bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing generative and extractive approaches to information extraction from abstracts describing randomized clinical trials
Authors: Witte Christian , Schmidt David M. , Cimiano Philipp 
Published: April 2024

Abstract
Background
Systematic reviews of Randomized Controlled Trials (RCTs) are an important part of the evidence-based medicine paradigm. However, the creation of such systematic reviews by clinical experts is costly as well as time-consuming, and results can get quickly outdated after publication. Most RCTs are structured based on the Patient, Intervention, Comparison, Outcomes (PICO) framework and there exist many approaches which aim to extract PICO elements automatically. The automatic extraction of PICO information from RCTs has the potential to significantly speed up the creation process of systematic reviews and this way also benefit the field of evidence-based medicine.

Results
Previous work has addressed the extraction of PICO elements as the task of identifying relevant text spans or sentences, but without populating a structured representation of a trial. In contrast, in this work, we treat PICO elements as structured templates with slots to do justice to the complex nature of the information they represent. We present two different approaches to extract this structured information from the abstracts of RCTs. The first approach is an extractive approach based on our previous work that is extended to capture full document representations as well as by a clustering step to infer the number of instances of each template type. The second approach is a generative approach based on a seq2seq model that encodes the abstract describing the RCT and uses a decoder to infer a structured representation of a trial including its arms, treatments, endpoints and outcomes. Both approaches are evaluated with different base models on a manually annotated dataset consisting of RCT abstracts on an existing dataset comprising 211 annotated clinical trial abstracts for Type 2 Diabetes and Glaucoma. For both diseases, the extractive approach (with ) reached the best $$F_1$$

F
1

score, i.e. 0.547 ($$\pm 0.006$$

±
0.006

) for type 2 diabetes and 0.636 ($$\pm 0.006$$

±
0.006

) for glaucoma. Generally, the $$F_1$$

F
1

scores were higher for glaucoma than for type 2 diabetes and the standard deviation was higher for the generative approach.

Conclusion
In our experiments, both approaches show promising performance extracting structured PICO information from RCTs, especially considering that most related work focuses on the far easier task of predicting less structured objects. In our experimental results, the extractive approach performs best in both cases, although the lead is greater for glaucoma than for type 2 diabetes. For future work, it remains to be investigated how the base model size affects the performance of both approaches in comparison. Although the extractive approach currently leaves more room for direct improvements, the generative approach might benefit from larger models.
Unveiling new horizons in heart research: the promise of multi-chamber cardiac organoids
Authors: Hou Junjie , Chen Ye-Guang , Xiong Jing-Wei 
Published: April 2024

AbstractHuman cardiac and other organoids have recently emerged as a groundbreaking tool for advancing our understanding the developmental biology of human organs. A recent paper from Sasha Mendjan’s laboratory published in the journal Cell on December 7, 2023, reported the generation of multi-chamber cardioids from human pluripotent stem cells, a transformative technology in the field of cardiology. In this short highlight paper, we summarize their findings. Their cardioids remarkably recapitulate the complexity of the human embryonic heart, including tissue architecture, cellular diversity, and functionality providing an excellent in vitro model for investigation of human heart development, disease modeling, precision medicine, and regenerative medicine. Thus, generating cardioids is an important step forward for understanding human heart development and developing potential therapies for heart diseases.
Blind Federated Learning without initial model
Authors: Salmeron Jose L. , Arévalo Irina 
Published: April 2024

AbstractFederated learning is an emerging machine learning approach that allows the construction of a model between several participants who hold their own private data. This method is secure and privacy-preserving, suitable for training a machine learning model using sensitive data from different sources, such as hospitals. In this paper, the authors propose two innovative methodologies for Particle Swarm Optimisation-based federated learning of Fuzzy Cognitive Maps in a privacy-preserving way. In addition, one relevant contribution this research includes is the lack of an initial model in the federated learning process, making it effectively blind. This proposal is tested with several open datasets, improving both accuracy and precision.
Radiomics signature for dynamic changes of tumor-infiltrating CD8+ T cells and macrophages in cervical cancer during chemoradiotherapy
Authors: Huang Kang , Huang Xuehan , Zeng Chengbing , Wang Siyan , Zhan Yizhou , Cai Qingxin , Peng Guobo , Yang Zhining , Zhou Li , Chen Jianzhou , Chen Chuangzhen 
Published: April 2024

Abstract
Background
Our previous study suggests that tumor CD8+ T cells and macrophages (defined as CD68+ cells) infiltration underwent dynamic and heterogeneous changes during concurrent chemoradiotherapy (CCRT) in cervical cancer patients, which correlated with their short-term tumor response. This study aims to develop a CT image-based radiomics signature for such dynamic changes.

Methods
Thirty cervical squamous cell carcinoma patients, who were treated with CCRT followed by brachytherapy, were included in this study. Pre-therapeutic CT images were acquired. And tumor biopsies with immunohistochemistry at primary sites were performed at baseline (0 fraction (F)) and immediately after 10F. Radiomics features were extracted from the region of interest (ROI) of CT images using Matlab. The LASSO regression model with ten-fold cross-validation was utilized to select features and construct an immunomarker classifier and a radiomics signature. Their performance was evaluated by the area under the curve (AUC).

Results
The changes of tumor-infiltrating CD8+T cells and macrophages after 10F radiotherapy as compared to those at baseline were used to generate the immunomarker classifier (AUC= 0.842, 95% CI:0.680–1.000). Additionally, a radiomics signature was developed using 4 key radiomics features to predict the immunomarker classifier (AUC=0.875, 95% CI:0.753-0.997). The patients stratified based on this signature exhibited significant differences in treatment response (p = 0.004).

Conclusion
The radiomics signature could be used as a potential predictor for the CCRT-induced dynamic alterations of CD8+ T cells and macrophages, which may provide a less invasive approach to appraise tumor immune status during CCRT in cervical cancer compared to tissue biopsy.
Artificial intelligence in chorioretinal pathology through fundoscopy: a comprehensive review
Authors: Driban Matthew , Yan Audrey , Selvam Amrish , Ong Joshua , Vupparaboina Kiran Kumar , Chhablani Jay 
Published: April 2024

Abstract
Background
Applications for artificial intelligence (AI) in ophthalmology are continually evolving. Fundoscopy is one of the oldest ocular imaging techniques but remains a mainstay in posterior segment imaging due to its prevalence, ease of use, and ongoing technological advancement. AI has been leveraged for fundoscopy to accomplish core tasks including segmentation, classification, and prediction.

Main body
In this article we provide a review of AI in fundoscopy applied to representative chorioretinal pathologies, including diabetic retinopathy and age-related macular degeneration, among others. We conclude with a discussion of future directions and current limitations.

Short conclusion
As AI evolves, it will become increasingly essential for the modern ophthalmologist to understand its applications and limitations to improve patient outcomes and continue to innovate.
A bonus task boosts people's willingness to offload cognition to an algorithm
Authors: Wahn Basil , Schmitz Laura 
Published: April 2024

AbstractWith the increased sophistication of technology, humans have the possibility to offload a variety of tasks to algorithms. Here, we investigated whether the extent to which people are willing to offload an attentionally demanding task to an algorithm is modulated by the availability of a bonus task and by the knowledge about the algorithm’s capacity. Participants performed a multiple object tracking (MOT) task which required them to visually track targets on a screen. Participants could offload an unlimited number of targets to a “computer partner”. If participants decided to offload the entire task to the computer, they could instead perform a bonus task which resulted in additional financial gain—however, this gain was conditional on a high performance accuracy in the MOT task. Thus, participants should only offload the entire task if they trusted the computer to perform accurately. We found that participants were significantly more willing to completely offload the task if they were informed beforehand that the computer’s accuracy was flawless (Experiment 1 vs. 2). Participants’ offloading behavior was not significantly affected by whether the bonus task was incentivized or not (Experiment 2 vs. 3). These results combined with those from our previous study (Wahn et al. in PLoS ONE 18:e0286102, 2023), which did not include a bonus task but was identical otherwise, show that the human willingness to offload an attentionally demanding task to an algorithm is considerably boosted by the availability of a bonus task—even if not incentivized—and by the knowledge about the algorithm’s capacity.
Epidemiology and clinical characteristics of headache among COVID-19 patients in Lebanon: a retrospective cohort study
Authors: Safawi Nour , Hasbini Jida , Khodor Hawaa , Atrouni Salim , Berjaoui Christin , ElJarkass Hania 
Published: April 2024

Abstract
Background
With the spread and rise in the number of infections of COVID-19 globally, patients experienced neurologic manifestations such as headache and dizziness, along with other serious medical conditions such as stroke and seizures. Many reported cases highlighted headache to be one of the most common COVID-19-related neurological symptoms. With the evolution of the pandemic, broad studies are needed to better understand the mechanism of headache with COVID-19. The aim of this study is to recognize the epidemiology, characteristic and progression of headache among patients with COVID-19 in Lebanon.

Methods
A retrospective cohort study was done to assess 439 patients for headache during the course of COVID-19. The Statistical Package for Social Sciences (SPSS) version 26 was used for descriptive analysis.

Results
A confirmed COVID-19 Infection by PCR test was confirmed among 86% of the participants. Tension-like headache was the most common type of headache experienced by participants during COVID-19. Pain was mainly diffuse (48.7%), and compressing in nature (77.0%). Moreover, about 29% required a physician consultation and 7.7% had emergency visits. Partial relief by analgesics was reported in 54.9%, and mainly by paracetamol (64.6%). Those who reported having a history of primary headache before contracting COVID-19 were 46.7%. Among them, 36.7% patients reported a change in the type of headache and about 49.6% reported increased severity.

Conclusion
Headache accompanied with COVID-19 is a common symptom during the early stages of illness. COVID-19 related headache was characterized as mainly involving the whole head region, pressuring, and partially relieved by analgesics. Thus, headache should raise early concern for the probability of being infected by COVID-19.
Progress in endophytic fungi secondary metabolites: biosynthetic gene cluster reactivation and advances in metabolomics
Authors: Zakariyah Rahmat Folashade , Ajijolakewu Kamoldeen Abiodun , Ayodele Ayomide Joseph , Folami-A Barnabas Ipinnuoluwa , Samuel Elohor Precious , Otuoze Sabdat Omeneke , Abdulrauf Lukman Bola , Ahmed Risikat Nike 
Published: April 2024

Abstract
Background
Fungal endophytes exhibit symbiotic relationships with their host plants but have recently emerged as sources for synthesizing important varieties of secondary metabolites (SMs). Many of these metabolites have shown significant importance as antibacterial, antifungal, antitumor, and anticancer drugs, leading to their exploration in medicine and pharmaceuticals.

Main body of the abstract
The endophytes' biosynthetic gene clusters (BGCs) are responsible for encoding enzymes that produce these SMs. The fungal endophytes' ability has been challenged due to their inability to trigger cryptic BGCs and their loss of ability to produce secondary metabolites over an extended period in an artificial culture medium. This review investigates the array of SMs produced by endophytic fungi. It identifies methods for awakening and exploiting silent BGCs to produce novel natural metabolites and explores recent advancements in metabolomics platforms used to profile SMs. Silent BGCs can be activated using various methods, including co-cultivation, one strain of many compounds, epigenetic modification, heterologous expression, and cluster-specific transcription factor methods.

Short conclusion
These methods reviewed effectively enhance the production of silent BGCs, leading to a significant increase in secondary metabolite production. Meanwhile, metabolomics profiling using liquid or gas chromatography coupled with mass spectrometry could provide several chances to discover bioactive compounds' complexity and chemical diversity. This review has, thus, given insight into the significance of methods used to reactivate BGCs from endophytes and the importance of varying techniques of their metabolomic profiling.
Inflammation-based Scores in Patients With Pheochromocytoma
Authors: Parazzoli Chiara , Prete Alessandro , Favero Vittoria , Aresta Carmen , Pucino Valentina , Ayuk John , Asia Miriam , Elhassan Yasir S , Chiodini Iacopo , Ronchi Cristina L 
Published: April 2024

Abstract

Background
Pheochromocytoma is associated with systemic inflammation but the underlying mechanisms are unclear. Therefore, we investigated the relationship between plasma metanephrine levels and hematological parameters—as a surrogate of inflammation—in patients with pheochromocytoma and the influence of preoperative α-blockade treatment.

Design and Methods
We retrospectively studied 68 patients with pheochromocytoma who underwent adrenalectomy (median age, 53 years; 64.7% females) and 2 control groups matched for age, sex, and body mass index: 68 patients with nonfunctioning adrenocortical tumors and 53 with essential hypertension. The complete blood count and several inflammation-based scores (neutrophil-to-lymphocyte ratio [NLR], platelet-to-lymphocyte ratio [PLR], lymphocyte-to-monocyte ratio [LMR], systemic-immune-inflammation index [SII], prognostic-nutrition index) were assessed in all patients and, in a subset of pheochromocytomas, after adrenalectomy (n = 26) and before and after preoperative α-blockade treatment (n = 29).

Results
A higher inflammatory state, as indicated by both complete blood count and inflammation-based scores, was observed in patients with pheochromocytoma compared with nonfunctioning adrenocortical tumors and essential hypertension. Plasma metanephrine levels showed a positive correlation with NLR (r = 0.4631), PLR (r = 0.3174), and SII (r = 0.3709) and a negative correlation with LMR (r = 0.4368) and prognostic-nutrition index (r = 0.3741), even after adjustment for age, sex, ethnicity, body mass index, and tumor size (except for PLR). After adrenalectomy, we observed a reduction in NLR (P = .001), PLR (P = .003), and SII (P = .004) and a concomitant increase in LMR (P = .0002). Similarly, α-blockade treatment led to a reduction in NLR (P = .007) and SII (P = .03).

Conclusion
Inflammation-based scores in patients with pheochromocytoma showed pro-inflammatory changes that correlated with plasma metanephrine levels and are ameliorated by adrenalectomy and α-blockade.
Modified Function-Preserving Endoscopic Endonasal Extracapsular Resection of a Large Orbital Apex Cavernous Hemangioma
Authors: Khaleghi Mehdi , Carlstrom Lucas P. , Callejas Claudio Andres , Kobalka Peter , Carrau Ricardo , Prevedello Daniel M. 
Published: April 2024

BACKGROUND AND IMPORTANCE:
Various invasive oculoplastic procedures are commonly utilized to control the rectus muscles and widen the surgical corridor through the endoscopic endonasal removal of large orbital apex cavernous hemangiomas (OACHs). They require additional transconjunctival incision, rectus muscle insertional retraction, or muscle deinsertion at the globe that might not be safe and lead to prolonged postoperative extraocular muscle dysfunction. In this article, the authors described a modified 3-handed extracapsular technique for the resection of a large OACH without an additional procedure for rectus muscle control. The aim is to achieve a safe gross total tumor removal while minimizing the procedure-related complications. An intraoperative video is included, along with a stepwise cadaveric dissection relevant to the approach.

CLINICAL PRESENTATION:
A 71-year-old female presented with progressive left-sided blurred vision, binocular diplopia, and mild proptosis. Contrast-enhanced brain MRI revealed a large heterogeneous enhanced inferomedial intraconal mass in the left orbital apex, mostly consistent with cavernous hemangioma. Gross total tumor removal was achieved through a modified 3-handed endoscopic endonasal extracapsular approach. The diplopia was resolved, and significant visual improvement was achieved. Computed tomography scan demonstrated complete tumor removal, and histological examination confirmed the diagnosis.

CONCLUSION:
Endoscopic endonasal resection of large OACH can be feasibly performed by using a modified 3-handed extracapsular technique through the generous use of Q-tip swab applicators within the natural separation plane around the tumor capsule and a sequential traction-countertraction method. Subsequently, a gross total removal and optimal postoperative functional outcome are attainable through minimal rectus muscle fiber violation and intraconal fat manipulation.
Exhaled and Systemic Biomarkers to Aid the Diagnosis of Bronchial Asthma in Elite Water Sports Athletes
Authors: CSOMA BALÁzs , SYDÓ NÓRA , SZŰcs GERGŐ , SERES ÉVA , ERDÉLYI TAMÁS , HORVÁTH GÁBOR , CSULAK EMESE , MERKELY BÉLA , MÜLLER VERONIKA 
Published: April 2024

ABSTRACT

Purpose
Our aim was to evaluate the accuracy of a combined airway inflammatory biomarker assessment in diagnosing asthma in elite water sports athletes.

Methods
Members of the Hungarian Olympic and Junior Swim Team and elite athletes from other aquatic disciplines were assessed for asthma by objective lung function measurements, and blood eosinophil count (BEC), serum total immunoglobulin E (IgE), fractional exhaled nitric oxide (FENO) measurements, and skin prick testing were performed. A scoring system from BEC, FENO, serum IgE, and skin test positivity was constructed by dichotomizing the variables and assigning a score of 1 if the variable is elevated. These scores were summed to produce a final composite score ranging from 0 to 4.

Results
A total of 48 participants were enrolled (age 21 ± 4 yr, 42% male), of which 22 were diagnosed with asthma. Serum total IgE and FENO levels were higher in asthmatic individuals (68 [27–176] vs 24 [1–43], P = 0.01; 20 [17–26] vs 15 [11–22], P = 0.02), and positive prick test was also more frequent (55% vs 8%, P < 0.01). Asthmatic participants had higher composite variable scores (2 [1–3] vs 1 [0–1], P = 0.02). Receiver operating characteristic analysis showed that total IgE, FENO, and composite variable were suitable
for identifying asthmatic participants (area under the curve = 0.72, P = 0.01; 0.70, P = 0.02, and 0.69, P = 0.03). A composite score of >2 reached a specificity of 96.2%, a sensitivity of 36.4%, and a likelihood ratio of 9.5. Logistic regression model revealed a strong association between the composite variable and the asthma diagnosis (OR = 2.71, 95% confidence interval = 1.17–6.23, P = 0.02).

Conclusions
Our data highlight the diagnostic value of combined assessment of Th2-type inflammation in elite water sports athletes. The proposed scoring system may be helpful in ruling in asthma in this population upon clinical suspicion.
Comparative efficacy of osteotome versus CAS kit-assisted indirect maxillary sinus lift and immediate implant placement in posterior atrophic maxilla: A clinico-radiological study
Authors: Shende Himanshu , Mundada Bhushan , Bhola Nitin 
Published: April 2024

Background: The aim of this study was to compare and evaluate clinical and radiological outcomes of conventional osteotome technique and CAS kit uses for indirect sinus lifting and immediate implant placement in atrophic posterior maxilla. Methods: A total of 20 patients aged <18 years in which 60% males and 40% of females were included in this study requiring implant prosthesis in atrophic (RBH > 3mm) posterior maxilla with a minimum width of 6mm were included in the study. They were randomly divided into two groups by computerised allocation into one group undergoing sinus lift with osteotome, and the other with CAS kit. Statistical analysis was done by using descriptive and inferential statistics. Qualitative data were analyzed using the Chi-square test. Dependent and independent variables were evaluated by the paired t-test and unpaired t-test respectively. A p<0.05 was set as the level of significance. Results: Mean duration for implant placement in the CAS group was 13.40±2.98 and in patients the osteotome group was 22.10±2.55. Mean primary stability in patients with CAS group was 44±6.14 and patients with osteotome group were 35.50±7.61. Mean amount of bone regeneration radiographic evaluation at three months in patients of CAS group was 4.99±0.86 and in patients of osteotome group was 5.59±1.21. The mean amount of bone regeneration radiographic evaluation at nine months in the CAS group was 5.53±0.77 and 6.34±1.11 in the osteotome group. Conclusions: CAS kit compared to osteotome was better in terms of operative time, primary stability, and marginal bone loss resulting in recommended modality.