bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational prediction of multiple antigen epitopes
Authors: Viswanathan Rajalakshmi , Carroll Moshe , Roffe Alexandra , Fajardo Jorge E , Fiser Andras 
Published: September 2024

Abstract

Motivation
Identifying antigen epitopes is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes. Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable.

Results
Here, we introduce the antigen epitope prediction program ISPIPab that combines information from two feature-based methods and a docking-based method. We demonstrate that ISPIPab outperforms each of its individual classifiers as well as other state-of-the-art methods, including those designed specifically for epitope prediction. By combining the prediction algorithm with hierarchical clustering, we show that we can effectively capture epitopes that align with available experimental data while also revealing additional novel targets for future experimental investigations.
Once upon a time: exploring the biogeographic history of the largest endemic lizard family in the Neotropics (Squamata: Gymnophthalmidae)
Authors: Vásquez-Restrepo Juan D , Ribeiro‑Júnior Marco A , Sánchez-Pacheco Santiago J 
Published: September 2024

Abstract
Gymnophthalmids are a diverse lineage of Neotropical lizards that present challenges in the understanding of their phylogenetic relationships and biogeographic history. Using a densely sampled phylogeny and distribution data, we investigated their biogeography at the family level. Dividing South and Central America into 12 regions, we tested six biogeographic models considering dispersal-extinction, vicariance, and founder events. Our analysis revealed high taxonomic and phylogenetic endemism in the Andes, Amazon, and Guiana Shield. The best-fit model identified the Guiana Shield as the likely ancestral area of the family, with dispersal events dominating over vicariance. Key areas for species interchange were the Amazon, Northern Andes, and Guiana Shield. The core regions of diversification included the Andes, Amazon, and Guiana Shield, with elevated species richness and biotic interchange events during the Eocene and Oligocene. The Guiana Shield stood out as a stronghold of gymnophthalmid diversity, driven by dispersal rates and ancient lineages. Our findings challenge previous hypotheses about the diversification of these lizards, suggesting a colonization pattern from lowlands to high elevations rather than the South-to-North Speciation Hypothesis for Andean lineages.
Adjusting for incomplete baseline covariates in randomized controlled trials: a cross-world imputation framework
Authors: Song Yilin , Hughes James P , Ye Ting 
Published: September 2024

ABSTRACT
In randomized controlled trials, adjusting for baseline covariates is commonly used to improve the precision of treatment effect estimation. However, covariates often have missing values. Recently, Zhao and Ding studied two simple strategies, the single imputation method and missingness-indicator method (MIM), to handle missing covariates and showed that both methods can provide an efficiency gain compared to not adjusting for covariates. To better understand and compare these two strategies, we propose and investigate a novel theoretical imputation framework termed cross-world imputation (CWI). This framework includes both single imputation and MIM as special cases, facilitating the comparison of their efficiency. Through the lens of CWI, we show that MIM implicitly searches for the optimal CWI values and thus achieves optimal efficiency. We also derive conditions under which the single imputation method, by searching for the optimal single imputation values, can achieve the same efficiency as the MIM. We illustrate our findings through simulation studies and a real data analysis based on the Childhood Adenotonsillectomy Trial. We conclude by discussing the practical implications of our findings.
Global, regional and national burdens of acne vulgaris in adolescents and young adults aged 10–24 years from 1990 to 2021: a trend analysis
Authors: Zhu Zhou , Zhong Xiaoying , Luo Zhongyu , Liu Mingjuan , Zhang Hanlin , Zheng Heyi , Li Jun 
Published: September 2024

Abstract

Background
Acne vulgaris is a common skin condition affecting adolescents and young adults worldwide, yet data on the burden and trends of this disease remain limited. We aimed to investigate trends in the burden of acne vulgaris among adolescents and young adults aged 10–24 years at global, regional and national levels.

Methods
We retrieved data from the Global Burden of Disease Study 2021 for individuals aged 10–24 years in 204 countries and territories from 1990 to 2021. We analysed the numbers, age-standardized rates and average annual percentage changes (AAPCs) of the prevalence, incidence and disability-adjusted life years (DALYs) for acne vulgaris at the global, regional and national levels. Additionally, we examined these global trends by age, sex and Sociodemographic Index (SDI).

Results
Globally, the age-standardized prevalence rate of acne vulgaris among adolescents and young adults increased from 8563.4 per 100 000 population [95% uncertainty interval (UI) 7343.5–9920.1] in 1990 to 9790.5 (95% UI 8420.9–11 287.2) per 100 000 population in 2021, with an AAPC of 0.43 [95% confidence interval (CI) 0.41–0.46]. The age-standardized incidence rate and age-standardized DALY rate also showed a similar upward trend. Regionally, Western Europe had the highest age-standardized prevalence, incidence and DALY rates, while North Africa and the Middle East had the largest increase in these rates. By SDI quintile, the high SDI region had the highest age-standardized prevalence, incidence and DALY rates from 1990 to 2021, whereas the low-middle SDI region had the lowest burden of acne vulgaris but experienced the most significant increase in these rates. Globally, the age-standardized prevalence rate of acne vulgaris in 2021 was approximately 25% higher in young women than in young men (10 911.8 per 100 000 population vs. 8727.8 per 100 000 population). Among all age groups, adolescents aged 15–19 years had the highest age-specific prevalence rate, while adolescents aged 10–14 years experienced the largest increase from 1990 to 2021 (AAPC 0.50, 95% CI 0.48–0.52).

Conclusions
The burden of acne vulgaris among adolescents and young adults has continued to increase in nearly all countries since the 1990s. Managing this condition remains a significant challenge, necessitating more effective and targeted interventions to control the acne burden.
Patterns of treatment failure in patients with sinonasal squamous cell carcinoma after chemoradiotherapy
Authors: Wang Li , Wang Jie , Wang Tian , Li Yi , Song Xinmao 
Published: September 2024

Abstract

Objectives
To investigate the failure patterns based on precision radiation treatment and to determine the predictive factors of treatment failure for sinonasal squamous cell carcinoma (SNSCC) patients.

Methods
This was a retrospective study that included 214 cases of treatment failure from 441 consecutive patients. Two experienced radiation oncologists evaluated the tumour volume of cases with local recurrence. The 5-year overall survival (OS), progression-free survival (PFS) rates, and distant-metastasis-free survival (DMFS) were estimated. Investigations were performed on the factors that predicted local failure or distant metastasis.

Results
About 140 (31.7%) patients developed local recurrence, 24 (5.4%) experienced regional failure, and 65 (14.7%) underwent distant metastasis. In-field, marginal, and out-of-field failures occurred in 55.7% (78/140), 33.6% (47/140), and 10.7% (15/140) of patients with local recurrence, respectively. In logistic regression analysis, factors statistically significant for total local failure included treatment mode (P &lt; .01), chemotherapy (P &lt; .01), and surgical margins (P &lt; .01). Primary tumours with poor differentiation (P = .018) and R2 resection margin (P = .009) were more prone to develop distant failure. The 5-year OS, PFS, and DMFS rates were 57.8%, 52.0%, and 56.7% for the whole cohort. In univariate and multivariate analysis, the skull base involvement was an independent predictor for poorer OS and PFS; orbital invasion was an independent predictor for poorer OS.

Conclusions
Local recurrence and distant metastasis were the most common failure modes. Treatment mode, chemotherapy, and surgical margins were related to local recurrence. Poor differentiation and R2 resection margin were predictors for distant failure.

Advances in knowledge
Local recurrence is the most common failure pattern in patients with SNSCC who accepted chemoradiotherapy, and marginal and out-of-field failures occurred in 44.3% of patients with local recurrence.
A national survey of interventional radiology trainees on peripheral and aortic endovascular training
Authors: Rao Mihir M , Zhong Jim , Mahay Usman , Haslam Philip , Patel Jai 
Published: September 2024

Abstract

Objectives
The development of technical skills in peripheral and aortic endovascular intervention is an essential part of interventional radiology (IR) training. Access to endovascular training remains contentious, with IR and vascular surgery (VS) trainees competing for opportunities. The Collaborative Peripheral and Aortic Endovascular Training Survey (CPAETS) aimed to evaluate IR trainees’ experiences, expectations, and barriers to endovascular training.

Methods
CPAETS was a joint survey between the British Society of Interventional Radiology and the Rouleaux Club (UK Vascular Trainees’ Association), open for 12 weeks and distributed to UK-based IR and VS trainees. This article focuses on IR trainee responses.

Results
Thirty-two responses were received from IR trainees across England, Scotland, and Wales. Overall, 59% of respondents were satisfied with their endovascular training. IR trainees reported less regular hands-on experience of aortic endovascular procedures (50%) compared to peripheral endovascular procedures (93%). Consequently fewer trainees (65%) felt confident in achieving the necessary aortic endovascular competencies by the end of their training, compared to peripheral procedures (89%).

Conclusion
Limited exposure to aortic endovascular procedures resulted in reduced confidence levels in performing aortic intervention as compared to peripheral procedures. Potential solutions to bridge some of these IR training gaps include greater pre-operative and post-operative presence, the use of simulators, and IR fellowships to ensure adequate training opportunities.

Advances in knowledge
This article provides a snapshot of the current gaps in IR endovascular training in the United Kingdom, with insight into solutions that can enable trainees to develop clinical and technical competencies required for IR consultant practice.
Accuracy of an artificial intelligence-enabled diagnostic assistance device in recognizing normal chest radiographs: a service evaluation
Authors: Kumar Amrita , Patel Puja , Robert Dennis , Kumar Shamie , Khetani Aneesh , Reddy Bhargava , Srivastava Anumeha 
Published: September 2024

Abstract

Objectives
Artificial intelligence (AI) enabled devices may be able to optimize radiologists’ productivity by identifying normal and abnormal chest X-rays (CXRs) for triaging. In this service evaluation, we investigated the accuracy of one such AI device (qXR).

Methods
A randomly sampled subset of general practice and outpatient-referred frontal CXRs from a National Health Service Trust was collected retrospectively from examinations conducted during November 2022 to January 2023. Ground truth was established by consensus between 2 radiologists. The main objective was to estimate negative predictive value (NPV) of AI.

Results
A total of 522 CXRs (458 [87.74%] normal CXRs) from 522 patients (median age, 64 years [IQR, 49-77]; 305 [58.43%] female) were analysed. AI predicted 348 CXRs as normal, of which 346 were truly normal (NPV: 99.43% [95% CI, 97.94-99.93]). The sensitivity, specificity, positive predictive value, and area under the ROC curve of AI were found to be 96.88% (95% CI, 89.16-99.62), 75.55% (95% CI, 71.34-79.42), 35.63% (95% CI, 28.53-43.23), and 91.92% (95% CI, 89.38-94.45), respectively. A sensitivity analysis was conducted to estimate NPV by varying assumptions of the prevalence of normal CXRs. The NPV ranged from 88.96% to 99.54% as prevalence increased.

Conclusions
The AI device recognized normal CXRs with high NPV and has the potential to increase radiologists’ productivity.

Advances in knowledge
There is a need for more evidence on the utility of AI-enabled devices in identifying normal CXRs. This work adds to such limited evidence and enables researchers to plan studies to further evaluate the impact of such devices.
How Family Group Conferencing Can Support a Contextual Safeguarding Response to Community-based Youth Harm: Lessons for Practice from a Participatory Study
Authors: Owens Rachael , Bradbury-Leather Vanessa 
Published: September 2024

Abstract
This article reports on a study that brought Family Group Conferencing (FGC) and Contextual Safeguarding together to create an innovative practice response to extra-familial harm. It took place as part of a wider research project into the implementation of Contextual Safeguarding—an ecological approach to creating safety for young people harmed outside the home. Whilst there is growing understanding in social care of the contextual dynamics of young people’s safeguarding needs beyond their homes, many remain unsure about what it means, in practice, for them to create safety in a context. Using data collected via participatory and embedded research methods, this article considers how FGCs were adapted to create responses to youth harm that shifted the focus from ‘family’ to ‘community’; addressed the ‘social conditions of harm’; and drew on practitioners’ existing FGC skills. It demonstrates conceptual alignment and practice benefits for bringing the two approaches together and argues that drawing on the value-base and skills of FGC coordinators has considerable potential. The article highlights three key elements that are needed to recreate similar responses, namely: organisational mandate/support; conceptual framework aligned to ecological theory; and skills and attributes that include facilitation, working restoratively and with authority in challenging situations.
A review of the genus Euterpe: botanical and genetic aspects of açai, the purple gold of the Amazon
Authors: Teixeira Bruno , Teixeira Gisele , Darnet Elaine , Schaller Hubert , Rogez Hervé , Darnet Sylvain 
Published: September 2024

Abstract
Achieving improved plant breeding is one of the most significant challenges facing efforts to ensure human nutrition and energy security over the next 30 years. The principal focus of plant breeding is to increase the production of conventional crops, but the domestication and breeding of lesser-known plants may also represent a source of food and energy. The African oil palm is an example of a cultivated plant that has reached the first rank of oil sources over the last four decades. Among palms, açai palm trees are highlighted due to the violet berries being commercialized internationally as functional foods. Açai palms are candidates for domestication and breeding and have a large area of cultivation. We reviewed the literature and technical reports concerning the açai genetic pool to detail the açai palm tree species and their biology, diversity centre, genetic resources, and existing breeding programmes.
Developing a calculable risk prediction model for sternal wound infection after median sternotomy: a retrospective study
Authors: Chen Yang , He Fei , Wu Fan , Hu Xiaolong , Zhang Wanfu , Li Shaohui , Zhang Hao , Duan Weixun , Guan Hao 
Published: September 2024

Abstract

Background
Diagnosing sternal wound infection (SWI) following median sternotomy remains laborious and troublesome, resulting in high mortality rates and great harm to patients. Early intervention and prevention are critical and challenging. This study aimed to develop a simple risk prediction model to identify high-risk populations of SWI and to guide examination programs and intervention strategies.

Methods
A retrospective analysis was conducted on the clinical data obtained from 6715 patients who underwent median sternotomy between January 2016 and December 2020. The least absolute shrink and selection operator (LASSO) regression method selected the optimal subset of predictors, and multivariate logistic regression helped screen the significant factors. The nomogram model was built based on all significant factors. Area under the curve (AUC), calibration curve and decision curve analysis (DCA) were used to assess the model's performance.

Results
LASSO regression analysis selected an optimal subset containing nine predictors that were all statistically significant in multivariate logistic regression analysis. Independent risk factors of SWI included female [odds ratio (OR) = 3.405, 95% confidence interval (CI) = 2.535–4.573], chronic obstructive pulmonary disease (OR = 4.679, 95% CI = 2.916–7.508), drinking (OR = 2.025, 95% CI = 1.437–2.855), smoking (OR = 7.059, 95% CI = 5.034–9.898), re-operation (OR = 3.235, 95% CI = 1.087–9.623), heart failure (OR = 1.555, 95% CI = 1.200–2.016) and repeated endotracheal intubation (OR = 1.975, 95% CI = 1.405–2.774). Protective factors included bone wax (OR = 0.674, 95% CI = 0.538–0.843) and chest physiotherapy (OR = 0.446, 95% CI = 0.248–0.802). The AUC of the nomogram was 0.770 (95% CI = 0.745–0.795) with relatively good sensitivity (0.798) and accuracy (0.620), exhibiting moderately good discernment. The model also showed an excellent fitting degree on the calibration curve. Finally, the DCA presented a remarkable net benefit.

Conclusions
A visual and convenient nomogram-based risk calculator built on disease-associated predictors might help clinicians with the early identification of high-risk patients of SWI and timely intervention.
Basiliximab induction alone vs a dual ATG–basiliximab approach in first live-donor non-sensitized kidney transplant recipients with low HLA matching
Authors: Hod Tammy , Levinger Shmuel , Askenasy Enosh , Siman-Tov Maya , Davidov Yana , Ghinea Ronen , Pencovich Niv , Nachmani Ido , Mor Eytan 
Published: September 2024

ABSTRACT

Background
Individualizing induction therapy based on immunological risk is crucial for optimizing outcomes in kidney transplantation.

Methods
A retrospective analysis included 157 first live-donor non-sensitized kidney transplant recipients (KTRs). Within this cohort, 96 individuals exhibited low human leukocyte antigen (HLA) matching (5–6 HLA mismatches). The low HLA match subgroup was categorized into 52 KTRs receiving basiliximab alone and 44 recipients treated with a combined single ATG dose of 1.5 mg/kg and basiliximab. The primary endpoint was early acute cellular rejection (ACR) within 6 months post-transplant while secondary outcomes encompassed infection rates, renal allograft function, length of stay (LOS) and readmissions post-transplant.

Results
The incidence of early ACR was decreased for low HLA match KTRs, who received ATG–basiliximab, when compared with low HLA-matched KTRs who received basiliximab alone (9.1% vs 23.9%, P = .067). Age was a predictor for rejection, and subgroup analysis showed consistent rejection reduction across age groups. No significant differences were observed in admission for transplant LOS or in peri-operative complications, nor in infections rate including BK and cytomegalovirus viremia, allograft function and number of readmissions post-transplant up to 6 months post-transplant.

Conclusion
In non-sensitized first live-donor KTRs with low HLA matching, a dual ATG–basiliximab induction approach significantly reduced early ACR without compromising safety.
The media literacy theory of change and the message interpretation process model
Authors: Austin Erica Weintraub , Domgaard Shawn 
Published: September 2024

Abstract
The Message Interpretation Process (MIP) model originated to explain how youth engaging with entertainment media messages make decisions about apparent reality and behavioral choices. Although it has been tested over several decades with various age groups, population types and content foci, it has never been fully explicated. As it has matured as a model, its principles and concepts have contributed to a complementary theoretical model referred to herein as the Media Literacy Theory of Change. Both stem from the overriding perspective that media literacy involves both cognitive and affective components of message interpretation processes and skills that can be taught, engaged, and adapted as a person develops physically, cognitively, emotionally, and socially. This article provides a formal explanation of the MIP model and the Media Literacy Theory of Change, exploring their assumptions and propositions, and referencing the research that has supported and extended the theoretical growth of each over time.
Early life food intake modulates effects of diet restriction on lifespan and fecundity in later life in a predatory mite (Acari: Phytoseiidae)
Authors: Xu Yun , Zhang Keshi , Han Xiao , Zhang Zhi-Qiang 
Published: September 2024

Abstract
The nutritional status of an individual can significantly influence its life history traits, including development, growth, reproduction, and survival. In the predatory mite Phytoseiulus persimilis Athias-Henriot (Acari: Phytoseiidae), the plasticity of life history traits, such as developmental time and size at maturity, is influenced by the quality and quantity of food. This study aimed to investigate the effects of dietary restriction at different life stages (i.e., juvenile, early adulthood, and later adulthood) on the lifespan and fecundity of P. persimilis. We found that reduced dietary intake during early adulthood resulted in a shorter lifespan for both male and female P. persimilis. Furthermore, this study demonstrated a sex-specific response to dietary restriction: it extended the lifespan of males but reduced that of females during later adulthood. Diet restriction during the postovipositional period of females showed the most variable life history trait response. Our results showed that the impact of diet restriction at different life stages can have combined influences on the postovipositional duration of P. persimilis, where the individuals receiving diet restriction during immature development and early adulthood had a greater reduction in ovipositional duration as those experiencing diet restriction during late adulthood. In addition, we observed a positive correlation between the lifespan and fecundity of females, with higher prey availability increasing both. The insights obtained from our research contribute to a better understanding of the aging process and dietary requirements of P. persimilis, which can facilitate the development of more effective biological control strategies using this predator for spider mites in agriculture.