bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft annotated genome of the entomopathogenic fungus
Metarhizium pingshaense
isolated from
Spodoptera
species
Authors: Apirajkamol Nonthakorn (Beatrice) , Bachler Andreas , Tay Wee Tek , Mainali Bishwo , Taylor Phillip , Walsh Thomas Kieran 
Published: December 2024

ABSTRACT

The entomopathogenic fungus
Metarhizium pingshaense
infects diverse insect host species. We present an annotated draft genome of
M. pingshaense
(Commonwealth Scientific and Industrial Research Organisation [CSIRO] strain M-1000) isolated from a
Spodoptera
species individual, thereby contributing to future research of
M. pingshaense
as a potential biological control agent.
Complete genome sequence of
Bacillus subtilis
bacteriophage Adastra
Authors: Herbig Andrew F. , Pendergrass Eliana M. 
Published: December 2024

ABSTRACT

Adastra is a lytic bacteriophage that infects
Bacillus subtilis
. Here, we report the sequencing and annotation of the 136,306-bp genome of Adastra and its similarity to other myophages in the SPO1 family.
Draft genome sequence of
Modicisalibacter
sp. strain Wilcox isolated from produced water
Authors: Ajagbe Damilare , Marsh William , Murdoch Robert , Fathepure Babu 
Published: December 2024

ABSTRACT

The draft genome sequence of
Modicisalibacter
sp. strain Wilcox, isolated from produced water, is presented. The genome is 3.6 Mb in size with 3,283 protein-coding genes, including genes for hydrocarbon degradation, heavy metal resistance, and adaptation to high salinity. This genome provides insights into molecular mechanisms of hydrocarbon degradation under hypersaline conditions.
Uncovering novel functions of the enigmatic, abundant, and active
Anaerolineae
in a salt marsh ecosystem
Authors: Payne Paige E. , Knobbe Loren N. , Chanton Patricia , Zaugg Julian , Mortazavi Behzad , Mason Olivia U. 
Published: December 2024

ABSTRACT

Anaerolineae
, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel
Anaerolineae
metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing
Anaerolineales
,
Promineifilales
, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and
Caldilineales
orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all
Anaerolineae
encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of
Anaerolineae
expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh
Anaerolineae
in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.

IMPORTANCE

Given that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular,
Anaerolineae
are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an ‘omics-based approach, we determined that
Anaerolineae
are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly,
Anaerolineae
encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of
Anaerolineae
appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.
Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity
Authors: Fang Yue , Meng Lingjie , Xia Jun , Gotoh Yasuhiro , Hayashi Tetsuya , Nagasaki Keizo , Endo Hisashi , Okazaki Yusuke , Ogata Hiroyuki 
Published: December 2024

ABSTRACT

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display seasonal fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics of these viruses remain largely unknown. In this study, we investigated the dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed computational pipeline generated 1,065 high-quality genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community structure at the study site and distinct dynamics of viral populations that were classified as persistent (
n
= 9), seasonal (
n
= 389), sporadic (
n
= 318), or others. By profiling the intra-species nucleotide-resolved microdiversity through read mapping, we also identified year-round recovery dynamics at subpopulation level for viruses classified as persistent or seasonal. Our results further indicated that giant viruses with broader niche breadth tended to exhibit higher levels of microdiversity. We argue that greater microdiversity of viruses likely enhances adaptability and thus survival under the virus–host arms race during prolonged interactions with their hosts.

IMPORTANCE
Recent genome-resolved metagenomic surveys have uncovered the vast genomic diversity of giant viruses, which play significant roles in aquatic ecosystems by acting as bloom terminators and influencing biogeochemical cycles. However, the relationship between the ecological dynamics of giant viruses and underlying genetic structures of viral populations remains unresolved. In this study, we performed deep metagenomic sequencing of seawater samples collected across a time-series from a coastal area in Japan. The results revealed a significant positive correlation between microdiversity and temporal persistence of giant virus populations, suggesting that population structure is a crucial factor for adaptation and survival in the interactions with their hosts.
Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase
Authors: Lim Hyun Gyu , Gao Ye , Rychel Kevin , Lamoureux Cameron , Lou Xuwen A. , Palsson Bernhard O. 
Published: December 2024

ABSTRACT

The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With
Escherichia coli
K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators (
e.g.
, Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria.

IMPORTANCE
Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.
Neospora caninum
infection specifically suppresses the expression of a host lncRNA
XR_001919077.1
to facilitate parasite propagation by modulating host cell mitochondrial function and autophagy
Authors: Zhao Shan-Shan , Tao De-Liang , Chen Jin-Ming , Zhang Ming-Yi , Yang Xin , Song Jun-Ke , Liu Qun , Zhao Guang-Hui 
Published: December 2024

ABSTRACT

Neospora caninum
is one of the most common pathogens causing reproductive failure in ruminants (e.g., cattle and goats) worldwide. However, due to a poor understanding of the pathogenic mechanisms of
N. caninum
infection, no effective drugs and vaccines are currently available. Long non-coding RNAs (lncRNAs) have been reported to be important regulators involved in a great number of physiological and pathological processes. Our previous study found that
N. caninum
infection induced significantly aberrant expression of lncRNA profiles in caprine endometrial epithelial cells (EECs). In the present study, we found that
N. caninum
infection specifically suppressed the expression of a novel lncRNA,
XR_001919077.1
, and knockdown of
XR_001919077.1
with small interfering RNA significantly promoted the propagation of
N. caninum
in caprine EECs. Rapid amplification of cDNA ends analysis generated six splice variants of
XR_001919077.1
, with lengths ranging from 592 to 694 nt. Transfection of the full length of each variant markedly inhibited the propagation of
N. caninum
in caprine EECs. Further study suggested that
XR_001919077.1
acted as a sponge of Chi-miR-93-5p to promote the expression of
sirt1
, and the
XR_001919077.1
/Chi-miR-93-5p/
sirt1
axis significantly delayed the
in vitro
growth of
N. caninum
in caprine EECs by regulating host cell mitochondrial function and autophagy. Our findings provide a novel insight to understand the interactions between
N. caninum
and host cells.

IMPORTANCE

The uterus is an indispensable reproductive organ for embryo implantation and fetal growth. The endometrium is more vulnerable to infection by pathogenic microorganisms resulting in an increased risk of miscarriage.
Neospora caninum
is one of the most common pathogens causing miscarriage in ruminants and is able to naturally inhabit the uterus, with
N. caninum
tissue cysts found in the endometrium. Recent advances in
N. caninum
research have revealed aberrant expression of long non-coding RNA (lncRNA) profiles in infected caprine endometrial epithelial cells. In the present study,
N. caninum
, but not
Toxoplasma gondii,
which has similar morphological and biological features to
N. caninum
, specifically suppresses the expression of a host lncRNA,
XR_ 001919077.1
, to impair host’s defense through the competitive endogenous RNA mechanism to modulate the host cell mitochondrial function and autophagy to facilitate parasite propagation. The findings suggest a novel immune evasion strategy of
N. caninum
to facilitate intracellular propagation and provide an alternative path to develop control strategies against neosporosis.
Identifying and counteracting fraudulent responses in online recruitment for health research: a scoping review
Authors: Comachio Josielli , Poulsen Adam , Bamgboje-Ayodele Adeola , Tan Aidan , Ayre Julie , Raeside Rebecca , Roy Rajshri , O’Hagan Edel 
Published: December 2024

ObjectivesThis study aimed to describe how health researchers identify and counteract fraudulent responses when recruiting participants online.DesignScoping review.Eligibility criteriaPeer-reviewed studies published in English; studies that report on the online recruitment of participants for health research; and studies that specifically describe methodologies or strategies to detect and address fraudulent responses during the online recruitment of research participants.Sources of evidenceNine databases, including Medline, Informit, AMED, CINAHL, Embase, Cochrane CENTRAL, IEEE Xplore, Scopus and Web of Science, were searched from inception to April 2024.Charting methodsTwo authors independently screened and selected each study and performed data extraction, following the Joanna Briggs Institute’s methodological guidance for scoping reviews and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews guidelines. A predefined framework guided the evaluation of fraud identification and mitigation strategies within the studies included. This framework, adapted from a participatory mapping study that identified indicators of fraudulent survey responses, allowed for systematic assessment and comparison of the effectiveness of various antifraud strategies across studies.Results23 studies were included. 18 studies (78%) reported encountering fraudulent responses. Among the studies reviewed, the proportion of participants excluded for fraudulent or suspicious responses ranged from as low as 3% to as high as 94%. Survey completion time was used in six studies (26%) to identify fraud, with completion times under 5 min flagged as suspicious. 12 studies (52%) focused on non-confirming responses, identifying implausible text patterns through specific questions, consistency checks and open-ended questions. Four studies examined temporal events, such as unusual survey completion times. Seven studies (30%) reported on geographical incongruity, using IP address verification and location screening. Incentives were reported in 17 studies (73%), with higher incentives often increasing fraudulent responses. Mitigation strategies included using in-built survey features like Completely Automated Public Turing test to tell Computers and Humans Apart (34%), manual verification (21%) and video checks (8%). Most studies recommended multiple detection methods to maintain data integrity.ConclusionThere is insufficient evaluation of strategies to mitigate fraud in online health research, which hinders the ability to offer evidence-based guidance to researchers on their effectiveness. Researchers should employ a combination of strategies to counteract fraudulent responses when recruiting online to optimise data integrity.
Sickle cell retinopathy among Ghanaian high school students: a school-based screening
Authors: Sedhom Jessica , Ahmed Akwasi , DesLauriers Andrew , Ahmed Eunice Agyeman , Ameyaw Baah Christabel , Ackah Peter , Appiah-Berko Maame Temah , Appiagyei Marion , Yeboah-Arhin Obed , Shah Sarthak , Pershing Suzann , Tabin Geoffrey C , Mruthyunjaya Prithvi , Brant Arthur 
Published: December 2024

IntroductionSickle cell disease (SCD) remains a significant health concern, particularly in Ghana and Sub-Saharan African countries. School-based ocular screenings provide a unique opportunity for early detection of sickle cell retinopathy (SCR).MethodsStudents from five major schools in the Kumasi Metropolitan District of Ghana were included. Research assistants educated students on SCD and type 1 diabetes (T1DM) during school-wide assemblies, emphasising destigmatisation and vision health. Students completed questionnaires to self-report SCD or T1DM. Those who self-reported underwent in-depth interviews and dilated fundus exams (DFE).ResultsOf 17 987 total student population, 8168 students completed the survey (45.4% response rate) of which 2.4% of students were aware of their SCD status, while most 69.3% were unaware. No students reported having T1DM. 24 students identified as having SCD (14 haemoglobin SS and 10 HbSC) resulting in a prevalence of 0.07% and 0.05% for SS and SC, respectively. Among the SCD cohort, four had Proliferative SCR (PSCR). Of the students with stage 3 PSCR, one was 15 years old with SS genotype and bilateral stage 3 PSCR; another was 18 years old with SC disease, unilateral stage 3 PSCR. Only one SCD patient (SS genotype) had a history of previous DFE. 20.8% of SCD students were aware of SCD ocular complications and 75% felt uncomfortable sharing their SCD status.ConclusionsWe conclude (1) an alarmingly low rate of self-reporting SCD (11× and 24× lower than expected for SS and SC-SCD, respectively), (2) low health literacy given 0% of students with SC-SCD had previously undergone a DFE and (3) 17% of students had PSCR and 8% of students had treatment-warranted PSCR (stage 3). These findings highlight the need for universal SCD screening, improved health education on the ocular complications of SCD and routine school-based vision screenings for patients with SCD.
How pragmatic are randomised controlled trials evaluating minimally invasive surgery for oesophageal cancer? A methodological review of trial design using the Pragmatic-Explanatory Continuum Indicator Summary-2 (PRECIS-2) tool
Authors: Chalmers Katy , Cousins Sian , Blencowe Natalie S , Blazeby Jane 
Published: December 2024

BackgroundSurgical interventions are inherently complex and designing and conducting surgical randomised controlled trials (RCTs) can be challenging. Trial design impacts the applicability of trial results to clinical practice. Given the recent growth in numbers of surgical RCTs, there is a need to better understand the validity and applicability of trials in this field.ObjectivesTo examine the applicability and validity of RCTs comparing minimally invasive and open surgery for oesophageal cancer and to delineate areas for future research.Eligibility criteriaRCTs comparing open with minimal invasive oesophagectomy, published January 2012–June 2023. Abstracts, pilot and feasibility studies, and systematic reviews were excluded.Sources of evidenceThree sequential searches of Ovid MEDLINE, Embase and CENTRAL electronic databases and clinical trials registry databases.Charting methodsTwo independent reviewers screened the articles and used appropriate, validated tools (Pragmatic-Explanatory Continuum Indicator Summary-2 (PRECIS-2) and Risk of Bias 2) to assess study quality. Trials were considered pragmatic if they were conducted in multiple centres and had a mean score of four or above on the PRECIS-2.ResultsNine RCTs were identified. One was judged to be pragmatic. The remaining eight were limited by narrow eligibility criteria, being single-centred or having strict intervention protocols. Two studies were low risk of bias, of which one was pragmatic, and three high, due to unblinded outcome assessment. The remaining four studies were of ‘some concern’ due to poor reporting.ConclusionsOnly one trial identified in this review was considered pragmatic. More lenient criteria, as used in other reviews, may increase the proportion. There is a need for clearer guidance on the cut-off values that define a trial as pragmatic. It is recommended that the intended purpose of the trial, whether explanatory or pragmatic, receives more attention during surgical trial study design and conduct.
Modified Delphi expert elicitation of the clinical and economic burden of obstructive hypertrophic cardiomyopathy in England and Northern Ireland
Authors: Hurst Michael , Zema Carla , Krause Taryn , Sandler Belinda , Lemmer Teresa , Noon Kathleen , Alexander Deepak , Osman Faizel 
Published: December 2024

ObjectiveTo estimate the resource use of patients with obstructive hypertrophic cardiomyopathy (HCM), stratified by New York Heart Association (NYHA) class, in the English and Northern Irish healthcare systems via expert elicitation.DesignModified Delphi framework methodology.SettingUK HCM secondary care centres (n=24).ParticipantsCardiologists who actively treated patients with HCM were eligible, of whom 10 from English and Northern Irish centres participated. Recruitment of participants to the study was limited to one expert per site.MethodsResponses were collected by electronic quantitative survey. Following the discussion of survey results in a virtual panel, aggregated responses from a final survey were analysed and stratified by NYHA class. Data were analysed without (base case) and with (scenario) interventional cardiologists who conduct septal reduction therapies (SRTs).ResultsBased on expert opinion, as NYHA class increased, so did the mean±95% CI number of primary care consultations (classes I–IV: 0.64±0.35; 1.07±0.33; 3.29±1.02; 6.00±2.46, respectively) per patient per annum. This was also observed across all types of secondary care consultations, such as mean±95% CI number of cardiovascular-related outpatient visits (classes I–IV: 0.69±0.26; 0.88±0.24; 2.13±0.78; 3.25±1.42, respectively) and inpatient admissions (classes I–IV: 0.01±0.01; 0.04±0.07; 0.94±0.39; 1.90±0.65, respectively) per annum. Patients in NYHA class III were most likely to undergo SRT in their lifetime (mean±95% CI proportion of patients:17.25%±7.19% or 26.30%±13.61% including interventionalists). Across NYHA, experts estimated that septal myectomy was more costly than alcohol septal ablation (mean±95% CI: £15 675±£10 556 vs £6750±£5900, respectively). Prescription of beta-blockers was higher than calcium channel blockers, irrespective of NYHA class.ConclusionsTreatment of obstructive HCM is associated with a substantial clinical and economic burden in England and Northern Ireland; the burden of the disease increasing with NYHA class is driven by the need for intensive disease management, hospitalisations and the potential burden of undertaking SRTs.
Development of measures to assess listening-related effort and fatigue in daily life among hearing aid users: protocol for a quantitative field trial
Authors: Micula Andreea , Høy Konvalinka Christensen Jeppe , Wendt Dorothea , Innes-Brown Hamish , Johnsrude Ingrid , Apps Matthew , Dau Torsten , Flensborg-Madsen Trine 
Published: December 2024

IntroductionIndividuals with hearing loss and hearing aid users report higher levels of listening effort and fatigue in daily life compared with those with normal hearing. However, there is a lack of objective measures to evaluate these experiences in real-world settings. Recent studies have found that higher sound pressure levels (SPL) and lower signal-to-noise ratios (SNR) are linked to increased heart rate and decreased heart rate variability, reflecting the greater effort required to process auditory information. This study aims to establish physiological and acoustic predictors of self-reported listening effort and fatigue in daily life. Additionally, the moderating effects of cognitive abilities, personality traits, stress, fatigue, suprathreshold abilities, noise annoyance, lifestyle and health on the development of listening effort and fatigue will be investigated.Methods and analysisA 4-week field trial will be conducted, in which physiological responses will be continuously recorded using Empatica Embrace Plus wristbands. Ambient acoustics will be captured every 20 s via the participants’ (n=60) personal hearing aids, and the participants will provide self-reported momentary assessments through a mobile app throughout the day. Questionnaires will be used to assess personality traits, fatigue, stress and noise annoyance, and gather relevant background information. Cognitive and suprathreshold abilities will also be evaluated. Associations between physiological responses, ambient acoustics and momentary assessments, as well as the potential influence of participant characteristics, will be analysed using multilevel regression models and time-series analyses.Ethics and disseminationInformed consent will be obtained from all participants. The study has been exempted from ethical application by the Science Ethics Committee for the Capital Region of Denmark (journal no. F-23028367). Results will be presented at conferences and submitted for publication in peer-reviewed journals.