bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction patterns and assembly mechanisms of dinoflagellates and diatoms in a coastal bay suffering from long-term eutrophication
Authors: Miao Wenfei , Wang Shuqi , Lin Tenghui , Yan Yi , Bao Zhen , Zhang Demin , Jiang Zhibing , Zhang Huajun 
Published: June 2024

ABSTRACT

Dinoflagellates and diatoms are highly prevalent and ecologically important phytoplankton in coastal waters, greatly contributing to primary productivity in marine ecosystems. Although their composition and diversity have been extensively elucidated in the open ocean, their interaction patterns and community assembly in long-term eutrophic coastal waters remain poorly understood. This investigation aimed to elucidate the seasonal successional patterns of dinoflagellates and diatoms by 18S rRNA gene amplicon sequencing in a semi-enclosed bay. The results revealed that dinoflagellate and diatom communities have pronounced seasonal succession patterns, which are primarily associated with temperature. Furthermore, the most prevalent species throughout the year were
Heterocapsa rotundata
and
Skeletonema costatum
. Moreover, the assembly of dinoflagellate and diatom communities was mainly dominated by stochastic processes, with drift being the major factor. The co-occurrence of dinoflagellates and diatoms showed seasonal patterns, with the highest interactions observed in autumn. In addition, interactions of Syndiniales with dinoflagellates and diatoms highlighted the roles of parasites in eutrophic conditions.
Flavobacteriaceae
and
Rhodobacteraceae
are the bacterial taxa that most frequently interacted with dinoflagellates and diatoms, with interactions between dinoflagellates and bacteria being more complex than those between diatoms and bacteria. Overall, this study provides results that deepen our understanding of the phytoplankton dynamics in coastal eutrophic waters.

IMPORTANCE
Dinoflagellates and diatoms are major phytoplankton groups in coastal waters. The composition and diversity of dinoflagellates and diatoms in the open ocean have been well documented; however, it remains uncertain to what extent their adaptation to long-term eutrophic conditions influences their response to environmental disturbances. Here, we investigated the interactions and assembly processes of dinoflagellates and diatoms in a eutrophic bay throughout the whole year. Our findings revealed that interactions between dinoflagellates and diatoms are primarily shaped by seasonal transitions, while prolonged eutrophic conditions tend to amplify stochastic processes in community assembly. These findings provide novel perspectives on the influence of long-term eutrophication on phytoplankton dynamics within eutrophic waters.
Distinct oral-associated gastric microbiota and
Helicobacter pylori
communities for spatial microbial heterogeneity in gastric cancer
Authors: Lei Lei , Zhao Lin-Yong , Cheng Ran , Zhang Hongyu , Xia Mengying , Chen Xiao-Long , Kudriashov Valentin , Liu Kai , Zhang Wei-Han , Jiang Han , Chen Yi , Zhu Liang , Zhou Hongmei , Yang Kun , Hu Tao , Hu Jian-Kun 
Published: June 2024

ABSTRACT

The gastric microbial community plays a fundamental role in gastric cancer (GC), and the two main anatomical subtypes of GC, non-cardia and cardia GC, are associated with different risk factors (
Helicobacter pylori
for non-cardia GC). To decipher the different microbial spatial communities of GC, we performed a multicenter retrospective analysis to characterize the gastric microbiota in 223 GC patients, including
H. pylori
-positive or -negative patients, with tumors and paired adjacent normal tissues, using third-generation sequencing. In the independent validation cohort, both dental plaque and GC tumoral tissue samples were collected and sequenced. The prevalence of
H. pylori
and oral-associated bacteria was verified using fluorescence
in situ
hybridization (FISH) assays in GC tumoral tissues and matched nontumoral tissues. We found that the vertical distribution of the gastric microbiota, at the upper, middle, and lower third sites of GC, was likely an important factor causing microbial diversity in GC tumor tissues. The oral-associated microbiota cluster, which included
Veillonella parvula
,
Streptococcus oralis
, and
Prevotella intermedia
, was more abundant in the upper third of the GC. However,
H. pylori
was more abundant in the lower third of the GC and exhibited a significantly high degree of microbial correlation. The oral-associated microbiota module was co-exclusive with
H. pylori
in the lower third site of the GC tumoral tissue. Importantly,
H. pylori
-negative GC patients with oral-associated gastric microbiota showed worse overall survival, while the increase in microbial abundance in
H. pylori
-positive GC patients showed no difference in overall survival. The prevalence of
V. parvula
in both the dental plaque and GC tissue samples was concordant in the independent validation phase. We showed that the oral-associated species
V. parvula
and
S. oralis
were correlated with overall survival. Our study highlights the roles of the oral-associated microbiota in the upper third of the GC. In addition, oral-associated species may serve as noninvasive screening tools for the management of GC and an independent prognostic factor for
H. pylori
-negative GCs.

IMPORTANCE

Our study highlights the roles of the oral-associated microbiota in the upper third of gastric cancer (GC).We showed that the oral-associated species
Veillonella parvula
and
Streptococcus oralis
were correlated with overall survival. In addition, oral-associated species may serve as noninvasive screening tools for the management of GC and an independent prognostic factor for
Helicobacter pylori
-negative GCs.
Distinct microbial nitrogen cycling processes in the deepest part of the ocean
Authors: Huang Yuhan , Zhang Xinxu , Xin Yu , Tian Jiwei , Li Meng 
Published: June 2024

ABSTRACT

The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600–10,500 m below sea level (mbsl)], surface sediments [0–46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200–306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment,
via
their CO
2
fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome
c
oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing
Ketobacter
species can fix inert N
2
released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.

IMPORTANCE

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O
2
fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing
Ketobacter
species could fix N
2
in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.
zDB: bacterial comparative genomics made easy
Authors: Marquis Bastian , Pillonel Trestan , Carrara Alessia , Bertelli Claire 
Published: June 2024

ABSTRACT

The analysis and comparison of genomes rely on diﬀerent tools for tasks such as annotation, orthology prediction, and phylogenetic inference. Most tools are specialized for a single task, and additional eﬀorts are necessary to integrate and visualize the results. To ﬁll this gap, we developed zDB, an application integrating a Nextﬂow analysis pipeline and a Python visualization platform built on the Django framework. The application is available on GitHub (
https://github.com/metagenlab/zDB
) and from the bioconda channel. Starting from annotated Genbank ﬁles, zDB identiﬁes orthologs and infers a phylogeny for each orthogroup. A species phylogeny is also constructed from shared single-copy orthologs. The results can be enriched with Pfam protein domain prediction, Cluster of Orthologs Genes and Kyoto Encyclopedia of Genes and Genomes annotations, and Swissprot homologs. The web application allows searching for speciﬁc genes or annotations, running Blast queries, and comparing genomic regions and whole genomes. The metabolic capacities of organisms can be compared at either the module or pathway levels. Finally, users can run queries to examine the conservation of speciﬁc genes or annotations across a chosen subset of genomes and display the results as a list of genes, Venn diagram, or heatmaps. Those features make zDB useful for both bioinformaticians and researchers more accustomed to laboratory research.

IMPORTANCE
Genome comparison and analysis rely on many independent tools, leaving to scientists the burden to integrate and visualize their results for interpretation. To alleviate this burden, we have built zDB, a comparative genomics tool that includes both an analysis pipeline and a visualization platform. The analysis pipeline automates gene annotation, orthology prediction, and phylogenetic inference, while the visualization platform allows scientists to easily explore the results in a web browser. Among other features, the interface allows users to visually compare whole genomes and targeted regions, assess the conservation of genes or metabolic pathways, perform Blast searches, or look for speciﬁc annotations. Altogether, this tool will be useful for a broad range of applications in comparative studies between two and hundred genomes. Furthermore, it is designed to allow sharing of data sets easily at a local or international scale, thereby supporting exploratory analyses for non-bioinformaticians on the genome of their favorite organisms.
On the road to genomically defining bacterial intra-species units
Authors: Castillo-Ramírez Santiago 
Published: June 2024

ABSTRACT

Over almost three decades, average nucleotide identity (ANI) analysis has been instrumental in operationally defining species in bacteria. However, barely any attention has been paid to soundly defining intra-species units employing ANI analyses until recently. Notably, some very recent publications are good steps forward in that direction. The level of granularity provided by these intra-species units will be relevant to understanding the eco-evolutionary dynamics and transmission of bacterial lineages and mobile genetic elements, antibiotic resistance, and virulence genes. These intra-species units will undoubtedly advance the genomic epidemiology of many bacterial pathogens. In the coming years, we anticipate that many studies will implement ANI-based definitions of different intra-species units, such as strains or sequence types, for many different bacterial species.
Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie
Authors: Denison Elizabeth R. , Zepernick Brittany N. , McKay R. Michael L. , Wilhelm Steven W. 
Published: June 2024

ABSTRACT

Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (
Caudoviricetes
), giant viruses (
Nucleocytoviricota
, or NCLDV), and RNA viruses (
Orthornavirae
). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.

IMPORTANCE
As seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems.
Pilot study to evaluate the use of remote patient monitoring to guide the timing of valve intervention in patients with severe asymptomatic aortic stenosis (APRAISE-AS): study protocol for a randomised controlled trial delivered in two tertiary cardiac centres in the UK
Authors: Khan Nazish , Steeds Richard P , Kyte Derek , Fabritz Larissa , Collis Philip , Chua Winnie , Stubbs Clive , Mehta Samir , Sun Yongzhong , Nulty Mary , Kirkham Katie , Cotton James M 
Published: June 2024

IntroductionAortic stenosis (AS) is common affecting >13% of adults over the age of 75 years. In people who develop symptoms, without valve replacement, prognosis is dismal with mortality as high as 50% at 1 year. In asymptomatic patients, the timing of valve intervention is less well defined and a strategy of watchful waiting is recommended. Many, however, may develop symptoms and attribute this to age related decline, rather than worsening AS. Timely intervention in asymptomatic severe AS is critical, since delayed intervention often results in poor outcomes. Proactive surveillance of symptoms, quality of life and functional capacity should enable timely identification of people who will benefit from aortic valve replacement. There are no data however, to support the clinical and cost effectiveness of such an approach in a healthcare setting in the UK. The aim of this pilot trial is to test the feasibility of a full-scale randomised controlled trial (RCT) to determine the utility of proactive surveillance in people with asymptomatic severe AS to guide the timing of intervention.Methods and analysisAPRAISE-AS is a multi-centre, non-blinded, two-arm, parallel group randomised controlled trial of up to 66 participants aged >18 years with asymptomatic severe AS. Participants will be randomised to either standard care or standard care supplemented with the APRAISE-AS intervention. Primary outcomes will capture; adherence to and participant acceptability of the intervention, recruitment and retention rates, and completeness of data collection. The findings will be used to inform the sample size and most appropriate outcome measure(s) for a full-scale RCT and health economic evaluation.Ethics and disseminationEthical approval was granted by the Black Country REC, reference: 22/WM/0214. Results will be submitted for publication in peer-reviewed journals and disseminated at local, regional and national meetings where appropriate.Trial registration numberISRCTN19413194.
Frontline nursing staff’s perceptions of intravenous medication administration: the first step toward safer infusion processes—a qualitative study
Authors: Uramatsu Masashi , Kimura Naoko , Kojima Takako , Fujisawa Yoshikazu , Oto Tomoko , Barach Paul 
Published: June 2024

ObjectivesIntravenous medication errors continue to significantly impact patient safety and outcomes. This study sought to clarify the complexity and risks of the intravenous administration process.DesignA qualitative focus group interview study.SettingFocused interviews were conducted using process mapping with frontline nurses responsible for medication administration in September 2020.ParticipantsFront line experiened nurses from a Japanese tertiary teaching hospital.Primary and secondary outcome measuresThe primary outcome measure was to identify the mental models frontline nurses used during intravenous medication administration, which influence their interactions with patients, and secondarily, to examine the medication process gaps between the mental models nurses perceive and the actual defined medication administration process.ResultsWe found gaps between the perceived clinical administration process and the real process challenges with an emphasis on the importance of verifying to see if the drug was ordered for the patient immediately before its administration.ConclusionsThis novel and applied improvement approach can help nurses and managers better understand the process vulnerability of the infusion process and develop a deeper understanding of the administration steps useful for reliably improving the safety of intravenous medications.
Optic nerve sheath diameter as a non-invasive tool to detect clinically relevant raised intracranial pressure in children: an observational analytical study
Authors: Bansal Anmol , Tiwari Lokesh Kumar , Kumar Pradeep , Jain Raina 
Published: June 2024

BackgroundRaised intracranial pressure (ICP) contributes to approximately 20% of the admissions in the paediatric intensive care unit (PICU) in our setting. Timely identification and treatment of raised ICP is important to prevent brain herniation and death in such cases. The objective of this study was to examine the role of optic nerve sheath diameter (ONSD) in detecting clinically relevant raised ICP in children.MethodsA hospital-based observational analytical study in a PICU of a tertiary care institute in India on children aged 2–14 years. ONSD was measured in all children on three time points that is, day 1, day 2 and between day 4 and 7 of admission. ONSD values were compared between children with and without clinical signs of raised ICP.ResultsOut of 137 paediatric patients recruited, 34 had signs of raised ICP. Mean ONSD on day 1 was higher in children with signs of raised ICP (4.99±0.57 vs 4.06±0.40; p<0.01). Mean ONSD on day 2 also was higher in raised ICP patients (4.94±0.55 vs 4.04±0.40; p<0.01). The third reading between days 4 and 7 of admission was less than the first 2 values but still higher in raised ICP patients (4.48±1.26 vs 3.99±0.57; p<0.001). The cut-off ONSD value for detecting raised ICP was 4.46 mm on the ROC curve with an area under curve 0.906 (95% CI 0.844 to 0.968), 85.3% sensitivity and 86.4% specificity. There was no difference in ONSD between the right and the left eyes at any time point irrespective of signs of raised ICP.ConclusionWe found that measurement of ONSD by transorbital ultrasound was able to detect clinically relevant raised ICP with an excellent discriminatory performance at the cut-off value of 4.46 mm.
Children with medical complexity receiving home healthcare devices in Japan: a retrospective cohort study
Authors: Shinjo Daisuke , Yotani Nobuyuki , Ito Ai , Isayama Tetsuya 
Published: June 2024

BackgroundLimited evidence exists regarding children receiving home healthcare devices (HHDs). This study aimed to describe the range and type of HHD use by children with chronic medical conditions in Japan and explore factors leading to increased use of these devices.MethodsThis retrospective cohort study was conducted using data from the National Database of Health Insurance Claims and Specific Health Checkups of Japan. Children receiving HHD aged ≤18 years between April 2011 and March 2019 were included. Children newly administered HHD between 2011 and 2013 were followed up for 5 years, and logistic regression analysis was performed to assess the relationship between increased HHD use and each selected risk factor (comorbidity or types of HHD). The models were adjusted for age category at home device introduction, sex and region.ResultsOverall, 52 375 children receiving HHD were identified. The number (proportion) of children receiving HHD increased during the study period (11 556 [0.05%] in 2010 and 25 593 [0.13%] in 2018). The most commonly administered HHD was oxygen (51.0% in 2018). Among the 12 205 children receiving HHD followed up for 5 years, 70.4% and 68.3% who used oxygen or continuous positive airway pressure, respectively, were released from the devices, while only 25.8% who used mechanical ventilation were released from the device. The following diagnosis/comorbidities were associated with increased HHD use: other neurological diseases (OR): 2.85, 95% CI): 2.54–3.19), cerebral palsy (OR: 2.16, 95% CI: 1.87 to 2.49), congenital malformations of the nervous system (OR: 1.70, 95% CI: 1.34 to 2.13) and low birth weight (OR: 1.68, 95% CI: 1.41 to 2.00).ConclusionsThis study provides nationwide population-based empirical data to clarify the detailed information regarding children receiving HHD in Japan. This information could assist healthcare professionals in improving the quality of life of these children and their families and help health policymakers consider measures.