bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Authors: Toro Sabrina , Anagnostopoulos Anna V. , Bello Susan M. , Blumberg Kai , Cameron Rhiannon , Carmody Leigh , Diehl Alexander D. , Dooley Damion M. , Duncan William D. , Fey Petra , Gaudet Pascale , Harris Nomi L. , Joachimiak Marcin P. , Kiani Leila , Lubiana Tiago , Munoz-Torres Monica C. , O‘Neil Shawn , Osumi-Sutherland David , Puig-Barbe Aleix , Reese Justin T. , Reiser Leonore , Robb Sofia MC. , Ruemping Troy , Seager James , Sid Eric , Stefancsik Ray , Weber Magalie , Wood Valerie , Haendel Melissa A. , Mungall Christopher J. 
Published: October 2024

Abstract
Background
Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources and necessitate substantial collaboration between domain experts, curators, and ontology experts.

We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). DRAGON-AI can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies and unstructured text sources.

Results
We assessed performance of DRAGON-AI on de novo term construction across ten diverse ontologies, making use of extensive manual evaluation of results. Our method has high precision for relationship generation, but has slightly lower precision than from logic-based reasoning. Our method is also able to generate definitions deemed acceptable by expert evaluators, but these scored worse than human-authored definitions. Notably, evaluators with the highest level of confidence in a domain were better able to discern flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues.

Conclusions
These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.
Investigation of parasite genetic variation and systemic immune responses in patients presenting with different clinical presentations of cutaneous leishmaniasis caused by Leishmania aethiopica
Authors: Yizengaw Endalew , Takele Yegnasew , Franssen Susanne , Gashaw Bizuayehu , Yimer Mulat , Adem Emebet , Nibret Endalkachew , Yismaw Gizachew , Cruz Cervera Edward , Ejigu Kefale , Tamiru Dessalegn , Munshea Abaineh , Müller Ingrid , Weller Richard , Cotton James A. , Kropf Pascale 
Published: October 2024

Abstract
Background
Cutaneous leishmaniasis (CL) is a neglected tropical skin disease, caused by the protozoan parasite Leishmania. In Ethiopia, CL is mainly caused by Leishmania aethiopica and can present in different clinical forms. The aim of this study was to assess whether these different forms are associated with differences in parasite genetic and host systemic immune signatures.

Methods
Here we analysed the whole genome sequence data for 48 clinical parasite isolates and the systemic immune signature from a cohort of CL patients, who were recruited in Nefas Mewcha, Northern Ethiopia, from January 2019 to January 2022.

Results
Our results show that parasites from CL cases with different presentations in a single Ethiopian setting are from the same genetic population based on a permutation test of genome-wide similarity. Furthermore, a logistic regression test for genome wide association did not identify any individual genetic variants significantly associated with disease presentation. We also measured plasma chemokine and cytokine levels of 129 CL patients presenting with different forms of CL. None of the chemokine [eotaxin, eotaxin-3, interleukin (IL)-8, interferon (IFN)-γ-induced protein-10 (IP-10), monocyte chemoattractant protein (MCP)-1, MCP-4, macrophage-derived chemokines (MDC), macrophage inflammatory protein (MIP)-1α, MIP-1β and thymus- and activation-regulated chemokine (TARC)] or cytokine (IFN-γ, IL-1β, interleukin-2, IL-4, IL-6, IL-10, IL-12p70, IL-13, tumor necrosis factor-α) levels measured were significantly different between the different clinical presentations of CL, as measured by Kruskal–Wallis test. We also compared those with healthy nonendemic controls: our results show a chemokine (IP-10, MCP-1, MCP-4, MDC, MIP-1α, MIP-1β and TARC) but not a cytokine immune signature in patients with CL as compared to healthy nonendemic controls, as measured by Mann-Whitney test.

Conclusions
The results of our study did not identify a systemic immune signature or parasite genetic factors associated with different clinical presentation of CL.

Graphical abstract
Brain-to-brain synchrony increased during interpersonal touch in romantic lovers: an EEG-based hyperscanning study
Authors: Zhou Chenghao , Jiang Xiaowei , Chen Yanan , Ge Chunlei , Ao Na , Du Feng 
Published: October 2024

Abstract
Background
Interpersonal touch is an essential element of human social life. It’s unclear whether the neural patterns of interpersonal touch are specific to intimate relationships or generally apply to other social relationships. Romantic lovers are typically intimate and have a high level of interpersonal touch. Currently, researchers focused on the neurobiological basis and neural processes of romantic love.

Methods
110 participants finished two resting-state blocks, no-handholding and handholding conditions, with Electroencephalogram (EEG). We aimed to explore the differences in the brain-brain synchrony pattern of interpersonal touch between romantic lovers and strangers by calculating dynamic interpersonal functional connectivity (dIFC) via EEG-based hyperscanning.

Results
Our results supported that the neural processing of interpersonal touch is a dynamic process. At first half, both groups tended to adapt, and then interpersonal touch increased the dIFC between romantic lovers and decreased the dIFC between strangers. Finally, we employed Support Vector Machine (SVM) to classify EEG signals into two different relationships. SVM recognized two relationships with an accuracy of 71% and 0.77 AUC of ROC at the first half, a 73% accuracy and 0.8 AUC of ROC at the second half.

Conclusions
Our study indicates that interpersonal touch may have different meanings between romantic lovers and strangers. Specifically, interpersonal touch enhances the dIFC between romantic lovers while reducing the dIFC between strangers. The research has important implications for planning touch-based interventions in social and medical care.
Experimental simulation of the ancient production of gold granules
Authors: Tan Panpan , Yang Junchang , Ji Juan 
Published: October 2024

Abstract
Granulation is an ancient and sophisticated decorative technique. The production of granules is a crucial part of this process but has rarely been studied. The present study employed three techniques—pouring method, heating method, and crucible method—to produce gold granules. The success ratio of granule formation, granule surface morphology, microstructure, and formation were analyzed to identify the techniques used in archaeological objects. The cooling medium significantly influenced small granule formation, microstructure, and grain size. Both heating and crucible methods could control the granule formation, but these methods produced distinct microstructures. Based on these experimental granules, the probable production methods of ancient gold balls were identified. The present study provided microscopic information for determining ancient gold granule production techniques.
An analytical study of the tabia mortar from Lin Yimu’s tomb, Zhejiang, China
Authors: Wu Xuan , Jin Cui , Jia Mengjun , Cui Biao , Grifa Celestino , Wang Jixin , Ma Xiao 
Published: October 2024

Abstract
The Lin Yimu’s tomb in Zhejiang Province, China, is a significant Qing Dynasty tabia structure that, despite relatively good preservation, has suffered damage from weathering, necessitating urgent restoration. In this study, we conducted a comprehensive scientific analysis of archaeological samples from the tabia of Lin Yimu’s tomb, employing a range of analytical techniques including X-ray diffraction (XRD), thermogravimetric analysis (TGA), scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM/EDX), Fourier transform infrared spectroscopy (FTIR), chemical methods, and measurements of hardness and strength. Analytical results revealed that the main phases of the sample are calcite, quartz, illite/mica, feldspar, with a minor presence of Tung oil. The proportion of calcium carbonate is approximately 27%, and the ratio of earth to sand is 1:2, suggesting a raw material formula mass ratio of lime-earth-sand of 3:4:8. The surface hardness of the sample is measured at 293 ± 15 HL, with a compressive strength of 5.5 ± 0.2 MPa. The sand used in the raw material has a medium particle size of 250 μm, while earth particles are predominantly around 17 μm. The sample exhibits a porosity of 27.5%, with pore sizes concentrated at 95 nm. These findings contribute significantly to our understanding of Qing dynasty tomb construction technologies and provide a solid scientific basis for the restoration of such historical sites.
A self-regulated expiratory flow device for mechanical ventilation: a bench study
Authors: Yang Lianye , Wiersema Ubbo F. , Bihari Shailesh , Broughton Roy , Roberts Andy , Kelley Nigel , McEwen Mark 
Published: October 2024

Abstract
Introduction
Unregulated expiratory flow may contribute to ventilator-induced lung injury. The amount of energy dissipated into the lungs with tidal mechanical ventilation may be used to quantify potentially injurious ventilation. Previously reported devices for variable expiratory flow regulation (FLEX) require, either computer-controlled feedback, or an initial expiratory flow trigger. In this bench study we present a novel passive expiratory flow regulation device.

Methods
The device was tested using a commercially available mechanical ventilator with a range of settings (tidal volume 420 ml and 630 ml, max. inspiratory flow rate 30 L/min and 50 L/min, respiratory rate 10 min−1, positive end-expiratory pressure 5 cmH2O), and a test lung with six different combinations of compliance and resistance settings. The effectiveness of the device was evaluated for reduction in peak expiratory flow, expiratory time, mean airway pressure, and the reduction of tidal dissipated energy (measured as the area within the airway pressure–volume loop).

Results
Maximal and minimal reduction in peak expiratory flow was from 97.18 ± 0.41 L/min to 25.82 ± 0.07 L/min (p < 0.001), and from 44.11 ± 0.42 L/min to 26.30 ± 0.06 L/min, respectively. Maximal prolongation in expiratory time was recorded from 1.53 ± 0.06 s to 3.64 ± 0.21 s (p < 0.001). As a result of the extended expiration, the maximal decrease in I:E ratio was from 1:1.15 ± 0.03 to 1:2.45 ± 0.01 (p < 0.001). The greatest increase in mean airway pressure was from 10.04 ± 0.03 cmH2O to 17.33 ± 0.03 cmH2O. Dissipated energy was significantly reduced with the device under all test conditions (p < 0.001). The greatest reduction in dissipated energy was from 1.74 ± 0.00 J to 0.84 ± 0.00 J per breath. The least reduction in dissipated energy was from 0.30 ± 0.00 J to 0.16 ± 0.00 J per breath. The greatest and least percentage reduction in dissipated energy was 68% and 33%, respectively.

Conclusions
The device bench tested in this study demonstrated a significant reduction in peak expiratory flow rate and dissipated energy, compared to ventilation with unregulated expiratory flow. Application of the device warrants further experimental and clinical evaluation.
Laparoscopic repair of gastric conduit obstruction after robot-assisted minimally invasive esophagectomy: a case report
Authors: Moriuchi Toshiyuki , Katsura Yuki , Shirakawa Yasuhiro , Uehara Ayane , Matsubara Kazuki , Ishida Michihiro , Choda Yasuhiro , Mashima Hiroaki , Sawada Hiroyuki , Yoshimitsu Masanori , Matsukawa Hiroyoshi , Shiozaki Shigehiro 
Published: October 2024

Abstract
Background
Gastric conduit obstruction (GCO) is a known complication after esophagectomy. Laparoscopic revision surgery for GCO is relatively rare, with limited reports in the literature. Here, we report a case of GCO after robot-assisted subtotal esophagectomy and posterior mediastinal gastric conduit reconstruction, which was successfully repaired laparoscopically.

Case presentation
A 66-year-old man presented with a passage disorder that became noticeable 14 months after surgery. Fluid passage was difficult, and the patient opted for revision surgery. The conduit had entered and deflected into the mediastinum; it also twisted due to band formation. The revision surgery was performed laparoscopically through five ports. The bands were dissected, esophageal hiatus was sutured, and conduit re-fixed. The intraoperative endoscopy was used to confirm that the obstruction had been released. The lack of adhesion of the posterior half of the gastric conduit wall, combined with postoperative weight loss leading to a decrease in omental volume, as well as inadequate fixation during the initial surgery, are believed to have contributed to the ease of the conduit deviation into the intrathoracic cavity. In addition, the twisting of the conduit due to band formation exacerbated the obstruction.

Conclusions
Laparoscopic revision surgery may become an effective treatment option as the number of minimally invasive esophagectomies is expected to increase in the future. Furthermore, the fixation method during initial surgery should be carefully considered and optimized to prevent gastric conduit obstruction. Additionally, the use of intraoperative endoscopy to evaluate the lumen of the conduit during surgery proved beneficial in this case, highlighting its potential value in identifying and addressing obstruction.
Cold-water coral mortality under ocean warming is associated with pathogenic bacteria
Authors: Chemel Mathilde , Peru Erwan , Binsarhan Mohammad , Logares Ramiro , Lartaud Franck , Galand Pierre E. 
Published: October 2024

AbstractCold-water corals form vast reefs that are highly valuable habitats for diverse deep-sea communities. However, as the deep ocean is warming, it is essential to assess the resilience of cold-water corals to future conditions. The effects of elevated temperatures on the cold-water coral Lophelia pertusa (now named Desmophyllum pertusum) from the north-east Atlantic Ocean were experimentally investigated at the holobiont level, the coral host, and its microbiome. We show that at temperature increases of + 3 and + 5 °C, L. pertusa exhibits significant mortality concomitant with changes in its microbiome composition. In addition, a metagenomic approach revealed the presence of gene markers for bacterial virulence factors suggesting that coral death was due to infection by pathogenic bacteria. Interestingly, different coral colonies had different survival rates and, colony-specific microbiome signatures, indicating strong colony-specific variability in their response to warming waters. These results suggest that L. pertusa can only survive a long-term temperature increase of < 3 °C. Therefore, regional variations in deep-sea temperature increase should be considered in future estimates of the global distribution of cold-water corals.
The composition of the arbuscular mycorrhizal fungal bacteriome is species dependent
Authors: Lahrach Zakaria , Legeay Jean , Ahmed Bulbul , Hijri Mohamed 
Published: October 2024

Abstract
Background
In addition to their role as endosymbionts for plant roots, arbuscular mycorrhizal fungi (AMF) engage in complex interactions with various soil microorganisms, the rhizosphere, and the root endosphere of host plants. They also host diverse prokaryotic groups within their mycelia, contributing to what is termed multipartite symbiosis. In this study, we examined the impact of three AMF species—Rhizophagus irregularis, R. clarus, and R. cerebriforme—combined with microbial bioaugmentation on the diversity and composition of bacterial communities in the mycelia and hyphosphere. Using a microcosm design to separate the influence of host plant roots from AMF mycelia and Illumina MiSeq amplicon sequencing to analyze the bacterial communities.

Results
Our results revealed that, while AMF identity and microbial bioaugmentation did not affect the structure of bacterial communities in the hyphosphere soil, they significantly altered the communities associated with their mycelia. Although all three AMF species belong to the same genus, with R. irregularis and R. clarus being closely related compared to R. cerebriforme, we observed variations in the bacterial communities associated with their mycelia. Interestingly, the mycelial bacterial community of R. cerebriforme contained 60 bacteriome core taxa exclusive to it, while R. clarus and R. irregularis had 25 and 9 exclusive taxa, respectively.

Conclusion
This study suggests that organismal phylogeny influences the bacterial communities associated with AMF mycelia. These findings provide new insights into AMF and bacterial interactions, which are crucial for the successful deployment of AMF inoculants. The taxonomic diversity of AMF inoculants is important for engineering the plant microbiome and enhancing ecosystem services.
Hybrid surgical approach for a large schwannoma from the cervical esophagus to the upper thoracic esophagus: a case report
Authors: Nakagawa Masashi , Mori Naoki , Saisyo Kohei , Yoshida Takehumi , Isobe Taro , Sakai Hisamune , Hisaka Toru , Ishibashi Nobuya , Fujita Fumihiko 
Published: October 2024

Abstract
Background
Esophageal schwannoma is an extremely rare esophageal submucosal tumor. We report a case of a hybrid surgery for a large esophageal schwannoma that had extended from the cervical to the upper thoracic esophagus by using thoracoscopic and cervical approaches.

Case presentation
A 58-year-old male was referred to our hospital for further examination and treatment of dysphagia and weight loss over the past 6 months. Upper gastrointestinal endoscopy revealed a 5.7-cm submucosal tumor from the cervical esophagus to the upper thoracic esophagus. The submucosal tumor was diagnosed as esophageal schwannoma by endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNA). Contrast-enhanced CT showed that the tumor had not invaded surrounding organs. Since the tumor extended from the cervical esophagus to the upper thoracic esophagus, we decided that it should be resected by not only the cervical but also the thoracoscopic approach. In operation, the patient was first placed in the prone position, and a thoracoscopic dissection of the upper thoracic esophagus containing the tumor was performed from the surrounding area. After changing the patient’s position from prone to supine, a cervical skin incision was performed, and we underwent the tumor enucleation. After enucleation, the esophageal wall was thinned, so the right sternocleidomastoid muscle was used to reinforce the esophageal wall. The tumor size of the specimen was 60 × 52 × 42 mm. The postoperative course was uneventful, and the patient was discharged on the 22nd day after surgery.

Conclusions
Enucleation of a large esophageal schwannoma from the cervical to the upper thoracic esophagus could be safely performed using both thoracoscopic and cervical approaches. The sternocleidomastoid muscle flap is useful in the occasion considering stenosis by muscular layer suture.
Distinguishing Genetic Alterations Versus (Epi)Mutations in Silver–Russell Syndrome and Focus on the IGF1R Gene
Authors: Vimercati Alessandro , Tannorella Pierpaola , Guzzetti Sara , Calzari Luciano , Gentilini Davide , Manfredini Emanuela , Gori Giulia , Gaudino Rossella , Antona Vincenzo , Piccione Maria , Daolio Cecilia , Auricchio Renata , Sirchia Fabio , Minelli Antonella , Rossi Elena , Bellini Melissa , Biasucci Giacomo , Raucci Annalisa Russo , Pozzobon Gabriella , Patti Giuseppa , Napoli Flavia , Larizza Lidia , Maghnie Mohamad , Russo Silvia 
Published: October 2024

Abstract

Context
Silver–Russell Syndrome (SRS) is a growth retardation disorder characterized by pre- and postnatal growth failure, relative macrocephaly at birth, prominent forehead, body asymmetry, and feeding difficulties. The main molecular mechanisms are imprinting alterations at multiple loci, though a small number of pathogenic variants have been reported in the SRS genes IGF2-PLAG1-HMGA2 and CDKN1C. However, around 40% of clinically suspected SRS cases do not achieve a molecular diagnosis, highlighting the necessity to uncover the underlying mechanism in unsolved cases.

Objective
Evaluate the frequency of genetic variants in undiagnosed SRS patients [Netchine–Harbison Clinical Scoring System (NH-CSS) ≥ 4], and investigate whether (epi)genetic patients may be distinguished from genetic patients.

Methods
One hundred thirty-two clinically SRS patients without (epi)genetic deregulations were investigated by whole-exome (n = 15) and targeted (n = 117) Sequencing. Clinical data from our cohort and from an extensive revision of the literature were compared.

Results
Pathogenic variants were identified in 9.1% of this cohort: 3% in IGF2, PLAG1, and HMGA2 genes and 3% in the IGF1R gene, associated with IGF-1 resistance (IGF1RES), an SRS differential diagnosis. Overall, IGF2-PLAG1-HMGA2 and IGF1R account for 3.6% of SRS with NH-CSS score ≥ 4. A clinical cross-comparison of (epi)genetic vs genetic SRS underlined (epi)genotype-phenotype correlation highlighted the prevalence of body asymmetry and relative macrocephaly in mosaic (epi)genetic SRS and recurrence of genetic familial cases. Furthermore, overlapping features were evidenced in (epi)genetic SRS and IGF1RES patients.

Conclusion
Our study explores the frequency of genetic SRS, underscores body asymmetry as a distinctive phenotype in (epi)genetic SRS and suggests IGF1R sequencing in a SRS diagnostic flowchart.