bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal coherence of circadian clocks and temporal control of differentiation in
Anabaena
filaments
Authors: Arbel-Goren Rinat , Dassa Bareket , Zhitnitsky Anna , Valladares Ana , Herrero Antonia , Flores Enrique , Stavans Joel 
Published: December 2023

ABSTRACT

Circadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacterium
Anabaena
sp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle, that gene expression in different vegetative intervals along a developed filament was discoordinated, and that the circadian clock was active in individual heterocysts. Furthermore,
Anabaena
mutants lacking the
kaiABC
genes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs in
Anabaena
, the temporal control of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen-deficient conditions, the clock coherent unit in
Anabaena
is reduced from a full filament under nitrogen-rich conditions to the vegetative cell interval between heterocysts.

IMPORTANCE

Circadian clocks, from unicellular organisms to animals, temporally align biological processes to day and night cycles. We study the dynamics of a circadian clock-controlled gene at the individual cell level in the multicellular filamentous cyanobacterium
Anabaena
, under nitrogen-stress conditions. Under these conditions, some cells along filaments differentiate to carry out atmospheric nitrogen fixation and lose their capability for oxygenic photosynthesis. We found that clock synchronization is limited to organismic units of contiguous photosynthetic cells, contrary to nitrogen-replete conditions in which clocks are synchronized over a whole filament. We provided evidence that the circadian clock regulates the process of differentiation, allowing it to occur preferentially within a limited time window during the circadian clock period. Lastly, we present evidence that the signal from the core clock to clock-regulated genes is conveyed in
Anabaena
as in unicellular cyanobacteria.
POOE: predicting oomycete effectors based on a pre-trained large protein language model
Authors: Zhao Miao , Lei Chenping , Zhou Kewei , Huang Yan , Fu Chen , Yang Shiping , Zhang Ziding 
Published: December 2023

ABSTRACT

Oomycetes are fungus-like eukaryotic microorganisms which can cause catastrophic diseases in many plants. Successful infection of oomycetes depends highly on their effector proteins that are secreted into plant cells to subvert plant immunity. Thus, systematic identification of effectors from the oomycete proteomes remains an initial but crucial step in understanding plant–pathogen relationships. However, the number of experimentally identified oomycete effectors is still limited. Currently, only a few bioinformatics predictors exist to detect potential effectors, and their prediction performance needs to be improved. Here, we used the sequence embeddings from a pre-trained large protein language model (ProtTrans) as input and developed a support vector machine-based method called POOE for predicting oomycete effectors. POOE could achieve a highly accurate performance with an area under the precision-recall curve of 0.804 (area under the receiver operating characteristic curve = 0.893, accuracy = 0.874, precision = 0.777, recall = 0.684, and specificity = 0.936) in the fivefold cross-validation, considerably outperforming various combinations of popular machine learning algorithms and other commonly used sequence encoding schemes. A similar prediction performance was also observed in the independent test. Compared with the existing oomycete effector prediction methods, POOE provided very competitive and promising performance, suggesting that ProtTrans effectively captures rich protein semantic information and dramatically improves the prediction task. We anticipate that POOE can accelerate the identification of oomycete effectors and provide new hints to systematically understand the functional roles of effectors in plant–pathogen interactions. The web server of POOE is freely accessible at
http://zzdlab.com/pooe/index.php
. The corresponding source codes and data sets are also available at
https://github.com/zzdlabzm/POOE
.

IMPORTANCE
In this work, we use the sequence representations from a pre-trained large protein language model (ProtTrans) as input and develop a Support Vector Machine-based method called POOE for predicting oomycete effectors. POOE could achieve a highly accurate performance in the independent test set, considerably outperforming existing oomycete effector prediction methods. We expect that this new bioinformatics tool will accelerate the identification of oomycete effectors and further guide the experimental efforts to interrogate the functional roles of effectors in plant-pathogen interaction.
Ultrasensitive one-pot detection of monkeypox virus with RPA and CRISPR in a sucrose-aided multiphase aqueous system
Authors: Wang Yue , Tang Yixin , Chen Yukang , Yu Guangxi , Zhang Xue , Yang Lihong , Zhao Chenjie , Wang Pei , Gao Song 
Published: December 2023

ABSTRACT
The monkeypox virus, which was declared as a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO), continues to cause infection cases worldwide. Given the risk of virus evolution, it is essential to identify monkeypox virus infection in a timely manner and isolate patients to prevent outbreaks so that the vulnerable population is protected and the emergence of dangerous monkeypox variants is restrained. In this study, a novel one-pot recombinase polymerase amplification-Clustered Regularly Interspaced Short Palindromic Repeats (RPA-CRISPR) assay for monkeypox based on a sucrose-aided multiphase aqueous system has been established with an ultra-high sensitivity of a single copy, which is 10 times higher than the existing RPA-CRISPR one-pot method. The entire reaction was completed within 60 min at 37°C. The detection method exhibited good specificity, effectively distinguishing monkeypox from other orthopoxviruses. The detection results could be observed by the naked eye under ultraviolet or blue light, making it highly suitable for home or limited healthcare settings. The assay has solved the incompatibility between the Cas12a cleavage reaction and the RPA reaction and shows good specificity, accuracy, and the rapidness and convenience important for point-of-care testing. It provides an effective tool for the early diagnosis of monkeypox and sets a technical example of using a multiphase aqueous system to establish one-pot RPA-CRISPR detection.

IMPORTANCE
The monkeypox virus was declared as a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO) and continues to cause infection cases worldwide. Given the risk of virus evolution, it is essential to identify monkeypox virus infection in a timely manner to prevent outbreaks. This study establishes a novel one-pot recombinase polymerase amplification-Clustered Regularly Interspaced Short Palindromic Repeats (RPA-CRISPR) assay for monkeypox virus with an ultra-high sensitivity. The assay shows good specificity, accuracy, and the rapidness and convenience important for point-of-care testing. It provides an effective tool for the early diagnosis of monkeypox, which is useful for the prevention of an epidemic.
Mobile class A β-lactamase gene
bla
GMA-1
Authors: Yano Hirokazu , Suzuki Masato , Nonaka Lisa 
Published: December 2023

ABSTRACT

The first reported
bla
GMA-1
gene encoding gammaproteobacterial mobile class A β-lactamase (GMA-1) was identified in a recently defined mobile DNA element, a strand-biased circularizing integrative element (SE). Increased genomic data revealed the presence of
bla
GMA-1
in marine bacteria, including pathogenic species such as
Vibrio parahaemolyticus
and
Photobacterium damselae
. Herein, we address the substrate range of GMA-1 and how frequently
bla
GMA-1
was acquired by the chromosomes or plasmids via SEs using sequences in a publicly available database. An
Escherichia coli
strain carrying
bla
GMA-1
exhibited resistance to amoxicillin, piperacillin, and carbenicillin, but it remained susceptible to cephalosporins, monobactam, and carbapenems, indicating that GMA-1 belongs to functional group 2c, narrow-spectrum β-lactamases.
bla
GMA-1
-flanking sequence analysis for sequences in the RefSeq/GenBank database revealed a total of eight distinct SE-mediated
bla
GMA-1
acquisition events and six SE-independent
bla
GMA-1
acquisition events, including
bla
GMA-1
alone translocation, without involving a specific insertion sequence, or integron. Thus, this study shows that GMA-1 is specialized for penicillin degradation and is mainly disseminated by SEs; however, SE is not the only genetic mechanism transmitting
bla
GMA-1
.

IMPORTANCE

Despite increasing reports, class A β-lactamases of environmental bacteria remain very poorly characterized, with limited understanding of their transmission patterns. To address this knowledge gap, we focused on a recently designated GMA family β-lactamase gene,
bla
GMA-1
, found in marine bacterial genera such as
Vibrio
. This study shows that gammaproteobacterial mobile class A β-lactamase is specialized for penicillin degradation, and
bla
GMA-1
is frequently linked to strand-biased circularizing integrative elements (SEs) in sequences in the RefSeq/GenBank database. Evidence for the implication of SEs in β-lactamase environmental transmission provides insights for future surveillance studies of antimicrobial resistance genes in human clinical settings.
Fast and sensitive differential diagnosis of pseudorabies virus-infected versus pseudorabies virus-vaccinated swine using CRISPR-Cas12a
Authors: Wang Hao , Li Hongzhao , Tang Bo , Ye Chen , Han Meiqing , Teng Lin , Yue Min , Li Yan 
Published: December 2023

ABSTRACT
Pseudorabies virus (PRV) is the causative pathogen of Aujeszky’s disease. It causes high mortality and miscarriage rates in the infected swine, leading to tremendous economic losses in the global swine industry. PRV has also been demonstrated to trigger viral encephalitis in humans. The eradication policy and large-scale vaccination have been adopted globally as the most effective strategy against PRV. A simple, fast, and sensitive diagnostic method is highly demanded to differentiate between vaccinated and infected swine. Herein, we designed a detection system combining multienzyme isothermal rapid amplification (MIRA) and CRISPR-Cas12a (termed MIRA-Cas12a), characterized by high sensitivity and specificity, low cost, less equipment, and convenient visualization. By targeting the gB, gE, and TK genes of PRV, the MIRA-Cas12a assay is able to distinguish the infected, uninfected, and vaccinated swine by the naked eyes in 40 min (from DNA extraction to result readout) and with comparable sensitivity to conventional quantitative PCR. A 37°C heater and a source of blue light are all the equipment required to detect PRV. Thus, the MIRA-Cas12a detection will facilitate PRV surveillance and minimize the financial losses to the swine industry.

IMPORTANCE
Pseudorabies virus (PRV) causes high mortality and miscarriage rates in the infected swine, and the eradication policy coupled with large-scale vaccination of live attenuated vaccines has been adopted globally against PRV. Differential diagnosis of the vaccinated and infected swine is highly demanded. Our multienzyme isothermal rapid amplification (MIRA)-Cas12a detection method described in this study can diagnose PRV with a superior sensitivity comparable to the quantitative PCR (qPCR) and a competitive detection speed (only half the time as qPCR needs). The portable feature and the simple procedure of MIRA-Cas12a make it easier to deploy for clinical diagnosis, even in resource-limited settings. The MIRA-Cas12a method would provide immediate and accurate diagnostic information for policymakers to respond promptly.
Diversity of
Salmonella enterica
phages isolated from chicken farms in Kenya
Authors: Gunathilake K. M. Damitha , Makumi Angela , Loignon Stéphanie , Tremblay Denise , Labrie Simon , Svitek Nicholas , Moineau Sylvain 
Published: December 2023

ABSTRACT

In this study, we describe the characterization of 67
Salmonella enterica
phages isolated from Kenya. Specifically, the phages were isolated from chicken feces as well as from swabs and water samples obtained from chicken farms and slaughterhouses in Nairobi and Kiambu counties. Genome sequencing and analysis revealed that 59 phage isolates were distinct and could be grouped into 17 clusters belonging to four major types of phages (MT1–4). Further taxonomic analysis showed that each MT represents one phage genus. Of the 17 selected representative genomes (one per cluster), seven phages belong to the MT1 group and to the genus
Jerseyvirus
. The MT2 cluster contained eight representative phages that were similar to Escherichia phage T5 and belong to the
Tequintavirus
genus. The unique MT3 cluster with one phage representative belongs to the
Zindervirus
genus, while the sole MT4 phage isolate is a member of the
Dhillonvirus
genus. All representative phages are siphophages, except MT3 phage which is a podophage. All genomes do not contain genes associated with lysogeny and therefore, they are considered exclusively lytic. No known virulence genes or antibiotic resistance genes were detected in any of the genomes. Phage DNA termini analyses showed that MT2 phages have a direct terminal repeat-based packaging mechanism while MT1 has a headful packaging mechanism. Host range studies showed that phages belonging to MT1 and MT3 appear to only infect
Salmonella
strains, while MT2 and MT4 phages were also capable of infecting
Escherichia
and
Shigella
strains.

IMPORTANCE

Non-typhoidal
Salmonella enterica
infections are one of the leading causes of diarrhoeal diseases that spread to humans from animal sources such as poultry. Hence, keeping poultry farms free of
Salmonella
is essential for consumer safety and for a better yield of animal products. However, the emergence of antibiotic resistance due to over usage has sped up the search for alternative biocontrol methods such as the use of bacteriophages. Isolation and characterization of novel bacteriophages are key to adapt phage-based biocontrol applications. Here, we isolated and characterized
Salmonella
phages from samples collected at chicken farms and slaughterhouses in Kenya. The genomic characterization of these phage isolates revealed that they belong to four ICTV (International Committee on Taxonomy of Viruses) phage genera. All these phages are lytic and possibly suitable for biocontrol applications because no lysogenic genes or virulence factors were found in their genomes. Hence, we recommend further studies on these phages for their applications in
Salmonella
biocontrol.
Holocene gigascale rock avalanches in Vaigat strait, West Greenland—Implications for geohazard
Authors: Svennevig Kristian , Owen Matthew J. , Citterio Michele , Nielsen Tove , Rosing Salik , Harff Jan , Endler Rudolf , Morlighem Mathieu , Rignot Eric 
Published: December 2023

Abstract
Rock avalanche–triggered displacement waves (also termed tsunamis) have recently occurred in Greenland and Alaska, and they illustrate the presence of such hazards in polar regions. To improve understanding of the magnitude of this hazard for these areas, we investigated gigascale subaerial rock avalanches impacting a partially confined water body within the Vaigat strait (western Greenland). We present a new combined subaerial to subaqueous digital elevation model, alongside a new compilation of seismic data, which revealed nine deglacial to Holocene rock avalanche complexes that are between one and two orders of magnitude larger than nearby historical rock avalanches. The three largest complexes have deposit thicknesses up to 300 m, runout distances reaching 19 km, and best-estimate volumes from 1.7 to 8.4 km3. Based on the morphology and the volume–angle of reach relations, it is likely that each complex represents a single or few events, thus making them among the largest displacement wave–generating subaerial to submarine rock avalanches on Earth. We estimated displacement wave magnitude up to 280 m on the opposite shore. The ages of the deposits are poorly constrained but the main rock avalanche activity is referable to early Holocene times. With significant climatic changes predicted in the Arctic, we recommend that hazard assessments account for events not only from the historical record but also those from the recent geological past.
Ultrasound-guided serratus anterior plane block to prevent neurocognitive impairment in elderly patients after thoracoscopic lobectomy: protocol for a single-centre, double-blind, randomised controlled trial
Authors: Wang Dan-Yang , Feng Di , Liu Mei-Yun , Wu Wei , Xu Huan , Shi Hong 
Published: December 2023

IntroductionPostoperative neurocognitive dysfunction (PND), including postoperative delirium (POD), is a common complication in elderly patients after major surgeries, often leading to poor postoperative recovery. Although the pathological mechanism underlying PND is still unclear, postoperative pain is strongly associated with the development of PND. The ultrasound-guided serratus anterior plane block (SAPB) has been reported to relieve postoperative pain in thoracic surgery. Therefore, this prospective trial hypothesises that SAPB may reduce the incidence of PND in the elderly undergoing thoracoscopic lobectomy.Methods and analysisThis study is designed as a single-centre, double-blind, randomised controlled clinical trial. A total of 256 elderly patients scheduled to undergo thoracoscopic lobectomy at Shanghai Pulmonary Hospital will be randomly assigned to general anaesthesia group or SAPB group. The primary outcome is the incidence of PND 7 days postoperatively or before discharge from hospital. The secondary outcomes include the occurrence of POD, the postoperative pain scores, Quality of Recovery at 1–2 days postoperatively and incidence of PND at 3 months postoperatively. The levels of fasting blood glucose in peripheral blood will be examined before and 1–2 days postoperatively.Ethics and disseminationThe trial has been approved by the Clinical Research Ethics Committee of Shanghai Pulmonary Hospital (identifier: K20-290). All participants will be required to provide written informed consent before any protocol-specific procedures. Findings will be disseminated in a peer-reviewed journal and in national and/or international meetings to guide future practice.Trial registration numberChiCTR2100052633.
Impact of health system governance on healthcare quality in low-income and middle-income countries: a scoping review
Authors: George Joby , Jack Susan , Gauld Robin , Colbourn Timothy , Stokes Tim 
Published: December 2023

IntroductionImproving healthcare quality in low-/middle-income countries (LMICs) is a critical step in the pathway to Universal Health Coverage and health-related sustainable development goals. This study aimed to map the available evidence on the impacts of health system governance interventions on the quality of healthcare services in LMICs.MethodsWe conducted a scoping review of the literature. The search strategy used a combination of keywords and phrases relevant to health system governance, quality of healthcare and LMICs. Studies published in English until August 2023, with no start date limitation, were searched on PubMed, Cochrane Library, CINAHL, Web of Science, Scopus, Google Scholar and ProQuest. Additional publications were identified by snowballing. The effects reported by the studies on processes of care and quality impacts were reviewed.ResultsThe findings from 201 primary studies were grouped under (1) leadership, (2) system design, (3) accountability and transparency, (4) financing, (5) private sector partnerships, (6) information and monitoring; (7) participation and engagement and (8) regulation.ConclusionsWe identified a stronger evidence base linking improved quality of care with health financing, private sector partnerships and community participation and engagement strategies. The evidence related to leadership, system design, information and monitoring, and accountability and transparency is limited.
mHealth application for improving treatment outcomes for patients with multidrug-resistant tuberculosis in Vietnam: an economic evaluation protocol for the V-SMART trial
Authors: Cheng Qinglu , Dang Tho , Nguyen Thu-Anh , Velen Kavindhran , Nguyen Viet Nhung , Nguyen Binh Hoa , Vu Dinh Hoa , Long Chuong Huynh , Do Thu Thuong , Vu Truong-Minh , Marks Guy B , Yapa Manisha , Fox Gregory J , Wiseman Virginia 
Published: December 2023

IntroductionThe Strengthen the Management of Multidrug-Resistant Tuberculosis in Vietnam (V-SMART) trial is a randomised controlled trial of using mobile health (mHealth) technologies to improve adherence to medications and management of adverse events (AEs) in people with multidrug-resistant tuberculosis (MDR-TB) undergoing treatment in Vietnam. This economic evaluation seeks to quantify the cost-effectiveness of this mHealth intervention from a healthcare provider and societal perspective.Methods and analysisThe V-SMART trial will recruit 902 patients treated for MDR-TB across seven participating provinces in Vietnam. Participants in both intervention and control groups will receive standard community-based therapy for MDR-TB. Participants in the intervention group will also have a purpose-designed App installed on their smartphones to report AEs to health workers and to facilitate timely management of AEs. This economic evaluation will compare the costs and health outcomes between the intervention group (mHealth) and the control group (standard of care). Costs associated with delivering the intervention and health service utilisation will be recorded, as well as patient out-of-pocket costs. The health-related quality of life (HRQoL) of study participants will be captured using the 36-Item Short Form Survey (SF-36) questionnaire and used to calculate quality-adjusted life-years (QALYs). Incremental cost-effectiveness ratios (ICERs) will be based on the primary outcome (proportion of patients with treatment success after 24 months) and QALYs gained. Sensitivity analysis will be conducted to test the robustness of the ICERs. A budget impact analysis will be conducted from a payer perspective to provide an estimate of the total budget required to scale-up delivery of the intervention.Ethics and disseminationEthical approval for the study was granted by the University of Sydney Human Research Ethics Committee (2019/676), the Scientific Committee of the Ministry of Science and Technology, Vietnam (08/QD-HDQL-NAFOSTED) and the Institutional Review Board of the National Lung Hospital, Vietnam (13/19/CT-HDDD). Study findings will be published in peer-reviewed journals and conference proceedings.Trial registration numberACTRN12620000681954.