution to enhance reproducibility and open science. This framework can be applied across various contexts, including software and machine learning model development stages, to foster a more transparent and collaborative scientific environment.
Artificial intelligence-generated feedback on social signals in patient–provider communication: technical performance, feedback usability, and impact
Authors: Bedmutha Manas Satish , Bascom Emily , Sladek Kimberly R , Tobar Kelly , Casanova-Perez Reggie , Andreiu Alexandra , Bhat Amrit , Mangal Sabrina , Wood Brian R , Sabin Janice , Pratt Wanda , Weibel Nadir , Hartzler Andrea L 
Published: October 2024

Abstract

Objectives
Implicit bias perpetuates health care inequities and manifests in patient–provider interactions, particularly nonverbal social cues like dominance. We investigated the use of artificial intelligence (AI) for automated communication assessment and feedback during primary care visits to raise clinician awareness of bias in patient interactions.

Materials and Methods
(1) Assessed the technical performance of our AI models by building a machine-learning pipeline that automatically detects social signals in patient–provider interactions from 145 primary care visits. (2) Engaged 24 clinicians to design usable AI-generated communication feedback for their workflow. (3) Evaluated the impact of our AI-based approach in a prospective cohort of 108 primary care visits.

Results
Findings demonstrate the feasibility of AI models to identify social signals, such as dominance, warmth, engagement, and interactivity, in nonverbal patient–provider communication. Although engaged clinicians preferred feedback delivered in personalized dashboards, they found nonverbal cues difficult to interpret, motivating social signals as an alternative feedback mechanism. Impact evaluation demonstrated fairness in all AI models with better generalizability of provider dominance, provider engagement, and patient warmth. Stronger clinician implicit race bias was associated with less provider dominance and warmth. Although clinicians expressed overall interest in our AI approach, they recommended improvements to enhance acceptability, feasibility, and implementation in telehealth and medical education contexts.

Discussion and Conclusion
Findings demonstrate promise for AI-driven communication assessment and feedback systems focused on social signals. Future work should improve the performance of this approach, personalize models, and contextualize feedback, and investigate system implementation in educational workflows. This work exemplifies a systematic, multistage approach for evaluating AI tools designed to raise clinician awareness of implicit bias and promote patient-centered, equitable health care interactions.
HR-pQCT reveals marked trabecular and cortical structural deficits in women with pregnancy and lactation-associated osteoporosis (PLO)
Authors: Agarwal Sanchita , El-Najjar Dany , Kondapalli Ananya , Kil Nayoung , Kamanda-Kosseh Mafo , Bucovsky Mariana , Colon Ivelisse , Lappe Joan M , Stubby Julie , Recker Robert R , Guo X Edward , Shane Elizabeth , Cohen Adi 
Published: October 2024

Abstract
Pregnancy and lactation-associated osteoporosis (PLO) is a rare presentation of early-onset osteoporosis characterized by low trauma and spontaneous fractures during late pregnancy/lactation. Herein, we report areal BMD (aBMD) by DXA and volumetric BMD (vBMD), microarchitecture, and strength at the distal radius and tibia by HR-pQCT in 59 women with PLO—in comparison to both healthy premenopausal controls (n = 28) and premenopausal women with idiopathic osteoporotic fractures not associated with pregnancy/lactation (non-PLO IOP; n = 50). Women with PLO (aged 34 ± 6 yr) had a more severe clinical presentation than non-PLO IOP: 80% had vertebral and 92% had multiple fractures (p&lt;.001). They had lower DXA aBMD at all sites vs Controls (all p&lt;.001) and non-PLO IOP (all p&lt;.05). By HR-pQCT, PLO had deficits in all radial/tibial density and most microarchitecture parameters and lower bone strength than controls (all p&lt;.001). Compared to non-PLO IOP, PLO had lower total and trabecular density at radius and tibia (all p ≤ .01) and significant deficits in trabecular microstructure and cortical thickness at the radius only. We studied PLO subgroups with clinical factors potentially related to bone physiology: Within PLO, women with vertebral fractures had lower spine aBMD and higher tibial cortical porosity but were otherwise structurally similar to the nonvertebral group. Those with prior heparin exposure had larger bone size and trabecular area, and those with renal stones had smaller bone size and lower 1/3 radius aBMD. We also compared groups based on postpartum timing: Recent PLO (n = 25) evaluated ≤12 M postpartum, before expected recovery of pregnancy/lactation bone loss, had significantly lower aBMD than distant PLO (n = 34) evaluated &gt;12 M postpartum. However, radial/tibial HR-pQCT measures did not differ, suggesting pre-existing and/or persistent structural deficits. This structural study increases our mechanistic understanding of the severe bone fragility presentation that characterizes PLO and also highlights areas of potential mechanistic heterogeneity that require additional investigation.
An enhanced slime mould algorithm with triple strategy for engineering design optimization
Authors: Wang Shuai , Zhang Junxing , Li Shaobo , Wu Fengbin , Li Shaoyang 
Published: October 2024

Abstract
This paper introduces an enhanced slime mould algorithm (EESMA) designed to address critical challenges in engineering design optimization. The EESMA integrates three novel strategies: the Laplace logistic sine map technique, the adaptive t-distribution elite mutation mechanism, and the ranking-based dynamic learning strategy. These enhancements collectively improve the algorithm’s search efficiency, mitigate convergence to local optima, and bolster robustness in complex optimization tasks. The proposed EESMA demonstrates significant advantages over many conventional optimization algorithms and performs on par with, or even surpasses, several advanced algorithms in benchmark tests. Its superior performance is validated through extensive evaluations on diverse test sets, including IEEE CEC2014, IEEE CEC2020, and IEEE CEC2022, and its successful application in six distinct engineering problems. Notably, EESMA excels in solving economic load dispatch problems, highlighting its capability to tackle challenging optimization scenarios. The results affirm that EESMA is a competitive and effective tool for addressing complex optimization issues, showcasing its potential for widespread application in engineering and beyond.
The Contrast Pressures on Consumer-Level Food Waste During a Pandemic: The Impact of Infection Salience Versus Lockdown Salience
Authors: Gao Huachao 
Published: October 2024

Abstract
Consumer food waste, with its extensive social, economic, and environmental implications, gained heightened attention during the COVID-19 pandemic, which disrupted food supply chains and exacerbated food insecurity. Amidst conflicting reports on the pandemic’s influences on consumer-level food waste, this research differentiates between the infection and lockdown facets of a pandemic. Specifically, we demonstrate that infection salience amplifies safety–health concerns, leading to increased consumer food waste, while lockdown salience raises concerns over resource scarcity, resulting in reduced consumer food waste. Considering that most pandemics or infectious diseases primarily increase infection salience without inducing lockdowns, we propose a safety–health intervention to mitigate the rise in consumer food waste driven by infection salience and the associated safety–health concerns. Through a large-scale field s tudy, a lab experiment measuring real food waste, a country-level secondary dataset, and three supplementary experiments, we provide converging supports for our theory. These studies also showcase various implementations of the safety–health intervention, such as table tents, napkins, and to-go boxes. This research reconciles divergent perspectives on the pandemic’s impact on consumer-level food waste, enriches the understanding of pandemics and associated food waste dynamics, and offers actionable strategies for businesses and policymakers to address consumer food waste during pandemics.
The bifurcation challenge at the Unified Patent Court
Authors: Dani Martina 
Published: October 2024

Abstract
Among the issues that have been examined during the preparatory phase for establishing the Unified Patent Court (UPC), bifurcation is one of the most discussed and criticized. In this article, the trends towards bifurcation developed during the first year of the UPC operations will be examined, thus offering valuable insights into what we can expect to see in the near future.