bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent trends in respirable crystalline silica and elemental carbon exposure in the Ontario, Canada mining industry
Authors: Arrandale Victoria H , Shakeel Ali , Hedges Kevin , O’Connell Kimberly , Gorman Ng Melanie 
Published: December 2024

Abstract

Introduction
Mining is a high-hazard industry with significant occupational disease risks. Despite this there is limited data describing current exposure conditions. The aim of this short communication is to share recent exposure data from underground mines in Ontario, Canada.

Methods
Data from underground mines were accessed through a freedom of information request. Data were cleaned and standardized. Data contained measurements of several hazards from 2013 to 2018; analysis focused on personal samples for respirable crystalline silica (RCS) and elemental carbon (EC) from 2014 to 2018. Descriptive statistics were calculated overall and by sampling year; comparisons were made to current occupational exposure limits. Linear regression models were constructed to examine time trends.

Results
EC exposures decreased significantly, ~10% per year over the measurement period (2014 to 2018). Overall 14% of EC measurements were above the current mining exposure limit (0.12 mg/m3 EC) in Ontario, Canada. Results for silica did not show a statistically significant trend but did suggest a reduction of ~1.8% per year. Almost one-third of the RCS measurements were above the American Conference of Governmental Industrial Hygienists (ACGIH) recommended threshold (0.025 mg/m3).

Conclusions
Current exposure data is needed to understand workers’ exposure and support occupational disease prevention. Recent data from the Ontario mining industry suggests that exposure to elemental carbon decreased significantly from 2014 to 2018, but the annual reduction for silica exposure was not nearly as substantial. Mining workers continue to be exposed to levels of EC and RCS that are hazardous to health.
A new phthalide derivative from the mushroom Cyclocybe cf. erebia culture filtrate affects the phase of circadian rhythms in mouse fibroblasts
Authors: Kobayashi Yusei , Lu Yuanyuan , Li Nan , Endo Naoki , Sotome Kozue , Ueno Kotomi , Tahara Yu , Ishihara Atsushi 
Published: December 2024

Abstract
Circadian rhythms are biological systems that provide approximately 24-h cycles for the behavior and physiological functions of organisms. As diverse modern lifestyles often cause disturbances in circadian rhythms, new approaches to their regulation are required. Therefore, new compounds that affect circadian rhythms have been explored in edible mushrooms. The extract from the culture filtrate of Cyclocybe cf. erebia showed activity that advanced the circadian rhythm in a bioassay with mouse fibroblasts expressing the LUCIFERASE protein under the control of the Period2 promoter. Bioassay-guided fractionation of the extract resulted in the isolation of the compound. Spectroscopic analyses identified the compound as a phthalide derivative, and the compound was named cyclocybelide. Treatment of mouse fibroblasts with the compound shifted the circadian rhythm forward, irrespective of the timing of treatment. In addition, some phthalide derivatives with hydroxy and methoxy groups showed similar effects on circadian rhythms.
Joint extraction of entity and relation based on fine-tuning BERT for long biomedical literatures
Authors: Gao Ting , Zhai Xue , Yang Chuan , Lv Linlin , Wang Han 
Published: December 2024

Abstract

Motivation
Joint extraction of entity and relation is an important research direction in Information Extraction. The number of scientific and technological biomedical literature is rapidly increasing, so automatically extracting entities and their relations from these literatures are key tasks to promote the progress of biomedical research.

Results
The joint extraction of entity and relation model achieves both intra-sentence extraction and cross-sentence extraction, alleviating the problem of long-distance information dependence in long literature. Joint extraction of entity and relation model incorporates a variety of advanced deep learning techniques in this paper: (i) a fine-tuning BERT text classification pre-training model, (ii) Graph Convolutional Network learning method, (iii) Robust Learning Against Textual Label Noise with Self-Mixup Training, (iv) Local regularization Conditional Random Fields. The model implements the following functions: identifying entities from complex biomedical literature effectively, extracting triples within and across sentences, reducing the effect of noisy data during training, and improving the robustness and accuracy of the model. The experiment results prove that the model performs well on the self-built BM_GBD dataset and public datasets, enabling precise large language model enhanced knowledge graph construction for biomedical tasks.

Availability and implementation
The model and partial code are available on GitHub at https://github.com/zhaix922/Joint-extraction-of-entity-and-relation.
Knowledge mining of brain connectivity in massive literature based on transfer learning
Authors: Chai Xiaokang , An Sile , Chen Simeng , Li Wenwei , Feng Zhao , Li Xiangning , Gong Hui , Luo Qingming , Li Anan 
Published: December 2024

Abstract

Motivation
Neuroscientists have long endeavored to map brain connectivity, yet the intricate nature of brain networks often leads them to concentrate on specific regions, hindering efforts to unveil a comprehensive connectivity map. Recent advancements in imaging and text mining techniques have enabled the accumulation of a vast body of literature containing valuable insights into brain connectivity, facilitating the extraction of whole-brain connectivity relations from this corpus. However, the diverse representations of brain region names and connectivity relations pose a challenge for conventional machine learning methods and dictionary-based approaches in identifying all instances accurately.

Results
We propose BioSEPBERT, a biomedical pre-trained model based on start-end position pointers and BERT. In addition, our model integrates specialized identifiers with enhanced self-attention capabilities for preceding and succeeding brain regions, thereby improving the performance of named entity recognition and relation extraction in neuroscience. Our approach achieves optimal F1 scores of 85.0%, 86.6%, and 86.5% for named entity recognition, connectivity relation extraction, and directional relation extraction, respectively, surpassing state-of-the-art models by 2.6%, 1.1%, and 1.1%. Furthermore, we leverage BioSEPBERT to extract 22.6 million standardized brain regions and 165 072 directional relations from a corpus comprising 1.3 million abstracts and 193 100 full-text articles. The results demonstrate that our model facilitates researchers to rapidly acquire knowledge regarding neural circuits across various brain regions, thereby enhancing comprehension of brain connectivity in specific regions.

Availability and implementation
Data and source code are available at: http://atlas.brainsmatics.org/res/BioSEPBERT and https://github.com/Brainsmatics/BioSEPBERT.
A cognitive and sensory approach based on workshops using the zebrafish model promotes the discovery of life sciences in the classroom
Authors: Bourcier Laure M , Babin Patrick J 
Published: December 2024

Abstract
The main objective of the ZebraCool programme was to create a positive attitude and curiosity towards science by bringing experimental activities within schools using an introductory cognitive and sensory approach. This innovative programme was offered at all levels of primary and secondary education including vocational high schools. Thematic workshops can be carried out on various themes such as comparative anatomy and embryology, molecular biology and evolution, or toxicology and endocrine disruptors. They were on an ad hoc basis or as part of an annual school project using zebrafish as a model. This animal was a very attractive entry point for the educator to motivate students to appreciate biology, in particular in the field of molecular biology and evolution. For each practical workshop, the student was an actor in his/her learning, which was intended to arouse the curiosity and desire to understand and learn. The programme was based on close collaboration between class teachers and programme educators to adapt workshops’ content to the school curriculum. Students conducted their own experiments, formulated and tested hypotheses, learned laboratory techniques, collected, and analysed data. ZebraCool scientific activities fell within a conceptual framework of evolutionary biology through which participants perceived their own inner fish through the comparison of biological processes between humans and zebrafish.
Geospatial analyses demonstrate variation of cutaneous T-cell lymphomas across Australia, providing insights into possible causes
Authors: Campbell Belinda A , Baade Peter D , Dasgupta Paramita , Cameron Jessica K , Porceddu Sandro V , Prince H Miles , Thursky Karin 
Published: December 2024

Abstract

Background
Cutaneous T-cell lymphomas (CTCL) are rare with distinct diagnostic challenges. Equitable access to cancer care is a recognised priority, internationally. To date, the geospatial distribution of CTCL has not been definitively studied. Understanding the incidence and geographical distribution of patients with CTCL are critical first steps towards the ultimate goal of equity of care. Geospatial analyses also allow the opportunity to explore environmental causative factors: for CTCL, the contribution of ultraviolet (UV) radiation on causation remains unclear.

Objectives
We investigate geospatial patterns of CTCL incidence across Australia, compare to all rare cancers, and consider solar UV exposure on causality and diagnosis rates.

Methods
All CTCL diagnoses (1/1/2000-31/12/2019) were obtained from the nation-wide dataset. Areas of residence were collected according to nationally-approved definitions. Bayesian spatial incidence models were applied. Geospatial distributions were visually analysed.

Results
The CTCL age-standardised incidence was 7.7 [95%CI:7.4-7.9] per million people in Australia. Diagnostic disparity was seen between Australian states/territories, with lower diagnosis rates in rural/remote and socio-economically disadvantaged areas. Incidence exceeded the national average within more densely populated capital cities. Visual comparisons of the geospatial distribution of CTCL revealed marked discordances with the geospatial patterns of all rare cancers and solar UV in Australia.

Conclusions
Geographical heterogeneity in CTCL exists across Australia. Incidence reflects population density. Geospatial patterns of CTCL substantially differ from all rare cancers, with implications for the unique diagnostic challenges and unmet needs of this patient population. The distribution of CTCL across Australia does not support a causative link with UV exposure. Further global evaluation of geospatial patterns is warranted.
Deciphering the temporal transcriptional landscape of human fetal leptomeninges
Authors: Sun Licheng , Liu Ping , Guo Jingjing , Fang Chuantao , Li Li , Liu Yi , Tan Yanfeng , Zhang Wei , Zhao Rui , Zhang Fayong , Xiao Jianbo , Dong Rui , Ma Shaojie , Mei Xinyu , Qi Dashi 
Published: December 2024

Abstract
The leptomeninges play a pivotal role in the central nervous system (CNS), serving both as a barrier and as a conduit for fluid and cellular transport. Despite their critical functions, our understanding of leptomeningeal development and maturation during human embryogenesis remains limited. This study seeks to bridge this gap.
We conducted single-nucleus RNA sequencing on leptomeningeal tissues from eight human embryos, capturing developmental stages from early fetal to late mid-fetal phases. Our bioinformatic analyses encompassed cell type classification, identification of layer-specific markers, mapping of the arachnoid barrier maturation trajectory, and joint analyses with mouse and aged human leptomeningeal scRNA datasets. Key bioinformatic findings were validated through immunostaining in selected samples.
Our study revealed a complex cellular heterogeneity within the developing leptomeninges, identifying distinct subpopulations of fibroblasts, immune cells, and vascular cells. We mapped the transcriptomic dynamics of fibroblast cell types throughout fetal brain development, highlighting a clear maturation process from early fetal to late mid-fetal stages. Comparative analysis with mouse data allowed us to distinguish human-specific layer markers while confirming several conserved markers shared between humans and mice. Joint analysis with aged human datasets identified two unique arachnoid clusters specific to aging leptomeninges. Moreover, we traced the developmental trajectory of the arachnoid barrier, detailing the transcriptomic shifts associated with its gradual formation. Notably, immune cells in early fetal stages were predominantly M2-type macrophages, underscoring a distinctive immune environment. Finally, we explored the molecular interactions between fibroblasts and other cell types, highlighting their coordinated roles in orchestrating leptomeningeal development.
Together, our findings provide a comprehensive overview of the cellular and molecular landscape of the developing human leptomeninges.
Alpha rhythm slowing in temporal lobe epilepsy across scalp EEG and MEG
Authors: Janiukstyte Vytene , Kozma Csaba , Owen Thomas W , Chaudhary Umair J , Diehl Beate , Lemieux Louis , Duncan John S , Rugg-Gunn Fergus , de Tisi Jane , Wang Yujiang , Taylor Peter N 
Published: December 2024

Abstract
EEG slowing is reported in various neurological disorders including Alzheimer’s, Parkinson’s and Epilepsy. Here, we investigate alpha rhythm slowing in individuals with refractory temporal lobe epilepsy compared with healthy controls, using scalp EEG and magnetoencephalography. We retrospectively analysed data from 17 (46) healthy controls and 22 (24) individuals with temporal lobe epilepsy who underwent scalp EEG and magnetoencephalography recordings as part of presurgical evaluation. Resting-state, eyes-closed recordings were source reconstructed using the standardized low-resolution brain electrographic tomography method. We extracted slow 6–9 Hz and fast 10–11 Hz alpha relative band power and calculated the alpha power ratio by dividing slow alpha by fast alpha. This ratio was computed for all brain regions in all individuals. Alpha oscillations were slower in individuals with temporal lobe epilepsy than controls (P&lt;0.05). This effect was present in both the ipsilateral and contralateral hemispheres and across widespread brain regions. Alpha slowing in temporal lobe epilepsy was found in both EEG and magnetoencephalography recordings. We interpret greater slow alpha as greater deviation from health.
Audit and Feedback Interventions for Antibiotic Prescribing in Primary Care: A Systematic Review and Meta-analysis
Authors: Xu Alice X T , Brown Kevin , Schwartz Kevin L , Aghlmandi Soheila , Alderson Sarah , Brehaut Jamie C , Brown Benjamin C , Bucher Heiner C , Clarkson Janet , De Sutter An , Francis Nick A , Grimshaw Jeremy , Gunnarsson Ronny , Hallsworth Michael , Hemkens Lars , Høye Sigurd , Khan Tasneem , Lecky Donna M , Leung Felicia , Leung Jeremy , Lindbæk Morten , Linder Jeffrey A , Llor Carl , Little Paul , O’Connor Denise , Pulcini Céline , Ramlackhan Kalisha , Ramsay Craig R , Sundvall Pär-Daniel , Taljaard Monica , Touboul Lundgren Pia , Vellinga Akke , Verbakel Jan Y , Verheij Theo J , Wikberg Carl , Ivers Noah 
Published: December 2024

Abstract

Background
This systematic review evaluates the effect of audit and feedback (A&F) interventions targeting antibiotic prescribing in primary care and examines factors that may explain the variation in effectiveness.

Methods
Randomized controlled trials (RCTs) involving A&F interventions targeting antibiotic prescribing in primary care were included in the systematic review. Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, CINAHL, and ClinicalTrials.gov were searched up to May 2024. Trial, participant, and intervention characteristics were extracted independently by 2 researchers. Random effects meta-analyses of trials that compared interventions with and without A&F were conducted for 4 outcomes: (1) total antibiotic prescribing volume; (2) unnecessary antibiotic initiation; (3) excessive prescription duration, and (4) broad-spectrum antibiotic selection. A stratified analysis was also performed based on study characteristics and A&F intervention design features for total antibiotic volume.

Results
A total of 56 RCTs fit the eligibility criteria and were included in the meta-analysis. A&F was associated with an 11% relative reduction in antibiotic prescribing volume (N = 21 studies, rate ratio [RR] = 0.89; 95% confidence interval [CI]: .84, .95; I2 = 97); 23% relative reduction in unnecessary antibiotic initiation (N = 16 studies, RR = 0.77; 95% CI: .68, .87; I2 = 72); 13% relative reduction in prolonged duration of antibiotic course (N = 4 studies, RR = 0.87 95% CI: .81, .94; I2 = 86); and 17% relative reduction in broad-spectrum antibiotic selection (N = 17 studies, RR = 0.83 95% CI: .75, .93; I2 = 96).

Conclusions
A&F interventions reduce antibiotic prescribing in primary care. However, heterogeneity was substantial, outcome definitions were not standardized across the trials, and intervention fidelity was not consistently assessed.
Clinical Trials Registration. Prospero (CRD42022298297).
The use of SGLT2 inhibitors and GLP-1 receptor agonists in older patients: a debate on approaches in CKD and non-CKD populations
Authors: Liabeuf Sophie , Minutolo Roberto , Floege Jürgen , Zoccali Carmine 
Published: December 2024

ABSTRACT
The management of CKD in older patients presents a significant challenge in modern medicine. As the global population ages, the prevalence of CKD among older adults is increasing, which demands effective and safe treatment strategies. The introduction of sodium-glucose cotransporter-2 (SGLT2) inhibitors and glucagon-like peptide-1 (GLP-1) receptor agonists has revolutionized the treatment of CKD, offering potential benefits beyond traditional therapies. However, their use in the older population raises essential questions about safety and efficacy, given the unique physiological changes and comorbidities associated with aging. In this CKJ controversy paper, Roberto Minutolo (PRO) and Sophie Liabeuf (CON) debate on the use of SGLT2 inhibitors and GLP-1 receptor agonists in older patients with CKD. Roberto Minutolo advocates the benefits of these medications, highlighting their role in improving cardiovascular outcomes and slowing CKD progression in older patients. He emphasizes the importance of personalized treatment plans based on the patient's cardio-renal risk profile and preferences. In contrast, Sophie Liabeuf expresses concerns about the safety of these drugs in older adults, citing risks such as fractures, acute kidney injury, and urinary tract infections. She argues that treatment decisions should be guided by patient frailty rather than chronological age, as frail individuals are more vulnerable to adverse drug effects. Both contenders agree on the need for more inclusive clinical trials to better understand the impact of these treatments on older populations. While Roberto Minutolo and Sophie Liabeuf present differing perspectives on the use of SGLT2 inhibitors and GLP-1 receptor agonists in older patients with CKD, their views can be seen as complementary rather than strictly opposing. Minutolo's focus on the benefits of these drugs underscores their potential to improve outcomes. Liabeuf's emphasis on caution and the consideration of frailty highlights the need for careful
patient assessment. Both agree on the importance of personalized treatment and the inclusion of older patients in future clinical trials, suggesting a shared goal of optimizing care for this vulnerable population. Their debate underscores the complexity of treatment decisions and the necessity of balancing risks and benefits in managing CKD in older adults.
NRF2 activation in the heart induces glucose metabolic reprogramming and reduces cardiac dysfunction via upregulation of the pentose phosphate pathway
Authors: Zoccarato Anna , Smyrnias Ioannis , Reumiller Christina M , Hafstad Anne D , Chong Mei , Richards Daniel A , Santos Celio X C , Visnagri Asjad , Verma Sharwari , Bromage Daniel I , Zhang Min , Zhang Xiaohong , Sawyer Greta , Thompson Richard , Shah Ajay M 
Published: December 2024

Abstract

Aims
The transcription factor nuclear factor erythroid–derived 2-like 2 (NRF2) is well recognized as a master regulator of antioxidant responses and cytoprotective genes. Previous studies showed that NRF2 enhances the resistance of mouse hearts to chronic haemodynamic overload, at least in part by reducing oxidative stress. Evidence from other tissues suggests that NRF2 may modulate glucose intermediary metabolism but whether NRF2 has such effects in the heart is unclear. Here, we investigate the role of NRF2 in regulating glucose intermediary metabolism and cardiac function during disease stress.

Methods and results
Cardiomyocyte-specific Keap1 knockout (csKeap1KO) mice, deficient in the endogenous inhibitor of NRF2, were used as a novel model of constitutively active NRF2 signalling. Targeted metabolomics and isotopomer analysis were employed in studies with 13C6-glucose in csKeap1KO and wild-type mice. Pharmacological and genetic approaches were utilized in neonatal rat ventricular myocytes (NRVMs) to explore molecular mechanisms. We found that cardiac-specific activation of NRF2 redirected glucose metabolism towards the pentose phosphate pathway (PPP), a branch pathway of glycolysis, and mitigated pressure overload-induced cardiomyocyte death and cardiac dysfunction. Activation of NRF2 also protected against myocardial infarction-induced DNA damage in remote myocardium and cardiac dysfunction. In vitro, knockdown of Keap1 upregulated PPP enzymes and reduced cell death in NRVM subjected to chronic neurohumoral stimulation. These pro-survival effects were abolished by pharmacological inhibition of the PPP or silencing of the PPP rate-limiting enzyme glucose-6-phosphate dehydrogenase. Knockdown of NRF2 in NRVM increased stress-induced DNA damage, which was rescued by supplementing the cells with either nicotinamide adenine dinucleotide phosphate (NADPH) or nucleosides, the two main products of the PPP.

Conclusion
These results indicate that NRF2 regulates cardiac metabolic reprogramming by stimulating the diversion of glucose into the PPP, thereby generating NADPH and providing nucleotides to prevent stress-induced DNA damage and cardiac dysfunction.