bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal dietary methionine restriction alters hepatic expression of one-carbon metabolism and epigenetic mechanism genes in the ducklings
Authors: Sécula Aurélie , Bluy Lisa E. , Chapuis Hervé , Bonnet Agnès , Collin Anne , Gress Laure , Cornuez Alexis , Martin Xavier , Bodin Loys , Bonnefont Cécile M. D. , Morisson Mireille 
Published: December 2022

AbstractBackgroundEmbryonic and fetal development is very susceptible to the availability of nutrients that can interfere with the setting of epigenomes, thus modifying the main metabolic pathways and impacting the health and phenotypes of the future individual. We have previously reported that a 38% reduction of the methyl donor methionine in the diet of 30 female ducks reduced the body weight of their 180 mule ducklings compared to that of 190 ducklings from 30 control females. The maternal methionine-restricted diet also altered plasmatic parameters in 30 of their ducklings when compared to that of 30 ducklings from the control group. Thus, their plasma glucose and triglyceride concentrations were higher while their free fatty acid level and alanine transaminase activity were decreased. Moreover, the hepatic transcript level of 16 genes involved in pathways related to energy metabolism was significantly different between the two groups of ducklings. In the present work, we continued studying the liver of these newly hatched ducklings to explore the impact of the maternal dietary methionine restriction on the hepatic transcript level of 70 genes mostly involved in one-carbon metabolism and epigenetic mechanisms.ResultsAmong the 12 genes (SHMT1,GART,ATIC,FTCD,MSRA,CBS,CTH,AHCYL1,HSBP1,DNMT3,HDAC9andEZH2) identified as differentially expressed between the two maternal diet groups (p-value < 0.05), 3 of them were involved in epigenetic mechanisms. Ten other studied genes (MTR,GLRX,MTHFR,AHCY,ADK,PRDM2,EEF1A1,ESR1,PLAGL1, andWNT11) tended to be differently expressed (0.05 < p-value < 0.10). Moreover, the maternal dietary methionine restriction altered the number and nature of correlations between expression levels of differential genes for one-carbon metabolism and epigenetic mechanisms, expression levels of differential genes for energy metabolism, and phenotypic traits of ducklings.ConclusionThis avian model showed that the maternal dietary methionine restriction impacted both the mRNA abundance of 22 genes involved in one-carbon metabolism or epigenetic mechanisms and the mRNA abundance of 16 genes involved in energy metabolism in the liver of the newly hatched offspring, in line with the previously observed changes in their phenotypic traits.
Sedation, sleep-promotion, and non-verbal and verbal communication techniques in critically ill intubated or tracheostomized patients: results of a survey
Authors: Waydhas Christian , Deffner Teresa , Gaschler Robert , Häske David , Hamsen Uwe , Herbstreit Frank , Hierundar Anke , Kumpf Oliver , Rohe Georg , Spiekermann Aileen , Vonderhagen Sonja , Waeschle Reiner M. , Riessen Reimer 
Published: December 2022

Abstract
Background
The aim of this survey was to describe, on a patient basis, the current practice of sedation, pharmacologic and non-pharmacologic measures to promote sleep and facilitation of communication in critically ill patients oro-tracheally intubated or tracheostomized.

Methods
Cross-sectional online-survey evaluating sedation, sleep management and communication in oro-tracheally intubated (IP) or tracheostomized (TP) patients in intensive care units on a single point.

Results
Eighty-one intensive care units including 447 patients (IP: n = 320, TP: n = 127) participated. A score of ≤ -2 on the Richmond Agitation Sedation Scale (RASS) was prevalent in 58.2% (IP 70.7% vs. TP 26.8%). RASS -1/0 was present in 32.2% (IP 25.9% vs. TP 55.1%) of subjects. Propofol and alpha-2-agonist were the predominant sedatives used while benzodiazepines were applied in only 12.1% of patients. For sleep management, ear plugs and sleeping masks were rarely used (< 7%). In half of the participating intensive care units a technique for phonation was used in the tracheostomized patients.

Conclusions
The overall rate of moderate and deep sedation appears high, particularly in oro-tracheally intubated patients. There is no uniform sleep management and ear plugs and sleeping masks are only rarely applied. The application of phonation techniques in tracheostomized patients during assisted breathing is low. More efforts should be directed towards improved guideline implementation. The enhancement of sleep promotion and communication techniques in non-verbal critically ill patients may be a focus of future guideline development.
Clinical outcomes of bicuspid versus tricuspid aortic valve stenosis after transcatheter aortic valve replacement with self-expandable valves
Authors: Jin Qinchun , Chen Shasha , Yang Xue , Li Mingfei , Li Wei , Zhang Xiaochun , Zhou Daxin , Lam Yat-Yin , Ge Junbo 
Published: December 2022

Abstract
Background
There is a lack of available data on specific prognostic comparisons between transcatheter aortic valve replacement (TAVR) using self-expandable valves (SEV) in patients with stenotic Type 0, Type 1 bicuspid aortic valve (BAV) and tricuspid aortic valve (TAV).

Objectives
To evaluate the association between aortic valve morphology and outcomes following self-expandable TAVR.

Methods
Consecutive patients with aortic stenosis(AS) undergoing self-expandable TAVR were enrolled and categorized into three groups (Type 0/Type 1 BAV or TAV) according to the Sievers classification. The primary endpoint was a composite of all-cause mortality and rehospitalization for heart failure (HF) within 2 years. Secondary outcomes included procedural complications and major cardiovascular events observed in clinical follow-ups. Clinical outcomes at 2 years following TAVR were compared among three groups using Kaplan-Meier curve and multivariable Cox proportional hazards regression models.

Results
A total of 344 AS patients (Type 0: 86; Type 1: 109; TAV: 149) were enrolled. The presence of moderate or severe paravalvular leak (PVL) was significantly higher in patients with Type 0 and Type 1 BAV versus TAV (10.47% vs. 16.51% vs. 6.71%, p = 0.043). All-cause 30-day mortality (2.33% vs. 0.92% vs. 2.68%, p = 0.626) and 2-year mortality (3.49% vs. 5.50% vs. 6.71%, p = 0.657) was comparable among the three groups. However, rehospitalization for HF within 2 years was significantly higher in Type 1 BAV (11.63% vs. 20.18% vs. 8.72%, p = 0.020). Multivariate Cox analysis showed that a higher STS score, Type 1 BAV morphology and excess leaflet calcification (≥ median calcium volume (CV) of the entire population) were independent predictors for HF rehospitalization. Additional intragroup Kaplan‒Meier analysis showed that excess leaflet calcification could predict higher long-term mortality and rehospitalization risk for HF(HR (95% CI): 3.430 (1.166–10.090), log rank p = 0.017) in Type 1 BAV patients.

Conclusion
Outcomes of self-expandable TAVR in BAV-AS patients might vary depending on valve subtypes. BAV patients with excess leaflet calcification and a raphe, especially calcified, had an increased risk of moderate PVL and HF readmission in mid-to-long term follow-ups.
Evaluating the predictive performance of gut microbiota for the early-stage colorectal cancer
Authors: Amini Maedeh , Rezasoltani Sama , Pourhoseingholi Mohamad Amin , Asadzadeh Aghdaei Hamid , Zali Mohammad Reza 
Published: December 2022

Abstract
Background
Colorectal cancer (CRC) has been regarded as one of the most frequently diagnosed malignancies among the leading causes of cancer-related morbidity and mortality globally. Diagnosis of CRC at the early-stages of tumour might improve the survival rate of patients. The current study sought to determine the performance of fecal Fusobacterium nucleatum (F. nucleatum) and Streptococcus bovis (S. bovis) for timely predicting CRC.

Methods
Through a case–control study, the fecal sample information of 83 individuals (38 females, 45 males) referring to a hospital in Tehran, Iran was used. All patients underwent a complete colonoscopy, regarded as a gold standard test. Bacterial species including S. bovis and F. nucleatum were measured by absolute quantitative real-time PCR. The Bayesian univariate and bivariate latent class models (LCMs) were applied to estimate the ability of the candidate bacterial markers in order to early detection of patients with CRC.

Results
Bayesian univariate LCMs demonstrated that the sensitivities of S. bovis and F. nucleatum were estimated to be 86% [95% credible interval (CrI) 0.82–0.91] and 82% (95% CrI 0.75–0.88); while specificities were 84% (95% CrI 0.78–0.89) and 80% (95% CrI 0.73–0.87), respectively. Moreover, the area under the receiver operating characteristic curves (AUCs) were 0.88 (95% CrI 0.83–0.94) and 0.80 (95% CrI 0.73–0.85) respectively for S. bovis and F. nucleatum. Based on the Bayesian bivariate LCMs, the sensitivities of S. bovis and F. nucleatum were calculated as 93% (95% CrI 0.84–0.98) and 90% (95% CrI 0.85–0.97), the specificities were 88% (95% CrI 0.78–0.93) and 87% (95% CrI 0.79–0.94); and the AUCs were 0.91 (95% CrI 0.83–0.99) and 0.88(95% CrI 0.81–0.96), respectively.

Conclusions
Our data has identified that according to the Bayesian bivariate LCM, S. bovis and F. nucleatum had a more significant predictive accuracy compared with the univariate model. In summary, these intestinal bacteria have been highlighted as novel tools for early-stage CRC diagnosis.
Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data
Authors: Zwaig Melissa , Baguette Audrey , Hu Bo , Johnston Michael , Lakkis Hussein , Nakada Emily M. , Faury Damien , Juretic Nikoleta , Ellezam Benjamin , Weil Alexandre G. , Karamchandani Jason , Majewski Jacek , Blanchette Mathieu , Taylor Michael D. , Gallo Marco , Kleinman Claudia L. , Jabado Nada , Ragoussis Jiannis 
Published: December 2022

Abstract
Background
Juvenile Pilocytic Astrocytomas (JPAs) are one of the most common pediatric brain tumors, and they are driven by aberrant activation of the mitogen-activated protein kinase (MAPK) signaling pathway. RAF-fusions are the most common genetic alterations identified in JPAs, with the prototypical KIAA1549-BRAF fusion leading to loss of BRAF’s auto-inhibitory domain and subsequent constitutive kinase activation. JPAs are highly vascular and show pervasive immune infiltration, which can lead to low tumor cell purity in clinical samples. This can result in gene fusions that are difficult to detect with conventional omics approaches including RNA-Seq.

Methods
To this effect, we applied RNA-Seq as well as linked-read whole-genome sequencing and in situ Hi-C as new approaches to detect and characterize low-frequency gene fusions at the genomic, transcriptomic and spatial level.

Results
Integration of these datasets allowed the identification and detailed characterization of two novel BRAF fusion partners, PTPRZ1 and TOP2B, in addition to the canonical fusion with partner KIAA1549. Additionally, our Hi-C datasets enabled investigations of 3D genome architecture in JPAs which showed a high level of correlation in 3D compartment annotations between JPAs compared to other pediatric tumors, and high similarity to normal adult astrocytes. We detected interactions between BRAF and its fusion partners exclusively in tumor samples containing BRAF fusions.

Conclusions
We demonstrate the power of integrating multi-omic datasets to identify low frequency fusions and characterize the JPA genome at high resolution. We suggest that linked-reads and Hi-C could be used in clinic for the detection and characterization of JPAs.
Downstaging and survival after Neoadjuvant chemotherapy for bladder cancer in Norway; a population-based study
Authors: Møller Christina Tanem , Støer Nathalie C. , Blindheim Augun , Berge Viktor , Tafjord Gunnar , Fosså Sophie D. , Andreassen Bettina Kulle 
Published: December 2022

Abstract
Background
Neoadjuvant chemotherapy (NAC) before radical cystectomy is associated with pathological downstaging (DS) and improved overall survival (OS) in patients with muscle-invasive bladder cancer (MIBC). Population-based studies have not unequivocally shown improved survival. The aim of this population-based study was to evaluate the effect of NAC on DS and OS in Norwegian patients with MIBC.

Methods
Patients in the Cancer Registry of Norway undergoing radical cystectomy (2008–2015) with or without NAC diagnosed with MIBC between 2008 and 2012 were included. Follow-up data were available until 31 December 2019. Logistic regression estimated the odds of DS with NAC, and a Cox model investigated the effect of DS on OS. Cox models, a mediator analysis and an instrumental variable approach were used to investigate the effect of NAC on OS.

Results
A total of 575 patients were included. NAC was administered to 82 (14%) patients. Compared to cystectomy only, NAC increased the proportion (43% vs. 22%) and the odds of DS (OR 2.51, CI 1.37–4.60, p = 0.003). Independent of NAC, the proportion of pN0 was higher in patients with DS (89% vs. 60%) and DS yielded a 78% mortality risk reduction (HR 0.22, CI 0.15–0.34, p = 1.9∙10–12), compared to patients without DS. We did not find an association between NAC and OS, neither by Cox regression (HR 1.16, CI 0.80–1.68, p = 0.417) nor by an instrumental variable approach (HR = 0.56, CI = 0.07–4.57, p = 0.586). The mediation analysis (p = 0.026) confirmed an indirect effect of NAC on OS through DS. Limitations include limited information of the primary tumour, details of NAC treatment and treatment indications.

Conclusions
NAC increases the probability of DS and is indirectly associated to OS. DS is related to the absence of regional lymph node metastases and is associated with an OS benefit. Improved staging and biomarkers are needed to identify patients most likely to achieve DS and to benefit from NAC.
Household level of air pollution and its impact on the occurrence of Acute Respiratory Illness among children under five: secondary analysis of Demographic and Health Survey in West Africa
Authors: Daffe Mouhamadou Lamine , Thiam Salimata , Bah Fatoumata , Ndong Awa , Cabral Mathilde , Diop Cheikh , Toure Aminata , Lam Absa , Fall Mamadou 
Published: December 2022

Abstract
Background
One out of ten deaths of children under five are attributable to indoor air pollution. And Acute Respiratory Illness (ARI) is among the direct causes.

Objective
This study showed the possibilities of characterizing indoor air pollution in West African Economic and Monetary Union (WAEMU) area and it also made it possible to estimate its impact on the occurrence of ARI in children under five.

Methods
It has been a secondary analysis based on Demographic and Health Surveys (DHSs) from WAEMU countries’ data.. “Household level of air pollution” is the created composite variable, from questions on the degradation factors of indoor air quality (domestic combustion processes) which served to characterize indoor air pollution and to measure its impact by a logistic regression.

Results
Burkina Faso stands out with a greater number of households with a high level of pollution (63.7%) followed by Benin (43.7%) then Togo (43.0%). The main exposure factor "Household level of air pollution" was associated with ARI symptoms (Togo: prevalence = 51.3%; chi-squared test’s p-value < 0.001). Exposure to high level of pollution constitutes a risk (AOR [95 CI]), even though it is not significant ( Ivory Coast: 1.29 [0.72–2.30], Senegal: 1.39 [0.94–2.05] and Togo: 1.15 [0.67–1.95]) and this could be explained by the high infectious etiology of the ARI.
The wellbeing paradox in Hungarian local sustainable agriculture: a health psychology approach
Authors: Birtalan Ilona Liliána , Fertő Imre , Neulinger Ágnes , Rácz József , Oláh Attila 
Published: December 2022

Abstract
Background
The literature suggests that farmers’ work involves a number of operational difficulties. Although alternative food networks address the majority of their problems, they can potentially generate new hardships. The aim of this study is to examine the situational and engagement-related work difficulties associated with the everyday world of Community Supported Agriculture (CSA) farmers.

Methods
This study used the health psychology approach, namely interpretive phenomenology, to understand the social determinants of farmers’ working lives in CSA and to explore mental health challenges within the practices of local sustainable farming. To collect data, semi-structured, in-person interviews were conducted with CSA farmers in Hungary.

Results
Our study shows that new modes of consumer-producer connectivity create novel situations and issues which farmers are forced to address. Three personal experiential themes emerge from the data to describe CSA farmers’ work difficulties: (1) Conflicted autonomy; (2) The pressure of boxes; (3) Social overload. The difficulties for CSA farmers seem to be rooted in the economic characteristics of alternative agriculture where farmers organize food production for the satisfaction of consumer needs. In addition, structural conditions require several different CSA farmer roles, which could even be conflicting.

Conclusion
This study provides participants’ perspectives on the health and wellbeing costs of sustainable farming. Newer producer-consumer connections require both time and experience and involve extra effort or skills, but farmers often lack these abilities. The results show how perceptions of work processes relate to the general framework of CSA, which necessitates a distinct strategy for farm management.
Stakeholder insights into implementing a systems-based suicide prevention program in regional and rural Tasmanian communities
Authors: Grattidge Laura , Purton Terry , Auckland Stuart , Lees David , Mond Jonathan 
Published: December 2022

Abstract
Purpose
With emerging evidence indicating that systems-based approaches help optimise suicide prevention efforts, the National Suicide Prevention Trial sought to gather evidence on the appropriateness of these approaches to prevent suicide among at-risk populations, in regional and rural communities throughout Australia. The Tasmanian component of the Trial implemented the LifeSpan systems framework across three distinct rural areas with priority populations of men aged 40–64 and people 65 and over. The University of Tasmania’s Centre for Rural Health undertook a local-level evaluation of the Trial.

Aims
To explore key stakeholder perceptions of implementing a systems-based suicide prevention program in regional and rural communities in Tasmania, Australia.

Method
This study utilised qualitative methods to explore in depth, stakeholder perspectives. Focus groups and interviews were conducted with 46 participants, comprising Trial Site Working Group members (n = 25), Tasmania’s Primary Health Network employees (n = 7), and other key stakeholders (n = 14). Approximately half of participants had a lived experience of suicide. Data were thematically analysed using NVivo.

Results
Key themes centred on factors impacting implementation of the Trial. These included how the Trial was established in Tasmania; Working Group governance structures and processes; communication and engagement processes; reaching priority population groups; the LifeSpan model and activity development; and the effectiveness, reach and sustainability of activities.

Discussion
Communities were acutely aware of the need to address suicide in their communities, with the Trial providing resources and coordination needed for community engagement and action. Strict adherence to the Lifespan model was challenging at the community level, with planning and time needed to focus on strategies influencing whole or multiple systems, for example health system changes, means restriction. Perceived limitations around implementation concerned varied community buy-in and stakeholder engagement and involvement, with lack of role clarity cited as a barrier to implementation within Working Groups. Barriers delivering activities to priority population groups centred around socio-cultural and technological factors, literacy, and levels of public awareness. Working Groups preferred activities which build on available capital and resources and which meet the perceived needs within the whole community. Approaches sought to increase awareness of suicide and its prevention, relationships and partnerships, and the lived experience capacity in Working Groups and communities.

Conclusion
Stakeholder insights of implementing the National Suicide Prevention Trial in regional and rural Tasmanian from this study can help guide future community-based suicide prevention efforts, in similar geographic areas and with high-risk groups.
Decline in older adults’ daily mobility during the COVID-19 pandemic: the role of individual and built environment factors
Authors: Choe Eun Yeong , Du Yao , Sun Guibo 
Published: December 2022

AbstractBackgroundExtensive research has shown that the COVID-19 pandemic dramatically impacted the daily mobility of older adults. However, very little attention has been paid to the role of individual and built environmental factors in decline in older adults’ daily mobility during the pandemic.MethodsBased on a cohort survey of 741 older adults in Hong Kong, we conducted a one-way ANOVA to explore the differences in determinants (individual or environmental factors) of older adults’ daily mobility between before and during the COVID-19 pandemic. Further, multilevel linear regression was performed to examine how individual characteristics and built environment factors are associated with changes in older adults’ daily mobility during the pandemic.ResultsResults show that the duration of active travel declined from 174.72 to 76.92 min per week, and that the public transport use frequency decreased from an average of 6.14 to 3.96 trips per week during the COVID-19 pandemic (before the rollout of vaccination programme). We also found residential density (p < 0.05) and the number of bus stop was negatively associated with the decline in their active travel (p < 0.01), while a higher destination mix was associated with more significant decrease in active travel (p < 0.01). A higher availability of recreational facilities in neighbourhoods was associated with a greater decrease in public transport use (p < 0.05). In addition, those who were older or having depressive symptoms, which are considered a vulnerable group, were negatively associated with decrease in their mobility (p < 0.001).ConclusionsMaintaining mobility and social interactions are crucial for older adults’ health during the COVID-19 pandemic. This study found that individual and environmental factors differentially affected older adults’ active travel and public transport use during the pandemic. Our findings contribute to understanding the COVID-19 impact on daily mobility in older adults and support more effective active travel promotion policies in the post-pandemic future.