bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrating aggression: spider males perform an unusual assessment strategy during contest displays
Authors: de Almeida João Gabriel Lacerda , Arnott Gareth , Peixoto Paulo Enrique Cardoso 
Published: April 2024

Abstract
A recurrent question in animal contests is whether individuals adopt a self or mutual assessment rule to decide to withdraw from a contest. However, many empirical studies fail to find conclusive support for one of these two possibilities. A possible explanation is that assessment strategies vary between individuals. In the contests of the orb-web spider Trichonephila clavipes, males perform a vibrational display on webs that may escalate to physical contact. Since all individuals perform the vibrational phase and only some of them escalate, we proposed 2 hypotheses: (1) all individuals perform mutual assessment during the vibrational phase, or (2) some individuals that do not escalate adopt self-assessment, while individuals that escalated adopt mutual assessment. To evaluate these hypotheses, we investigated the relationship between the duration of the vibrational phase and frontal leg length (a proxy of male fight capacity) of loser and winner males in contests that escalated and did not escalate to the physical contact phase. We found a non-significant relationship between duration and losers leg length for both contests that escalate and did not escalate. While we found a positive relationship between duration and winners leg length, particularly in contests that did not escalate. These results do not provide support for mutual assessment or for a mix of different assessment rules among individuals. We suggest that in T. clavipes, the dynamics of the vibrational phase may be explained by two different contest strategies (opponent-only assessment or size-based aggressiveness) that are dependent on intruder motivation to escalate.
IBPGNET: lung adenocarcinoma recurrence prediction based on neural network interpretability
Authors: Xu Zhanyu , Liao Haibo , Huang Liuliu , Chen Qingfeng , Lan Wei , Li Shikang 
Published: April 2024

Abstract
Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer. Early-stage patients have a 30–50% probability of metastatic recurrence after surgical treatment. Here, we propose a new computational framework, Interpretable Biological Pathway Graph Neural Networks (IBPGNET), based on pathway hierarchy relationships to predict LUAD recurrence and explore the internal regulatory mechanisms of LUAD. IBPGNET can integrate different omics data efficiently and provide global interpretability. In addition, our experimental results show that IBPGNET outperforms other classification methods in 5-fold cross-validation. IBPGNET identified PSMC1 and PSMD11 as genes associated with LUAD recurrence, and their expression levels were significantly higher in LUAD cells than in normal cells. The knockdown of PSMC1 and PSMD11 in LUAD cells increased their sensitivity to afatinib and decreased cell migration, invasion and proliferation. In addition, the cells showed significantly lower EGFR expression, indicating that PSMC1 and PSMD11 may mediate therapeutic sensitivity through EGFR expression.
SEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data
Authors: Huang Jinze , Zhao Yang , Meng Bo , Lu Ao , Wei Yaoguang , Dong Lianhua , Fang Xiang , An Dong , Dai Xinhua 
Published: April 2024

Abstract
Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without clear labels, their effectiveness might be compromised. Single models are susceptible to the randomness of parameters and initialization, which can result in a high rate of false positives. Ensemble models, on the other hand, have shown capabilities in effectively mitigating the impacts of such randomness and assisting in accurately detecting true outliers. Therefore, we introduced SEAOP, a Python toolbox that utilizes an ensemble mechanism by integrating multi-round data management and a statistics-based decision pipeline with multiple models. Specifically, SEAOP uses multi-round resampling to create diverse sub-data spaces and employs outlier detection methods to identify candidate outliers in each space. Candidates are then aggregated as confirmed outliers via a chi-square test, adhering to a 95% confidence level, to ensure the precision of the unsupervised approaches. Additionally, SEAOP introduces a visualization strategy, specifically designed to intuitively and effectively display the distribution of both outlier and non-outlier samples. Optimal hyperparameter models of SEAOP for outlier detection were identified by using a gradient-simulated standard dataset and Mann–Kendall trend test. The performance of the SEAOP toolbox was evaluated using three experimental datasets, confirming its reliability and accuracy in handling quantitative proteomics.
Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology
Authors: Arulraj Theinmozhi , Wang Hanwen , Ippolito Alberto , Zhang Shuming , Fertig Elana J , Popel Aleksander S 
Published: April 2024

Abstract
Understanding the intricate interactions of cancer cells with the tumor microenvironment (TME) is a pre-requisite for the optimization of immunotherapy. Mechanistic models such as quantitative systems pharmacology (QSP) provide insights into the TME dynamics and predict the efficacy of immunotherapy in virtual patient populations/digital twins but require vast amounts of multimodal data for parameterization. Large-scale datasets characterizing the TME are available due to recent advances in bioinformatics for multi-omics data. Here, we discuss the perspectives of leveraging omics-derived bioinformatics estimates to inform QSP models and circumvent the challenges of model calibration and validation in immuno-oncology.
PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data
Authors: Yu Chunjiang , Zong Hui , Chen Yalan , Zhou Yibin , Liu Xingyun , Lin Yuxin , Li Jiakun , Zheng Xiaonan , Min Hua , Shen Bairong 
Published: April 2024

Abstract
Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer (PCa), large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. A formal representation of PCa-associated knowledge will be essential to the diverse data standardization, data sharing and the future knowledge graph extraction, deep phenotyping and explainable artificial intelligence developing. In this study, we constructed an updated PCa ontology (PCAO2) based on the ontology development life cycle. An online information retrieval system was designed to ensure the usability of the ontology. The PCAO2 with a subclass-based taxonomic hierarchy covers the major biomedical concepts for PCa-associated genotypic, phenotypic and lifestyle data. The current version of the PCAO2 contains 633 concepts organized under three biomedical viewpoints, namely, epidemiology, diagnosis and treatment. These concepts are enriched by the addition of definition, synonym, relationship and reference. For the precision diagnosis and treatment, the PCa-associated genes and lifestyles are integrated in the viewpoint of epidemiological aspects of PCa. PCAO2 provides a standardized and systematized semantic framework for studying large amounts of heterogeneous PCa data and knowledge, which can be further, edited and enriched by the scientific community. The PCAO2 is freely available at https://bioportal.bioontology.org/ontologies/PCAO, http://pcaontology.net/ and http://pcaontology.net/mobile/.
Multilevel superposition for deciphering the conformational variability of protein ensembles
Authors: Amisaki Takashi 
Published: April 2024

AbstractThe dynamics and variability of protein conformations are directly linked to their functions. Many comparative studies of X-ray protein structures have been conducted to elucidate the relevant conformational changes, dynamics and heterogeneity. The rapid increase in the number of experimentally determined structures has made comparison an effective tool for investigating protein structures. For example, it is now possible to compare structural ensembles formed by enzyme species, variants or the type of ligands bound to them. In this study, the author developed a multilevel model for estimating two covariance matrices that represent inter- and intra-ensemble variability in the Cartesian coordinate space. Principal component analysis using the two estimated covariance matrices identified the inter-/intra-enzyme variabilities, which seemed to be important for the enzyme functions, with the illustrative examples of cytochrome P450 family 2 enzymes and class A $\beta$-lactamases. In P450, in which each enzyme has its own active site of a distinct size, an active-site motion shared universally between the enzymes was captured as the first principal mode of the intra-enzyme covariance matrix. In this case, the method was useful for understanding the conformational variability after adjusting for the differences between enzyme sizes. The developed method is advantageous in small ensemble-size problems and hence promising for use in comparative studies on experimentally determined structures where ensemble sizes are smaller than those generated, for example, by molecular dynamics simulations.
Brain and cognitive changes in patients with long COVID compared with infection-recovered control subjects
Authors: Serrano del Pueblo Víctor M , Serrano-Heras Gemma , Romero Sánchez Carlos M , Landete Pepa Piqueras , Rojas-Bartolome Laura , Feria Inmaculada , Morris Richard G M , Strange Bryan , Mansilla Francisco , Zhang Linda , Castro-Robles Beatriz , Arias-Salazar Lourdes , López-López Susana , Payá María , Segura Tomás , Muñoz-López Mónica 
Published: April 2024

Abstract
Between 2.5% and 28% of people infected with SARS-CoV-2 suffer long COVID or persistence of symptoms for months after acute illness. Many symptoms are neurological, but the brain changes underlying the neuropsychological impairments remain unclear. This study aimed to provide a detailed description of the cognitive profile, the pattern of brain alterations in long COVID and the potential association between them.
To address these objectives, 83 patients with persistent neurological symptoms after COVID-19 were recruited, and 22 now healthy control subjects chosen because they had suffered COVID-19 but did not experience persistent neurological symptoms. Patients and controls were matched for age, sex and educational level. All participants were assessed by clinical interview, comprehensive standardized neuropsychological tests and structural MRI.
The mean global cognitive function of patients with long COVID assessed by Addenbrooke’s Cognitive Examination-III screening test [overall cognitive level (OCLz) = −0.39 ± 0.12] was significantly below the infection recovered-controls (OCLz = +0.32 ± 0.16, P &lt; 0.01). We observed that 48% of patients with long COVID had episodic memory deficit, with 27% also with impaired overall cognitive function, especially attention, working memory, processing speed and verbal fluency. The MRI examination included grey matter morphometry and whole brain structural connectivity analysis. Compared to infection recovered controls, patients had thinner cortex in a specific cluster centred on the left posterior superior temporal gyrus. In addition, lower fractional anisotropy and higher radial diffusivity were observed in widespread areas of the patients’ cerebral white matter relative to these controls. Correlations between cognitive status and brain abnormalities revealed a relationship between altered connectivity of white matter regions and impairments of episodic memory, overall cognitive function, attention and verbal fluency.
This study shows that patients with neurological long COVID suffer brain changes, especially in several white matter areas, and these are associated with impairments of specific cognitive functions.
Flexibility of brain dynamics is increased and predicts clinical impairment in relapsing–remitting but not in secondary progressive multiple sclerosis
Authors: Cipriano Lorenzo , Minino Roberta , Liparoti Marianna , Polverino Arianna , Romano Antonella , Bonavita Simona , Pirozzi Maria Agnese , Quarantelli Mario , Jirsa Viktor , Sorrentino Giuseppe , Sorrentino Pierpaolo , Troisi Lopez Emahnuel 
Published: April 2024

Abstract
Large-scale brain activity has long been investigated under the erroneous assumption of stationarity. Nowadays, we know that resting-state functional connectivity is characterized by aperiodic, scale-free bursts of activity (i.e. neuronal avalanches) that intermittently recruit different brain regions. These different patterns of activity represent a measure of brain flexibility, whose reduction has been found to predict clinical impairment in multiple neurodegenerative diseases such as Parkinson’s disease, amyotrophic lateral sclerosis and Alzheimer’s disease. Brain flexibility has been recently found increased in multiple sclerosis, but its relationship with clinical disability remains elusive. Also, potential differences in brain dynamics according to the multiple sclerosis clinical phenotypes remain unexplored so far. We performed a brain dynamics study quantifying brain flexibility utilizing the ‘functional repertoire’ (i.e. the number of configurations of active brain areas) through source reconstruction of magnetoencephalography signals in a cohort of 25 multiple sclerosis patients (10 relapsing–remitting multiple sclerosis and 15 secondary progressive multiple sclerosis) and 25 healthy controls. Multiple sclerosis patients showed a greater number of unique reconfigurations at fast time scales as compared with healthy controls. This difference was mainly driven by the relapsing–remitting multiple sclerosis phenotype, whereas no significant differences in brain dynamics were found between secondary progressive multiple sclerosis and healthy controls. Brain flexibility also showed a different predictive power on clinical disability according to the multiple sclerosis type. For the first time, we investigated brain dynamics in multiple sclerosis patients through high temporal resolution techniques, unveiling differences in brain flexibility according to the multiple sclerosis phenotype and its relationship with clinical disability.
Diphenylanthracene-based amorphous molecular fluorophores for triplet–triplet annihilation upconversion system
Authors: Naemura Shungo , Matsui Ryoma , Matsumoto Ikumi , Iimori Toshifumi , Nakano Hideyuki 
Published: April 2024

Abstract
Novel diphenylanthracene-based amorphous molecular fluorophores have been designed and synthesized. They were found to exhibit fluorescence emission with fairly high quantum efficiencies both in solution, crystalline state, and amorphous state. Triplet–triplet annihilation upconversion emissions have been achieved not only in toluene solutions but also as amorphous solids using present novel fluorophores as acceptors combined with platinum(II) octaethylporphyrin as a donor.
Moderate salt restriction in primary aldosteronism improves bone metabolism through attenuation of urinary calcium and phosphate losses
Authors: Schneider Holger , Brüdgam Denise , Nowotny Hanna F , Schmidmaier Ralf , Reincke Martin , Adolf Christian 
Published: April 2024

Abstract
Accumulating evidence links osteoporosis and dietary salt consumption. Primary aldosteronism (PA) is a model disease with increased dietary salt intake and constitutes an independent risk factor for osteoporosis. We, thus, assessed whether a short-term moderate reduction in salt intake in PA results in detectable osteoanabolic effects. Forty-one patients with PA on stable mineralocorticoid receptor antagonist therapy were subjected to a 12-week salt restriction. Serum and urinary electrolytes, markers of bone turnover, and a 15 steroids plasma profile were registered. After 12 weeks, urinary calcium and phosphate decreased, while plasma testosterone, serum phosphate, and bone alkaline phosphatase (BAP) all increased significantly. Longitudinal changes in BAP were independently correlated with changes in serum phosphate, parathyroid hormone, and urinary calcium in multivariate analysis. Salt restriction in PA limits urinary calcium and phosphate losses and may confer favorable osteoanabolic effects. Our findings suggest that salt restriction should be considered in patients with PA to improve bone health.
Long-term reliability of the phospholamban (PLN) p.(Arg14del) risk model in predicting major ventricular arrhythmia: a landmark study
Authors: van der Heide Myrthe Y C , Verstraelen Tom E , van Lint Freyja H M , Bosman Laurens P , de Brouwer Remco , Proost Virginnio M , van Drie Esmée , Taha Karim , Zwinderman Aeilko H , Dickhoff Cathelijne , Schoonderwoerd Bas A , Germans Tjeerd , Houweling Arjan C , Gimeno-Blanes Juan R , van der Zwaag Paul A , de Boer Rudolf A , Cox Moniek G P J , van Tintelen J Peter , Wilde Arthur A M 
Published: April 2024

Abstract

Aims
Recently, a genetic variant-specific prediction model for phospholamban (PLN) p.(Arg14del)-positive individuals was developed to predict individual major ventricular arrhythmia (VA) risk to support decision-making for primary prevention implantable cardioverter defibrillator (ICD) implantation. This model predicts major VA risk from baseline data, but iterative evaluation of major VA risk may be warranted considering that the risk factors for major VA are progressive. Our aim is to evaluate the diagnostic performance of the PLN p.(Arg14del) risk model at 3-year follow-up.

Methods and results
We performed a landmark analysis 3 years after presentation and selected only patients with no prior major VA. Data were collected of 268 PLN p.(Arg14del)-positive subjects, aged 43.5 ± 16.3 years, 38.9% male. After the 3 years landmark, subjects had a mean follow-up of 4.0 years (± 3.5 years) and 28 (10%) subjects experienced major VA with an annual event rate of 2.6% [95% confidence interval (CI) 1.6–3.6], defined as sustained VA, appropriate ICD intervention, or (aborted) sudden cardiac death. The PLN p.(Arg14del) risk score yielded good discrimination in the 3 years landmark cohort with a C-statistic of 0.83 (95% CI 0.79–0.87) and calibration slope of 0.97.

Conclusion
The PLN p.(Arg14del) risk model has sustained good model performance up to 3 years follow-up in PLN p.(Arg14del)-positive subjects with no history of major VA. It may therefore be used to support decision-making for primary prevention ICD implantation not merely at presentation but also up to at least 3 years of follow-up.
Light conditions and the evolution of the visual system in birds
Authors: Fröhlich Arkadiusz , Ducatez Simon , Neˇmec Pavel , Sol Daniel 
Published: April 2024

Abstract
Despite vision being an essential sense for many animals, the intuitively appealing notion that the visual system has been shaped by environmental light conditions is backed by insufficient evidence. Based on a comprehensive phylogenetic comparative analysis of birds, we investigate if exposure to different light conditions might have triggered evolutionary divergence in the visual system through pressures on light sensitivity, visual acuity, and neural processing capacity. Our analyses suggest that birds that have adopted nocturnal habits evolved eyes with larger corneal diameters and, to a lesser extent, longer axial length than diurnal species. However, we found no evidence that sensing and processing organs were selected together, as observed in diurnal birds. Rather than enlarging the processing centers, we found a tendency among nocturnal species to either reduce or maintain the size of the two main brain centers involved in vision—the optic tectum and the wulst. These results suggest a mosaic pattern of evolution, wherein optimization of the eye optics for efficient light capture in nocturnal species may have compromised visual acuity and central processing capacity.
Sacred Space, Mourning and the War Dead in Protestant Germany, 1945–
Authors: Brodie Thomas 
Published: April 2024

Abstract
Using the Flensburg Memorial Dispute of 1967 as a microstudy, this article explores how Germany’s twentieth-century war dead have been represented within Protestant sacred space since 1945. It highlights the central role played by church spaces in the mourning and commemoration of Germany’s war dead and the tremendous difficulties accompanying attempts to redesign these iconographies in the later twentieth century in the face of popular sentiment.
Associations of Social Support With Physical and Mental Health Symptom Burden After COVID-19 Hospitalization Among Older Adults
Authors: Lee Seohyuk , McAvay Gail J , Geda Mary , Chattopadhyay Sumon , Acampora Denise , Araujo Katy , Charpentier Peter , Gill Thomas M , Hajduk Alexandra M , Cohen Andrew B , Ferrante Lauren E 
Published: April 2024

Abstract

Background
Despite significant support system disruptions during the coronavirus 2019 (COVID-19) pandemic, little is known about the relationship between social support and symptom burden among older adults following COVID-19 hospitalization.

Methods
From a prospective cohort of 341 community-living persons aged ≥60 years hospitalized with COVID-19 between June 2020 and June 2021 who underwent follow-up at 1, 3, and 6 months after discharge, we identified 311 participants with ≥1 follow-up assessment. Social support prehospitalization was ascertained using a 5-item version of the Medical Outcomes Study Social Support Survey (range, 5–25), with low social support defined as a score ≤15. At hospitalization and each follow-up assessment, 14 physical symptoms were assessed using a modified Edmonton Symptom Assessment System inclusive of COVID-19-relevant symptoms. Mental health symptoms were assessed using Patient Health Questionnaire-4. Longitudinal associations between social support and physical and mental health symptoms, respectively, were evaluated through multivariable regression.

Results
Participants’ mean age was 71.3 years (standard deviation, 8.5), 52.4% were female, and 34.2% were of Black race or Hispanic ethnicity. 11.8% reported low social support. Over the 6-month follow-up period, low social support was independently associated with higher burden of physical symptoms (adjusted rate ratio [aRR], 1.26; 95% confidence interval [CI], 1.05–1.52), but not mental health symptoms (aRR, 1.14; 95% CI, 0.85–1.53).

Conclusions
Low social support is associated with greater physical, but not mental health, symptom burden among older survivors of COVID-19 hospitalization. Our findings suggest a potential need for social support screening and interventions to improve post-COVID-19 symptom management in this vulnerable group.