bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation
Authors: Midot Frazer , Goh Kian Mau , Liew Kok Jun , Lau Sharon Yu Ling , Espenberg Mikk , Mander Ülo , Melling Lulie 
Published: December 2024

ABSTRACT

Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH
4
), and nitrous oxide (N
2
O) fluxes. Soil CO
2
emission increased (doubling from approximately 200 mg C m
−2
h
−1
), while CH
4
emissions decreased (from 200 µg C m
−2
h
−1
to slightly negative) following land use changes. The N
2
O emissions in the oil palm plantation reached approximately 1,510 µg N m
−2
h
−1
, significantly higher than previous land uses. The CH
4
fluxes were driven by groundwater table, humification levels, and C:N ratio, with
Methanomicrobia
populations dominating methanogenesis and
Methylocystis
as the main CH
4
oxidizer. The N
2
O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant
nirK
-type denitrifiers (13-fold
nir
to
nosZ
) and a minor role by nitrification (a threefold increase in
amoA
) in the plantation.
Proteobacteria
and
Acidobacteria
encoding incomplete denitrification genes potentially impact N
2
O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.

IMPORTANCE
Tropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.
Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes
Authors: Beizman-Magen Yana , Orevi Tomer , Kashtan Nadav 
Published: December 2024

ABSTRACT

Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing
Bacillus velezensis
FZB42 and two bacterial strains susceptible to its antibiotics:
Xanthomonas euvesicatoria
85-10 and
Pseudomonas syringae
DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably
, X. euvesicatoria
shows increased protection against both the cells and supernatants of
B. velezensis
under wet-dry cycles, while
P. syringae
cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between
P. syringae
and
B. velezensis
, where
P. syringae
inhibits
B. velezensis
under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.

IMPORTANCE

Our study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by
Bacillus velezensis
against two susceptible bacterial species:
Xanthomonas
and
Pseudomonas
varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.
The CP123L protein of African swine fever virus is a membrane-associated, palmitoylated protein required for viral replication
Authors: Guan Xiangyu , Wang Tao , Gao Yuxuan , Zhai Huanjie , Jiang Fengwei , Hou Qinghe , Yang Xiaoke , Wu Hongxia , Li Lian-Feng , Luo Yuzi , Li Su , Sun Yuan , Qiu Hua-Ji , Li Yongfeng 
Published: December 2024

ABSTRACT

African swine fever (ASF) is a highly contagious and often lethal disease caused by African swine fever virus (ASFV) in pigs. Protein palmitoylation is a prevalent posttranslational lipid modification that can modulate viral replication. In this study, we investigated the palmitoylation of ASFV proteins. The results revealed that the CP123L protein (pCP123L) of ASFV was palmitoylated at the cysteine residue at position 18 (C18). To further elucidate the functional significance of this posttranslational modification, abolishing palmitoylation through a cysteine-to-serine mutation at C18 (C18S) of pCP123L (pCP123L/C18S) or treatment with 2-bromopalmitate (2-BP), a palmitoylation inhibitor, led to altered cytomembrane localization and migration rate of pCP123L. Furthermore, depalmitoylation achieved through 2-BP treatment significantly suppressed ASFV replication and exerted a profound impact on virus budding. Remarkably, blocking pCP123L palmitoylation
via
the C18S mutation resulted in decreased replication of ASFV. Our study represents the first evidence for the presence of palmitoylation in ASFV proteins and underscores its crucial role in viral replication.

IMPORTANCE
African swine fever (ASF) poses a significant threat to the global pig industry. The causative agent of ASF is African swine fever virus (ASFV), which encodes more than 165 proteins. Protein palmitoylation, a common posttranslational lipid modification, can modulate viral infection. To date, the ASFV proteins that undergo palmitoylation and their impacts on viral replication remain elusive. In this study, the CP123L protein (pCP123L) of ASFV was identified as a palmitoylated protein, and the cysteine residue at position 18 of pCP123L is responsible for its palmitoylation. Notably, our findings demonstrate that palmitoylation plays significant roles in ASFV protein functions and facilitates viral replication.
Role of Vigilin and RACK1 in dengue virus-
Aedes aegypti-Wolbachia
interactions
Authors: Wang Guijie , Hussain Mazhar , Qi Zhi , Asgari Sassan 
Published: December 2024

ABSTRACT

Vigilin is a large and evolutionary conserved RNA-binding protein (RBP), which can interact with RNA through its KH domain. Vigilin is, therefore, a multifunctional protein reported to be associated with RNA transport and metabolism, sterol metabolism, chromosome segregation, carcinogenesis, and heterochromatin-mediated gene silencing. The receptor for activated C kinase 1 (RACK1) is another highly conserved protein involved in many cellular pathways. Functional studies in human cells indicated that RACK1 interacts with Vigilin to promote dengue virus (DENV) replication. Both proteins are associated with the endoplasmic reticulum. Here, we investigated the significance of Vigilin and RACK1 homologs in
Aedes aegypti
mosquitoes concerning DENV replication and
Wolbachia
infection. We identified the homologs of the two genes in
Ae. aegypti
(
AeVigilin
and
AeRACK1
), which were upregulated in DENV-infected Aag2 cells and mosquitoes, and silencing them in Aag2 cells resulted in reduced DENV replication. Co-immunoprecipitation showed that AeRACK1 and AeVigilin interact in mosquito cells. Interestingly, we also found upregulation of both genes in a
Wolbachia
-infected cell line (Aag2.
w
AlbB). Furthermore, silencing
AeVigilin
and
AeRACK1
in Aag2.
w
AlbB cells reduced DENV replication but increased
Wolbachia
density. However, we did not find a significant effect on DENV replication after silencing both genes in
Ae. aegypti
mosquitoes. Overall, our results support the involvement and significance of AeVigilin and AeRACK1 in DENV replication in
Ae. aegypti
.

IMPORTANCE

Dengue virus (DENV), transmitted mainly by
Aedes aegypti
mosquitoes, poses significant health risks. Identifying factors involved in the virus replication in mosquitoes and human hosts is essential for devising control measures. In this study, we show that Vigilin and the receptor for activated C kinase 1 (RACK1), two proteins shown to play a role in the replication of DENV in human cells, are induced in mosquitoes and cell lines following DENV replication. Both proteins reside in the cytoplasm, where they interact similarly to human cells. Silencing the genes in mosquito cells significantly reduced virus replication. Furthermore, we found that both genes are induced in mosquito cells transinfected with
Wolbachia
, a bacterium that blocks DENV replication. The results help better understand the role of the common factors supporting DENV replication in mosquitoes and human cells.
Hindguts of
Kyphosus sydneyanus
harbor phylogenetically and genomically distinct
Alistipes
capable of degrading algal polysaccharides and diazotrophy
Authors: Facimoto Cesar T. , Clements Kendall D. , White W. Lindsey , Handley Kim M. 
Published: December 2024

ABSTRACT

The genus
Alistipes
(
Bacteroidota
) is most often associated with human clinical samples and livestock. However,
Alistipes
are also prevalent in the hindgut of the marine herbivorous fish
Kyphosus sydneyanus
(Silver Drummer), and analysis of their carbohydrate-active enzyme (CAZyme) encoding gene repertoires suggests
Alistipes
degrade macroalgal biomass to support fish nutrition. To further explore host-associated traits unique to
K. sydneyanus
-derived
Alistipes
, we compared 445 high-quality genomes of
Alistipes
available in public databases (e.g., human and ruminant associated) with 99 metagenome-assembled genomes (MAGs) from the
K. sydneyanus
gut. Analyses showed that
Alistipes
from
K. sydneyanus
are phylogenetically distinct from other hosts and comprise 26 species based on genomic average nucleotide identity (ANI) analyses. Ruminant- and fish-derived
Alistipes
had significantly smaller genomes than human-derived strains, and lower GC contents, possibly reflecting a symbiotic relationship with their hosts. The fish-derived
Alistipes
were further delineated by their genetic capacity to fix nitrogen, biosynthesize cobalamin (vitamin B12), and utilize marine polysaccharides (e.g., alginate and carrageenan). The distribution of CAZymes encoded by
Alistipes
from
K. sydneyanus
was not phylogenetically conserved. Distinct CAZyme gene compositions were observed between closely related species. Conversely, CAZyme gene clusters (operons) targeting the same substrates were found across diverse species. Nonetheless, transcriptional data suggest that closely related
Alistipes
target specific groups of substrates within the fish hindgut. Results highlight host-specific adaptations among
Alistipes
in the fish hindgut that likely contribute to
K. sydneyanus
digesting their seaweed diet, and diverse and redundant carbohydrate-degrading capabilities across these
Alistipes
species.

IMPORTANCE

Despite numerous reports of the
Alistipes
genus in humans and ruminants, its diversity and function remain understudied, and there is no clear consensus on whether it positively or negatively impacts host health. Given the symbiotic role of gut communities in the
Kyphosus sydneyanus
hindgut, where
Alistipes
are prevalent, and the diversity of carbohydrate-active enzymes (CAZymes) encoded that likely contribute to the breakdown of important substrates in the host diet, it is likely that this genus provides essential services to the fish host. Therefore, considering its metabolism in various contexts and hosts is crucial for understanding the ecology of the genus. Our study highlights the distinct genetic traits of
Alistipes
based on host association, and the potential of fish-associated
Alistipes
to transform macroalgae biomass into nutraceuticals (alginate oligosaccharides, β-glucans, sulfated galactans, and sulfated fucans).
Effect of electroacupuncture on discomfort in patients undergoing colonoscopy: protocol for a multicentre, randomised, controlled clinical trial
Authors: Sun Xiangyu , Lu Liyue , Wang Yongqiang , Wang Chunchun , Lin Chao , Xu Kuangdi , Yong Yue , Chen Wenting , Song Jiangang 
Published: December 2024

IntroductionColonoscopy is currently the most commonly used and effective method for early detection, diagnosis and treatment of tumours of the colon and rectum. However, similar to other invasive procedures, it is associated with adverse reactions such as pain and abdominal distension. Electroacupuncture (EA) has been proposed as a potential treatment for relieving this discomfort; however, there is limited evidence supporting its efficacy. Therefore, the aim of this study is to investigate the effectiveness of EA when used prior to colonoscopy.Methods and analysisThis multicentre, randomised, controlled, patient–assessor-blinded trial will be conducted at three hospitals in China. A total of 500 participants will be randomly assigned to either the EA group or sham EA (SEA) group, in a 1:1 ratio. EA will be administered for 30 min before the colonoscopy. Participants will be asked to complete detailed questionnaires within 10 min after the procedure and 24 hours after the procedure to record their symptoms. The primary outcome will be assessed using discomfort numeric rating scale (NRS) scores. Secondary outcomes will include participants’ tolerance levels, including standard NRS scores for abdominal pain, bloating and anal discomfort reported by the participants, as well as heart rate(HR), blood pressure(BP), surgical pleth index, participant satisfaction, nurses’ and endoscopists’ evaluations, incidence of adverse events and salivary cortisol levels collected before EA and after colonoscopy.Ethics and disseminationEthics approval was obtained from the Ethics Committee of Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine (number 2023-1327-94-01), Ethics Committee of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine (number 2023LCSY059) and Ethics Committee of Wuxi Hospital Affiliated to Nanjing University of Traditional Chinese Medicine (number 2023-062-01). The results of this study will be disseminated in peer-reviewed publications. All potential participants will be provided informed consent before participating in the study.Trial registration numberChiCTR2300073485.
Comparison of I-gel and Baska mask in elective surgery: a meta-analysis
Authors: Shen Jiaxin , Miao Xiaoyun , Wang Hao , Zhao Jinglin , Shi Jiaxiao , Dai Qingchun 
Published: December 2024

ObjectiveThe supraglottic airway device is a viable alternative to tracheal intubation for elective surgery. To conduct a comparative analysis of the advantages and disadvantages associated with use of the Baska mask and I-gel across various dimensions.DesignA comprehensive search was conducted across PubMed, Embase, Cochrane Library, Web of Science, and other relevant databases to identify randomised controlled trials (RCTs) involving patients who used the Baska mask and I-gel.Main resultsTwelve studies were identified for comparison of clinical indices. The Baska mask device demonstrated general feasibility in oropharyngeal leak pressure at insertion time and 30 min post-insertion, as well as in the assessment of dysphonia. However, the I-gel had superior efficacy in reducing sore throat compared with the Baska mask.ConclusionsBased on current evidence, the Baska mask demonstrates superior intraoperative performance compared with I-gel; however, it is associated with a higher incidence of a sore throat post-extubation. Nevertheless, the overall quality of existing studies is suboptimal, underscoring the need for additional high-quality RCTs to substantiate these findings.
DIAMACC: protocol of a prospective diagnostic accuracy study of the maximal systolic acceleration to detect peripheral arterial disease in patients with diabetes-related foot ulceration in the Netherlands
Authors: Willems Siem , Schepers Abbey , Hamming Jaap , Brouwers Jeroen J W M 
Published: December 2024

IntroductionFoot ulcers are one of the most serious complications of diabetes, leading to significant risks on amputation and mortality. Peripheral arterial disease (PAD) is an important factor for the development and the outcome of diabetic foot ulcers (DFU). Although prompt and accurate detection of PAD is critical to reduce complications, its diagnosis can be challenging with currently used bedside tests (such as ankle–brachial index and toe pressure) due to medial arterial calcification. A new and promising bedside test for the detection of PAD is the maximal systolic acceleration (ACCmax), measured by duplex ultrasonography (DUS). The primary aim of this study is to assess the diagnostic performance of the ACCmaxto detect PAD in patients with DFU, in comparison with commonly used bedside tests. Secondary aims include the correlation between diagnostic test accuracy and patient comorbidities. Tertiary objectives focus on collecting (follow-up) data for prognostic evaluation, such as ulcer healing, revascularisation feasibility, amputation risk, cardiovascular events and mortality.Methods and analysisA multicentre prospective diagnostic accuracy study with 198 patients will be conducted to assess the diagnostic performance of multiple index tests to detect PAD in patients with DFU, with special emphasis on ACCmax. A full lower limb arterial DUS will serve as reference test.Ethics and disseminationStudy protocol approval was gained from the Medical Ethical Committee Leiden/Den Haag/Delft and registered at ClinicalTrials.gov. The findings of this study will be reported through peer-reviewed publications and (inter)national conferences.Trial registration numberNCT05646147.
Antireflux mucosal valvuloplasty versus proton pump inhibitors for the treatment of patients with gastro-oesophageal reflux disease in a tertiary healthcare centre in China: study protocol for a randomised controlled trial
Authors: Lv Xiaofen , Ma Wenlong , Zeng Yunqing , Lu Jiaoyang 
Published: December 2024

IntroductionEndoscopic antireflux therapy has shown promising potential in the treatment for gastro-oesophageal reflux disease (GERD). However, there is currently no universally accepted standard for endoscopic surgery. Therefore, we introduced antireflux mucosal valvuloplasty (ARMV), an innovative endoscopic treatment for GERD. We have conducted a cohort study to assess the association between ARMV and clinical outcomes, including risks and benefits. The objective of this trail is to compare the efficacy of ARMV with proton pump inhibitors (PPIs) therapy.Methods and analysis74 patients with chronic GERD will be randomised (1:1) to undergo either ARMV or continue PPI therapy. The primary endpoint is the GERD health-related quality of life score, measured 6 months postprocedure. Secondary endpoints include the GERD questionnaire score, presence of reflux oesophagitis, appearance of the mucosal flap, DeMeester score, PPI usage and the incidence of adverse events. After 6 months, crossover is allowed for the PPI group. Assessments will occur at baseline and at 3, 6, 12, 24 and 36 months postintervention.Ethics and disseminationThe study protocol has been approved by the Institutional Review Board of Qilu Hospital, Shandong University. Study results will be disseminated through peer-reviewed journals and presented at scientific conferences.Trial registration numberClinicalTrials.gov (NCT 06348420).
Trends, outcomes and knowledge gaps in mobile apps for reproductive endocrinology and infertility: a scoping review protocol
Authors: dos Santos Emerson Roberto , de Gouvêa Aline Russomano , Castro Natália Almeida de Arnaldo Silva Ro , Souza Menezes João Daniel de , Querino da Silva Matheus , Cristóvão Helena Landin Gonçalves , Martins Cíntia Canato , Oliveira Jéssica Gisleine de , Fucuta Patrícia da Silva , Werneck Alexandre Lins , Filho Gerardo Maria de Araújo , Lima Alba Regina de Abreu , Caldas Heloisa Cristina , Brienze Vânia Maria Sabadoto , André Júlio César , Oliani Antônio Hélio 
Published: December 2024

IntroductionInfertility is a complex condition that affects millions worldwide, with significant physical, emotional and social implications. Mobile apps have emerged as potential tools to assist in the management of infertility by offering features such as menstrual cycle tracking, ovulation prediction, fertility education, lifestyle modification guidance and emotional support, thereby promoting reproductive health. Despite promising advancements such as the development of apps with sophisticated algorithms for ovulation prediction and comprehensive platforms offering integrated fertility education and emotional support, there remain gaps in the literature regarding the comprehensive evaluation of mobile apps for reproductive endocrinology and infertility. This scoping review distinguishes itself by systematically mapping and synthesising evidence on mobile apps specifically for reproductive endocrinology and infertility, unlike previous reviews that may not have focused exclusively on this intersection. This review aims to analyse recent trends, identify outcomes used to assess usability and highlight knowledge gaps.Methods and analysisThis scoping review will adhere to the methodological frameworks outlined by Arksey and O'Malley and Levacet al, alongside the Joanna Briggs Institute’s recommendations. The research question, ‘What is known about mobile apps in reproductive health and infertility?’ was formulated using the Population, Concept, Context (PCC) strategy. We will include studies published from January 2019 to April 2024 in English, Portuguese and Spanish that focus on the use of mobile apps in reproductive health and infertility. Searches will be conducted across electronic databases (EMBASE, ERIC, PubMed, Science Direct, Scopus and Web of Science) and grey literature sources. Two independent reviewers will carry out the study selection using Covidence software. Data extraction will follow a standardised format and will be synthesised narratively using tables and graphs. Expert consultations will be conducted to validate the findings.Ethics and disseminationEthical approval is not required for this scoping review as it will only use published data. The findings will be disseminated through publication in a peer-reviewed journal, conference presentations and stakeholder meetings. The review protocol will be registered with the Open Science Framework to ensure transparency and reproducibility.