bluuebunny/crossref_metadata_2025 huggingface dataset:
A modified petal and stamen dimorphism interact to enhance pollen placement by a buzz-pollinated flower
Authors: Monteiro Thainã R , Gonçalves Rogério V S , Telles Francismeire J , Barônio Gudryan J , Nogueira Anselmo , Brito Vinícius L G
Published: December 2024

Background

Floral adaptations supposedly help pollen grains to cross the numerous barriers faced during their journey to stigmas. Stamen dimorphism and specialized petals, like the cucculus in the Cassieae tribe (Fabaceae), are commonly observed in flowers that offer only pollen as a resource for bee pollinators. Here, we experimentally investigated whether stamen dimorphism and the cucculus enhance pollen placement on the bee’s body.

Methods

We used 3-D-printed bee models to apply artificial vibrations to the flowers of Chamaechrista latistipula with their cucculus deflected or maintained in its original position and their anther pores manipulated. After each simulated flower visit, we captured photographs of the artificial bee from four distinct angles. Employing digital imaging techniques, we documented the presence and location of pollen and stigma on the bee’s body.

Key Results

Our findings reveal that the cucculus redistributes pollen grains on the bee’s body. There is a remarkable increase in pollen density (~10-fold) on the lateral side adjacent to the cucculus, precisely where the stigma contacts the bee when the cucculus is unmanipulated. Furthermore, the cucculus also enhances pollen placement on the ventral region of the bee, indicating its additional function. The cucculus also increases the accuracy of pollen grains on the adjacent lateral region of the bee’s body, irrespective of the pollen grains released by small or large anthers.

Conclusions

Floral specialized traits, such as modified petals and stamen dimorphism, can modify the fate of pollen grains and ultimately contribute to male reproductive performance in pollen flowers with poricidal anthers. The cucculus exhibits a dual role by promoting pollen placement in optimal regions for pollination and probably supporting pollen grains for bee feeding. These findings provide valuable insights into the adaptive significance of floral traits and their impact on the reproductive success of pollen flowers.
Helium Plasma Effect on Breast Stromal-Enriched Lipograft: A Case Report
Authors: Sterodimas Aris
Published: December 2024

Autologous fat transfer for large volume augmentation, reconstructive, and cosmetic purposes has become more popular due to the inherent biocompatibility, accessibility, and low cost. For volume augmentation, the retention of grafted fat is unpredictable. Several approaches to autologous fat transfer have prepared the donor fat and/or the recipient-site increase fat graft retention as well as the predictability of the retention. This study is the first clinical report on the combination of radiofrequency helium plasma pretreatment of the recipient site and a cell-assisted lipotransfer technique for enhanced fat graft retention. One patient underwent autologous breast augmentation using the stromal-enriched lipograft technique to process the fat prior to injection. Only the right breast received pretreatment using radiofrequency helium plasma after infiltration. The processed fat was injected using a droplet style injector. The patient was followed for 2 years and underwent breast MRI examinations for measurement of the graft volume. The overall fat graft survival after 12 months for the stromal-enriched lipograft was 63%, whereas the survival for the stromal-enriched lipograft in combination with radiofrequency helium plasma was 89%. The addition of biostimulatory techniques to prepare the recipient site for breast augmentation enhanced the fat graft retention. Further clinical studies using radiofrequency helium plasma are required to justify using this modality as a recipient-site preparation technique.

Level of Evidence: 5 (Therapeutic)
HLA-EpiCheck: novel approach for HLA B-cell epitope prediction using 3D-surface patch descriptors derived from molecular dynamic simulations
Authors: Amaya-Ramirez Diego , Devriese Magali , Lhotte Romain , Usureau Cédric , Smaïl-Tabbone Malika , Taupin Jean-Luc , Devignes Marie-Dominique
Published: December 2024

Motivation

The human leukocyte antigen (HLA) system is the main cause of organ transplant loss through the recognition of HLAs present on the graft by donor-specific antibodies raised by the recipient. It is therefore of key importance to identify all potentially immunogenic B-cell epitopes on HLAs in order to refine organ allocation. Such HLAs epitopes are currently characterized by the presence of polymorphic residues called “eplets”. However, many polymorphic positions in HLAs sequences are not yet experimentally confirmed as eplets associated with a HLA epitope. Moreover, structural studies of these epitopes only consider 3D static structures.

Results

We present here a machine-learning approach for predicting HLA epitopes, based on 3D-surface patches and molecular dynamics simulations. A collection of 3D-surface patches labeled as Epitope (2117) or Nonepitope (4769) according to Human Leukocyte Antigen Eplet Registry information was derived from 207 HLAs (61 solved and 146 predicted structures). Descriptors derived from static and dynamic patch properties were computed and three tree-based models were trained on a reduced non-redundant dataset. HLA-Epicheck is the prediction system formed by the three models. It leverages dynamic descriptors of 3D-surface patches for more than half of its prediction performance. Epitope predictions on unconfirmed eplets (absent from the initial dataset) are compared with experimental results and notable consistency is found.

Availability and implementation

Structural data and MD trajectories are deposited as open data under doi: 10.57745/GXZHH8. In-house scripts and machine-learning models for HLA-EpiCheck are available from https://gitlab.inria.fr/capsid.public_codes/hla-epicheck.
CCfrag: scanning folding potential of coiled-coil fragments with AlphaFold
Authors: Martinez-Goikoetxea Mikel
Published: December 2024

Motivation

Coiled coils are a widespread structural motif consisting of multiple α-helices that wind around a central axis to bury their hydrophobic core. While AlphaFold has emerged as an effective coiled-coil modeling tool, capable of accurately predicting changes in periodicity and core geometry along coiled-coil stalks, it is not without limitations, such as the generation of spuriously bent models and the inability to effectively model globally non-canonical-coiled coils. To overcome these limitations, we investigated whether dividing full-length sequences into fragments would result in better models.

Results

We developed CCfrag to leverage AlphaFold for the piece-wise modeling of coiled coils. The user can create a specification, defined by window size, length of overlap, and oligomerization state, and the program produces the files necessary to run AlphaFold predictions. The structural models and their scores are then integrated into a rich per-residue representation defined by sequence- or structure-based features. Our results suggest that removing coiled-coil sequences from their native context can improve prediction confidence and results in better models. In this article, we present various use cases of CCfrag and propose that fragment-based prediction is useful for understanding the properties of long, fibrous coiled coils by revealing local features not seen in full-length models.

Availability and implementation

The program is implemented as a Python module. The code and its documentation are available at https://github.com/Mikel-MG/CCfrag.
MSA clustering enhances AF-Multimer’s ability to predict conformational landscapes of protein–protein interactions
Authors: Rustamov Khondamir R , Baev Artyom Y
Published: December 2024

Motivation

Understanding the conformational landscape of protein–ligand interactions is critical for elucidating the binding mechanisms that govern these interactions. Traditional methods like molecular dynamics (MD) simulations are computationally intensive, leading to a demand for more efficient approaches. This study explores how multiple sequence alignment (MSA) clustering enhance AF-Multimer’s ability to predict conformational landscapes, particularly for proteins with multiple conformational states.

Results

We verified this approach by predicting the conformational landscapes of chemokine receptor 4 (CXCR4) and glucagon receptor (GCGR) in the presence of their agonists and antagonists. In our experiments, AF-Multimer predicted the structures of CXCR4 and GCGR predominantly in active state in the presence of agonists and in inactive state in the presence of antagonists. Moreover, we tested our approach with proteins known to switch between monomeric and dimeric states, such as lymphotactin, SH3, and thermonuclease. AFcluster-Multimer accurately predicted conformational states during oligomerization, which AFcluster with AlphaFold2 alone fails to achieve. In conclusion, MSA clustering enhances AF-Multimer’s ability to predict protein conformational landscapes and mechanistic effects of ligand binding, offering a robust tool for understanding protein–ligand interactions.

Availability and implementation

Code for running AFcluster-Multimer is available at https://github.com/KhondamirRustamov/AF-Multimer-cluster
Pod5Viewer: a GUI for inspecting raw nanopore sequencing data
Authors: Dietrich Vincent , Alagna Nicolò , Helm Mark , Gerber Susanne , Butto Tamer
Published: December 2024

Motivation

Oxford Nanopore Technologies recently adopted the POD5 file format for storing raw nanopore sequencing data. The information stored in these files provides detailed insights into the sequencing features and enhances the understanding of raw nanopore data. However, the process of visualizing the data can be cumbersome, especially for users without programming skills. To address this issue, we developed the pod5Viewer, a GUI application for inspecting POD5 files.

Results

The pod5Viewer offers straightforward access to raw sequencing data and associated metadata in POD5 files. It includes functionalities for viewing, plotting, and exporting individual reads. Designed with user-friendliness in mind, the pod5Viewer is easy to install and use, making it suitable for users with all technical backgrounds.

Availability and implementation

The pod5Viewer is available as open source from the pod5Viewer Github repository (https://github.com/dietvin/pod5Viewer)
TargetSA: adaptive simulated annealing for target-specific drug design
Authors: Xue Zhe , Sun Chenwei , Zheng Wenhao , Lv Jiancheng , Liu Xianggen
Published: December 2024

Motivation

The burgeoning field of target-specific drug design has attracted considerable attention, focusing on identifying compounds with high binding affinity toward specific target pockets. Nevertheless, existing target-specific deep generative models encounter notable challenges. Some models heavily rely on elaborate datasets and complicated training methodologies, while others neglect the multi-constraint optimization problem inherent in drug design, resulting in generated molecules with irrational structures or chemical properties.

Results

To address these issues, we propose a novel framework (TargetSA) that leverages adaptive simulated annealing (SA) for target-specific molecular generation and multi-constraint optimization. The SA process explores the discrete structural space of molecules, progressively converging toward the optimal solution that fulfills the predefined objective. To propose novel compounds, we first predict promising editing positions based on historical experience, and then iteratively edit molecular graphs through four operations (insertion, replacement, deletion, and cyclization). Together, these operations collectively constitute a complete operation set, facilitating a thorough exploration of the drug-like space. Furthermore, we introduce a reversible sampling strategy to re-accept currently suboptimal solutions, greatly enhancing the generation quality. Empirical evaluations demonstrate that TargetSA achieves state-of-the-art performance in generating high-affinity molecules (average vina dock −9.09) while maintaining desirable chemical properties.

Availability and implementation

https://github.com/XueZhe-Zachary/TargetSA
The athletes heart—from acute stimulus to chronic adaptation
Authors: Maxwell Joseph D , Oxborough David
Published: December 2024

Introduction

The complex phenomenon of the athlete’s heart (AH) describes the chronic physiological structural and functional adaptation secondary to repeated exposure of an acute exercise stimulus.

Sources of Data

This narrative review is based on published evidence.

Areas of agreement

Highly trained athletic individuals frequently display cardiac parameters which are suggestive of an AH and can exceed the traditional ‘normal’ limits.

Area of controversy

The physiological processes underpinning the extent of cardiac adaption and how this is closely linked to exercise type, but also sex, ethnicity, and body size.

Growing points

Since its seminal description by Morganroth and colleagues in 1975, our understanding of the AH has evolved in tandem with improvements in cardiac imaging techniques alongside the exploration of more diverse athletic populations. This narrative review aims to provide a balanced discussion of the multi-factorial nature of structure and function of the AH with specific reference to the unique physiological exercise stimuli.

Areas timely for developing research

Despite great interest in cardiac adaptations across a broad spectrum of athletic populations, future research designs should consider the use of new and novel imaging techniques to enhance our understanding of the acute cardiovascular responses which ultimately mediates such adaptations, especially in athletic populations underrepresented in the literature.
Prevalence of hypothyroidism in older adults and its association with cognition: a cross-sectional study from a South Indian ageing urban cohort
Authors: Jessy Angeline S , G. Sandhya , S. Monisha , S. Sundarakumar Jonas , Stezin Albert , Issac Thomas Gregor
Published: December 2024

The study conducted on a South Indian urban cohort aimed to emphasize the prevalence and patterns of hypothyroidism and its association with cognition among individuals aged 45 years and above. A cross-sectional design was adopted, utilizing data from the Tata Longitudinal Study of Aging cohort, comprising 1201 non-demented participants in Bangalore, South India. The study contains detailed clinical assessments, including medical history, physical examination and cognitive tests such as the COGNITO battery, Hindi Mental State Examination and Addenbrooke’s Cognition Examination III. Biochemical tests were utilized to quantify plasma levels of thyroid-stimulating hormone, triiodothyronine and thyroxine. Participants were categorized based on medication history and thyroid hormone levels. The study findings showed a 17.69% prevalence of hypothyroidism, with 6.22% being classified as overt hypothyroidism and 93.78% as subclinical hypothyroidism. The prevalence was significantly higher in females compared with males (P = 0.043). Individuals with hypothyroidism are more frequently diagnosed with mild cognitive impairment than people with euthyroid (P = 0.008). Furthermore, on the classification based on thyroid medication history, the ineffective treatment group performed poorer in Addenbrooke’s Cognition Examination III fluency (P = 0.006), auditory attention (P = 0.001) and form matching (P = 0.024) tasks compared with the adequately treated group. The partially treated group performed poorer in visual attention (P = 0.005) and vocabulary (P = 0.043) compared with the effectively treated group. The study identified a notable prevalence of hypothyroidism in the cohort, with females exhibiting a higher prevalence. Our study suggests that the timely management of thyroid disorders with medications is crucial not only to prevent hormonal imbalances but also to improve cognitive functioning.
Evaluating clinical meaningfulness of anti-β-amyloid therapies amidst amyloid-related imaging abnormalities concern in Alzheimer’s disease
Authors: Aljuhani Manal , Ashraf Azhaar , Edison Paul
Published: December 2024

Alzheimer’s disease is the most prevalent form of dementia in the elderly, which is clinically characterized by a gradual and progressive deterioration of cognitive functions. The central and early role of β-amyloid in the pathogenesis of Alzheimer’s disease is supported by a plethora of studies including genetic analyses, biomarker research and genome-wide association studies in both familial (early-onset) and sporadic (late-onset) forms of Alzheimer’s. Monoclonal antibodies directed against β-amyloid demonstrate slowing of the clinical deterioration of patients with early Alzheimer’s disease. Aducanumab, lecanemab and donanemab clinical trials showed slowing of Alzheimer’s disease progression on composite scores by 25–40% based on the measure used. Anti-β-amyloid antibodies can cause side effects of bleeding and swelling in the brain, called amyloid-related imaging abnormalities. Amyloid-related imaging abnormalities typically occur early in treatment and are often asymptomatic, and though in rare cases, they can lead to serious or life-threatening events. The aim of this review is to evaluate the clinical meaningfulness of anti-β-amyloid therapies amidst amyloid-related imaging abnormalities concern in Alzheimer’s disease.
Rewiring the disordered connectome with circuit-based paired stimulation after stroke—a randomized, double-blind and controlled Phase II trial
Authors: Xing Xiang-Xin , Wu Jia-Jia , Qu Jiao , Ma Jie , Xu Rong , Zhu Yu , Zheng Mou-Xiong , Hua Xu-Yun , Xu Jian-Guang
Published: December 2024

The cortico-cortical paired associative stimulation, a combined stimulation based on two brain regions, may be an effective strategy for stroke rehabilitation. Our aim was to confirm that the cortico-cortical paired associative stimulation strengthens the connection between brain regions in the motor circuit and promotes improvements in motor function. This was a randomized double-blind, controlled Phase II trial. 44 Stroke patients were treated in a rehabilitation hospital from October 2020 to January 2021 and were randomly assigned to the sham stimulation group and the cortico-cortical paired associative stimulation group. Patients in both groups received 12 days of rehabilitation therapy. Cortico-cortical paired associative stimulation group received one treatment of cortico-cortical paired associative stimulation invention. Both groups received behavioural assessments such as the Fugl–Meyer upper-extremity scale and resting-state functional MRI scans prior to the intervention and on Day 14. 40 patients completed the intervention session. The results of Fugl–Meyer upper-extremity scale showed a more significant improvement in motor function in the cortico-cortical paired associative stimulation group (6.33 ± 1.29) than in the sham stimulation group (3.16 ± 1.38) (P < 0.001). The functional connectivity showed that cortico-cortical paired associative stimulation strengthens connections between brain regions. Correlation analysis confirmed that the enhancement of functional connectivity was positively correlated with the recovery of Fugl–Meyer upper-extremity scale (r2 = 0.146, P = 0.034; r2 = 0.211, P = 0.0093). The results of functional connectivity suggest that cortico-cortical paired associative stimulation strengthens connections between brain regions. It is expected that this study will provide a positive viewpoint for the neurorehabilitation of stroke patients based on the circuit-level plasticity. (Chinese Clinical Trial Registry: ChiCTR2000036685).
Harnessing the power of machine learning into tissue engineering: current progress and future prospects
Authors: Wu Yiyang , Ding Xiaotong , Wang Yiwei , Ouyang Defang
Published: December 2024

Tissue engineering is a discipline based on cell biology and materials science with the primary goal of rebuilding and regenerating lost and damaged tissues and organs. Tissue engineering has developed rapidly in recent years, while scaffolds, growth factors, and stem cells have been successfully used for the reconstruction of various tissues and organs. However, time-consuming production, high cost, and unpredictable tissue growth still need to be addressed. Machine learning is an emerging interdisciplinary discipline that combines computer science and powerful data sets, with great potential to accelerate scientific discovery and enhance clinical practice. The convergence of machine learning and tissue engineering, while in its infancy, promises transformative progress. This paper will review the latest progress in the application of machine learning to tissue engineering, summarize the latest applications in biomaterials design, scaffold fabrication, tissue regeneration, and organ transplantation, and discuss the challenges and future prospects of interdisciplinary collaboration, with a view to providing scientific references for researchers to make greater progress in tissue engineering and machine learning.
Impact of Clinician Feedback Reports on Antibiotic Use in Children Hospitalized With Community-acquired Pneumonia
Authors: Chiotos Kathleen , Dutcher Lauren , Grundmeier Robert W , Meyahnwi Didien , Lautenbach Ebbing , Neuhauser Melinda M , Hicks Lauri A , Hamilton Keith W , Li Yun , Szymczak Julia E , Muller Brandi M , Congdon Morgan , Kane Emily , Hart Jessica , Utidjian Levon , Cressman Leigh , Jaskowiak-Barr Anne , Gerber Jeffrey S
Published: December 2024

Background

Feedback reports summarizing clinician performance are effective tools for improving antibiotic use in the ambulatory setting, but the effectiveness of feedback reports in the hospital setting is unknown.

Methods

Quasi-experimental study conducted between December 2021 and November 2023 within a pediatric health system measuring the impact of clinician feedback reports delivered by email and reviewed in a monthly meeting on appropriate antibiotic use in children hospitalized with community-acquired pneumonia (CAP). We used an interrupted time series analysis (ITSA) to estimate the immediate change and change over time in the proportion of CAP encounters adherent to validated metrics of antibiotic choice and duration, then used Poisson regression to estimate intervention effect as a risk ratio (RR).

Results

Preintervention, 213 of 413 (52%) encounters received the appropriate antibiotic choice and duration, which increased to 308 of 387 (80%) postintervention. The ITSA demonstrated an immediate 18% increase in the proportion of CAP encounters receiving both the appropriate antibiotic choice and duration (95% confidence interval [CI]: 3–33%), with no further change over time (−0.3% per month, 95% CI: −2%–2%). In the Poisson model adjusted for age, sex, race, season, site, and intensive care unit admission, the intervention was associated with a 32% increase in the rate of appropriate antibiotic choice and duration (RR 1.32, 95% CI: 1.12–1.56, P < .01). No difference in length of stay or revisits were detected postintervention.

Conclusions

The intervention was associated with an increase in clinician adherence to antibiotic choice and duration recommendations for children hospitalized with CAP.
Multiethnic prevalence of the APOL1 G1 and G2 variants among the Israeli dialysis population
Authors: Ben-Ruby Dror , Atias-Varon Danit , Kagan Maayan , Chowers Guy , Shlomovitz Omer , Slabodnik-Kaner Keren , Mano Neta , Avayou Shany , Atsmony Yariv , Levin Dana , Dotan Edo , Calderon-Margalit Ronit , Shnaider Alla , Haviv Yosef S , Birk Ohad S , Hadar Noam , Anikster Yair , Berar Yanay Noa , Chernin Gil , Kruzel-Davila Etty , Beckerman Pazit , Rozen-Zvi Benaya , Doctor Gabriel T , Stanescu Horia C , Shemer Revital , Pras Elon , Reznik-Wolf Haike , Nahum Ayelet Hashahar , Dominissini Dan , Skorecki Karl , Vivante Asaf
Published: December 2024

Background and hypothesis

The two apolipoprotein L1 (APOL1) variants, G1 and G2, are common in populations of sub-Saharan African ancestry. Individuals with two of these alleles (G1 or G2) have an increased risk for a spectrum of non-diabetic chronic kidney diseases. However, these variants are typically not observed outside of populations that self-identify as current continental Africans or having clear recent African ancestry such as, most notably, African Americans, and other large population groups in the Americas and several European countries. We hypothesized that the diverse ethnic groups within the Israeli population may exhibit varying levels of recent African ancestry. Therefore, it is plausible that APOL1 risk alleles might be present even in individuals who do not self-identify as being of sub-Saharan African descent.

Methods

We non-selectively screened people with kidney failure across Israel for APOL1 risk variants using restriction fragment length polymorphism.

Results

We recruited 1744 individuals from 38 dialysis units in Israel. We identified eight patients of Moroccan Jewish, Bedouin, or Muslim Arab ancestry, who carry at least one G1 or G2 allele. None of the eight patients carried the protective APOL1 p.N264K variant. Furthermore, despite all Bedouin individuals being G2 heterozygous, the G2 minor allele frequency was significantly enriched in kidney failure cases compared to ethnically matched controls (P = .006).

Conclusions

These findings show that APOL1 G1 and G2 allelic variants are present in populations previously not appreciated to possess recent sub-Saharan ancestry and suggest that a single G2 risk variant may confer increased risk for chronic kidney disease in certain population contexts.
FLDS: differentially private federated learning with double shufflers
Authors: Qi Qingqiang , Yang Xingye , Hu Chengyu , Tang Peng , Su Zhiyuan , Guo Shanqing
Published: December 2024

Federated learning (FL) often uses local differential privacy (LDP) to prevent leaking data privacy through gradients. However, due to the high dimension of gradients, LDP will encounter the problem of privacy budget explosion in the application, resulting in low accuracy of the training model. To overcome this shortcoming, we propose a differential privacy FL protocol incorporating a control matrix and double shuffles. The control matrix, generated by the analyzer, is responsible for governing the selection and upload of clients’ gradients. Double shufflers shuffle the control matrix and clients’ gradients, respectively, so that the control matrix is invisible to the server and the gradient is anonymous to the server. In addition, the existing differential private FL often uses the same clipping scale for gradients clipping to facilitate determining the noise scale. However, this will bring too many clipping errors for the large gradients and too many noise errors for the small ones. To solve these problems, we propose an adaptive clipping scheme. Experiments on the real-world datasets show that our proposed methods achieve higher testing accuracy.
Mycophenolate Mofetil Appears Effective for the Treatment of Patients With Refractory Crohn’s Disease
Authors: Rosenfeld Sam , Clark-Snustad Kindra , Kamp Kendra J , Jacobs Jeffrey , Barahimi Mitra , Harper Jason , Lee Scott David
Published: December 2024

Background

Medically refractory Crohn’s disease (CD) is associated with a high risk of complications. Mycophenolate mofetil (MMF), a small molecule immunosuppressant, has limited data in patients with CD, and objective endoscopic response to MMF has not been reported.

Aims

We evaluated the safety and clinical, endoscopic, and biochemical effectiveness of off-label MMF for refractory CD as monotherapy or in combination with a biologic in patients with CD.

Methods

We retrospectively assessed adverse events (AEs), clinical response (Harvey–Bradshaw index), endoscopic response (simple endoscopic score in Crohn’s disease), and physician global assessment at an academic medical center and county hospital.

Results

60 patients received MMF as monotherapy (n = 40) or in combination with a biologic (n = 20) between 2008 and 2021 at a dose ranging from 1000 to 4000 mg daily. Median age was 39 years and median disease duration was 12 years. All patients previously failed ≥ 1 advanced therapy (median = 4). The median MMF therapy duration was 27 weeks. 54% achieved clinical response and 19% achieved clinical remission after a mean of 19.5 weeks (SD 14.5). Endoscopic response occurred in 32%, endoscopic remission in 16%, and endoscopic healing in 4% after a mean of 46.6 weeks (SD 31.0). 48% of patients experienced AEs, most commonly mild infection, nausea/vomiting, and headache. One serious AE occurred, which was assessed as unrelated to MMF.

Conclusions

MMF resulted in clinical, endoscopic, and biochemical benefits in some patients with refractory CD, and was tolerated by most patients. Further randomized controlled trials are needed to define optimal dosing and long-term efficacy and safety.
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology
Authors: Ma Hetong , Shen Liu , Wang Jiayang , Wang Shilong , Wang Min , Wang Meng , Li Zixiao , Li Jiao
Published: December 2024

Atherosclerotic cerebrovascular disease could result in a great number of deaths and disabilities. However, it did not acquire enough attention. Less information, statistics, or data on the disease has been revealed. Thus, no systematic concept datasets were released to help clinicians clarify the scope, assist research, and offer maximized value. This study aimed to develop a cross-lingual atherosclerotic cerebrovascular disease ontology; describe the workflow, schema, hierarchical structure, and the highlighted content; design a brand-new rehabilitation ontology; implement the ontology evaluation; and illustrate the application scenarios in real-world scenarios. We implemented nine steps based on the Ontology Development 101 methodologies combined with expert opinions. The ontology included collection and specification of clinical requirements, background investigation and knowledge acquisition, ontology selection and reuse, scope identification, schema definition, concept extraction, concept extension, ontology verification, and ontology evaluation. We evaluated the proposed ontology in the literature classification task. The current ontology included 10 top-level classes, respectively, clinical manifestation, comorbidity, complication, diagnosis, model of atherosclerotic cerebrovascular disease, pathogenesis, prevention, rehabilitation, risk factor, and treatment. There are 1715 concepts in the 11-level ontology, covering 4588 Chinese terms, 6617 English terms, and 972 definitions. The ontology could be applied in real-world scenarios such as information retrieval, new expression discovery, named entity recognition, and knowledge fusion, and the use case proved that it could offer satisfying support to related medical scenarios. The ontology was proven to be useful in text classification tasks, and the weight-F1 score could reach >80% combined with the pretrained model. The proposed ontology provided a clear set of cross-lingual concepts and terms with an explicit hierarchical structure, helping scientific researchers to quickly retrieve relevant medical literature, assisting data scientists to efficiently identify relevant contents in electronic health records, and providing a clear domain framework for academic reference.

Database URL: https://bioportal.bioontology.org/ontologies/ACVD_ONTOLOGY
Ulcerative Colitis Severity Classification and Localized Extent (UC-SCALE): An Artificial Intelligence Scoring System for a Spatial Assessment of Disease Severity in Ulcerative Colitis
Authors: Gutierrez-Becker Benjamin , Fraessle Stefan , Yao Heming , Luscher Jerome , Girycki Rafal , Machura Bartosz , Czornik Janusz , Goslinsky Jaroslaw , Pitura Marek , Levitte Steven , Arús-Pous Josep , Fisher Emily , Bojic Daniela , Richmond David , Bigorgne Amelie E , Prunotto Marco
Published: December 2024

Background and Aims

Validated scoring methods such as the Mayo Clinic Endoscopic Subscore (MCES) evaluate ulcerative colitis (UC) severity at the worst colon segment, without considering disease extent. We present the Ulcerative Colitis Severity Classification and Localized Extent (UC-SCALE) algorithm, which provides a comprehensive and automated evaluation of endoscopic severity and disease extent in UC.

Methods

Ulcerative Colitis Severity Classification and Localized Extent consists of 3 main elements: (1) a quality filter selecting readable images (frames) from colonoscopy videos, (2) a scoring system assigning an MCES to each readable frame, and (3) a camera localization algorithm assigning each frame to a location within the colon. Ulcerative Colitis Severity Classification and Localized Extent was trained and tested using 4326 sigmoidoscopy videos from phase III Etrolizumab clinical trials.

Results

The high agreement between UC-SCALE and central reading at the level of the colon section (𝜅 = 0.80), and the agreement between central and local reading (𝜅 = 0.84), suggested a similar inter-rater agreement between UC-SCALE and experienced readers. Furthermore, UC-SCALE correlated with disease activity markers such calprotectin, C-reactive protein and patient-reported outcomes, Physician Global Assessment and Geboes Histologic scores (rs 0.40-0.55, ps < 0.0001). Finally, the value of using UC-SCALE was demonstrated by assessing individual endoscopic severity between baseline and induction.

Conclusions

Our fully automated scoring system enables accurate, objective, and localized assessment of endoscopic severity in UC patients. In addition, we provide a topological representation of the score as a marker of disease severity that correlates highly with clinical metrics. Ulcerative Colitis Severity Classification and Localized Extent reproduces central reading and holds promise to enhance disease severity evaluation in both clinical trials and everyday practice.
Global longitudinal strain is a predictor of mortality in patients with cardiogenic shock
Authors: Berg-Hansen Kristoffer , Ito Saki , Oh Jae , Yang Jeong Hoon , Wiggers Henrik , Jentzer Jacob C
Published: December 2024

Aims

Cardiogenic shock (CS) is a critical manifestation of severe cardiac dysfunction, necessitating precise evaluation of left ventricular (LV) function by transthoracic echocardiography. The prognostic value of global longitudinal strain (GLS) has not been examined in patients with CS. Therefore, we aimed to assess the prognostic significance of GLS in patients with CS.

Methods and results

This was a retrospective study of patients with CS from 2007 to 2018 who had a transthoracic echocardiography performed within 24 h of admission. GLS was measured, and conventional parameters were obtained. LV dysfunction was categorized by GLS: > 9.7% (Quartile 1), 7.0% < GLS ≤ 9.7% (Quartile 2), 5.0% < GLS ≤ 7.0% (Quartile 3), and ≤5.0% (Quartile 4). Outcomes included in-hospital and 1-year all-cause mortality. Among 623 patients with CS with the median LVEF of 31% [inter-quartile range (IQR): 24–41%] and the median GLS of 7.0% (IQR: 5.0–9.7%), in-hospital mortality was 29%. Mortality increased across GLS quartiles: Quartile 1: 17%; Quartile 2: 22%; Quartile 3: 35%; and Quartile 4: 42%. GLS remained the only independent echocardiographic predictor of in-hospital mortality after adjusting for clinical covariates (adjusted odds ratio: 1.23 per 1% decrease, 95% confidence interval: 1.04–1.46, P = 0.015). GLS independently predicted 1-year all-cause mortality (P < 0.001). The prognostic value of GLS was superior in cases with acute coronary syndrome. A classification and regression tree analysis identified GLS as the most important echocardiographic variable for predicting in-hospital mortality.

Conclusion

GLS independently predicted short- and long-term mortality in patients with CS, surpassing conventional echocardiographic parameters in prognostic value, supporting its potential role in risk stratification in this population.
Predictors of coronary atherosclerosis in middle-aged and older athletes: the MARC-2 study
Authors: Berge Kristian , Janssen Sylvan L J E , Velthuis Birgitta K , Myhre Peder Langeland , Mosterd Arend , Omland Torbjørn , Eijsvogels Thijs M H , Aengevaeren Vincent L
Published: December 2024

Aims

Exercise improves cardiovascular health, but high-volume high-intensity exercise is associated with increased coronary artery calcification (CAC). We aimed to identify predictors of CAC in athletes.

Methods and results

We assessed the association of traditional and non-traditional cardiovascular risk factors with CAC using linear and logistic regression. A total of 289 male athletes from the MARC-2 study were included, with a median age of 60 (Q1–3 56–66) years, lifelong weekly training load of 26 (17–35) metabolic equivalent of task hours, body mass index of 24.5 (22.9–26.6) kg/m2, systolic blood pressure of 139 ± 18 mmHg, and reported 0.0 (0.0–8.0) smoking pack years. Thirty-one per cent had a CAC score > 100 and 13% > 400. Among traditional cardiovascular risk factors, higher age, systolic blood pressure, smoking pack years, and family history of coronary artery disease independently predicted greater CAC scores, while body mass index, low-density lipoprotein cholesterol, and diabetes mellitus did not. Among non-traditional risk factors, higher training loads, serum phosphate, and lower adjusted energy intake and fat percentage of energy intake independently predicted greater CAC scores. The full model with all traditional and non-traditional risk factors had higher accuracy in predicting CAC > 100 [receiver operating characteristic area under the curve 0.76, 95% confidence interval (0.70–0.82)] and CAC > 400 [0.85 (0.77–0.92)] than traditional cardiovascular risk factors alone [0.72 (0.65–0.78), P = 0.012, and 0.81 (0.74–0.90), P = 0.038, respectively].

Conclusion

Non-traditional risk factors, including training load, dietary patterns, and serum phosphate, were independently associated with CAC in aging male athletes. Prediction accuracy for CAC increased when including these variables in a prediction model with traditional risk factors.
A shot through the heart: a case report on retained bullet causing cardiac tamponade
Authors: Shah Rakesh , Dacey Thomas , Sebastian Joseph , Zehr Kenton , Cardozo Shaun
Published: December 2024

Background

As a rare complication of penetrating chest trauma, one can occasionally find foreign bodies inside the pericardium. Even rarer is finding an intact bullet inside the pericardial cavity following the gunshot injury.

Case summary

A 17-year-old male presented to the emergency department as a Level 1 trauma for multiple gunshot wounds. Upon arrival, the patient was tachycardic but normotensive. Physical exam was notable for several penetrating wounds to the chest and right clavicle. The initial chest X-ray demonstrated a metallic foreign body consistent with a bullet overlying the cardiac silhouette. Approximately 24 h into the hospital course, ST-segment elevation was noted on telemetry. An electrocardiogram demonstrated sinus tachycardia with diffuse ST-segment elevation in all leads, consistent with acute pericarditis. Over the following several hours, the patient gradually developed tamponade physiology, prompting a more emergent median sternotomy.

Discussion

Although penetrating cardiac injury carries a high mortality rate, management of these patients and complications that may arise during their hospital course are rarely explained. The diagnosis of projectile chest trauma starts with history and physical examination. The primary diagnostic modalities are the X-ray, computed tomography scan of the chest, electrocardiogram, and echocardiogram. Management of a patient with cardiac gunshot depends largely on haemodynamic status. As in our case, a patient with haemodynamic instability is managed with emergency exploration and removal of the foreign body.
A case report of familial catecholaminergic polymorphic ventricular tachycardia with a novel mutation in the ryanodine receptor 2
Authors: Shoji Yoshikuni , Hayashida Satoshi , Masuda Hikaru , Tachibana Eizo , Okumura Yasuo
Published: December 2024

Background

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is suspected by clinical characteristics involving fatal arrhythmic events in childhood and adolescence. On the other hand, genetic testing is also important because the mutation site in the specific genes of CPVT is related to the risk of ventricular arrhythmias and gene penetrance.

Case summary

We present a case of a 15-year-old male with a familial history of CPVT and a history of syncope at the age of 5. He experienced a cardiac arrest prompting out-of-hospital cardiopulmonary resuscitation, and his circulatory dynamics recovered. Multiple premature ventricular contractions inducted by a treadmill exercise test disappeared after a dosage of verapamil, flecainide, and nadolol, and a subcutaneous implantable cardioverter defibrillator was implanted. The novel pathogenic mutation with an insertion of histidine near the C-terminus of the RYR2 protein was identified by genetic testing in this case and his mother.

Discussion

The RYR2 mutation in this case has not been previously reported and may be an intractable phenotype of CPVT associated with a strong familial history and fatal cardiac events even under adequate medical therapy.
Congenital absence of the left atrial appendage: a positive coincidence for the electrophysiologist? A case report
Authors: Batista Lage João Gabriel , Rangel Rafael Augusto Lethier , de Oliveira Júnior Nilson Araújo , Tavares Pinheiro Martha Valeria , de Souza Olga Ferreira
Published: December 2024

Background

The congenital absence of the left atrial appendage (LAA) is an extremely rare anatomical anomaly, with only 23 cases documented in medical literature. The LAA plays a critical role in thrombus formation, particularly in patients with atrial fibrillation (AF), thus impacting stroke prevention strategies and the management of anticoagulation.

Case summary

We report a 48-year-old male with a 2-year history of hypertension and prior episodes of tachycardic palpitations, who presented with AF and chest pain. During catheter ablation for AF, a transoesophageal echocardiogram revealed the absence of the LAA, initially suspected to be a thrombus. The procedure was suspended until a computed tomography confirmed the congenital absence of the LAA. The patient successfully underwent pulmonary vein isolation with radiofrequency and, after a shared decision-making process, discontinued anticoagulation. He remains asymptomatic without AF recurrence.

Discussion

The congenital absence of the LAA raises important considerations for managing stroke risk in AF patients, as standard thromboembolic risk scores do not account for such anatomical variations. Despite the LAA being the most common site for thrombus formation, stroke risk in AF results from multiple factors beyond a single site of thrombus formation. Left atrial appendage occlusion is a viable alternative for stroke prevention in patients contraindicated for anticoagulation. Recent guidelines recommend individualized risk assessment using scores such as CHA2DS2-VA, even in atypical cases, ensuring that management strategies are tailored to each patient’s risk profile.
Ex vivo imaging of subacute myocardial infarction with ultra-short echo time 3D quantitative T1- and T1ρ-mapping magnetic resonance imaging in mice
Authors: Räty Iida , Aarnio Antti , Nissi Mikko J , Kettunen Sanna , Ruotsalainen Anna-Kaisa , Laidinen Svetlana , Ylä-Herttuala Seppo , Ylä-Herttuala Elias
Published: December 2024

Aims

The aim of this study was to develop an ultra-short echo time 3D magnetic resonance imaging (MRI) method for imaging subacute myocardial infarction (MI) quantitatively and in an accelerated way. Here, we present novel 3D T1- and T1ρ-weighted Multi-Band SWeep Imaging with Fourier Transform and Compressed Sensing (MB-SWIFT-CS) imaging of subacute MI in mice hearts ex vivo.

Methods and results

Relaxation time–weighted and under-sampled 3D MB-SWIFT-CS MRI were tested with manganese chloride (MnCl2) phantom and mice MI model. MI was induced in C57BL mice, and the hearts were collected 7 days after MI and then fixated. The hearts were imaged with T1 and adiabatic T1ρ relaxation time–weighted 3D MB-SWIFT-CS MRI, and the contrast-weighted image series were estimated with a locally low-rank regularized subspace constrained reconstruction. The quantitative parameter maps, T1 and T1ρ, were then obtained by performing non-linear least squares signal fitting on the image estimates. For comparison, the hearts were also imaged using 2D fast spin echo-based T2 and T1ρ mapping methods. The relaxation rates varied linearly with the MnCl2 concentration, and the T1 and T1ρ relaxation time values were elevated in the damaged areas. The ischaemic areas could be observed visually in the 3D T1, 3D T1ρ, and 2D MRI maps. The scar tissue formation in the anterior wall of the left ventricle and inflammation in the septum were confirmed by histology, which is in line with the results of MRI.

Conclusion

MI with early fibrosis, increased inflammatory activity, and interstitial oedema were determined simultaneously with T1 and T1ρ relaxation time constants within the myocardium by using the 3D MB-SWIFT-CS method, allowing quantitative isotropic 3D assessment of the entire myocardium.
Acute cardiovascular effects of electronic cigarettes: a systematic review and meta-analysis
Authors: Cheraghi Mahdis , Amiri Mehrnaz , Omidi Fatemeh , Shahidi Bonjar Amir Hashem , Bakhshi Hooman , Vaezi Atefeh , Nasiri Mohammad Javad , Mirsaeidi Mehdi
Published: December 2024

Electronic cigarette (EC) is widely advertised as a safe alternative to traditional cigarette (TC). We aimed to investigate the cardiovascular effect of EC with/without nicotine compared with TC. We systematically searched PubMed/MEDLINE, EMBASE, and Cochrane CENTRAL for randomized controlled trials that compared the effect of different smoking modalities on cardiovascular function up to 1 October 2024. Analysis used the weighted mean difference (WMD) with a 95% confidence interval (CI) via Comprehensive Meta-Analysis software, version 3.0. The study evaluated key cardiovascular parameters, including pulse wave velocity (PWV), augmentation index at 75 beats/min (AIx75), flow-mediated dilation (FMD), heart rate (HR), systolic blood pressure, and diastolic blood pressure. We analysed 9 trials involving 370 participants. Acute exposure to EC with nicotine (ECN) compared with nicotine-free EC (EC0) increased PWV (WMD = 0.26; 95% CI: 0.14–0.38, P < 0.001), AIx75 (WMD = 4.29; 95% CI: 2.07–6.51, P < 0.001), and HR (WMD = 5.06; 95% CI: 2.13–7.98, P = 0.001), significantly. In contrast, comparison between ECN and TC revealed no significant differences in FMD (WMD = 0.80; 95% CI: −0.09–1.70, P = 0.08). Our meta-analysis suggests that ECN acutely increases arterial stiffness more than EC0 does. Additionally, we found that the acute effect of ECN on endothelial dysfunction is not different from TC. Therefore, our study suggests that vaping cannot be considered as a safe substitute for TC. Further investigation is needed to explore the long-term cardiovascular effects of vaping and its modalities.