bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and spatial characteristics of tumor evolution in a mouse model of oral squamous cell carcinoma
Authors: Cao Yong , Dong Hao , Li Guangyu , Wei Huiping , Xie Cheng , Tuo Yangjuan , Chen Nian , Yu Dahai 
Published: November 2022

AbstractObjectivesWe aimed to elucidate the temporal and spatial characteristics of tumor evolution in an oral squamous cell carcinoma (OSCC) mouse model with higher burden of lymphatic metastasis through high-throughput sequencing.MethodsThe OSCC model was established in 9 mice. DNA was extracted from the tumors of primary tongue lesions and disseminated tumor cells (DTCs) of submandibular gland lymph nodes and bone marrow, and then whole genome sequencing was performed. After bioinformatics analysis, somatic single-nucleotide variants (SSNVs) and copy number variations (CNVs) data were obtained. Based on SSNVs, clonal architecture and ancestor-descendant relationships among tumor cell subclones were elucidated.ResultsA total of 238 tumor-related SSNVs with 120 high-frequency mutated genes were obtained from 36 samples of 9 mice by whole-genome sequencing. The number of unique SSNVs in the primary lesion, submandibular lymph node and bone marrow was greater than the number of shared SSNVs. Furthermore, the primary lesion-originated subclones, which were identified by SSNVs, were also detected in submandibular lymph nodes in the early stage of oral carcinogenesis. Moreover, at different histopathological stages, unique subclones were also identified in DTCs isolated from lymph nodes.ConclusionTumor heterogeneity is significant in primary tumor cells and disseminated tumor cells. OSCC cells probably disseminate to lymph nodes in the early stage of oral carcinogenesis. OSCC is characterized by polyclonal dissemination, and the evolutionary trajectory of DTCs is potentially dominated by the tumor microenvironment.
The contribution of peer research in evaluating complex public health interventions: examples from two UK community empowerment projects
Authors: Southby Kris , Coan Susan , Rushworth Sara , South Jane , Bagnall Anne-Marie , Lam Tiffany , Woodward Jenny , Button Danial 
Published: November 2022

Abstract
Background
Peer-research is steered and conducted by people with lived experience of the issues being researched. This paper explores the value of peer-research in two complex public health intervention evaluations in the UK.

Methods
Reports from 18 peer research projects, completed by residents from 12 communities in the UK taking part in two community empowerment interventions, were analysed using cross-case analysis.

Results
Undertaking peer research helped to build the evaluation and research skills within individual projects as well as providing data on other outcomes related to the programmes Theory of Change. Some peer researchers, however, felt unprepared for the activity despite support from the academic team and were unsatisfied with project outcomes. While peer research projects provided more opportunities for local residents to engage with the overall evaluations, there was an overreliance on people closely connected to the programmes to be peer researchers. The peer research projects explored topics that were broader than the aims and objectives of the overall programme evaluations. All provided insight into the context in which projects occurred, while some also informed understanding of programme change mechanisms.

Conclusions
Including peer research as part of complex public health intervention evaluations can help uncover important contextual and ecological details beyond the reach of more traditional evaluation data collection. Peer research can also empower and build research/evaluation capacity within communities, which is particularly pertinent for community empowerment interventions.
Just and inclusive end-of-life decision-making for long-term care home residents with dementia: a qualitative study protocol
Authors: Sutherland N. , St. Amant O. , Dupuis S. , Kontos P. , Wiersma E. , Brennan M. 
Published: November 2022

AbstractBackgroundMany people living with dementia eventually require care services and spend the remainder of their lives in long-term care (LTC) homes. Yet, many residents with dementia do not receive coordinated, quality palliative care. The stigma associated with dementia leads to an assumption that people living in the advanced stages of dementia are unable to express their end-of-life needs. As a result, people with dementia have fewer choices and limited access to palliative care. The purpose of this paper is to describe the protocol for a qualitative study that explores end-of-life decision-making processes for LTC home residents with dementia.Methods/designThis study is informed by two theoretical concepts. First, it draws on a relational model of citizenship. The model recognizes the pre-reflective dimensions of agency as fundamental to being human (irrespective of cognitive impairment) and thereby necessitates that we cultivate an environment that supports these dimensions. This study also draws from Smith’s critical feminist lens to foreground the influence of gender relations in decision-making processes towards palliative care goals for people with dementia and reveal the discursive mediums of power that legitimize and sanction social relations.This study employs a critical ethnographic methodology. Through data collection strategies of interview, observation, and document review, this study examines decision-making for LTC home residents with dementia and their paid (LTC home workers) and unpaid (family members) care partners.DiscussionThis research will expose the embedded structures and organizational factors that shape relationships and interactions in decision-making. This study may reveal new ways to promote equitable decision-making towards palliative care goals for LTC home residents with dementia and their care partners and help to improve their access to palliative care.
Low rates of structured advance care planning documentation in electronic health records: results of a single-center observational study
Authors: Wu Adela , Huang Robert J. , Colón Gabriela Ruiz , Zembrzuski Chris , Patel Chirag B. 
Published: November 2022

Abstract
Background
Proper advance care planning (ACP) documentation both improves patient care and is increasingly seen as a marker of high quality by governmental payers. The transition of most medical documentation to electronic health records (EHR) allows for ACP documents to be rapidly disseminated across diverse ambulatory practice settings. At the same time, the complexity and heterogeneity of the EHR, as well as the multiple potential storage locations for documentation, may lead to confusion and inaccessibility. There has been movement to promote structured ACP (S-ACP) documentation within the EHR.

Methods
We performed a retrospective cohort study at a single, large university medical center in California to analyze rates of S-ACP documentation. S-ACP was defined as ACP documentation contained in standardized locations, auditable, and not in free-text format. The analytic cohort composed of all patients 65 and older with at least one ambulatory encounter at Stanford Health Care between 2012 and 2020, and without concurrent hospice care. We then analyzed clinic-level, provider-level, insurance, and temporal factors associated with S-ACP documentation rate.

Results
Of 187,316 unique outpatient encounters between 2012 and 2020, only 7,902 (4.2%) contained S-ACP documentation in the EHR. The most common methods of S-ACP documentation were through problem list diagnoses (3,802; 40.3%) and scanned documents (3,791; 40.0%). At the clinic level, marked variability in S-ACP documentation was observed, with Senior Care (46.6%) and Palliative Care (25.0%) demonstrating highest rates. There was a temporal trend toward increased S-ACP documentation rate (p < 0.001).

Conclusion
This retrospective, single-center study reveals a low rate of S-ACP documentation irrespective of clinic and specialty. While S-ACP documentation rate should not be construed as a proxy for ACP documentation rate, it nonetheless serves as an important quality metric which may be reported to payers. This study highlights the need to both centralize and standardize reporting of ACP documentation in complex EHR systems.
Beyond challenges and enrichment: a qualitative account of cross-cultural experiences of nursing patients with an ethnic minority background in Norway
Authors: Alkhaled Tariq , Rohde Gudrun , Lie Birgit , Johannessen Berit 
Published: November 2022

Abstract
Background
Substantial mass migrations to the Scandinavian countries have made them heterogeneous and multicultural societies. Migration has also influenced the workforce, especially the healthcare system that has had to accommodate a culturally diverse population. This qualitative study aimed to explore nurses’ experiences in caring for patients with an ethnic minority background.

Methods
Focus group interviews with a total of 21 nurses were conducted. Thematic analysis was performed on the transcribed and translated interviews.

Results
The findings of this study revealed three major themes: various experiences concerning language barriers and the use of interpreters, the impact of religious and cultural values, and caring for patients with an ethnic minority background is professionally interesting but demanding.

Conclusions
Caring for culturally diverse patients offers both challenges and opportunities to enhance cultural competence and cultural sensitivity among nurses. Various culturally divergent needs of patients such as family visits, food preferences, expression of pain, and gender sensitivity are interlinked and depend on effective communication during encounters with nurses and the healthcare system at large.
Delirium in the intensive care unit: identifying difficulties in applying the Confusion Assessment Method for the Intensive Care Unit (CAM-ICU)
Authors: dos Santos Fernanda Cecília Monroe , Rêgo Adriana Sousa , Montenegro Widlani Sousa , de Carvalho Sarah Tarcisia Rabelo Ferreira , Cutrim Rodrigo Costa , Júnior Abraão Albino Mendes , Pereira Fábio Henrique Ferreira , Dibai-Filho Almir Vieira , Bassi-Dibai Daniela 
Published: November 2022

Abstract
Background
Delirium is an underdiagnosed condition and this may be related, among other causes, to the incorrect use of assessment tools due to lack of knowledge about cognitive assessment and lack of training of the care team. The aim of this study was to investigate the difficulties encountered by the nursing team in the application of the Confusion Assessment Method for the Intensive Care Unit (CAM-ICU) in patients on mechanical ventilation.

Methods
This is descriptive study with a qualitative approach in a private tertiary hospital located in northeast Brazil. Data collection took place from July 2018 to January 2019. We included 32 nurses and used face-to-face semi-structured interviews. The recorded data were analysed using content analysis. This study followed the recommendations of the Standards for Reporting Qualitative Research (SRQR).

Results
We identified three major categories: lack of knowledge of professionals, subdivided into deficit in academic formation, difficulty in the differential diagnosis of delirium and delusion, and lack of knowledge about the steps of the CAM-ICU; difficulty in patient cooperation; and lack of adequate training to apply the CAM-ICU.

Conclusion
Nurses have a deficit in academic formation on delirium and need adequate training for the correct and frequent use of the CAM-ICU.
An examination of health care utilization during the COVID-19 pandemic among women with early-stage hormone receptor-positive breast cancer
Authors: Paladino Andrew J. , Pebley Kinsey , Kocak Mehmet , Krukowski Rebecca A. , Waters Teresa M. , Vidal Gregory , Schwartzberg Lee S. , Curry Andrea N. , Graetz Ilana 
Published: November 2022

Abstract
Background
Women undergoing treatment for breast cancer require frequent clinic visits for maintenance of therapy. With COVID-19 causing health care disruptions, it is important to learn about how this population’s access to health care has changed. This study compares self-reported health care utilization and changes in factors related to health care access among women treated at a cancer center in the mid-South US before and during the pandemic.

Methods
Participants (N = 306) part of a longitudinal study to improve adjuvant endocrine therapy (AET) adherence completed pre-intervention baseline surveys about their health care utilization prior to AET initiation. Questions about the impact of COVID-19 were added after the pandemic started assessing financial loss and factors related to care. Participants were categorized into three time periods based on the survey completion date: (1) pre-COVID (December 2018 to March 2020), (2) early COVID (April 2020 – December 2020), and later COVID (January 2021 to June 2021). Negative binomial regression analyses used to compare health care utilization at different phases of the pandemic controlling for patient characteristics.

Results
Adjusted analyses indicated office visits declined from pre-COVID, with an adjusted average of 17.7 visits, to 12.1 visits during the early COVID period (p = 0.01) and 9.9 visits during the later COVID period (p < 0.01). Hospitalizations declined from an adjusted average 0.45 admissions during early COVID to 0.21 during later COVID, after vaccines became available (p = 0.05). Among COVID period participants, the proportion reporting changes/gaps in health insurance coverage increased from 9.5% participants during early-COVID to 14.8% in the later-COVID period (p = 0.05). The proportion reporting financial loss due to the pandemic was similar during both COVID periods (34.3% early- and 37.7% later-COVID, p = 0.72). The proportion of participants reporting delaying care or refilling prescriptions decreased from 15.2% in early-COVID to 4.9% in the later-COVID period (p = 0.04).

Conclusion
COVID-19 caused disruptions to routine health care for women with breast cancer. Patients reported having fewer office visits at the start of the pandemic that continued to decrease even after vaccines were available. Fewer patients reported delaying in-person care as the pandemic progressed.
Knowledge, attitude and application towards fast track surgery among operating room paramedics: a cross-sectional study
Authors: Huang Ting , Wang Jingming , Chen Yuanyao , Ye Zhen , Fang Yiwei , Xia Yuze 
Published: November 2022

Abstract
Background
Fast track surgery has shown its effectiveness to accelerate recovery and gained acceptance in many operations. However, data for paramedics using fast track surgery are limited in China. The aims of our study are to evaluate the knowledge, attitude and application status of fast track surgery in paramedics and to provide suggestions for the better application of fast track surgery.

Methods
Two Hundred Ninety-one operating room paramedics were investigated by simple random sampling from October 20 to December 20, 2019 time. A self-reported questionnaire was used to collect data with five dimensions: demographic data, cognitive level, knowledge, attitude and application of fast track surgery. Data were analyzed using qualitative and quantitative methods.

Results
19.93% of participants never heard fast track surgery and only 3.32% of participants were very familiar with it. Gender (0.702, 95% CI 0.109–1.294), technical title (0.342, 95% CI 0.126–0.558) and awareness of the concept of fast track surgery (0.471, 95% CI 0.165–0.776) had a correlation with the knowledge level of paramedics towards fast track surgery. In terms of attitude towards fast track surgery, gender (− 1.944, 95% CI -3.830- -0.058), age (0.303, 95% CI 0.021–0.585) and knowledge score of fast track surgery (0.426, 95% CI 0.014–0.838) are related. Half of the paramedics believe the most difficult problem in the application of fast track surgery was the lack of multi-team communication and cooperation.

Conclusion
The knowledge of fast track surgery among paramedics in Wuhan is poor, and some paramedics have a negative attitude towards it. As the attitude is positively correlated with the knowledge, it is necessary to improve the knowledge level of fast track surgery among paramedics in Wuhan.
Application of decision analytical models to diabetes in low- and middle-income countries: a systematic review
Authors: Twumwaa Tagoe Eunice , Justice Nonvignon , Robert van Der Meer , Itamar Megiddo 
Published: November 2022

AbstractBackgroundDecision analytical models (DAMs) are used to develop an evidence base for impact and health economic evaluations, including evaluating interventions to improve diabetes care and health services—an increasingly important area in low- and middle-income countries (LMICs), where the disease burden is high, health systems are weak, and resources are constrained. This study examines how DAMs–in particular, Markov, system dynamic, agent-based, discrete event simulation, and hybrid models–have been applied to investigate non-pharmacological population-based (NP) interventions and how to advance their adoption in diabetes research in LMICs.MethodsWe systematically searched peer-reviewed articles published in English from inception to 8th August 2022 in PubMed, Cochrane, and the reference list of reviewed articles. Articles were summarised and appraised based on publication details, model design and processes, modelled interventions, and model limitations using the Health Economic Evaluation Reporting Standards (CHEERs) checklist.ResultsTwenty-three articles were fully screened, and 17 met the inclusion criteria of this qualitative review. The majority of the included studies were Markov cohort (7, 41%) and microsimulation models (7, 41%) simulating non-pharmacological population-based diabetes interventions among Asian sub-populations (9, 53%). Eleven (65%) of the reviewed studies evaluated the cost-effectiveness of interventions, reporting the evaluation perspective and the time horizon used to track cost and effect. Few studies (6,35%) reported how they validated models against local data.ConclusionsAlthough DAMs have been increasingly applied in LMICs to evaluate interventions to control diabetes, there is a need to advance the use of DAMs to evaluate NP diabetes policy interventions in LMICs, particularly DAMs that use local research data. Moreover, the reporting of input data, calibration and validation that underlies DAMs of diabetes in LMICs needs to be more transparent and credible.
The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors
Authors: Joubert Pierre M. , Krasileva Ksenia V. 
Published: November 2022

Abstract
Background
One of the ways genomes respond to stress is by producing extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat.

Results
We present a whole circularome sequencing study of the rice blast pathogen, Magnaporthe oryzae. We find that M. oryzae has a highly diverse circularome that contains many genes and shows evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs in M. oryzae occur in genomic regions prone to presence-absence variation and that disease-associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs in our data, which indicates that the presence of these genes on eccDNAs is selected against.

Conclusions
Our study paves the way to understanding how eccDNAs contribute to adaptation in M. oryzae. Our analysis also reveals how M. oryzae eccDNAs differ from those of other species and highlights the need for further comparative characterization of eccDNAs across species to gain a better understanding of these molecules.
Folate regulates RNA m5C modification and translation in neural stem cells
Authors: Xu Xiguang , Johnson Zachary , Wang Amanda , Padget Rachel L. , Smyth James W. , Xie Hehuang 
Published: November 2022

Abstract
Background
Folate is an essential B-group vitamin and a key methyl donor with important biological functions including DNA methylation regulation. Normal neurodevelopment and physiology are sensitive to the cellular folate levels. Either deficiency or excess of folate may lead to neurological disorders. Recently, folate has been linked to tRNA cytosine-5 methylation (m5C) and translation in mammalian mitochondria. However, the influence of folate intake on neuronal mRNA m5C modification and translation remains largely unknown. Here, we provide transcriptome-wide landscapes of m5C modification in poly(A)-enriched RNAs together with mRNA transcription and translation profiles for mouse neural stem cells (NSCs) cultured in three different concentrations of folate.

Results
NSCs cultured in three different concentrations of folate showed distinct mRNA methylation profiles. Despite uncovering only a few differentially expressed genes, hundreds of differentially translated genes were identified in NSCs with folate deficiency or supplementation. The differentially translated genes induced by low folate are associated with cytoplasmic translation and mitochondrial function, while the differentially translated genes induced by high folate are associated with increased neural stem cell proliferation. Interestingly, compared to total mRNAs, polysome mRNAs contained high levels of m5C. Furthermore, an integrative analysis indicated a transcript-specific relationship between RNA m5C methylation and mRNA translation efficiency.

Conclusions
Altogether, our study reports a transcriptome-wide influence of folate on mRNA m5C methylation and translation in NSCs and reveals a potential link between mRNA m5C methylation and mRNA translation.