bluuebunny/crossref_metadata_2025_split huggingface dataset:
The systemic evolutionary theory of the origin of cancer (SETOC): an update
Authors: Mazzocca Antonio , Ferraro Giovanni , Misciagna Giovanni 
Published: January 2025

Abstract
The Systemic Evolutionary Theory of the Origin of Cancer (SETOC) is a recently proposed theory founded on two primary principles: the cooperative and endosymbiotic process of cell evolution as described by Lynn Margulis, and the integration of complex systems operating in eukaryotic cells, which is a core concept in systems biology. The SETOC proposes that malignant transformation occurs when cells undergo a continuous adaptation process in response to long-term injuries, leading to tissue remodeling, chronic inflammation, fibrosis, and ultimately cancer. This process involves a maladaptive response, wherein the 'endosymbiotic contract’ between the nuclear-cytoplasmic system (derived from the primordial archaeal cell) and the mitochondrial system (derived from the primordial α-proteobacterium) gradually breaks down. This ultimately leads to uncoordinated behaviors and functions in transformed cells. The decoupling of the two cellular subsystems causes transformed cells to acquire phenotypic characteristics analogous to those of unicellular organisms, as well as certain biological features of embryonic development that are normally suppressed. These adaptive changes enable cancer cells to survive in the harsh tumor microenvironment characterized by low oxygen concentrations, inadequate nutrients, increased catabolic waste, and increased acidity. De-endosymbiosis reprograms the sequential metabolic functions of glycolysis, the TCA cycle, and oxidative phosphorylation (OxPhos). This leads to increased lactate fermentation (Warburg effect), respiratory chain dysfunction, and TCA cycle reversal. Here, we present an updated version of the SETOC that incorporates the fundamental principles outlined by this theory and integrates the epistemological approach used to develop it.
Mobility as a Service (MaaS) bundle uptake: a case study in Milan, Italy
Authors: Silvestri Fulvio , Silvestri Federico , Coppola Pierluigi 
Published: January 2025

Abstract
Recent applications of Mobility as a Service (MaaS) platforms have highlighted certain limitations in accurately identifying integrated mobility packages (MaaS bundles) that align with users’ needs and preferences while also supporting the financial viability of businesses. This study explores the interest of university community members in adopting and paying for MaaS bundles, aiming to determine whether their preferences differ from those of the general population commonly analyzed in existing research. The research method involved the design and administration of a survey instrument, resulting in 1949 completed computer-assisted web interviews collected between May and June 2023. The willingness to pay (WTP) for different MaaS bundles was estimated based on users’ responses to stated preference choice tree experiments. Results reveal that 45.2% of respondents showed no interest in any proposed MaaS bundle, 29.5% towards only one specific MaaS bundle. Conversely, 25.3% of respondents expressed interest in two or more MaaS bundles. Public transport (PT) pass holders showed a higher WTP for MaaS bundles compared to PT pass non-holders, with a WTP an additional 17.5–28.3% over what they currently pay for their PT pass. The findings reveal a positive attitude among university community members toward MaaS bundles, especially among PT pass holders. This underscores an opportunity for MaaS providers to target this group with tailored bundles that complement existing transport choices, thereby increasing user satisfaction and financial viability.
Pseudocitrobacter cyperus, a novel bacterial species recovered from Cyperus alternifolius in Egypt
Authors: Hamed Samira M. , Amer Mai A. 
Published: January 2025

Abstract

Background
Strain Cyp38ST was isolated as an endophyte from the plant Cyperus alternifolius, collected along the banks of the River Nile in 2019. Preliminary analysis tentatively identified Cyp38ST as belonging to the genus Pseudocitrobacter.

Methods
The preliminary identification of Cyp38ST was performed using the VITEK®2 identification system, MALDI-TOF-MS, and 16S rRNA gene sequencing. To confirm its taxonomic classification, the draft genome of Cyp38ST was generated using DNBseq, and the genome-based taxonomic evaluation was conducted by calculating the overall genome-relatedness indices (OGRIs) such as Average Nucleotide Identity (ANI), digital DNA-DNA hybridization (dDDH), and the tetra-nucleotide signatures (Tetra). Additionally, the biochemical features, antimicrobial susceptibility profiles, and fatty acid methyl ester content of Cyp38ST were characterized.

Results
VITEK®2 misidentified Cyp38ST as Citrobacter werkmanii, MALDI-TOF-MS identified it as Pseudocitrobacter faecalis. While the 16S rRNA gene showed more than 99.0% similarity to other Pseudocitrobacter species, the calculated OGRIs were lower than the thresholds recommended for species assignment to all currently known Pseudocitrobacter species. Furthermore, the phylogenomic analysis revealed that Cyp38ST forms a distinct species cluster within the genus Pseudocitrobacter. Cyp38ST was predicted as a potential human pathogen and carried a unique ß-lactamase-coding gene.

Conclusion
Here we present Cyp38ST (= CCASU-2024-73T) as the type strain of a novel species within the genus Pseudocitrobacter to which we propose the name Pseudocitrobacter cyperus sp. nov. We provide a full description of the novel species and present its genome sequence and annotation. The discovery of this novel species highlights the potential of endophytic bacteria associated with unique plant hosts to harbor previously uncharacterized microbial diversity.
Service delivery and the role of clinical pharmacists in UK primary care for older people, including people with dementia: a scoping review
Authors: Burnand Alice , Woodward Abi , Kolodin Vladimir , Manthorpe Jill , Jani Yogini , Orlu Mine , Bhanu Cini , Samsi Kritika , Vickerstaff Victoria , Wilcock Jane , Ward Jane , Rait Greta , Davies Nathan 
Published: January 2025

Abstract

Objective
As populations age globally, there is increasing prevalence of multiple long-term conditions, such as dementia, leading to many challenges. The burden on health and care services, economic pressures, and the necessity for innovative policies to better support older people and people with dementia becomes paramount. This review explores how clinical pharmacists working in UK primary care support older people and people with dementia.

Design
Scoping review.

Method
This review was conducted following the framework for scoping reviews in accordance with the Joanna Briggs Institute (JBI) methodology. The search of Scopus, EMBASE, CINAHL, Web of Science, PsycINFO, and Cochrane was initially conducted in September 2022, and updated in August 2024. Searches included literature exploring the landscape of clinical pharmacy services for older people in the UK, focusing on roles and services delivered, perceptions, and experiences.

Results
A total of 30 articles were included. These detail the multifaceted responsibilities of clinical pharmacists in primary care for older people. Stakeholder perspectives, including healthcare professionals and patients, emphasised the positive outcomes of clinical pharmacist involvement, from reducing other practitioners’ workloads to improving patient safety. However, communication gaps, concerns about competence from other healthcare professionals, and the need for clear role definitions emerged as challenges. Research focused on the experiences of underserved groups, such as people with dementia or from minority ethnic backgrounds, is lacking.

Conclusions and implications
The review enhances our understanding of the primary care clinical pharmacist service in the UK and identifies gaps in evidence, emphasising the need for empirical studies on the experiences of older people with cognitive impairment and those from minority ethnic backgrounds. It provides insights into what makes an effective clinical pharmacist service, such as training and communication, which may help to inform international policy and practice and improve service provision globally.
Association between COVID-19 anxiety syndrome and COVID-19 vaccine hesitancy in the postpandemic era: a cross-sectional study in Hong Kong
Authors: Wu Timothy Chung Ming , Ho Jonathan Ka Ming , Choi Sai Kit , Chan Yanki Hiu Yan , Chan Bella Wing Sze , Li Timmy Tim Ming , Tam Fu Po , Wong Ivan Man Chun , Wing Chan Alex Siu 
Published: January 2025

Abstract

Background
The COVID-19 pandemic has had profound psychophysiological and socioeconomic effects worldwide. COVID-19 anxiety syndrome (CAS) is a specific cluster of maladaptive coping strategies, including perseveration and avoidance behaviours, in response to the perceived threat and fear of COVID-19. CAS is distinct from general COVID-19 anxiety. The level of CAS in the postpandemic era remained unknown. Despite extensive research on general COVID-19 anxiety and COVID-19 vaccine hesitancy (CVH), few studies have investigated the association between CAS and CVH. The present study aimed to assess the level of CAS and the prevalence of CVH and explore the association between CAS and CVH in the general population of Hong Kong.

Methods
This cross-sectional study was conducted in Hong Kong. Participants were recruited using convenience and snowball sampling methods and completed an online or a paper-based questionnaire comprising two well-validated instruments. The COVID-19 Anxiety Syndrome Scale (C-19ASS), which includes the C-19ASS-P and C-19ASS-A subscales, was used to evaluate CAS in terms of perseveration and avoidance behaviours. The COVID-19 Vaccine Hesitancy Scale (CVHS) was used to determine the presence of CVH.

Results
This study included 389 participants. The median C-19ASS-P and C-19ASS-A scores were 8 (Interquartile range (IQR) 5–13) and 3 (IQR 0–6), respectively. The CVHS scores revealed a CVH prevalence of 68.1%. A significantly larger proportion of participants with CVH rated “hesitant” compared with those without CVH across all the CVHS items. Furthermore, the median C-19ASS-P and C-19ASS-A scores were significantly higher for participants without CVH than for those with CVH.

Conclusions
Our findings revealed that CAS persists and CVH is common in the postpandemic era and that CAS is associated with CVH. Comprehensive interventions addressing both informational and psychological aspects are needed to increase the rate of vaccine acceptance and to mitigate the effect of CAS on public health outcomes.
AmelOBP4: an antenna-specific odor-binding protein gene required for olfactory behavior in the honey bee (Apis mellifera)
Authors: Liu Fang , Lai Yu , Wu Lixian , Li Qiang , Lei Linyue , Yin Wei , Zhang Yuan , Huang Zachary Y. , Zhao Hongxia 
Published: January 2025

Abstract

Background
Odorant binding proteins (OBPs) initiate the process of odorant perception. Numerous investigations have demonstrated that OBPs bind a broad variety of chemicals and are more likely to carry pheromones or odor molecules with high binding affinities. However, few studies have investigated its effects on insect behavior. Previously, we found that AmelOBP4 has a significantly higher expression in the heads of foragers than that of nurses regardless of their ages, revealing its importance in foraging behaviour of the honey bee. RNA interference (RNAi) is the induction of sequence specific gene silencing by double-stranded RNA (dsRNA), it is a powerful tool that makes gene inactivation possible in organisms that were not amenable to genetic analysis before.

Results
In this study, we found that AmelOBP4 had high expression levels in the antennae of both nurses and foragers, and could be successfully inhibited by feeding double stranded RNA of AmelOBP4 (dsAmelOBP4). Foragers with inhibited AmelOBP4 showed significantly lower sugar responsiveness than control bees, and also significantly reduced EAG response to plant volatiles of nonanal, linalool and 1-Octen-3ol. On the other hand, nurses with inhibited AmelOBP4 showed significantly reduced EAG response to brood pheromone of ethyl oleate, methyl linoleate, methyl palmitate and β-ocimene. Finally, the Y-tube choice assay showed nurses only exhibited a significantly reduced preference to ethyl oleate, but foragers exhibited significantly reduced preference to all these three plant volatiles.

Conclusions
The findings of our study suggested that AmelOBP4 plays an important role in the odorant binding process, especially in modulating olfactory behaviour in workers. Our results provide a foundation for exploring the olfactory mechanism of Apis mellifera.
SenPred: a single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden
Authors: Hughes Bethany K. , Davis Andrew , Milligan Deborah , Wallis Ryan , Mossa Federica , Philpott Michael P. , Wainwright Linda J. , Gunn David A. , Bishop Cleo L. 
Published: January 2025

Abstract

Background
Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets have enabled an increased understanding of senescent cell heterogeneity.

Methods
Here we present SenPred, a machine-learning pipeline which identifies fibroblast senescence based on single-cell transcriptomics from fibroblasts grown in 2D and 3D.

Results
Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental fibroblast senescence to a high degree of accuracy (> 99% true positives). Applying SenPred to in vivo whole skin scRNA-seq datasets reveals that cells grown in 2D cannot accurately detect fibroblast senescence in vivo. Importantly, utilising scRNA-seq from 3D deeply senescent fibroblasts refines our ML model leading to improved detection of senescent cells in vivo. This is context specific, with the SenPred pipeline proving effective when detecting senescent human dermal fibroblasts in vivo, but not the senescence of lung fibroblasts or whole skin.

Conclusions
We position this as a proof-of-concept study based on currently available scRNA-seq datasets, with the intention to build a holistic model to detect multiple senescent triggers using future emerging datasets. The development of SenPred has allowed for the detection of an in vivo senescent fibroblast burden in human skin, which could have broader implications for the treatment of age-related morbidities.
All code for the SenPred pipeline is available at the following URL: https://github.com/bethk-h/SenPred_HDF.
Standard: Human gastric organoids
Authors: Hong Fan , Tan Ronghui , Wang Ting , Zhong Nanshan , Zhao Hongling , Xu Rui-hua , Shen Lin , Liu Yingbin , Yao Xuebiao , Xiang Dongxi , Hui Lijian , Xiong Jianping , Gao Dong , Zhao Bing , Miao Zhifeng , Hao Jie , Li Yong , Hu Shijun , Fu Boqiang , Hua Guoqiang , Wang Lei , Zeng Zhao-Lei , Chen Chong , Wu Jianmin , Wang Changlin , Wang Chunnian , Zhan Xianbao , Song Chen , Yu Chunping , Yang Yingying , Niu Gengming , Wang Yalong , Zhao Tongbiao , Chen Ye-Guang 
Published: January 2025

Abstract
Organoid technology provides a transformative approach to understand human physiology and pathology, offering valuable insights for scientific research and therapeutic development. Human gastric organoids, in particular, have gained significant interest for applications in disease modeling, drug discovery, and studies of tissue regeneration and homeostasis. However, the lack of standardized quality control has limited their extensive clinical applications. The “Human Gastric Organoids” is part of a series of guidelines for human gastric organoids in China, which establishes comprehensive standards on terminology, technical specifications, testing methods, inspection rules, usage instructions, labeling, transportation, and storage, developed by experts from the Chinese Society for Cell Biology and its branch societies. Released on October 29, 2024, this guideline aims to establish standardized protocols, enhance institutional practices, and promote international standardization for clinical and research applications of human gastric organoids.
Patient centered medication treatment for opioid use disorder in rural Vermont: a qualitative study
Authors: Hichborn Emily G. , Murray Owen B. , Murphy Eilis I. , Gallant Tess E. , Moore Sarah K. , McLeman Bethany M. , Saroyan John , Folland Anthony , Mitchell Megan , Marsch Lisa A. 
Published: January 2025

Abstract

Background
Opioid-related fatal overdoses are occurring at historically high levels and increasing each year. Accessible social and financial support are imperative to the initiation and success of treatment for Opioid Use Disorder (OUD). Medications for Opioid Use Disorder (MOUD) offer effective treatment but there are many more people with untreated OUD than receiving evidence-based medication. Patient-centered care is associated with increased care utilization for substance use disorders. This qualitative study explored the patient perspective of OUD care through a Patient-Centered Care (PCC) framework to illuminate patients’ sense of engagement in care.

Methods
Fifteen semi-structured telephone interviews were conducted from August through November of 2021 regarding patient experiences receiving MOUD in 13 Vermont Hub and Spoke clinics. Emergent themes were deductively mapped to PCC domains of Therapeutic Alliance, Individualized Care, Shared Decision-Making, and Holistic Care.

Results
Participants indicated that PCC fostered engagement and often characterized MOUD clinics they no longer attended as lacking in PCC. Themes related to Therapeutic Alliance were the most prevalent and suggest pathways to retention. Individualizing care through flexible appointment scheduling was strongly valued, while inflexible scheduling fostered fear of not getting medication. Some participants indicated they were less likely to remain in care when providers did not include them in decisions about medication type, dose, or formulation. Participants also appreciated holistic biopsychosocial care and care referrals.

Conclusions
Patient-centered MOUD care was important to participants and encouraged engagement in care. Prioritizing alliance with patients, adapting care to patient needs and preferences particularly when scheduling, including patients in medication decisions, and biopsychosocial attention to patients are congruent with patient perception of desirable MOUD care. Having this understanding of an established, leading MOUD treatment system may serve to benefit states looking to implement this model, or for states who are looking to improve the model they already have in place, potentially leading to higher treatment and retention rates.

Trial registration
This was not a clinical trial involving an intervention, and therefore registration was not required.
Early systemic insults following severe sepsis-associated encephalopathy of critically ill patients: association with mortality and awakening—an analysis of the OUTCOMEREA database
Authors: Thy Michael , Sonneville Romain , Ruckly Stéphane , Mourvillier Bruno , Schwebel Carole , Cohen Yves , Garrouste-Orgeas Maité , Siami Shidasp , Bruel Cédric , Reignier Jean , Azoulay Elie , Argaud Laurent , Goldgran-Toledano Dany , Laurent Virginie , Dupuis Claire , Poujade Julien , Bouadma Lila , de Montmollin Etienne , Timsit Jean-François ,   on the behalf of the OUTCOME R. E. A. network
Published: January 2025

Abstract

Background
Sepsis-associated encephalopathy (SAE) may be worsened by early systemic insults. We aimed to investigate the association of early systemic insults with outcomes of critically ill patients with severe SAE.

Methods
We performed a retrospective analysis using data from the French OUTCOMEREA prospective multicenter database. We included patients hospitalized in intensive care unit (ICU) for at least 48 h with severe SAE (defined by a score on the Glasgow Coma Scale (GCS) ≤ 13 and severe sepsis or septic shock (SEPSIS 2.0 criteria)) requiring invasive ventilation and who had no primary brain injury.
We analyzed early systemic insults (abnormal glycemia (< 3 mmol/L or ≥ 11 mmol/L), hypotension (diastolic blood pressure ≤ 50 mmHg), temperature abnormalities (< 36 °C or ≥ 38.3 °C), anemia (hematocrit < 21%), dysnatremia (< 135 mmol/L or ≥ 145 mmol/L), oxygenation abnormalities (PaO2 < 60 or > 200 mmHg), carbon dioxide abnormalities (< 35 mmHg or ≥ 45 mmHg), and the impact of their correction at day 3 on day-28 mortality and awakening, defined as a recovery of GCS > 13.

Results
We included 995 patients with severe SAE, of whom 883 (89%) exhibited at least one early systemic insult that persisted through day 3. Compared to non-survivors, survivors had significantly less early systemic insults (hypoglycemia, hypotension, hypothermia, and anemia) within the first 48 h of ICU admission. The absence of correction of the following systemic insults at day 3 was independently associated with mortality: blood pressure (adjusted hazard ratio (aHR) = 1.77, 95% confidence interval (CI) 1.34–2.34), oxygenation (aHR = 1.78, 95% CI 1.20–2.63), temperature (aHR = 1.46, 95% CI 1.12–1.91) and glycemia (aHR = 1.41, 95% CI 1.10–1.80). Persistent abnormal blood pressure, temperature and glycemia at day 3 were associated with decreased chances of awakening.

Conclusions
In patients with severe SAE, the persistence of systemic insults within the first three days of ICU admission is associated with increased mortality and decreased chances of awakening.
Analysis of faculty readiness for online teaching: assessing impact and adaptability in diverse educational contexts
Authors: Alcaide-Pulido Purificación , Gutiérrez-Villar Belén , Ordóñez-Olmedo Eva , Pérez-Escolar Marta 
Published: January 2025

Abstract
In recent years, educators have encountered significant shifts in teaching methodologies driven by rapid technological advancements and evolving demands in higher education. This transition has prompted adaptations in teaching practices and digital approaches, resulting in a broader paradigm shift across institutions. This study explores faculty perceptions and attitudes toward emerging pedagogies, focusing on their preparedness for digital and hybrid learning environments and the dynamics of teacher-student collaborative learning in these contexts. The research examines how faculty readiness can enhance adaptation to modern educational demands beyond any specific event or period. Utilising the FROCT scale—measuring readiness through comfort with risk, identity disruption, teaching norms, and equity and tenure norms—this research, conducted among Spanish university teachers, that highlight significant shifts in readiness perceptions after 2 years of compulsory online education. Furthermore, the study identifies gender and age disparities in teachers’ perceptions of online education readiness. These findings contributing to a better understanding of teacher preparation and performance in the post-pandemic educational landscape, specifically in online and blended education, where cognitive, metacognitive, and emotional dimensions play integral roles in fostering socialisation online and collaborative learning between educators and students.