bluuebunny/crossref_metadata_2025_split huggingface dataset:
A knowledge graph approach to predict and interpret disease-causing gene interactions
Authors: Renaux Alexandre , Terwagne Chloé , Cochez Michael , Tiddi Ilaria , Nowé Ann , Lenaerts Tom 
Published: August 2023

Abstract
Background
Understanding the impact of gene interactions on disease phenotypes is increasingly recognised as a crucial aspect of genetic disease research. This trend is reflected by the growing amount of clinical research on oligogenic diseases, where disease manifestations are influenced by combinations of variants on a few specific genes. Although statistical machine-learning methods have been developed to identify relevant genetic variant or gene combinations associated with oligogenic diseases, they rely on abstract features and black-box models, posing challenges to interpretability for medical experts and impeding their ability to comprehend and validate predictions. In this work, we present a novel, interpretable predictive approach based on a knowledge graph that not only provides accurate predictions of disease-causing gene interactions but also offers explanations for these results.

Results
We introduce BOCK, a knowledge graph constructed to explore disease-causing genetic interactions, integrating curated information on oligogenic diseases from clinical cases with relevant biomedical networks and ontologies. Using this graph, we developed a novel predictive framework based on heterogenous paths connecting gene pairs. This method trains an interpretable decision set model that not only accurately predicts pathogenic gene interactions, but also unveils the patterns associated with these diseases. A unique aspect of our approach is its ability to offer, along with each positive prediction, explanations in the form of subgraphs, revealing the specific entities and relationships that led to each pathogenic prediction.

Conclusion
Our method, built with interpretability in mind, leverages heterogenous path information in knowledge graphs to predict pathogenic gene interactions and generate meaningful explanations. This not only broadens our understanding of the molecular mechanisms underlying oligogenic diseases, but also presents a novel application of knowledge graphs in creating more transparent and insightful predictors for genetic research.
Expression profile and bioinformatics analysis of circRNA and its associated ceRNA networks in longissimus dorsi from Lufeng cattle and Leiqiong cattle
Authors: Yang Chuang , Wu Longfei , Guo Yongqing , Li Yaokun , Deng Ming , Liu Dewu , Liu Guangbin , Sun Baoli 
Published: August 2023

AbstractThis paper aims to explore the role of circRNA expression profiles and circRNA-associated ceRNA networks in the regulation of myogenesis in the longissimus dorsi of cattle breeds surviving under subtropical conditions in southern China by RNA sequencing and bioinformatics analysis. It also aims to provide comprehensive understanding of the differences in muscle fibers in subtropical cattle breeds and to expand the knowledge of the molecular networks that regulate myogenesis. With regard to meat quality indicators, results showed that the longissimus dorsi of LQC had lower pH (P < 0.0001), lower redness (P < 0.01), lower shear force (P < 0.05), and higher brightness (P < 0.05) than the longissimus dorsi of LFC. With regard to muscle fiber characteristics, the longissimus dorsi of LQC had a smaller diameter (P < 0.0001) and higher density of muscle fibers (P < 0.05). The analysis results show that the function of many circRNA-targeted mRNAs was related to myogenesis and metabolic regulation. Furthermore, in the analysis of the function of circRNA source genes, we hypothesized that btacirc_00497 and btacirc_034497 may regulate the function and type of myofibrils by affecting the expression of MYH6, MYH7, and NEB through competitive linear splicing.
Microbiota-derived short chain fatty acids in fermented Kidachi Aloe promote antimicrobial, anticancer, and immunomodulatory activities
Authors: Al-Madboly Lamiaa A. , Yagi Akira , Kabbash Amal , El-Aasr Mona A. , El-Morsi Rasha M. 
Published: August 2023

AbstractBackgroundFermented Aloe leaf juice is a commonly used food supplement in Japan. In a previous study, fermentation ofA. arborescencejuice was performed and the presence of short-chain fatty acids (SCFAs) was confirmed and quantified. Samples were collected before and after the fermentation process to be subjected, in the present study, to DNA extraction, 16S rRNA gene (V3–V4 regions) amplification, and sequencing by the next-generation Illumina MiSeq sequencer. Our work aims to analyze the sequences to assess the bacterial diversity in the juice before and after fermentation, identify the beneficial microbes responsible for the production of SCFAs, and evaluate some of the biological activities of the fermented juice.ResultsData revealed the richness and diversity of the bacterial community in the fermented juice compared to the unfermented control. Relative abundance of bacterial phyla showed that the majority of the microbial community in the test samples corresponded toPseudomonadota(unfermented; 10.4%, fermented; 76.36%), followed by Bacillota (unfermented; 4.71%, fermented; 17.13%) and thenBacteroidota(unfermented; 0.57%, fermented; 1.64%). For the fermented sample, 84% of Bacillota were lactobacilli. A hierarchically clustered heatmap revealed thatLactobacilluswas the most abundant genus in both samples suggesting its involvement in the production of SCFAs.To assess potential health benefits, the anticancer efficacy of the fermented product ofA. arborescenswas investigated against colorectal cancer (IC50 = 3.5 µg/ml) and liver cancer (IC50 = 6.367 µg/ml) compared to the normal peripheral blood mononuclear cells (PBMCs). Flow cytometric analysis of the cell cycle pattern revealed remarkable population arrest in G0 and G1, however, the highest percentages were mainly in the G1 phase for Hep-G2 (40.1%) and HCT-116 (53.2%) cell lines. This effect was accompanied by early apoptotic profiles of HCT-116 (36.9%) and late apoptosis for Hep-G2 (17.3%). Furthermore, immunomodulatory properties demonstrated a significantly (p < 0.001) reduced percentage of induced TNF-α while enhancing IFN-γ dramatically. For antimicrobial activities, marked broad-spectrum activities were recorded against some bacterial and fungal pathogens (17–37 mm inhibition zone diameter range).ConclusionTherefore, this study affords the basis of bacterial community composition in fermentedA. arborescensjuice as well as its potential biological benefits.
Randomized comparison of effects of two different remifentanil dose on surgical conditions during endoscopic sinus surgery
Authors: Jeong JinHyeok , Park ChanWoo , Yoon YoungJoon , Lee DoJae , Cho SangYun 
Published: August 2023

Abstract
Background
The combination of propofol and remifentanil results in better surgical field conditions during endoscopic sinus surgery than inhalation anesthesia. This study compared surgical field conditions between two groups receiving low or high concentration of remifentanil and hemodynamic variables using non-invasive cardiac monitoring.

Methods
Fifty-four patients between ASA I or II, were randomly assigned to either the high-concentration remifentanil group (HR), effect-site concentration of 8 ng/mL or the low-concentration remifentanil group(LR), effect-site concentration of 4 ng/mL. Surgical condition was evaluated using the Boezaart Surgical Field Grading Scale presented by Boezaart. Cardiac output was measured using non-invasive cardiac monitoring (CSN-1901).

Results
In terms of surgical conditions, the HR group showed significantly lower values than the LR group (p = 0.021) at 90 min after the start of surgery. Heart rate was significantly lower in the HR group than the LR group at 30, 60, and 90 min after the start of surgery (30 min; p = 0.005, 60 min; p = 0.002, 90 min; p = 0.001). There was a statistically significant decrease of cardiac output in the HR group compared to the LR group immediately after endotracheal intubation and at 30, 60, and 90 min after the start of surgery (Base; P = 0.222, Intubation; P = 0.016, 30 min; p = 0.014, 60 min; P = 0.012, 90 min; P = 0.008). However, in the case of stroke volume, there was no significant difference between the two groups in all measurements.

Conclusion
When comparing the HR group and the LR group, the surgical condition was improved at 90 min after the start of surgery. MAP was lower in the HR group and this was a result of reduction in cardiac output primarily attributed to the decrease in heart rate rather than a decrease in stroke volume.

Trial registration
Clinical Trial Registry of the Republic of Korea (KCT0006453).
Medical care and biomarker-based assessment of mortality in two cohorts of patients with chronic coronary syndrome 10 years apart
Authors: Rehm Martin , Jaensch Andrea , Schöttker Ben , Mons Ute , Hahmann Harry , Koenig Wolfgang , Brenner Hermann , Rothenbacher Dietrich 
Published: August 2023

Abstract
Background
This study aimed to describe the characteristics and mortality of two cohorts of patients with chronic coronary syndrome (CCS) recruited with identical study designs in the same rehabilitation clinics but approximately 10 years apart.

Methods
The KAROLA cohorts included patients with CCS participating in an inpatient cardiac rehabilitation programme in Germany (KAROLA-I: years 1999/2000, KAROLA-II: 2009–2011). Blood samples and information on sociodemographic factors, lifestyle, and medical treatment were collected at baseline, at the end of rehabilitation, and after one year of follow-up. A biomarker-based risk model (ABC-CHD model) and Cox regression analysis were used to evaluate cardiovascular (CV) and non-CV mortality risk.

Results
We included 1130 patients from KAROLA-I (mean age 58.7 years, 84.4% men) and 860 from KAROLA-II (mean age 60.4 years, 83.4% men). Patients in the KAROLA-I cohort had significantly higher concentrations of CV biomarkers and fewer patients were taking CV medications, except for statins. The biomarker-based ABC-CHD model provided a higher estimate of CV death risk for patients in the KAROLA-I cohort (median 3-year risk, 3.8%) than for patients in the KAROLA-II cohort (median 3-year risk, 2.7%, p-value for difference < 0.001). After 10 years of follow-up, 91 (8.1%) patients in KAROLA-I and 45 (5.2%) in KAROLA-II had died from a CV event.

Conclusions
Advances in disease management over the past 20 years may have led to modest improvements in pharmacological treatment during cardiac rehabilitation and long-term outpatient care for patients with CCS. However, modifiable risk factors such as obesity have increased in the more recent cohort and should be targeted to further improve the prognosis of these patients.
An innovative sequential mixed-methods approach to evaluating clinician acceptability during implementation of a standardized labor induction protocol
Authors: Hamm Rebecca Feldman , Levine Lisa D. , Szymczak Julia E. , Parry Samuel , Srinivas Sindhu K. , Beidas Rinad S. 
Published: August 2023

Abstract
Background
Implementation outcomes, including acceptability, are of critical importance in both implementation research and practice. The gold standard measure of acceptability, Acceptability of Intervention Measure (AIM), skews positively with a limited range. In an ongoing hybrid effectiveness-implementation trial, we aimed to evaluate clinician acceptability of induction standardization. Here, we describe an innovative mixed-methods approach to maximize the interpretability of the AIM using a case study in maternal health.

Methods
In this explanatory sequential mixed methods study, we distributed the validated, 4-question AIM (total 4–20) to labor and delivery clinicians 6 months post-implementation at 2 sites (Site 1: 3/2021; Site 2: 6/2021). Respondents were grouped by total score into tertiles. The top (“High” Acceptability) and bottom (“Low” Acceptability) tertiles were invited to participate in a 30-minute semi-structured qualitative interview from 6/2021 to 10/2021 until thematic saturation was reached in each acceptability group. Participants were purposively sampled by role and site. Interviews were coded using an integrated approach, incorporating a priori attributes (Consolidated Framework for Implementation Research constructs) into a modified content analysis approach.

Results
104 clinicians completed the initial survey; 24 were interviewed (12 “High” and 12 “Low” Acceptability). Median total AIM scores were 20/20 IQR[20–20] in the High and 12.5/20 IQR[11–14] in the Low Acceptability groups. In both groups, clinicians were enthusiastic about efforts to standardize labor induction, believing it reduces inter-clinician variability and improves equitable, evidence-based care. In the Low Acceptability group, clinicians stated the need for flexibility and consideration for patient uniqueness. Rarely, clinicians felt labor induction could not or should not be standardized, citing discomfort with medicalization of labor, and concerns with “bulldozing” the patient with interventions. Suggested strategies for overcoming negative sentiment included comprehensive clinician education, as well as involving patients as active participants in the protocol prenatally.

Conclusions
This study utilized AIM in an innovative sequential mixed-methods approach to characterize clinician acceptability, which may be generalizable across implementation endeavors. By performing this work during a hybrid trial, implementation strategies to improve acceptability emerged (clinician education focusing on respect for flexibility; involving patients as active participants prenatally) for year 2, which will inform future multi-site work.
Link between the referring physician and breast and cervical cancers screening: a cross-sectional study in France
Authors: Ouanhnon Lisa , Bugat Marie-Eve Rouge , Druel Vladimir , Grosclaude Pascale , Delpierre Cyrille 
Published: August 2023

Abstract
Background
The aims of the “médecin traitant” or referring physician (RP) reform, introduced in France in 2004, were to improve the organisation and quality of care and to allow for greater equity, particularly in terms of prevention. The objective of our study was to evaluate the effect of having a declared RP on the uptake of screening for breast and cervical cancers, and to explore the mechanisms involved.

Methods
We used an existing dataset of 1,072,289 women, which combines data from the Health Insurance information systems, with census data. We built multivariable logistic regression models to study the effect of having a RP on the uptake of mammography and pap smear, adjusted for age, socio-economic level, health status and healthcare provision. We secondarily added to this model the variable “having consulted a General Practitioner (GP) within the year”. Finally, we evaluated the interaction between the effect of having a referring physician and the area of residence (metropolitan/urban/rural).

Results
Patients who had a declared RP had a significantly higher uptake of mammography and pap smear than those who did not. The strength of the association was particularly important in very urban areas. The effect of having visited a GP seemed to explain a part of the correlation between having a RP and uptake of screening.

Conclusions
Lower rates of gynaecological screening among women without an RP compared to those with an RP may partly reflect a specific behaviour pattern in women less adherent to the health care system. However, this result also shows the importance of the RP, who assumes the key role of relaying public health information in a more personalised and adapted way.
Burden in caregivers of primary care patients with dementia: influence of neuropsychiatric symptoms according to disease stage (NeDEM project)
Authors: García-Martín Victoria , de Hoyos-Alonso M Canto , Delgado-Puebla Rosalía , Ariza-Cardiel Gloria , del Cura-González Isabel 
Published: August 2023

Abstract
Background
Caregiver burden is related to personal factors and patient characteristics and is greater when neuropsychiatric symptoms (NPSs) are present. Objective: Estimate the prevalence of burden among caregivers of dementia patients and its association with NPSs and identify NPSs causing greater caregiver distress according to dementia stage.

Methods
A cross-sectional observational study in caregivers of noninstitutionalized dementia patients was conducted. Caregiver variables were sociodemographic, time of care, NPS-associated distress based on the Neuropsychiatric Inventory Caregiver Distress Scale (NPI-D) and burden based on the Zarit Burden Interview (ZBI). Patient variables were time since disease onset, Global Deterioration Scale (GDS) disease stage, functional assessment and NPS presence and intensity according to the Neuropsychiatric Inventory (NPI). The mean ZBI score, prevalence of burden and NPI-D score with 95% CIs at each dementia stage were estimated. Factors associated with burden were identified by multivariate analysis.

Results
Of the 125 caregivers included, 77.6% were women, with a mean age of 60.7 (± 14.3) years; 78.4% (95%CI: 71.0; 86.0) experienced burden. The mean ZBI score was 12.3 (95%CI: 11.6; 12.9) and increased according to NPS number (p = 0.042). The NPSs causing the most burden were disinhibition (93.5%), irritability (87.3%) and agitation (86.1%). Agitation, apathy, and sleep disorders were the NPSs generating the greatest overall caregiver distress; depression (max NPI-D 1.9), hyperactivity (max NPI-D 2.1), and psychosis symptoms (max NPI-D 1.6) generated the greatest distress at stage GDS 3, stages GDS 4–5, and stages GDS 6–7, respectively. The NPI score (OR = 1.0, 95%CI 1.0; 1.1), intensity of irritability (OR = 1.2, 95%CI 1.0; 1.6), disinhibition (OR = 2.6, 95%CI 1.1; 5.8) and hyperactivity subsyndrome (OR = 1.1, 95%CI 1.0; 1.2) were associated with caregiver burden. Other associated factors were female gender (OR = 6.0, 95%CI 1.6; 22.8), ≥ 8 h daily care (OR = 5.6, 95%CI 1.4; 22.8), working outside the home (OR = 7.6, 95%CI 1.8; 31.8), living with the patient (OR = 4.5, 95%CI 1.1; 19.6), kinship (OR = 5.4, 95%CI 1.0; 28.2) and lower patient education (OR = 8.3, 95%CI 2.3; 30.3).

Conclusions
The burden on caregivers of dementia patients is high and associated with NPS presence and intensity. Disinhibition and irritability caused the highest burden. Depression, hyperactivity and psychosis produce more distress in mild, mild-moderate and severe dementia, respectively.
The effect of follow-up blood cultures on mortality and antibiotic use in gram-negative bloodstream infections
Authors: Yildiz Mehmet , Habibi Hamid , Altin Fatma Betul , Corbacioglu Seref Kerem , Ozger Hasan Selcuk 
Published: August 2023

Abstract
Background
Gram-negative bloodstream infections (GN-BSIs) are a significant clinical challenge. The utility of follow-up blood cultures (FUBCs) in GN-BSIs and their impact on mortality and antibiotic consumption are areas of debate. This study aimed to evaluate the effect of FUBCs on mortality and antibiotic consumption in patients with GN-BSIs.

Methods
This single-center, retrospective study was conducted in aged > 18 years of patients with GN-BSIs. FUBC was defined as a blood culture performed 2–7 days after the first blood culture. Patients were grouped as FUBC and no FUBC and compared. A 1:1 match analysis was performed between the groups according to the SOFA score. The matched subgroup was compared for mortality risk factors with logistic regression models. The two groups were compared for the duration of effective antibiotic therapy and total antibiotic consumption (days of therapy per 1000 patient days (DOT/1000 PD)).

Results
FUBC was performed in 564 (69.4%) of 812 patients. Persistent, positive and negative FUBC rates were 7.9%, 14%, and 78%, respectively. The frequency of persistent GN-BSI in patients with appropriate antibiotic therapy was 3.9%. SOFA score (OR:1.33; 95% CI, 1.23–1.44), Charlson comorbidity index score (OR:1.18; 95% CI, 1.08–1.28), hospital-acquired infections (OR:1.93; 95% CI, 1.08–3.46) and carbapenem-resistant GN-BSI (OR: 2.92; 95% CI, 1.72–4.96) were independent risk factors for mortality. No relationship was found between FUBC and mortality (p > 0.05). Duration of effective antibiotic therapy (10(4–16) vs. 15(9–20), p < 0.001) and DOT/1000 PD (1609 (1000–2178) vs. 2000 (1294–2769), p < 0.001) were longer in the FUBC group.

Conclusion
Routine FUBC should not be recommended because of the low prevalence of persistent infections in patients under appropriate antibiotic therapy and FUBC increases antibiotic consumption.
Comparative study of diagnostic efficacy of sputum and bronchoalveolar lavage fluid specimens in community-acquired pneumonia children treated with fiberoptic bronchoscopy
Authors: Wang Le , Lu Sukun , Guo Yinghui , Liu Jianhua , Wu Peng , Yang Shuo 
Published: August 2023

Abstract
Background
Community-acquired pneumonia (CAP) is usually diagnosed in children, and the type of respiratory specimen is critical. Differences in pathogens detection between induced sputum (IS) and bronchoalveolar lavage fluid (BALF) have not been evaluated.

Methods
In 2018, paired sputum and BALF samples from CAP hospitalised children with indications for bronchoalveolar lavage (BAL) were subjected to multiplex PCR for the detection of 11 common respiratory pathogens.

Results
A total of 142 children with paired sputum and BALF were tested. The overall positivity rate was 85.9% (122/142) for sputum and 80.3% (114/142) for BALF. The two specimens presented almost perfect agreement between the detection on M. pneumoniae, influenza A, influenza B, bocavirus and RSV. In contrast, adenovirus had the lowest kappa value of 0.156, and a false negative rate (FNR) of 66.7%. Rhinovirus had the highest false positive rate (FPR) as 18.5%. The consistent rate was significantly higher in school-age children than those under 1 year old (p = .005). Bacterial co-infection in BALF specimens were observed in 14.8% (21/142). Of the 11 discordant pairs of specimens, 9 cases were sputum(+)/BALF(-) with adenovirus predominating.

Conclusion
Our findings suggest that the consistency of results between sputum and BALF is pathogen specific. Careful consideration needs to be given to whether sputum can be used as a substitute for BALF when children are young or co-infections with bacteria are suspected.