bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel phage infecting the
Roseobacter
CHUG lineage reveals a diverse and globally distributed phage family
Authors: Wu Zuqing , Guo Luyuan , Wu Ying , Yang Mingyu , Du Sen , Shao Jiabing , Zhang Zefeng , Zhao Yanlin 
Published: June 2024

ABSTRACT

Bacteriophages play an essential role in shaping the diversity and metabolism of bacterial communities. Marine
Roseobacter
group is an abundant heterotrophic bacterial group that is involved in many major element cycles, especially carbon and sulfur. Members of the
Roseobacter
CHUG (Clade Hidden and Underappreciated Globally) lineage are globally distributed and are activated in pelagic marine environments. In this study, we isolated and characterized a phage, CRP-810, that infects the CHUG strain FZCC0198. The genome of CRP-810 was dissimilar to those of other known phages. Additionally, 251 uncultured viral genomes (UViGs) closely related to CRP-810 were obtained from the uncultivated marine viral contig databases. Comparative genomic and phylogenetic analyses revealed that CRP-810 and these related UViGs exhibited conserved genome synteny, representing a new phage family with at least eight subgroups. Most of the CRP-810-type phages contain an integrase gene, and CRP-810 can be integrated into the host genome. Further analysis revealed that three CRP-810-type members were prophages found in the genomes of marine SAR11,
Poseidonocella
, and
Sphingomonadaceae
. Finally, viromic read-mapping analysis showed that CRP-810-type phages were globally distributed and displayed distinct biogeographic patterns related to temperature and latitude. Many members with a lower G + C content were mainly distributed in the trade station, whereas members with a higher G + C content were mainly distributed in polar and westerlies station, indicating that the niche differentiation of phages was subject to host adaptation. Collectively, these findings identify a novel phage family and expand our understanding of phylogenetic diversity, evolution, and biogeography of marine phages.

IMPORTANCE

The
Roseobacter
CHUG lineage, affiliated with the Pelagic
Roseobacter
Cluster (PRC), is widely distributed in the global oceans and is active in oligotrophic seawater. However, knowledge of the bacteriophages that infect CHUG members is limited. In this study, a CHUG phage, CRP-810, that infects the CHUG strain FZCC0198, was isolated and shown to have a novel genomic architecture. In addition, 251 uncultured viral genomes closely related to CRP-810 were recovered and included in the analyses. Phylogenomic analyses revealed that the CRP-810-type phages represent a new phage family containing at least eight genus-level subgroups. Members of this family were predicted to infect various marine bacteria. We also demonstrated that the CRP-810-type phages are widely distributed in global oceans and display distinct biogeographic patterns related to latitude. Collectively, this study provides important insights into the genomic organization, diversity, and ecology of a novel phage family that infect ecologically important bacteria in the global ocean.
PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides
Authors: Ramos-Llorens Marc , Bello-Madruga Roberto , Valle Javier , Andreu David , Torrent Marc 
Published: June 2024

ABSTRACT

The alarming rise of antibiotic-resistant bacterial infections is driving efforts to develop alternatives to conventional antibiotics. In this context, antimicrobial peptides (AMPs) have emerged as promising candidates for their ability to target a broad range of microorganisms. However, the development of AMPs with optimal potency, selectivity, and/or stability profiles remains a challenge. To address it, computational tools for predicting AMP properties and designing novel peptides have gained increasing attention. PyAMPA is a novel platform for AMP discovery. It consists of five modules, namely AMPScreen, AMPValidate, AMPSolve, AMPMutate, and AMPOptimize, that allow high-throughput proteome inspection, candidate screening, and optimization through point-mutation and genetic algorithms. The platform also offers additional tools for predicting and evaluating AMP properties, including antimicrobial and cytotoxic activity, and peptide half-life. By providing innovative and accessible inroads into AMP motifs in proteomes, PyAMPA will enable advances in AMP development and potential translation into clinically useful molecules. PyAMPA is available at:
https://github.com/SysBioUAB/PyAMPA

IMPORTANCE
This paper introduces PyAMPA, a new bioinformatics platform designed for the discovery and optimization of antimicrobial peptides (AMPs). It addresses the urgent need for new antimicrobials due to the rise of antibiotic-resistant infections. PyAMPA, with its five predictive modules -AMPScreen, AMPValidate, AMPSolve, AMPMutate and AMPOptimize, enables high-throughput screening of proteomes to identify potential AMP motifs and optimize them for clinical use. Its unique approach, combining prediction, design, and optimization tools, makes PyAMPA a robust solution for developing new AMP-based therapies, offering a significant advance in combatting antibiotic resistance.
Comparative genomic analysis of an emerging Pseudomonadaceae member,
Thiopseudomonas alkaliphila
Authors: Burcham Zachary M. 
Published: June 2024

ABSTRACT

Thiopseudomonas alkaliphila
, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how
T. alkaliphila
functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of
T. alkaliphila
includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in
T. alkaliphila
genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of
T. alkaliphila
, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.

IMPORTANCE

As the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact.
Thiopseudomonas alkaliphila
is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification,
T. alkaliphila
has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that
T. alkaliphila
is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting
T. alkaliphila
may operate as an undescribed opportunistic pathogen.
Resistance to ceftazidime–avibactam and other new β-lactams in
Pseudomonas aeruginosa
clinical isolates: a multi-center surveillance study
Authors: Valzano Felice , La Bella Gianfranco , Lopizzo Teresa , Curci Anna , Lupo Laura , Morelli Elisabetta , Mosca Adriana , Marangi Marianna , Melfitano Raffaela , Rollo Tiziana , De Nittis Rosella , Arena Fabio 
Published: June 2024

ABSTRACT

New β-lactam–β-lactamase inhibitor combinations represent last-resort antibiotics to treat infections caused by multidrug-resistant
Pseudomonas aeruginosa
. Carbapenemase gene acquisition can limit their spectrum of activity, and reports of resistance toward these new molecules are increasing. In this multi-center study, we evaluated the prevalence of resistance to ceftazidime–avibactam (CZA) and comparators among
P. aeruginosa
clinical isolates from bloodstream infections, hospital-acquired or ventilator-associated pneumonia, and urinary tract infections, circulating in Southern Italy. We also investigated the clonality and content of relevant β-lactam resistance mechanisms of CZA-resistant (CZA
R
) isolates. A total of 120
P
.
aeruginosa
isolates were collected. CZA was among the most active β-lactams, retaining susceptibility in the 81.7% of cases, preceded by cefiderocol (95.8%) and followed by ceftolozane–tazobactam (79.2%), meropenem–vaborbactam (76.1%), imipenem–relebactam (75%), and aztreonam (69.6%). Among non-β-lactams, colistin and amikacin were active against 100% and 85.8% of isolates respectively. In CZA
R
strains subjected to whole-genome sequencing (
n
= 18), resistance was mainly due to the expression of metallo-β-lactamases (66.6% VIM-type and 5.5% FIM-1), followed by PER-1 (16.6%) and GES-1 (5.5%) extended-spectrum β-lactamases, mostly carried by international high-risk clones (ST111 and ST235). Of note, two strains producing the PER-1 enzyme were resistant to all β-lactams, including cefiderocol. In conclusion, the CZA resistance rate among
P. aeruginosa
clinical isolates in Southern Italy remained low. CZA
R
isolates were mostly metallo-β-lactamases producers and belonging to ST111 and ST253 epidemic clones. It is important to implement robust surveillance systems to monitor emergence of new resistance mechanisms and to limit the spread of
P. aeruginosa
high-risk clones.

IMPORTANCE

Multidrug-resistant
Pseudomonas aeruginosa
infections are a growing threat due to the limited therapeutic options available. Ceftazidime–avibactam (CZA) is among the last-resort antibiotics for the treatment of difficult-to-treat
P. aeruginosa
infections, although resistance due to the acquisition of transferable β-lactamase genes is increasing. With this work, we report that CZA represents a highly active antipseudomonal β-lactam compound (after cefiderocol), and that metallo-β-lactamases (VIM-type) and extended-spectrum β-lactamases (GES and PER-type) production is the major factor underlying CZA resistance in isolates from Southern Italian hospitals. In addition, we reported that such resistance mechanisms were mainly carried by the international high-risk clones ST111 and ST235.
High-pressure, low-temperature metamorphism preserved in the Indus-Yarlung suture zone of the eastern Himalaya: Overprinting at amphibolite facies and comparison with occurrences in the western Himalaya
Authors: Li Wangchao , Yin Changqing , Yakymchuk Chris , Ding Lin , Li Shun , Qian Jiahui , Gao Peng , Zhang Yanling 
Published: June 2024

Abstract
Eclogite and blueschist are important monitors of subduction zone processes and can record complex polymetamorphic histories during the protracted evolution of subduction systems. However, the rarity of such high-pressure, low-temperature metamorphic rocks in the Indus-Yarlung suture zone of the Himalaya hinders our understanding of the convergence of India and Asia. Here, we examine high-pressure, low-temperature metamorphic rocks from the Milin area of the eastern Indus-Yarlung suture zone. A comprehensive microtextural, mineral chemistry, and phase-equilibrium modeling investigation shows that low-temperature eclogite-facies metapelites with different parageneses (garnet-mica schists) experienced a cold subduction history along a low-thermal gradient, with peak pressures of ~1.6 GPa at ~550 °C. This represents an approximate thermal gradient of ~10 °C km−1. After peak pressure, these rocks underwent a two-step exhumation history with initial exhumation accompanying heating at ~590–600 °C and ~0.8–1.0 Gpa; this was followed by the second stage of exhumation to lower amphibolite-facies conditions. We interpret these low-temperature eclogite-facies metapelites to represent sedimentary rocks that overlaid Neo-Tethyan oceanic crust during subduction. Exhumation paths of high-pressure, low-temperature rocks in the eastern Indus-Yarlung suture zone include an amphibolite-facies overprint, which is absent from high-pressure, low-temperature rocks in the western Indus-Yarlung suture zone. This result is caused by the different timing of exhumation relative to the terminal collision of India and Asia.
Hydrological phenomena related to elevation head on the Arabian Plate
Authors: Stewart S.A. 
Published: June 2024

Abstract
Arabian Plate geology consists of exposed basement in the west overlain by a Phanerozoic sequence in the east that reaches 10 km in thickness and incorporates the Zagros fold-and-thrust belt on the northeast margin of the plate. The Phanerozoic wedge results from Neogene to Recent plate tilt and consequent uplift and erosion, exposing most of the Phanerozoic formations at outcrop, becoming progressively older from the east coast of Saudi Arabia, to the Arabian Shield at an altitude of ~900 m. Reservoirs in this Phanerozoic sequence that have top and base seals but are laterally extensive and open to the land surface have active hydrodynamics, with flow driven up to 1000 km northeastward into the basin by elevation head, discharging into the Arabian Gulf via topseal failures deep in the basin. Deep wells and seismic reflection data originally acquired for hydrocarbon exploration have been repurposed to investigate the basin-scale hydrogeology. This data has revealed previously undescribed phenomena including intra-reservoir haloclines separating fresh and saline water layers more than 1000 m below sea level, and quantified regional hydraulic gradients and an area of over 60,000 km2 where the vadose zone is up to 450 in thickness. Hydraulic gradients have been measured by wells at ~1 m/km in several different reservoirs.
The role of Fe(II)-silicate gel in the generation of Archean and Paleoproterozoic chert
Authors: Tostevin Rosalie , Sevgen Serhat 
Published: June 2024

Abstract
Chert is abundant in Archean and Paleoproterozoic rocks and is commonly densely packed with authigenic Fe(II)-silicate nanoparticles such as greenalite, indicating a close relationship between iron and silica deposition. We investigate the relationship between Fe(II)-silicate minerals and dissolved silica during precipitation, settling, and diagenesis using anoxic synthesis, sorption, and heating experiments. Excess silica is associated with the solid during precipitation, resulting in high molar Si/Fe ratios (&lt;1.52) that exceed that of stoichiometric greenalite (0.67). At pH 8–8.5, silica sorbs to the surface, reaching sorption densities of 0.68 mmol Si per mmol Fe(II)-silicate. Furthermore, excess Si is released upon heating as the Fe(II)-silicate gel crystallizes. We suggest that Fe(II)-silicate minerals acted as an effective Si shuttle between the water column and the sediments in Archean and Paleoproterozoic marine environments, providing sites for the growth of early diagenetic chert, consistent with observations from the sedimentary record. Our results explain the exceptional preservation of greenalite in early chert and indicate that these minerals could provide a robust archive of marine geochemical data.
Determining the age and origin of a Tertiary karstic system by in situ U-Pb geochronology on speleothems
Authors: Moreau Kévin , Brigaud Benjamin , Andrieu Simon , Briais Justine , Quesnel Florence 
Published: June 2024

Abstract
Dating the onset of ancient (&gt;1 Ma) karstification is a challenge. One approach is to date the earliest calcite cements in speleothems. We show the benefits of in situ U-Pb dating directly on thin sections from ancient (ca. 30 Ma) thin (&lt;1 mm) speleothems in the karstified Lower Oligocene lacustrine-palustrine carbonates of the Paris Basin (France), which cannot be dated using other methods. We dated 32 calcite rafts (a type of speleothem), one geopetal cement, and 10 calcite cements precipitated along the karstic walls. The ages of the calcite rafts and cements at 29 ± 1 Ma (Lower Oligocene) fall within the age range of the host deposits (≈29 Ma) previously deduced from palaeontological evidence. We demonstrate that cementation of the carbonate host rock, its dissolution, and the speleothem precipitation occurred within 2 m.y. after deposition. Ostracods and intraclasts trapped within Rupelian calcite rafts clearly indicate that the karst developed deep underground shortly before a phase of lacustrine-palustrine sedimentation at the surface. This very early dissolution episode is attributed to the uplift of the Paris Basin as a result of the far-field intraplate deformation induced by the alpine orogenesis. This study shows that in situ U-Pb geochronology on ancient calcite rafts is a promising technique for the indirect dating of karstification and, more broadly, for dating geodynamic events and diagenetic evolution of sedimentary basins.
Paediatric opioid poisoning in the UK: a retrospective analysis of clinical enquiries to the National Poisons Information Service
Authors: Yard Hannah Elisabeth , Thompson John P , Gray Laurence , Coulson James M , Bradberry Sally M , Sandilands Euan , Thanacoody Ruben , Tuthill David 
Published: June 2024

ObjectiveTo evaluate a decade of reported paediatric opioid poisoning cases in the UK.MethodsThe National Poisons Information Service (NPIS) telephone enquiries database (UK Poisons Information Database) was searched for calls regarding opioid poisoning in children under 18 years from 2012 to 2021. The NPIS online clinical guidance database TOXBASE was searched for accesses relating to opioids for both adults and children. The Office of National Statistics provided paediatric data for hospital admissions and deaths in those aged under 20 years old due to opioids.ResultsThe NPIS received 426 774 telephone enquiries from 2012 to 2021 from across the UK, 3600 in relation to opioid exposures regarding children under 18 years. Annual telephone enquiries regarding paediatric opiate poisoning reduced year on year, from around 450 to 300 calls/year. A rise in all age TOXBASE annual accesses relating to opioids from 71 642 in 2012 to 87 498 in 2021 was noted, a total of 838 455 during the study period. Hospital admissions from opioid poisoning remained consistent, with around 1500 admissions/year. Deaths were uncommon, but averaged 18 deaths annually. Co-codamol was the most reported substance to NPIS, with 1193 calls (36.5%), followed by codeine with 935 (26.1%).ConclusionsOpioid poisoning in children is not uncommon. There is a general downward trend in telephone enquiries to NPIS, but many childhood exposures may have been dealt with through consultations via TOXBASE, where accesses relating to opioids have increased. Unfortunately, children still die from opioid exposure each year in the UK and this figure has changed little during 2012–2021.
Development of a survey to support assessment of safety learning systems
Authors: Mahmoud Hassan Assem , Mulpuru Sunita , Thavorn Kednapa , McIsaac Daniel , Forster Alan J 
Published: June 2024

BackgroundPatient safety learning systems play a critical role in supporting safety culture in healthcare organisations. A lack of explicit standards leads to inconsistent implementation across organisations, causing uncertainty about their roles and impact. Organisations can address inconsistent implementation by using a self-assessment tool based on agreed-on best practices. Therefore, we aimed to create a survey instrument to assess an organisation’s approach to learning from safety events.MethodsThe foundation for this work was a recent systematic review that defined features associated with the performance of a safety learning system. We organised features into themes and rephrased them into questions (items). Face validity was checked, which included independent pre-testing to ensure comprehensibility and parsimony. It also included clinical sensibility testing in which a representative sample of leaders in quality at a large teaching hospital (The Ottawa Hospital) answered two questions to judge each item for clarity and necessity. If more than 20% of respondents judged a question unclear or unnecessary, we modified or removed that question accordingly. Finally, we checked the internal consistency of the questionnaire using Cronbach’s alpha.ResultsWe initially developed a 47-item questionnaire based on a prior systematic review. Pre-testing resulted in the modification of 15 of the questions, 2 were removed and 2 questions were added to ensure comprehensiveness and relevance. Face validity was assessed through yes/no responses, with over 80% of respondents confirming the clarity and 85% the necessity of each question, leading to the retention of all 47 questions. Data collected from the five-point responses (strongly disagree to strongly agree) for each question were used to assess the questionnaire’s internal consistency. The Cronbach’s alpha was 0.94, indicating a high internal consistency.ConclusionThis self-assessment questionnaire is evidence-based and on preliminary testing is deemed valid, comprehensible and reliable. Future work should assess the range of survey responses in a large sample of respondents from different hospitals.
Neighbourhood inequities in the availability of retailers selling tobacco products: a systematic review
Authors: Kong Amanda Y , Lee Joseph G L , Halvorson-Fried Sarah M , Sewell Kerry B , Golden Shelley Diane , Henriksen Lisa , Herbert Lily , Ribisl Kurt M 
Published: June 2024

ObjectiveTo examine inequities in tobacco retailer availability by neighbourhood-level socioeconomic, racial/ethnic and same-sex couple composition.Data sourcesWe conducted a 10 November 2022 search of PubMed, PsycINFO, Global Health, LILACS, Embase, ABI/Inform, CINAHL, Business Source Complete, Web of Science and Scopus.Study selectionWe included records from Organisation for Economic Co-operation and Development member countries that tested associations of area-level measures of tobacco retailer availability and neighbourhood-level sociodemographic characteristics. Two coders reviewed the full text of eligible records (n=58), including 41 records and 205 effect sizes for synthesis.Data extractionWe used dual independent screening of titles, abstracts and full texts. One author abstracted and a second author confirmed the study design, location, unit of analysis, sample size, retailer data source, availability measure, statistical approach, sociodemographic characteristic and unadjusted effect sizes.Data synthesisOf the 124 effect sizes related to socioeconomic inequities (60.5% of all effect sizes), 101 (81.5%) indicated evidence of inequities. Of 205 effect sizes, 69 (33.7%) tested associations between retailer availability and neighbourhood composition of racially and ethnically minoritised people, and 57/69 (82.6%) documented inequities. Tobacco availability was greater in neighbourhoods with more Black, Hispanic/Latine and Asian residents (82.8%, 90.3% and 40.0% of effect sizes, respectively). Two effect sizes found greater availability with more same-sex households.ConclusionsThere are stark inequities in tobacco retailer availability. Moving beyond documenting inequities to partnering with communities to design, implement, and evaluate interventions that reduce and eliminate inequities in retail availability is needed to promote an equitable retail environment.PROSPERO registration numberCRD42019124984.