bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees
Authors: Lu LinQin , Li GuoQing , Liu FeiFei 
Published: January 2024

Abstract
Objectives
Lasiodiplodia pseudotheobromae is an important fungal pathogen associated with die-back, canker and shoot blight in many plant hosts with a wide geographic distribution. The aim of our study was to provide high-quality genome assemblies and sequence annotation resources of L. pseudotheobromae, to facilitate future studies on the systematics, population genetics and genomics of the fungal pathogen L. pseudotheobromae.

Data description
High-quality genomes of five L. pseudotheobromae isolates were sequenced based on Oxford Nanopore technology (ONT) and Illumina HiSeq sequencing platform. The total size of each assembly ranged from 43 Mb to 43.86 Mb and over 11,000 protein-coding genes were predicted from each genome. The proteins of predicted genes were annotated using multiple public databases, among the annotated protein-coding genes, more than 4,300 genes were predicted as potential virulence genes by the Pathogen Host Interactions (PHI) database. Moreover, the genome comparative analysis among L. pseudotheobromae and other closely related species revealed that 7,408 gene clusters were shared among them and 152 gene clusters unique to L. pseudotheobromae. This genome and associated datasets provided here will serve as a useful resource for further analyses of this fungal pathogen species.
A preliminary exploration on the mechanism of the carbapenem-resistance transformation of Serratia marcescens in vivo
Authors: Xu Qian , Zheng Beiwen , Li Kaixuan , Shen Ping , Xiao Yonghong 
Published: January 2024

Abstract
Background
The infection of carbapenem-resistant organisms was a huge threat to human health due to their global spread. Dealing with a carbapenem-resistant Serratia marcescens (CRSM) infection poses a significant challenge in clinical settings. This study aims to provide insights into strategies for controlling CRSM infection by exploring the transformation mechanism of carbapenem-resistance.

Methods
We used whole genome sequencing (WGS) to investigate the mechanism of carbapenem resistance in 14 S. marcescens isolates in vivo. The expression level of related genes and the minimum inhibitory concentration of meropenem (MICMEM) were also evaluated to confirm the mechanism of carbapenem resistance.

Results
Seven groups of S. marcescens, each consisting of two strains, were collected from a hospital and displayed a shift in MICMEM from low to high levels. Homology analysis revealed that the isolates in five groups were significantly different from the remaining two. WGS and experimental evidence indicated that four groups of strains developed carbapenem resistance by acquiring the blaKPC (obtaining group), while two groups (persisting group) increased the expression level of the blaKPC. In contrast, isolates in the last group (missing group) did not carry the blaKPC. All strains possessed multiple β-lactamase genes, including blaCTX−M−14, blaSRT−1, and blaSRT−2. However, only in the missing group, the carbapenem-resistant strain lost an outer membrane protein-encoding gene, leading to increased blaCTX−M−14 expression compared to the carbapenem-susceptible strain.

Conclusion
The study findings suggest that S. marcescens strains developed diverse carbapenem resistance in vivo through the evolution of drug resistance, rather than through clone replacement. We hypothesize that carbapenem resistance in S. marcescens was due to certain clonal types with a distinct mechanism.
Genomic insights into Penicillium chrysogenum adaptation to subseafloor sedimentary environments
Authors: Liu Xuan , Wang Xinran , Zhou Fan , Xue Yarong , Liu Changhong 
Published: January 2024

Abstract
Background
Penicillium chrysogenum is a filamentous fungal species with diverse habitats, yet little is known about its genetics in adapting to extreme subseafloor sedimental environments.

Results
Here, we report the discovery of P. chrysogenum strain 28R-6-F01, isolated from deep coal-bearing sediments 2306 m beneath the seafloor. This strain possesses exceptional characteristics, including the ability to thrive in extreme conditions such as high temperature (45 °C), high pressure (35 Mpa), and anaerobic environments, and exhibits broad-spectrum antimicrobial activity, producing the antibiotic penicillin at a concentration of 358 μg/mL. Genome sequencing and assembly revealed a genome size of 33.19 Mb with a GC content of 48.84%, containing 6959 coding genes. Comparative analysis with eight terrestrial strains identified 88 unique genes primarily associated with penicillin and aflatoxins biosynthesis, carbohydrate degradation, viral resistance, and three secondary metabolism gene clusters. Furthermore, significant expansions in gene families related to DNA repair were observed, likely linked to the strain’s adaptation to its environmental niche.

Conclusions
Our findings provide insights into the genomic and biological characteristics of P. chrysogenum adaptation to extreme anaerobic subseafloor sedimentary environments, such as high temperature and pressure.
Effect of ultrasound-guided stellate ganglion block on inflammatory cytokines and postoperative recovery after partial hepatectomy: a randomised clinical trial
Authors: Lao Wei-long , Sang Shuang , Huang Li-cai , Yi Sheng-hua , Guo Mo-chi , Dong Hui-min , Zhou Guo-zhong , Chen Zhong-hua 
Published: January 2024

Abstract
Background
Stellate ganglion block (SGB) has been shown to reduce perioperative complications in various surgeries. Because laparoscopic techniques and instruments have advanced during the past two decades, laparoscopic liver resection is being increasingly adopted worldwide. Lesser blood loss, fewer postoperative complications, and shorter postoperative hospital stays are the advantages of laparoscopic liver resection, as compared to conventional open surgery. There is an urgent need for an effective intervention to reduce perioperative complications and accelerate postoperative recovery. This study investigated the effect of ultrasound-guided SGB on enhanced recovery after laparoscopic partial hepatectomy.

Methods
We compared patients who received SGB with 0.5% ropivacaine (group S) with those who received SGB with 0.9% saline (group N). A total of 58 patients with partial hepatectomy were enrolled (30 S) and (28 N). Before induction of anesthesia, SGB was performed with 0.5% ropivacaine in group S and 0.9% saline in group N. Main outcome: Comparison of serum inflammatory cytokines concentration at each time point.

Results
Main outcome: When comparing IL-6 and IL-10 concentrations among groups, group S showed less variation over time compared to group N. For comparison between groups, the serum IL-6 concentration in group S was lower than that in group N at 6 and 24 h after operation (P < 0.01), and there was a significant linear relationship between serum IL-6 concentration at 24 h after operation and hospitalization situation.

Conclusions
Ultrasound-guided SGB can stabilize perioperative inflammatory cytokines plays a positive role in the enhanced recovery of patients after laparoscopic partial hepatectomy. The serum IL-6 level within 24 h after surgery may be used as a predictor of hospitalization.

Trial registration
The study was registered at the ClinicalTrials.gov (Registration date: 13/09/2021; Trial ID: NCT05042583).
A case of endocardial dissection caused by Micra implantation
Authors: Zhang Jianghua , Shang Shuai , Dong Zhenyu , Zhou Xianhui , Li Yaodong , Lu Yanmei , Xing Qiang , Tuerhong Zukela , Guo Yankai , Xiaokereti Jiasuoer , Tang Baopeng 
Published: January 2024

Abstract
Background
Leadless pacemakers are a recent technological advancement. It has many advantages, but there are still a few serious complications.

Case presentation
This article reports the case of a patient with an endocardial tear and dissection caused by contact with the tip of the Micra cup during surgery and summarises the relevant data.

Conclusions
This case report details the occurrence and management of the incident and provides some guidance for future clinical management.
Characteristics and correlation of body fat distribution and brachial-ankle pulse wave velocity in adults aged 20–59 years: a cross-sectional study
Authors: Wang Shengya , Shi Haiyan , Luo Laiyuan , He Hui 
Published: January 2024

Abstract
Background
Fat distribution is closely related to vascular stiffness. This study aimed to investigate age and sex differences in fat distribution and brachial-ankle pulse wave velocity (baPWV), and the association between fat parameters and baPWV.

Methods
A total of 10,811 participants aged 20–59 years were recruited. Measures included waist and hip circumference, waist-to-hip ratio (WHR), body mass index (BMI), percentage body fat (PBF), subcutaneous fat area (SFA), visceral fat area (VFA), and baPWV.

Results
The results confirm that fat accumulates with age and that men tend to carry more abdominal fat than women in the same age group. The findings also indicate that baPWV increases with age and is significantly higher in men than in women in the same age group. In addition, WHR, VFA, and baPWV were more strongly correlated than baPWV and BMI, SFA, and PBF. Finally, the effects of age, PBF, WHR, and VFA on baPWV were greater for the higher quantiles.

Conclusions
There are age and sex differences in fat distribution and baPWV. Abdominal obesity is more closely linked to arterial stiffness than overall obesity, and people with higher baPWV are more affected by obesity parameters.
Long term all-cause mortality after myocardial infarction with non-obstructed vs obstructed coronary artery disease: a meta-analysis of adjusted data
Authors: Lu Xueli , Zhu Shengnan , Lu Yanjiao , Li Yanming 
Published: January 2024

Abstract
Background
The difference in the long-term outcomes of myocardial infarction in patients with non-obstructed coronary arteries (MINOCA) and patients with myocardial infarction with obstructed coronary artery disease (MI-CAD) is not clear. The current study aimed to pool adjusted data to compare long-term outcomes of MINOCA vs MI-CAD.

Methods
Electronic literature search of PubMed, Embase, CENTRAL, and Google Scholar databases was done for publications up to 18th June 2023. Only studies reporting multivariable-adjusted data with > 1 year of follow-up were included.

Results
Sixteen studies met the inclusion criteria. Our meta-analysis revealed no statistically significant difference in the risk of all-cause mortality between MINOCA and MI-CAD patients (HR: 0.90 95% CI 0.68, 1.19 I2 = 94% p = 0.48). Analysis of the limited data showed a reduced combined risk of all-cause mortality and MI (HR: 0.54 95% CI 0.39, 0.76 I2 = 72% p = 0.003) and major adverse cardiac events (MACE) (HR: 0.66 95% CI 0.51, 0.84 I2 = 51% p = 0.0009) in patients with MINOCA vs MI-CAD, and no difference in the risk of cardiovascular mortality (HR: 0.81 95% CI 0.54, 1.22 I2 = 0% p = 0.31) and readmission between the two groups (HR: 0.85 95% CI 0.61, 1.19 I2 = 90% p = 0.35).

Conclusion
A pooled analysis of adjusted outcomes from the available studies indicated that MINOCA and MI-CAD patients have similar long-term all-cause mortality risk. Our conclusions on the risk of cardiovascular mortality, MACE and readmission rates need to be taken with caution due to a lack of adequate studies. Further research is needed to strengthen the evidence on this important subject.
A novel pathogenic variant in the carnitine transporter gene, SLC22A5, in association with metabolic carnitine deficiency and cardiomyopathy features
Authors: Jolfayi Amir Ghaffari , Naderi Niloofar , Ghasemi Serwa , Salmanipour Alireza , Adimi Sara , Maleki Majid , Kalayinia Samira 
Published: January 2024

Abstract
Background
Primary carnitine deficiency (PCD) denotes low carnitine levels with an autosomal recessive pattern of inheritance. Cardiomyopathy is the most common cardiac symptom in patients with PCD, and early diagnosis can prevent complications. Next-generation sequencing can identify genetic variants attributable to PCD efficiently.

Objective
We aimed to detect the genetic cause of the early manifestations of hypertrophic cardiomyopathy and metabolic abnormalities in an Iranian family.

Methods
We herein describe an 8-year-old boy with symptoms of weakness and lethargy diagnosed with PCD through clinical evaluations, lab tests, echocardiography, and cardiac magnetic resonance imaging. The candidate variant was confirmed through whole-exome sequencing, polymerase chain reaction, and direct Sanger sequencing. The binding efficacy of normal and mutant protein-ligand complexes were evaluated via structural modeling and docking studies.

Results
Clinical evaluations, echocardiography, and cardiac magnetic resonance imaging findings revealed hypertrophic cardiomyopathy as a clinical presentation of PCD. Whole-exome sequencing identified a new homozygous variant, SLC22A5 (NM_003060.4), c.821G > A: p.Trp274Ter, associated with carnitine transport. Docking analysis highlighted the impact of the variant on carnitine transport, further indicating its potential role in PCD development.

Conclusions
The c.821G > A: p.Trp274Ter variant in SLC22A5 potentially acted as a pathogenic factor by reducing the binding affinity of organic carnitine transporter type 2 proteins for carnitine. So, the c.821G > A variant may be associated with carnitine deficiency, metabolic abnormalities, and cardiomyopathic characteristics.
Primary care occupational, physical, and respiratory therapy role adaptation in the first year of the COVID-19 pandemic
Authors: Brown Cara L. , Chartrand Louise , Vollebregt Brontë , Kaur Dayajyot , Crawford Tory , Thille Patricia 
Published: January 2024

Abstract
Background
Occupational, physical and respiratory therapists are relatively new to primary care settings, and thus their roles are still emerging. The COVID-19 pandemic was a time of abrupt changes in professional roles. Professional role adaptations are integral to the ability of health care teams to respond to day-to-day care delivery challenges, such as the current physician and nurse shortage, as well as disaster situations. This study explored the role adaptation of occupational, physical, and respiratory therapists in Canadian primary care settings throughout the first year of the COVID-19 pandemic, as well as barriers and facilitators to adaptation.

Methods
This longitudinal interpretative descriptive study purposively sampled primary care occupational, physical, and respiratory therapists from two Canadian provinces (Manitoba and Ontario). We asked participants to prepare at least 10 semi-structured audio-diary entries during a 12-week period (April – Oct 2020), followed by two semi-structured interviews (Dec 2020, Apr 2021). Questions focused on changes happening in their practice over time. Analysis was iterative, including developing a individual summaries and coding data using both inductive and pre-determined codes. We then entered an immersion/crystallization process to develop key themes related to role adaptation.

Results
We represent our findings with the metaphor of the game of Role Adaptation Snakes and Ladders (aka Chutes and Ladders). The pandemic was certainly not a game, but this metaphor represents the tension of being a pawn to circumstance while also being expected to take control of one’s professional and personal life during a disaster. The object of the game is to move through three phases of role adaptation, from Disorienting, through Coping and Waiting, to Adapting. In the Adapting phase, the therapists creatively found ways to provide vital services for the pandemic response. The therapists were influenced both negatively and positively (snakes and ladders) by their personal circumstances, and professional meso and macro contexts. Each therapist moved across the board in a unique trajectory and timeline based on these contexts.

Conclusions
Rehabilitation professionals, with adequate meso and macro system supports, can maximize their role on primary care teams by adapting their services to work to their full scope of practice.
Experiences with smoking habits and the need for cessation among habitual smokers in Japan: a qualitative study based on semi-structured interviews
Authors: Shiratani Kae , Shimasawa Junko , Mizutani Mayumi 
Published: January 2024

Abstract
Background
Although more than half of the habitual smokers recognize that they want to quit smoking cigarettes, approximately half have failed to quit and experienced distress relapse; therefore, there is an urgent need to focus on these populations. When chronic behavior occurs, it is necessary to view the behavior in the context of the entire life of the person involved, considering the history of the person. In this study, we aimed to describe experiences with smoking from the onset to the present and the need for smoking cessation among habitual smokers in Japan and to explore efforts to address them.

Methods
Semi-structured interviews that lasted for 55–90 min were conducted with the cooperation of 16 habitual smokers who smoked cigarettes daily. The content of the interviews included demographic characteristics, experiences with smoking from the onset to the present, whether they have attempted to quit and related experiences, and their thoughts on smoking. Interviews were transcribed verbatim and analyzed qualitatively. The Medical Research Ethics Review Committee of Jikei University approved this study (approval number: 33–384(11008)).

Results
The participants were aged 26–59 years (mean ± SD: 40.8 ± 8.9 years) and included 10 men and 6 women. The participants started smoking between age 13 and 24 years. The highest number of cigarettes smoked in the participants’ lives ranged from 10 to 80 daily, and 12 participants had attempted to quit smoking so far without success. Regarding experiences with smoking from the onset to the present, four themes of “expand one’s world,” “unconscious attachment,” “attempts and failures,” and “losing oneself” were extracted. Regarding the need for smoking cessation, four themes of “empowerment from experts,” “peer interaction,” “social commitment,” and “recovery of confidence” were extracted.

Conclusion
To support smoking cessation from the perspective of habitual smokers, in addition to improvements through the existing approaches, it is important to recover their confidence using ongoing activities in peer groups according to the target background and support from experts incorporating visual assessments of lung function, along with multiple short-term goals. It is also necessary to raise awareness in communities through activities.
A retrospective cohort study on oesophageal food bolus obstruction in the North Denmark region in 2021—two thirds were never diagnosed with a cause
Authors: Terkelsen Jacob Holmen , Hollænder Martin , Bredal Kasper , Nielsen Sara Munk , Thomsen Kristoffer Vittrup Koed , Baggerman Amanda , Ofverlind Emilia , Koc Alptug Mertcan , Pakes Hannah , Mahdi Marco Bassam , Larsen Sanne Ørnfeldt , Gonzalez Vanessa Parra , Riis Johannes , Frandsen Line Tegtmeier , Melgaard Dorte , Krarup Anne Lund 
Published: January 2024

Abstract
Background
Food bolus obstruction (FBO) leading to hospital treatment is often associated with eosinophilic oesophagitis (EoE), stenosis, or oesophageal cancer (1). Danish national guidelines recommend that patients with FBO undergo a diagnostic upper endoscopy within two weeks of presentation to exclude possible malignancy, and histological evaluation of eight biopsies (2, 3).

Aims
The aims of this study were to (1) report the incidence and describe the causes and treatment of FBO in the North Denmark Region (NDR), (2) determine the proportion of patients who underwent upper endoscopy and biopsy according to regional and national guidelines, and (3) identify International Classification of Diseases 10th Revision (ICD-10) diagnosis and procedure codes applied to the hospital visits due to FBO in the NDR.

Methods
Among all acute hospital visits in the NDR in 2021, all visits with ICD-10 codes possibly reflecting FBO, as well as a random sample of 14,400 visits with unspecific ICD-10 codes (R and Z codes), were screened manually for possible FBO. Diagnosis, follow-up, and treatment of all patients with FBO were recorded.

Results
The median patient age was 66.0 (Q1-Q3: 49.8–81.0) years, and half of the patients had experienced FBO before. Two thirds of patients (66.0%) were never diagnosed with a cause of FBO, followed by 17.3% with EoE. 30% of patients did not undergo upper endoscopy within two weeks of the hospital visit, and 50.7% were never biopsied in the oesophagus. Of 1886 hospital visits with registry ICD-10 codes that possibly reflected FBO, 8.4% were due to FBO, while FBO was present in 0.028% of the random sample of unspecific ICD-10 codes.

Conclusions
Most hospitalized FBO patients in the NDR in 2021 were never diagnosed with a cause. In these patients there is a high risk of overlooked EoE or upper gastrointestinal cancers. The area needs immediate focus and changed routines to improve treatment and prevent new FBO.
Analysis of HIV drug prophylaxis services cascade in healthcare workers: a cross-sectional study in China
Authors: Hu Jingkun , Kang Wenting , Guo Jiahuan , Xu Jie , Lyu Fan , Zhang Guang 
Published: January 2024

Abstract
Background
Human immunodeficiency virus (HIV) drug prophylaxis, including post-exposure prophylaxis (PEP) and pre-exposure prophylaxis (PrEP), has not yet been generally recognized and accepted by the whole society in China, and the utilization coverage among high-risk populations is low. Healthcare workers (HCWs) are important to the promotion and implementation of HIV drug prophylaxis strategy. This study analyzed the HIV drug prophylaxis services cascade (knowledge, attitude, and service) in HCWs, and explored the correlations between PEP and PrEP.

Methods
A cross-sectional study was conducted among 1066 HCWs in 20 designated hospitals for HIV antiretroviral therapy in 20 cities in China. We collected information on participants’ essential characteristics, HIV drug prophylaxis services cascade (knowledge, attitude, and service) and so on. The Chi-square test was used to analyse whether the differences and correlations between categorical variables were statistically significant, and Pearson contingency coefficient was used to analyse the strength of correlations. Multivariable logistic regression was used to analyse associated factors.

Results
Among three stages of HIV drug prophylaxis services cascade, a high percentage of 1066 participants had knowledge of HIV drug prophylaxis (PEP: 78.2%, PrEP: 80.0%). Of them, almost all had supportive attitudes towards HIV drug prophylaxis (PEP: 99.6%, PrEP: 98.6%). Only about half of them would provide HIV drug prophylaxis services (PEP: 53.5%, PrEP: 48.5%). There were positive correlations between knowledge of PEP and PrEP (r = 0.292), between attitudes toward PEP and PrEP (r = 0.325), and between provision of PEP services and PrEP services (r = 0.555) in HCWs.

Conclusions
There was a positive correlation between PEP and PrEP in HCWs. At the stage of providing HIV drug prophylaxis services, training, advocacy and education for HCWs, should be targeted and also combine PEP and PrEP to maximize the effects, so as to improve the enthusiasm of HCWs to provide HIV drug prophylaxis services.