bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are there conserved biosynthetic genes in lichens? Genome-wide assessment of terpene biosynthetic genes suggests ubiquitous distribution of the squalene synthase cluster
Authors: Singh Garima , Pasinato Anna , Yriarte Alejandra López-Chicheri , Pizarro David , Divakar Pradeep K. , Schmitt Imke , Dal Grande Francesco 
Published: October 2024

AbstractLichen-forming fungi (LFF) are prolific producers of functionally and structurally diverse secondary metabolites, most of which are taxonomically exclusive and play lineage-specific roles. To date, widely distributed, evolutionarily conserved biosynthetic pathways in LFF are not known. However, this idea stems from polyketide derivatives, since most biochemical research on lichens has concentrated on polyketide synthases (PKSs). Here, we present the first systematic identification and comparison of terpene biosynthetic genes of LFF using all the available Lecanoromycete reference genomes and 22 de novo sequenced ones (111 in total, representing 60 genera and 23 families). We implemented genome mining and gene networking approaches to identify and group the biosynthetic gene clusters (BGCs) into networks of similar BGCs. Our large-scale analysis led to the identification of 724 terpene BGCs with varying degrees of pairwise similarity. Most BGCs in the dataset were unique with no similarity to a previously known fungal or bacterial BGC or among each other. Remarkably, we found two BGCs that were widely distributed in LFF. Interestingly, both conserved BGCs contain the same core gene, i.e., putatively a squalene/phytoene synthase (SQS), involved in sterol biosynthesis. This indicates that early gene duplications, followed by gene losses/gains and gene rearrangement are the major evolutionary factors shaping the composition of these widely distributed SQS BGCs across LFF. We provide an in-depth overview of these BGCs, including the transmembrane, conserved, variable and LFF-specific regions. Our study revealed that lichenized fungi do have a highly conserved BGC, providing the first evidence that a biosynthetic gene may constitute essential genes in lichens.
Participants’ baseline characteristics and feedback of the nature-based social intervention “friends in nature” among lonely older adults in assisted living facilities in finland: a randomised controlled trial of the RECETAS EU-project
Authors: Pitkala Kaisu H. , Rautiainen Laura , Aalto Ulla L. , Kautiainen Hannu , Kolster Annika , Laakkonen Marja-Liisa , Partonen Timo , Roitto Hanna-Maria , Strandberg Timo E. , Opacin Nerkez , Puntscher Sibylle , Siebert Uwe , Coll-Planas Laura , Sachs Ashby L. , Litt Jill S. , Jansson Anu H. ,   For the RECETAS project, David Acurio , Alzbeta Bártová , Lucie Cattaneo , Iva Holmerova , Gabriela Garcia 
Published: October 2024

Abstract
Background
Loneliness is common among older adults in institutional settings. It leads to adverse effects on health and wellbeing, for which nature contact with peers in turn may have positive impact. However, the effects of nature engagement among older adults have not been studied in randomised controlled trials (RCT). The “Friends in Nature” (FIN) group intervention RCT for lonely older adults in Helsinki assisted living facilities (ALFs) aims to explore the effects of peer-related nature experiences on loneliness and health-related quality of life (HRQoL). In this study we aim describe the participants’ baseline characteristics of the RCT, feasibility of FIN intervention and intervention participants’ feedback on the FIN.

Methods
Lonely participants were recruited from 22 ALFs in Helsinki area, Finland, and randomised into two groups: 1) nature-based social intervention once a week for nine weeks (n = 162) and 2) usual care (n = 157). Demographics, diagnoses and medication use were retrieved from medical records, and baseline cognition, functioning, HRQoL, loneliness and psychological wellbeing were assessed. Primary trial outcomes will be participants’ loneliness (De Jong Giervald Loneliness Scale) and HRQoL (15D).

Results
The mean age of participants was 83 years, 73% were female and mean Minimental State Examination of 21 points. The participants were living with multiple co-morbidities and/or disabilities. The intervention and control groups were comparable at baseline. The adherence with intervention was moderate, with a mean attendance of 6.8 out of the nine sessions. Of the participants, 14% refused, fell ill or were deceased, and therefore, participated three sessions or less. General subjective alleviation of loneliness was achieved in 57% of the intervention participants. Of the respondents, 96% would have recommended a respective group intervention to other older adults. Intervention participants appreciated their nature excursions and experiences.

Conclusions
We have successfully randomised 319 lonely residents in assisted living facilities into a trial about the effects of nature experiences in a group-format. The feedback from participants was favourable. The trial will provide important information about possibilities of alleviating loneliness with peer-related nature-based experiences in frail residents.

Trial registration
ClinicalTrials.gov, ID: NCT05507684. Registration 19/08/2022.
Associations between clinical data, vaccination status, antibody responses, and post-COVID-19 symptoms in Thais infected with SARS-CoV-2 Delta and Omicron variants: a 1-year follow-up study
Authors: Khongsiri Wathusiri , Poolchanuan Prapassorn , Dulsuk Adul , Thippornchai Narin , Phunpang Rungnapa , Runcharoen Chakkaphan , Boonprakob Thitiya , Hemtong Onura , Chowplijit Suchada , Chuapaknam Vachara , Siripoon Tanaya , Piyaphanee Watcharapong , Luvira Viravarn , Rotejanaprasert Chawarat , Leaungwutiwong Pornsawan , Chantratita Wasun , Chantratita Narisara , Kosoltanapiwat Nathamon 
Published: October 2024

Abstract
Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), led to a global pandemic from 2020. In Thailand, five waves of outbreaks were recorded, with the fourth and fifth waves driven by the Delta and Omicron variants, resulting in over 20,000 new confirmed cases daily at their peaks.

Methods
This cross-sectional study investigated the associations between clinical symptoms, vaccination status, antibody responses, and post-COVID-19 sequelae in COVID-19 patients. Plasma samples and clinical data were collected from participants admitted to hospitals in Thailand between July 2021 and August 2022, with follow-ups conducted for one year. The study included 110 participants infected with either the Delta (n = 46) or Omicron (n = 64) variants. Virus genotypes were confirmed by RT-PCR of nasal swab RNA and partial nucleotide sequencing of the S gene. IgG and IgA antibody levels against the receptor-binding domain (RBD) of SARS-CoV-2 Delta and Omicron variants were measured in plasma samples using ELISA.

Results
Pneumonia was found to be associated with Delta variant infections, while sore throat, congestion or runny nose, and headache were linked to Omicron infections. Vaccination with fewer than two doses and diabetes mellitus were significantly associated with higher disease severity. Specific IgG and IgA antibodies against the RBD of the Delta variant generally rose by day 14 and were maintained for up to two months, whereas the pattern of antibody response to the Omicron variant was less clear. Antibody risings were found to be positively associated with pneumonia, certain underlying conditions (obesity, hypertension, dyslipidemia, and diabetes mellitus), and age ≥ 60 years. Delta variant infections were associated with forgetfulness, hair loss, and headache during the 1-year post-infection period. Females were more likely to experience hair loss, forgetfulness, and joint pain, while older age was associated with joint pain.

Conclusions
This study enhances our understanding of SARS-CoV-2 infections in Thais, particularly concerning the Delta and Omicron variants. The findings can inform public health planning and response strategies for future outbreaks of SARS-CoV-2 or other emerging viral diseases.
Surgeon handedness affects the acetabular cup positioning during primary total hip arthroplasty regardless of the surgical approach. a systematic review and metanalysis
Authors: Khalifa Ahmed A. , Hassan Ahmed Abdelazim 
Published: October 2024

Abstract
Purpose
The aim was to investigate the effect of surgeon handedness on acetabular cup positioning, functional outcomes, and dislocation incidence during primary THA.

Methods
A systematic review was conducted according to the PRISMA guidelines. Studies published in English were searched in three databases (PubMed, Embase, and Scopus). A dominant side is a right-handed (RHD) or left-handed (LHD) surgeon who operates on the right or left hip, respectively. The opposite is considered to be the non-dominant side. We used odds ratios for dichotomous data and mean differences for continuous data, with 95% confidence intervals for quantitative data synthesis. Heterogeneity was assessed using the I² test, with outcomes graphically represented in a forest plot and a p-value of < 0.05 considered statistically significant; analyses were performed using Review Manager 5.4 (RevMan 5.4.1). >.

Result
Four observational studies were included out of 98 articles. Ten experienced surgeons participated (8 RHD and 2 LHD) and operated on 822 patients (1484 hips), divided equally between dominant and non-dominant sides, and the posterolateral approach was utilized in 80.9% of THAs. RHD surgeons operated on 1404 (94.6%) THAs. The pooled synthesis for inclination indicated no significant difference between either side [MD: 0.10 (95% CI -2.10 to 2.30, P = 0.93, I² = 91%)]. While the difference was significant for anteversion [MD: -2.37 (95% CI -3.82 to -0.93, P = 0.001, I² = 31%)]. The functional outcome was better on the dominant side [MD: 1.44 (95% CI 0.41 to 2.48, P = 0.006, I² = 0%)], and the dislocation incidence was significantly higher on the non-dominant side [OR: 0.45 (95% CI 0.25 to 0.81, P = 0.008, I² = 0%)].

Conclusion
Surgeon handedness and whether operating on the dominant or non-dominant side could affect the acetabular cup positioning and outcomes during primary THAs, even in the hands of high-volume surgeons.
Imbalances in the oral health workforce: a Canadian population-based study
Authors: Gupta Neeru , Miah Pablo 
Published: October 2024

Abstract
Background
In Canada, a new federal public dental insurance plan, being phased in over 2022–2025, may help enhance financial access to dental services. However, as in many other countries, evidence is limited on the supply and distribution of human resources for oral health (HROH) to meet increasing population needs. This national observational study aimed to quantify occupational, geographical, institutional, and gender imbalances in the Canadian dental workforce to help inform benchmarking of HROH capacity for improving service coverage.

Methods
Sourcing microdata from the 2021 Canadian population census, we described workforce imbalances for three groups of postsecondary-qualified dental professionals: dentists, dental hygienists and therapists, and dental assistants. To assess geographic maldistribution relative to population, we linked the person-level census data to the geocoded Index of Remoteness for all inhabited communities. To assess gender-based inequities in the dental labour market, we performed Blinder-Oaxaca decompositions for examining differences in professional earnings of women and men.

Results
The census data tallied 3.4 active dentists aged 25–54 per 10,000 population, supported by an allied workforce of 1.7 dental hygienists/therapists and 1.6 dental assistants for every dentist. All three professional groups were overrepresented in heavily urbanized communities compared with more rural and remote areas. Almost all dental service providers worked in ambulatory care settings, except for male dental assistants. The dentistry workforce was found to have achieved gender parity numerically, but women dentists still earned 21% less on average than men, adjusting for other characteristics. Despite women representing 97% of dental hygienists/therapists, they earned 26% less on average than men, a significant difference that was largely unexplained in the decomposition analysis.

Conclusions
Accelerating universal coverage of oral healthcare services is increasingly advocated as an integral, but often neglected, component toward achieving the health-related Sustainable Development Goals. In the Canadian context of universal coverage for medical (but not dentistry) services, the oral health workforce was found to be demarcated by considerable geographic and gendered imbalances. More cross-nationally comparable research is needed to inform innovative approaches for equity-oriented HROH planning and financing, often critically overlooked in public policy for health systems strengthening.
CAM: a novel aid system to analyse the coloration quality of thick blood smears using image processing and machine learning techniques
Authors: Fong Amaris W. M. , Suárez Daniel R. , Cortés-Cortés Liliana J. , Martinez Carol 
Published: October 2024

Abstract
Background
Battling malaria’s morbidity and mortality rates demands innovative methods related to malaria diagnosis. Thick blood smears (TBS) are the gold standard for diagnosing malaria, but their coloration quality is dependent on supplies and adherence to standard protocols. Machine learning has been proposed to automate diagnosis, but the impact of smear coloration on parasite detection has not yet been fully explored.

Methods
To develop Coloration Analysis in Malaria (CAM), an image database containing 600 images was created. The database was randomly divided into training (70%), validation (15%), and test (15%) sets. Nineteen feature vectors were studied based on variances, correlation coefficients, and histograms (specific variables from histograms, full histograms, and principal components from the histograms). The Machine Learning Matlab Toolbox was used to select the best candidate feature vectors and machine learning classifiers. The candidate classifiers were then tuned for validation and tested to ultimately select the best one.

Results
This work introduces CAM, a machine learning system designed for automatic TBS image quality analysis. The results demonstrated that the cubic SVM classifier outperformed others in classifying coloration quality in TBS, achieving a true negative rate of 95% and a true positive rate of 97%.

Conclusions
An image-based approach was developed to automatically evaluate the coloration quality of TBS. This finding highlights the potential of image-based analysis to assess TBS coloration quality. CAM is intended to function as a supportive tool for analyzing the coloration quality of thick blood smears.
Adenoviral fiber-knob based vaccination elicits efficient neutralizing antibodies and T cell responses against adenovirus infection
Authors: Orabi Ahmed , Shameli Kamyar , Protzer Ulrike , Moeini Hassan 
Published: October 2024

Abstract
Background
Human adenoviruses (HAdVs) frequently cause common respiratory or gastrointestinal infections among children, adults, individuals with immune deficiencies, and other vulnerable populations with varying degree of symptoms, ranging from mild to server, and in some cases, even fatalities. Despite the significant clinical impact of HAdVs, there is currently no approved vaccine available.

Methods
This study explores the potential of the adenovirus type 5 fiber knob (Ad5-FK) to stimulate the production of Ad-specific neutralizing antibodies and T-cell responses in mice. Based on structure predictions, we first expressed Ad5-FK in E. coli and confirmed the assembly of FK into its trimeric form. After testing the binding capability of the trimeric FK to susceptible cells, the immunogenicity of the protein in combination with the c-di-AMP adjuvant was assessed in BALB/c mice.

Results
The purified Ad5-FK exhibited self-trimerization and maintained correct conformation akin to the authentic FK structure. This facilitated effective binding to susceptible HEK293 cells. Notably, the protein demonstrated significant inhibition of HEK293 cells infection by rAd5-GFP. Immunization of BALB/c mice with Ad5-FK, or Ad5-FK mixed with c-di-AMP yielded FK-specific antibodies with potent neutralization capacity. Significantly, Ad5-FK was found to elicit a vigorous CD4+ T-cell response in the immunized mice.

Conclusion
Our findings underscore the efficacy of FK-based vaccine in eliciting anti-Ad humoral immune response and CD4 T-cell immune reactions essential for protection against viral infections.
Burnout amongst chiropractic faculty, practitioners, and trainees: a scoping review
Authors: Partridge Brittni L. , Scott Zachary E. , Roecker Christopher B. , Walters Sheryl A. , Daniels Clinton J. 
Published: October 2024

AbstractObjectiveThe purpose of this scoping review was to summarize the literature pertaining to burnout and chiropractic.MethodsA literature review was performed in accordance with Preferred Reporting of Systematic Reviews and Meta-Analysis Extension for Scoping Reviews (PRISMA-ScR). A literature review was performed by combining the term “chiropractic” with terms relevant to professional burnout (e.g., “work-related stress,” “emotional exhaustion”). We included all publications addressing burnout within the chiropractic profession, including all study designs in only peer-reviewed literature.ResultsOur search yielded 126 citations and 10 met the inclusion criteria. The studies identified consisted of eight surveys and two narrative reviews published from 2011 to 2024. Six of the studies utilized the Maslach Burnout Inventory to assess burnout. Chiropractic students reported greater burnout than the general population. Factors reported to increase burnout risk include higher workload, insurance mandates, and physical demands of daily practice. Factors reported to be protective against burnout included longer duration in clinical practice and philosophy-based practices.ConclusionsResearch on burnout within the chiropractic profession is limited and may not be generalizable. However, the reported factors contributing to burnout are well-documented. Future research should be conducted to improve understanding of the prevalence and causes of burnout in chiropractic.
Nuts and bolts of lung ultrasound: utility, scanning techniques, protocols, and findings in common pathologies
Authors: Beshara Michael , Bittner Edward A. , Goffi Alberto , Berra Lorenzo , Chang Marvin G. 
Published: October 2024

AbstractPoint of Care ultrasound (POCUS) of the lungs, also known as lung ultrasound (LUS), has emerged as a technique that allows for the diagnosis of many respiratory pathologies with greater accuracy and speed compared to conventional techniques such as chest x-ray and auscultation. The goal of this narrative review is to provide a simple and practical approach to LUS for critical care, pulmonary, and anesthesia providers, as well as respiratory therapists and other health care providers to be able to implement this technique into their clinical practice. In this review, we will discuss the basic physics of LUS, provide a hands-on scanning technique, describe LUS findings seen in normal and pathological conditions (such as mainstem intubation, pneumothorax, atelectasis, pneumonia, aspiration, COPD exacerbation, cardiogenic pulmonary edema, ARDS, and pleural effusion) and also review the training necessary to achieve competence in LUS.
Exploring transmission dynamics of the Sarcoptes scabiei mite in humans by combining molecular typing and epidemiological variables, the Netherlands 2016–2023
Authors: Vink Martijn , Coppoolse Hester , Bergmans Anneke , Wennekes Meike , Pas Suzan , Pattipeilohy-van Ommen Jane , Braks Marieta , Bruisten Sylvia , Galimont-Collen Annemie , Wintermans Bas , Fanoy Ewout 
Published: October 2024

Abstract
Background
Scabies, an infestation of the mite Sarcoptes scabiei, has seen an increase in clinical diagnoses in the Netherlands since 2011. This study aimed to analyse PCR-positive S. scabiei skin samples through partial genome sequencing and to link findings to patient epidemiological characteristics.

Methods
Skin samples were collected from individuals in the Netherlands between January 2016 and January 2023. On the PCR-positive S. scabiei skin samples, partial mitochondrial cytochrome c oxidase subunit 1 gene (cox1) sequencing was performed to assess genetic variability. Epidemiological information was collected through interviews. We examined associations between cox1 subtypes, epidemiological factors and treatment outcomes.

Results
Sequencing results were obtained from 128 patients, with epidemiological information available for 55 (43%) of these patients. Fifteen distinct cox1 subtypes were identified. Subtype 01 was most prevalent (45%) and present across all age groups and social settings. The remaining subtypes were less common and not consistently found in all contexts. Five clusters were identified, each with identical cox1 subtypes. Comparative analysis with GenBank sequences revealed genetic similarities with strains from Australia, the USA and China, suggesting the global distribution and transmission of specific subtypes. A substantial proportion (73%) of patients with scabies required multiple treatments to eradicate the infestation, with no subtype-related differences.

Conclusions
This is the first study linking S. scabiei sequencing results to patient epidemiological data. Several subtypes clustered in specific geographic regions and social contexts, underscoring localised transmission patterns. Further research with larger sample sizes is needed to enhance our understanding of the transmission of this mite. This study provides valuable insights that will strengthen scabies control efforts.

Graphical Abstract
High density genomic surveillance and risk profiling of clinical Listeria monocytogenes subtypes in Germany
Authors: Halbedel Sven , Wamp Sabrina , Lachmann Raskit , Holzer Alexandra , Pietzka Ariane , Ruppitsch Werner , Wilking Hendrik , Flieger Antje 
Published: October 2024

Abstract
Background
Foodborne infections such as listeriosis caused by the bacterium Listeria monocytogenes represent a significant public health concern, particularly when outbreaks affect many individuals over prolonged time. Systematic collection of pathogen isolates from infected patients, whole genome sequencing (WGS) and phylogenetic analyses allow recognition and termination of outbreaks after source identification and risk profiling of abundant lineages.

Methods
We here present a multi-dimensional analysis of > 1800 genome sequences from clinical L. monocytogenes isolates collected in Germany between 2018 and 2021. Different WGS-based subtyping methods were used to determine the population structure with its main phylogenetic sublineages as well as for identification of disease clusters. Clinical frequencies of materno-foetal and brain infections and in vitro infection experiments were used for risk profiling of the most abundant sublineages. These sublineages and large disease clusters were further characterised in terms of their genetic and epidemiological properties.

Results
The collected isolates covered 62% of all notified cases and belonged to 188 infection clusters. Forty-two percent of these clusters were active for > 12 months, 60% generated cases cross-regionally, including 11 multinational clusters. Thirty-seven percent of the clusters were caused by sequence type (ST) ST6, ST8 and ST1 clones. ST1 was identified as hyper- and ST8, ST14, ST29 as well as ST155 as hypovirulent, while ST6 had average virulence potential. Inactivating mutations were found in several virulence and house-keeping genes, particularly in hypovirulent STs.

Conclusions
Our work presents an in-depth analysis of the genomic characteristics of L. monocytogenes isolates that cause disease in Germany. It supports prioritisation of disease clusters for epidemiological investigations and reinforces the need to analyse the mechanisms underlying hyper- and hypovirulence.