bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics of quinolone-resistant Escherichia coli from broilers and humans in Norway
Authors: Slettemeås Jannice Schau , Sekse Camilla , Sunde Marianne , Norström Madelaine , Wester Astrid Louise , Naseer Umaer , Simonsen Gunnar Skov , Ulstad Charlotte Rosenberg , Urdahl Anne Margrete , Lagesen Karin 
Published: July 2024

Abstract
Background
The usage of fluoroquinolones in Norwegian livestock production is very low, including in broiler production. Historically, quinolone-resistant Escherichia coli (QREC) isolated from Norwegian production animals rarely occur. However, with the introduction of a selective screening method for QREC in the Norwegian monitoring programme for antimicrobial resistance in the veterinary sector in 2014; 89.5% of broiler caecal samples and 70.7% of broiler meat samples were positive. This triggered the concern if there could be possible links between broiler and human reservoirs of QREC. We are addressing this by characterizing genomes of QREC from humans (healthy carriers and patients) and broiler isolates (meat and caecum).

Results
The most frequent mechanism for quinolone resistance in both broiler and human E. coli isolates were mutations in the chromosomally located gyrA and parC genes, although plasmid mediated quinolone resistance (PMQR) was also identified. There was some relatedness of the isolates within human and broiler groups, but little between these two groups. Further, some overlap was seen for isolates with the same sequence type isolated from broiler and humans, but overall, the SNP distance was high.

Conclusion
Based on data from this study, QREC from broiler makes a limited contribution to the incidence of QREC in humans in Norway.
Simulated complexes formed from a set of postsynaptic proteins suggest a localised effect of a hypomorphic Shank mutation
Authors: Miski Marcell , Weber Áron , Fekete-Molnár Krisztina , Keömley-Horváth Bence Márk , Csikász-Nagy Attila , Gáspári Zoltán 
Published: July 2024

Abstract
Background
The postsynaptic density is an elaborate protein network beneath the postsynaptic membrane involved in the molecular processes underlying learning and memory. The postsynaptic density is built up from the same major proteins but its exact composition and organization differs between synapses. Mutations perturbing protein: protein interactions generally occurring in this network might lead to effects specific for cell types or processes, the understanding of which can be especially challenging.

Results
In this work we use systems biology-based modeling of protein complex distributions in a simplified set of major postsynaptic proteins to investigate the effect of a hypomorphic Shank mutation perturbing a single well-defined interaction. We use data sets with widely variable abundances of the constituent proteins. Our results suggest that the effect of the mutation is heavily dependent on the overall availability of all the protein components of the whole network and no trivial correspondence between the expression level of the directly affected proteins and overall complex distribution can be observed.

Conclusions
Our results stress the importance of context-dependent interpretation of mutations. Even the weakening of a generally occurring protein: protein interaction might have well-defined effects, and these can not easily be predicted based only on the abundance of the proteins directly affected. Our results provide insight on how cell-specific effects can be exerted by a mutation perturbing a generally occurring interaction even when the wider interaction network is largely similar.
Genome-wide analysis of MYB transcription factor family and AsMYB1R subfamily contribution to ROS homeostasis regulation in Avena sativa under PEG-induced drought stress
Authors: Chen Yang , Li Aixue , Yun Ping , Chen Quan , Pan Dayu , Guo Rui , Zhang Han , Ahmed Hassan Ahmed Ibraheem , Hu Haiying , Peng Yuanying , Wang Cheng , Dong Hongtu , Qiu Chaoyang , Shabala Lana , Shabala Sergey , Luo Bin , Hou Peichen 
Published: July 2024

Abstract
Background
The myeloblastosis (MYB) transcription factor (TF) family is one of the largest and most important TF families in plants, playing an important role in a life cycle and abiotic stress.

Results
In this study, 268 Avena sativa MYB (AsMYB) TFs from Avena sativa were identified and named according to their order of location on the chromosomes, respectively. Phylogenetic analysis of the AsMYB and Arabidopsis MYB proteins were performed to determine their homology, the AsMYB1R proteins were classified into 5 subgroups, and the AsMYB2R proteins were classified into 34 subgroups. The conserved domains and gene structure were highly conserved among the subgroups. Eight differentially expressed AsMYB genes were screened in the transcriptome of transcriptional data and validated through RT-qPCR. Three genes in AsMYB2R subgroup, which are related to the shortened growth period, stomatal closure, and nutrient and water transport by PEG-induced drought stress, were investigated in more details. The AsMYB1R subgroup genes LHY and REV 1, together with GST, regulate ROS homeostasis to ensure ROS signal transduction and scavenge excess ROS to avoid oxidative damage.

Conclusion
The results of this study confirmed that the AsMYB TFs family is involved in the homeostatic regulation of ROS under drought stress. This lays the foundation for further investigating the involvement of the AsMYB TFs family in regulating A. sativa drought response mechanisms.
Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae
Authors: Huang Yue , Jin Xin-Jie , Zhang Can-Yu , Li Pan , Meng Hong-Hu , Zhang Yong-Hua 
Published: July 2024

Abstract
Background
Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family.

Results
The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn’t support rapid radiation occurred in the evolution history of Engelhardia.

Conclusion
Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.
Ecological stress memory in wood architecture of two Neotropical hickory species from central-eastern Mexico
Authors: Rodríguez-Ramírez Ernesto C. , Frei Jonas , Ames-Martínez Fressia N. , Guerra Anthony , Andrés-Hernández Agustina R. 
Published: July 2024

Abstract
Background
Drought periods are major evolutionary triggers of wood anatomical adaptive variation in Lower Tropical Montane Cloud Forests tree species. We tested the influence of historical drought events on the effects of ecological stress memory on latewood width and xylem vessel traits in two relict hickory species (Carya palmeri and Carya myristiciformis) from central-eastern Mexico. We hypothesized that latewood width would decrease during historical drought years, establishing correlations between growth and water stress conditions, and that moisture deficit during past tree growth between successive drought events, would impact on wood anatomical features. We analyzed latewood anatomical traits that developed during historical drought and pre- and post-drought years in both species.

Results
We found that repeated periods of hydric stress left climatic signatures for annual latewood growth and xylem vessel traits that are essential for hydric adaptation in tropical montane hickory species.

Conclusions
Our results demonstrate the existence of cause‒effect relationships in wood anatomical architecture and highlight the ecological stress memory linked with historical drought events. Thus, combined time-series analysis of latewood width and xylem vessel traits is a powerful tool for understanding the ecological behavior of hickory species.
Combined analysis of the metabolome and transcriptome reveals the metabolic characteristics and candidate genes involved in alkaloid metabolism in Heuchera micrantha Douglas ex Lindl
Authors: Gong Weichang , Xiong Lina , Fu Hongbo 
Published: July 2024

Abstract
Background
Alkaloids, important secondary metabolites produced by plants, play a crucial role in responding to environmental stress. Heuchera micrantha, a well-known plant used in landscaping, has the ability to purify air, and absorb toxic and radioactive substances, showing strong environmental adaptability. However, there is still limited understanding of the accumulation characteristics and metabolic mechanism of alkaloids in H. micrantha.

Results
In this study, four distinct varieties of H. micrantha were used to investigate the accumulation and metabolic traits of alkaloids in its leaves. We conducted a combined analysis of the plant’s metabolome and transcriptome. Our analysis identified 44 alkaloids metabolites in the leaves of the four H. micrantha varieties, with 26 showing different levels of accumulation among the groups. The HT and JQ varieties exhibited higher accumulation of differential alkaloid metabolites compared to YH and HY. We annotated the differential alkaloid metabolites to 22 metabolic pathways, including several alkaloid metabolism. Transcriptome data revealed 5064 differentially expressed genes involved in these metabolic pathways. Multivariate analysis showed that four key metabolites (N-hydroxytryptamine, L-tyramine, tryptamine, and 2-phenylethylamine) and three candidate genes (Cluster-15488.116815, Cluster-15488.146268, and Cluster-15488.173297) that merit further investigation.

Conclusions
This study provided preliminarily insight into the molecular mechanism of the biosynthesis of alkaloids in H. micrantha. However, further analysis is required to elucidate the specific regulatory mechanisms of the candidate gene involved in the synthesis of key alkaloid metabolites. In summary, our findings provide important information about how alkaloid metabolites build up and the metabolic pathways involved in H. micrantha varieties. This gives us a good starting point for future research on the regulation mechanism, and development, and utilization of alkaloids in H. micrantha.
Network analyses predict major regulators of resistance to early blight disease complex in tomato
Authors: Tominello-Ramirez Christopher S. , Muñoz Hoyos Lina , Oubounyt Mhaned , Stam Remco 
Published: July 2024

Abstract
Background
Early blight and brown leaf spot are often cited as the most problematic pathogens of tomato in many agricultural regions. Their causal agents are Alternaria spp., a genus of Ascomycota containing numerous necrotrophic pathogens. Breeding programs have yielded quantitatively resistant commercial cultivars, but fungicide application remains necessary to mitigate the yield losses. A major hindrance to resistance breeding is the complexity of the genetic determinants of resistance and susceptibility. In the absence of sufficiently resistant germplasm, we sequenced the transcriptomes of Heinz 1706 tomatoes treated with strongly virulent and weakly virulent isolates of Alternaria spp. 3 h post infection. We expanded existing functional gene annotations in tomato and using network statistics, we analyzed the transcriptional modules associated with defense and susceptibility.

Results
The induced responses are very distinct. The weakly virulent isolate induced a defense response of calcium-signaling, hormone responses, and transcription factors. These defense-associated processes were found in a single transcriptional module alongside secondary metabolite biosynthesis genes, and other defense responses. Co-expression and gene regulatory networks independently predicted several D clade ethylene response factors to be early regulators of the defense transcriptional module, as well as other transcription factors both known and novel in pathogen defense, including several JA-associated genes. In contrast, the strongly virulent isolate elicited a much weaker response, and a separate transcriptional module bereft of hormone signaling.

Conclusions
Our findings have predicted major defense regulators and several targets for downstream functional analyses. Combined with our improved gene functional annotation, they suggest that defense is achieved through induction of Alternaria-specific immune pathways, and susceptibility is mediated by modulating hormone responses. The implication of multiple specific clade D ethylene response factors and upregulation of JA-associated genes suggests that host defense in this pathosystem involves ethylene response factors to modulate jasmonic acid signaling.
Impact of non-emergency surgical timing on postoperative recovery quality in mild or asymptomatic SARS-CoV-2 infected patients: a grouped cohort study
Authors: Wang Qiu-Bo , Wang Yu-Long , Wang Yue-Feng , Chen Hua , Chen Wei , Chen Yong-Quan 
Published: July 2024

Abstract
Objective
To explore the relationship between the timing of non-emergency surgery in mild or asymptomatic SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infected individuals and the quality of postoperative recovery from the time of confirmed infection to the day of surgery.

Methods
We retrospectively reviewed the medical records of 300 cases of mild or asymptomatic SARS-CoV-2 infected patients undergoing elective general anaesthesia surgery at Yijishan Hospital between January 9, 2023, and February 17, 2023. Based on the time from confirmed SARS-CoV-2 infection to the day of surgery, patients were divided into four groups: ≤2 weeks (Group A), 2–4 weeks (Group B), 4–6 weeks (Group C), and 6–8 weeks (Group D). The primary outcome measures included the Quality of Recovery-15 (QoR-15) scale scores at 3 days, 3 months, and 6 months postoperatively. Secondary outcome measures included postoperative mortality, ICU admission, pulmonary complications, postoperative length of hospital stay, extubation time, and time to leave the PACU.

Results
Concerning the primary outcome measures, the QoR-15 scores at 3 days postoperatively in Group A were significantly lower compared to the other three groups (P < 0.05), while there were no statistically significant differences among the other three groups (P > 0.05). The QoR-15 scores at 3 and 6 months postoperatively showed no statistically significant differences among the four groups (P > 0.05). In terms of secondary outcome measures, Group A had a significantly prolonged hospital stay compared to the other three groups (P < 0.05), while other outcome measures showed no statistically significant differences (P > 0.05).

Conclusion
The timing of surgery in mild or asymptomatic SARS-CoV-2 infected patients does not affect long-term recovery quality but does impact short-term recovery quality, especially for elective general anaesthesia surgeries within 2 weeks of confirmed infection. Therefore, it is recommended to wait for a surgical timing of at least greater than 2 weeks to improve short-term recovery quality and enhance patient prognosis.
Comparison of remimazolam tosilate and propofol during induction and maintenance of general anesthesia in patients undergoing laparoscopic cholecystectomy: a prospective, single center, randomized controlled trial
Authors: Luo Zhuxin , Cao Hai , Luo Li , Chen Long , Feng Dian , Huang Guihua 
Published: July 2024

Abstract
Background
Remimazolam tosilate (RT) is a new, ultrashort-acting benzodiazepine. Here, we investigated the efficacy and safety of RT for general anesthesia in patients undergoing Laparoscopic Cholecystectomy (LC).

Methods
In this study, 122 patients undergoing laparoscopic cholecystectomy were randomly allocated to receive either remimazolam tosilate (Group RT) or propofol group (Group P). RT was administered as a slow bolus of 0.3 mg kg− 1 for induction, followed by 1.0–2.0 mg kg− 1 h− 1 for maintenance of general anesthesia. Propofol was started at 2 mg kg− 1 and followed by 4–10 mg kg− 1 h− 1 until the end of surgery. The primary outcome was the time to bispectral index (BIS) ≤ 60. The secondary outcome included the time to loss of consciousness (LoC), and the time to extubation. Adverse events were also assessed.

Results
A total of 112 patients were recruited for study participation. Among them, the time to BIS ≤ 60 in Group RT was longer than that in Group P (Group RT: 89.3 ± 10.7 s; Group P: 85.9 ± 9.7 s, P > 0.05). While the time to LoC comparing remimazolam and propofol showed no statistical significance (Group RT: 74.4 ± 10.3 s; Group P: 74.7 ± 9.3 s, P > 0.05). The time to extubation in Group RT was significantly longer than that in Group P (Group RT: 16.0 ± 2.6 min; Group P: 8.8 ± 4.3 min, P < 0.001). Remimazolam tosilate had more stable hemodynamics and a lower incidence of hypotension during general anesthesia.

Conclusions
Remimazolam tosilate can be safely and effectively used for general anesthesia in patients undergoing Laparoscopic Cholecystectomy. It maintains stable hemodynamics during induction and maintenance of general anesthesia compared with propofol. Further studies are needed to validate the findings.

Trial registration
Chictr.org.cn ChiCTR2300071256 (date of registration: 09/05/2023).
The use of diagnostic ultrasound by primary care physicians in Switzerland – a cross-sectional study
Authors: Zumstein Nico , Merlo Christoph , Essig Stefan , Auer Reto , Tal Kali , Hari Roman 
Published: July 2024

Abstract
Background
Diagnostic ultrasound has become a bedside tool widely available to many primary care physicians (PCPs) in Europe. It is often used as point-of-care ultrasonography (POCUS) in this setting. In Switzerland, certain POCUS examinations are listed as learning objectives in existing ultrasound training programs (we defined these examinations as swissPOCUS = sPOCUS). Ultrasound performed by PCPs can lead to faster diagnostic workup and reduce referral to secondary care units. However, adequate training is crucial to guarantee high quality. To guide the development of ultrasound training programs for PCPs, this study explores the use of ultrasound in primary care in Switzerland.

Methods
This was a cross-sectional study. We invited PCPs from the Swiss practice-based research network “Sentinella” to collect data on the first 5 daily ultrasounds they ordered or performed themselves. Participating PCPs collected data for 3 months – divided into 4 groups to account for seasonal differences.

Results
Out of 188 PCPs invited, 81.9% provided data through an initial questionnaire. 46.8% provided data on 1616 ultrasounds. 56.5% of PCPs had access to ultrasound machines, while 29.8% had completed formal training. 77% of the reported ultrasounds were self-performed; 27% of the reported scans (35% of all self-performed scans) were performed by PCPs with incomplete or no formal training.
The main areas of interest were the abdominal (57.9%) and the musculoskeletal (22%) region. 36.9% of reported examinations were sPOCUS exams. Among PCPs with access to US machines, the percentages of referred examinations were similar for sPOCUS (11.9%) and non-sPOCUS (11.3%) indications. However, some sPOCUS musculoskeletal ultrasounds were often referred (e.g. tendon/ligament/muscle injuries or cutaneous/subcutaneous tumour).

Conclusion
Most Swiss PCPs had access to ultrasound equipment and performed a majority of both sPOCUS and non-sPOCUS scans themselves, often without or with incomplete training. This reflects the fact that POCUS was only recently introduced in Switzerland. There is a need for easily accessible POCUS training programs aimed at PCPs in Switzerland.
Training courses for PCPs should focus on abdominal and musculoskeletal ultrasound, because these were the most common sites for scans, and because some sPOCUS musculoskeletal examinations showed a particularly high percentage of referral.
Adjusting the 15-method to Danish general practice: identification of barriers, facilitators, and user needs
Authors: Schøler Peter Næsborg , Søndergaard Jens , Rasmussen Sanne , Nielsen Anette Søgaard 
Published: July 2024

Abstract
Background
The 15-method is an opportunistic screening and brief intervention tool for alcohol-related problems in primary healthcare. A Danish feasibility study of the 15-method indicated that adjustments were needed to improve its contextual fit to Danish general practice. This adjustment process was conducted in two parts. The first part focused on identifying barriers, facilitators, and user needs for addressing alcohol using the 15-method. The second part will address the identified barriers and user needs to finalize a Danish version of the method. This study reports on part one of the adjustment process.

Methods
Semi-structured individual interviews and focus group interviews with healthcare professionals (n = 8) and patients (n = 5) from general practice in Denmark. Data analysis was conducted using thematic content analysis. The results were condensed into two focus areas that will form the basis for user workshops in part two of the adjustment process.

Results
The main barriers for addressing alcohol using the 15-method were patients and healthcare professionals not having the same agenda, having difficulty opening a conversation on alcohol, and workflow in the practices. Main facilitators included high interpersonal skills, taking the patient’s perspective, and good routines and interdisciplinary work. Suggested adjustments and additions to the method included digitalization, visual icebreakers, quotes and examples, and development of a quick guide. The identified focus areas for user workshops were Communication and Material, and Integration to Workflows.

Conclusion
Healthcare professionals found the opportunistic screening approach exemplified by the 15-method to be beneficial in identifying and addressing alcohol-related problems. They appreciate the method’s structured framework that assists in presenting treatment options. Identified adjustment areas to the 15-method will lay the groundwork for future efforts to develop a finalized Danish version of the 15-method.