bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models
Authors: Li Jianfu , Li Yiming , Pan Yuanyi , Guo Jinjing , Sun Zenan , Li Fang , He Yongqun , Tao Cui 
Published: August 2024

Abstract
Background
Vaccines have revolutionized public health by providing protection against infectious diseases. They stimulate the immune system and generate memory cells to defend against targeted diseases. Clinical trials evaluate vaccine performance, including dosage, administration routes, and potential side effects. ClinicalTrials.gov is a valuable repository of clinical trial information, but the vaccine data in them lacks standardization, leading to challenges in automatic concept mapping, vaccine-related knowledge development, evidence-based decision-making, and vaccine surveillance.

Results
In this study, we developed a cascaded framework that capitalized on multiple domain knowledge sources, including clinical trials, the Unified Medical Language System (UMLS), and the Vaccine Ontology (VO), to enhance the performance of domain-specific language models for automated mapping of VO from clinical trials. The Vaccine Ontology (VO) is a community-based ontology that was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Our methodology involved extracting and annotating data from various sources. We then performed pre-training on the PubMedBERT model, leading to the development of CTPubMedBERT. Subsequently, we enhanced CTPubMedBERT by incorporating SAPBERT, which was pretrained using the UMLS, resulting in CTPubMedBERT + SAPBERT. Further refinement was accomplished through fine-tuning using the Vaccine Ontology corpus and vaccine data from clinical trials, yielding the CTPubMedBERT + SAPBERT + VO model. Finally, we utilized a collection of pre-trained models, along with the weighted rule-based ensemble approach, to normalize the vaccine corpus and improve the accuracy of the process. The ranking process in concept normalization involves prioritizing and ordering potential concepts to identify the most suitable match for a given context. We conducted a ranking of the Top 10 concepts, and our experimental results demonstrate that our proposed cascaded framework consistently outperformed existing effective baselines on vaccine mapping, achieving 71.8% on top 1 candidate’s accuracy and 90.0% on top 10 candidate’s accuracy.

Conclusion
This study provides a detailed insight into a cascaded framework of fine-tuned domain-specific language models improving mapping of VO from clinical trials. By effectively leveraging domain-specific information and applying weighted rule-based ensembles of different pre-trained BERT models, our framework can significantly enhance the mapping of VO from clinical trials.
Epigallocatechin-3-gallate protects bovine ruminal epithelial cells against lipopolysaccharide-induced inflammatory damage by activating autophagy
Authors: Zhao Wanli , Shen Taiyu , Zhao Bichen , Li Moli , Deng Zhaoju , Huo Yihui , Aernouts Ben , Loor Juan J. , Psifidi Androniki , Xu Chuang 
Published: August 2024

Abstract
Background
Subacute ruminal acidosis (SARA) causes an increase in endotoxin, which can induce immune and inflammatory responses in the ruminal epithelium of dairy cows. In non-ruminants, epigallocatechin-3-gallate (EGCG), a major bioactive ingredient of green tea, is well-known to alleviate inflammation. Whether EGCG confers protection against SARA-induced inflammation and the underlying mechanisms are unknown.

Results
In vivo, eight ruminally cannulated Holstein cows in mid-lactation were randomly assigned to either a low-concentrate (40%) diet (CON) or a high-concentrate (60%) diet (HC) for 3 weeks to induce SARA (n = 4). Cows with SARA had greater serum concentrations of tumor necrosis factor (TNF)-α and interleukin-6, and epithelium had histological signs of damage. In vitro, immortalized bovine ruminal epithelial cells (BREC) were treated with lipopolysaccharide (LPS) to imitate the inflammatory damage caused by SARA. Our data revealed that BREC treated with 10 µg/mL LPS for 6 h successfully induce a robust inflammatory response as indicated by increased phosphorylation of IκBα and nuclear factor kappa-B (NF-κB) p65. Pre-treatment of BREC with 50 µmol/L EGCG for 6 h before LPS challenge promoted the degradation of NLR family pyrin domain containing 3 (NLRP3) inflammasome through activation of autophagy, which further repressed activation of NF-κB pathway targeting Toll-like receptor 4 (TLR4). Analyses also revealed that the ECGG upregulated tight junction (TJ) protein expression upon incubation with LPS.

Conclusions
Subacute ruminal acidosis causes ruminal epithelium injury and systemic inflammation in dairy cows. However, the anti-inflammatory effects of EGCG help preserve the integrity of the epithelial barrier through activating autophagy when BREC are exposed to LPS. Thus, EGCG could potentially serve as an effective therapeutic agent for SARA-associated inflammation.

Graphical Abstract
Clinical trauma severity of indoor and outdoor injurious falls requiring emergency medical service response
Authors: Burford Kathryn G. , Itzkowitz Nicole G. , Crowe Remle P. , Wang Henry E. , Lo Alexander X. , Rundle Andrew G. 
Published: August 2024

Abstract
Background
Injurious falls represent a significant public health burden. Research and policies have primarily focused on falls occurring indoors despite evidence that outdoor falls account for 47–58% of all falls requiring some medical attention. This study described the clinical trauma severity of indoor versus outdoor injurious falls requiring Emergency Medical Services (EMS) response.

Methods
Using the 2019 National Emergency Medical Services Information System (NEMSIS) dataset, we identified the location of patients injured from falls that required EMS response. We classified injury severity using (1) the Revised Trauma Score for Triage (T-RTS): ≤ 11 indicated the need for transport to a Trauma Center; (2) Glasgow Coma Scale (GCS): ≤ 8 and 9–12 indicated severe and moderate neurologic injury; and (3) patient clinical acuity by EMS: Dead, Critical, Emergent, Low.

Results
Of 1,854,909 encounters for patients with injurious falls, the vast majority occurred indoors (n = 1,596,860) compared to outdoors (n = 152,994). For patients who fell indoors vs outdoors on streets or sidewalks, the proportions were comparable for moderate or severe GCS scores (3.0% vs 3.9%), T-RTS scores indicating need for transport to a Trauma Center (5.2% vs 5.9%) and EMS acuity rated as Emergent or Critical (27.7% vs 27.1%). Injurious falls were more severe among male patients compared to females and males injured by falling on streets or sidewalks had higher percentages for moderate or severe GCS scores (5.2% vs 1.9%) and T-RTS scores indicating the need for transport to a Trauma Center (7.3% vs 3.9%) compared to falling indoors. Young and middle-aged patients who fell on streets or sidewalks had higher proportions for a T-RTS score indicating the need for Trauma Center care compared to those in this subgroup who fell indoors. Yet older patients injured by falling indoors were more likely to have a T-RTS score indicating the need for transport to a Trauma Center than older patients who fell on streets or sidewalks.

Conclusions
There was a similar proportion of patients with severe injurious falls that occurred indoors and outdoors on streets or sidewalks. These findings suggest the need to determine outdoor environmental risks for outdoor falls to support location-specific interventions.
The symbiotic alga Trebouxia fuels a coherent soil ecosystem on the landscape scale in the Atacama Desert
Authors: Jung Patrick , Brand Rebekah , Briegel-Williams Laura , Werner Lina , Jost Emily , Lentendu Guillaume , Singer David , Athavale Rujuta , Nürnberg Dennis J. , Alfaro Fernando D. , Büdel Burkhard , Lakatos Michael 
Published: August 2024

AbstractBiocrusts represent associations of lichens, green algae, cyanobacteria, fungi and other microorganisms, colonizing soils in varying proportions of principally arid biomes. The so-called grit crust represents a recently discovered type of biocrust situated in the Coastal Range of the Atacama Desert (Chile) made of microorganisms growing on and in granitoid pebbles, resulting in a checkerboard pattern visible to the naked eye on the landscape scale. This specific microbiome fulfills a broad range of ecosystem services, all probably driven by fog and dew-induced photosynthetic activity of mainly micro-lichens. To understand its biodiversity and impact, we applied a polyphasic approach on the phototrophic microbiome of this biocrust, combining isolation and characterization of the lichen photobionts, multi-gene phylogeny of the photobionts and mycobionts based on a direct sequencing and microphotography approach, metabarcoding and determination of chlorophylla+b contents. Metabarcoding showed that yet undescribed lichens within the Caliciaceae dominated the biocrust together with Trebouxia as the most abundant eukaryote in all plots. Together with high mean chlorophylla+b contents exceeding 410 mg m−2, this distinguished the symbiotic algae Trebouxia as the main driver of the grit crust ecosystem. The trebouxioid photobionts could be assigned to the I (T. impressa/gelatinosa) and A (T. arboricola) clades and represented several lineages containing five potential species candidates, which were identified based on the unique phylogenetic position, morphological features, and developmental cycles of the corresponding isolates. These results designate the grit crust as the only known coherent soil layer with significant landscape covering impact of at least 440 km2, predominantly ruled by a single symbiotic algal genus.
Agreement between child self-report and parent-proxy report for functioning in pediatric chronic pain
Authors: Hanania Joan W. , George Jessica Edwards , Rizzo Christie , Manjourides Justin , Goldstein Laura 
Published: August 2024

Abstract
Purpose
Accurate assessment of chronic pain and functional disability in children and adolescents is imperative for guiding pain management interventions. Parents have multifaceted roles in their child’s pain experience and frequently provide parent-proxy reports of pain-related functioning. However, cross-informant variance is often observed with limited understanding of contributing factors. This study aims to examine the degree of alignment between child and parent-proxy reports for Patient-Reported Outcomes Measurement Information System (PROMIS) pain interference domain among children with chronic pain and to identify factors associated with improved child-parent agreement.

Methods
This study includes a sample of 127 youth (66.1% female) with mixed etiology chronic pain, ranging in age from 8 to 17 (M = 12.24; SD = 1.598), and their parent. Data was collected at an interdisciplinary pediatric pain clinic and online peer support groups. Measures of demographic, pain intensity, and functioning were collected.

Results
Means of parent-proxy reports were significantly lower than child self-reports on the PROMIS (p < 0.05). A statistically significant association between child’s pain intensity (β = 0.953, P < 0.05) and the difference between child self-reported and parent-proxy reported PROMIS functional interference scores was found.

Conclusion
Parents underestimated pain-related functional disability relative to children’s self-reports. The difference between the paired child self-report and parent-proxy report of functional disability was significantly associated with greater child self-reported pain intensity. Although parent-proxy reports in pediatric chronic pain is often used in research and practice, findings underscore the importance of incorporating child and adolescent self-report, when possible, to comprehensively capture the child’s pain experience and best inform clinical interventions.
Predictive ability of the REMS and HOTEL scoring systems for mortality in geriatric patients with pulmonary embolism
Authors: Özkan Abuzer , Özdemir Serdar 
Published: August 2024

Abstract
Background
Pulmonary embolism (PE) is an important cause of mortality and morbidity in the geriatric population. We aimed to compare the ability of the pulmonary embolism severity index (PESI), rapid emergency medicine score (REMS), and hypotension, oxygen saturation, low temperature, electrocardiogram change, and loss of independence (HOTEL) to predict prognosis and intensive care requirement in geriatric patient with PE.

Results
The median age of 132 patients was 77 (71–82) years. PESI was higher in the non-survivor group [132 (113–172)] (P =0.001). The median REMS was 8 (7–10), and it was higher in the non-survivor group [10 (7.5–12.0)] (p = 0.005). The median HOTEL score was 1 (0–2) in the whole cohort and 2 (1–3) in the non-survivor group, indicating significant difference compared to the survivor group (P = 0.001). The area under the curve (AUC) values of HOTEL, REMS, and PESI were determined as 0.72, 0.65, and 0.71, respectively. For the prediction of intensive care requirement, the AUC values of HOTEL, REMS, and PESI were 0.76, 0.75, and 0.76, respectively, with no significant difference in pairwise comparisons (PESI vs. REMS: p = 0.520, HOTEL vs. PESI: P = 0.526, REMS vs. HOTEL: P = 0.669, overall test: P = 0.96, DeLong’s test). The risk ratios of HOTEL and PESI were parallel to each other [5.31 (95% confidence interval (CI): 2.53–11.13) and 5.34 (95% CI: 2.36–12.08), respectively].

Conclusion
HOTEL and REMS were as successful as PESI in predicting short-term mortality and intensive care requirement in geriatric patients with PE. These scores are also more practical since they have fewer parameters than PESI.
Quantification of liver fat using non-invasive MRI-PDFF technique versus guided biopsy in potential liver donor
Authors: El-Assaly Hany , El-Adawy Laila Abd El-Moaty Ali , El-Latif Reda Saad Abd , Fawzi Mohamed Mohsen , Osama Ayman 
Published: August 2024

Abstract
Introduction
Significant hepatic steatosis affects the outcome of surgery when living donors are transplanted. The gold standard for diagnosing and evaluating hepatic steatosis is hepatic imaging-guided biopsy. Hepatic steatosis assessment using MR spectroscopy and the proton density fat fraction (MR-PDFF) method has produced positive findings.

Objectives
Is to compare the pre-operative assessment of liver fat quantification using MRI-PDFF methods, a non-invasive method, with histopathology.

Subjects and methods
A 42 potential donors were then operated surgically for liver transplantation, consequently, were available for the assessment of the efficiency and sensitivity of the radiological findings MRI-PDFF procedures and imaging-guided liver biopsy. This radiological workup of these donors was done through a period of 7 months.

Results
In many liver transplantations centers, liver imaging-guided biopsy histopathological examination is the gold standard. The study examined the MR proton density fat fraction modality, a recently developed test for hepatic steatosis measurement. The findings indicate 86.8% sensitivity, 50% specificity, 94.2% PDV, 28.5% NPV, 83.3% accuracy, and 0.684 AUC. On analyzing the fat percent, we found that the recorded fat percent using liver imaging-guided biopsy ranges between 1 and 10% with a median of 3. On the other hand, the recorded fat percent using MRI ranged between 2 and 15% with a median of 5.

Conclusion
The non-invasive magnetic resonance hepatic proton density fat fraction approach using IDEAL sequence is a reliable and accurate means of quantitatively evaluating hepatic steatosis with excellent sensitivity, specificity, and accuracy.
A local review of section 17 leave forms in conjunction with the Mental Health Act Code of Practice: recommendations for future practice
Authors: Pathmanathan Shayanthan , Edgerley Harris Georgina , Townsend Giles 
Published: August 2024

Aims and methodThe aim of this project was to set out recommendations for the section 17 leave form to reflect guidance provided in the Mental Health Act 1983: Code of Practice, following local Care Quality Commission feedback. We reviewed guidance in the Code and publicly available leave forms to identify items to include in the leave form. Then, we determined which publicly available leave forms included each item and reviewed whether the item should be included in the leave form and whether any reformulation was needed.ResultsUsing the method described, we identified a list of items that should be included in the leave form. When comparing the leave forms of different trusts, there was considerable variation with respect to which items were included in each form.Clinical implicationsWe provide some recommendations for future practice regarding section 17 leave forms to facilitate consistency with the Code and between different trusts.
A systematic review and meta-analysis of the traumatogenic phenotype hypothesis of psychosis
Authors: Onyeama Franca , Melegkovits Eirini , Yu Nicole , Parvez Ameerah , Rodrigues Artur , Billings Jo , Kelleher Ian , Cannon Mary , Bloomfield Michael A. P. 
Published: August 2024

Background
Developmental trauma increases psychosis risk and is associated with poor prognosis. It has been proposed that psychosis in survivors of developmental trauma gives rise to a distinct ‘traumatogenic’ phenotype.

Aims
Given the implications for personalised treatment, we sought to explore the traumatogenic psychosis phenotype hypothesis in a systematic review and meta-analysis of studies comparing psychotic presentations between adults with and without developmental trauma histories.

Method
We registered the systematic review on PROSPERO (CRD42019131245) and systematically searched EMBASE, Medline and PsycINFO. The outcomes of interests were quantitative and qualitative comparisons in psychotic symptom expression (positive, negative, cognitive) and other domains of psychopathology, including affect regulation, sleep, depression and anxiety, between adults with and without experience of developmental trauma.

Results
Of 34 studies included (N = 13 150), 11 were meta-analysed (n = 2842). A significant relationship was found between developmental trauma and increased symptom severity for positive (Hedge's g = 0.27; 95% CI 0.10–0.44; P = 0.002), but not negative symptoms (Hedge's g = 0.13; 95% CI −0.04 to 0.30; P = 0.14). Developmental trauma was associated with greater neurocognitive, specifically executive, deficits, as well as poorer affect, dissociation and social cognition. Furthermore, psychotic symptom content thematically related to traumatic memories in survivors of developmental trauma.

Conclusions
Our findings that developmental trauma is associated with more severe positive and affective symptoms, and qualitative differences in symptom expression, support the notion that there may be a traumatogenic psychosis phenotype. However, underdiagnosis of post-traumatic stress disorder may also explain some of these findings. More research is needed to explore this further.
TSH Receptor Oligomers Associated With the TSH Receptor Antibody Reactome
Authors: Mezei Mihaly , Latif Rauf , Davies Terry F 
Published: August 2024

Abstract
The TSH receptor (TSHR) and its many forms are the primary antigens of Graves' disease as evidenced by the presence of TSHR antibodies of differing biological activity. The TSH holoreceptor undergoes complex posttranslational changes including cleavage of its ectodomain and oligomer formation. We have previously shown that the TSHR exists in both monomeric and dimeric structures in the thyroid cell membrane and have demonstrated, by modeling, that the transmembrane domains (TMD) can form stable dimeric structures. Based on these earlier simulations of the TSHR-TMD structure and our most recent model of the full-length TSHR, we have now built models of full-length TSHR multimers with and without TSH ligand in addition to multimers of the extracellular leucine-rich domain, the site of TSH and autoantibody binding. Starting from these models we ran molecular dynamics simulations of the receptor oligomers solvated with water and counterions; the full-length oligomers also were embedded in a dipalmitoylphosphatidylcholine bilayer. The full-length TSHR dimer and trimer models stayed in the same relative orientation and distance during 2000 ns (or longer) molecular dynamics simulation in keeping with our earlier report of TMD dimerization. Simulations were also performed to model oligomers of the leucine-rich domain alone; we found a trimeric complex to be even more stable than the dimers. These data provide further evidence that different forms of the TSHR add to the complexity of the immune response to this antigen that, in patients with autoimmune thyroid disease, generate an autoantibody reactome with multiple types of autoantibody to the TSHR.
Structure and Function of Somatostatin and Its Receptors in Endocrinology
Authors: Zhang Bo , Xue Li , Wu Zhe Bao 
Published: August 2024

Abstract
Somatostatin analogs, such as octreotide, lanreotide, and pasireotide, which function as somatostatin receptor ligands (SRLs), are the main drugs used for the treatment of acromegaly. These ligands are also used as important molecules for radiation therapy and imaging of neuroendocrine tumors. Somatostatin receptors (SSTRs) are canonical G protein-coupled proteins that play a role in metabolism, growth, and pathological conditions such as hormone disorders, neurological diseases, and cancers. Cryogenic electron microscopy combined with the protein structure prediction platform AlphaFold has been used to determine the 3-dimensional structures of many proteins. Recently, several groups published a series of papers illustrating the 3-dimensional structure of SSTR2, including that of the inactive/activated SSTR2-G protein complex bound to different ligands. The results revealed the residues that contribute to the ligand binding pocket and demonstrated that Trp8-Lys9 (the W-K motif) in somatostatin analogs is the key motif in stabilizing the bottom part of the binding pocket. In this review, we discuss the recent findings related to the structural analysis of SSTRs and SRLs, the relationships between the structural data and clinical findings, and the future development of novel structure-based therapies.
Metabolic states influence chicken retinal pigment epithelium cell fate decisions
Authors: Perez-Estrada J. Raúl , Tangeman Jared A. , Proto-Newton Maeve , Sanaka Harshavardhan , Smucker Byran , Del Rio-Tsonis Katia 
Published: August 2024

ABSTRACT
During tissue regeneration, proliferation, dedifferentiation and reprogramming are necessary to restore lost structures. However, it is not fully understood how metabolism intersects with these processes. Chicken embryos can regenerate their retina through retinal pigment epithelium (RPE) reprogramming when treated with fibroblast factor 2 (FGF2). Using transcriptome profiling, we uncovered extensive regulation of gene sets pertaining to proliferation, neurogenesis and glycolysis throughout RPE-to-neural retina reprogramming. By manipulating cell media composition, we determined that glucose, glutamine or pyruvate are individually sufficient to support RPE reprogramming, identifying glycolysis as a requisite. Conversely, the activation of pyruvate dehydrogenase by inhibition of pyruvate dehydrogenase kinases, induces epithelial-to-mesenchymal transition, while simultaneously blocking the activation of neural retina fate. We also identified that epithelial-to-mesenchymal transition fate is partially driven by an oxidative environment. Our findings provide evidence that metabolism controls RPE cell fate decisions and provide insights into the metabolic state of RPE cells, which are prone to fate changes in regeneration and pathologies, such as proliferative vitreoretinopathy.