bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the lemon (Citrus limon) epiphytic microbiome: impact of the biocontrol yeast Clavispora lusitaniae 146
Authors: Rasuk Maria Cecilia , Irazoqui José Matías , Perez María Florencia , Pereyra Martina María , Sineli Pedro Eugenio , Poehlein Anja , Daniel Rolf , Dib Julian Rafael 
Published: January 2025

Abstract

Background
Postharvest lemons are affected by several fungal infections, and as alternatives to chemical fungicides for combating these infections, different microbial biocontrol agents have been studied, with the Clavispora lusitaniae 146 strain standing out. Although strain 146 has proven to be an effective agent, the influence of a microbial biological control agent on the postharvest lemon microbiome has not been studied until now. Thus, this study aimed to evaluate how the epiphytic microbiome of postharvest lemons is affected by the application of the biocontrol yeast C. lusitaniae 146.

Results
In terms of bacterial composition, the most abundant genera were Sphingomonas, Pelomonas, and Bacillus and no significant differences in the composition were detected between the treated and control samples. Among fungi, Clavispora was predominant not only in the treated samples but also in the control, and statistics indicated differences, suggesting its significant role in modulating the epiphytic community composition of lemon. Understanding fruit microbiomes is vital for effective disease control, and this study provides insights into the microbial composition of the surface of lemon and the role of C. lusitaniae 146.
Validation of a hypomorphic variant in CDK13 as the cause of CHDFIDD with autosomal recessive inheritance through determination of an episignature
Authors: Fischer Jan , Alders Mariëlle , Mannens Marcel M. A. M. , Genevieve David , Hackmann Karl , Schröck Evelin , Sadikovic Bekim , Porrmann Joseph 
Published: January 2025

Abstract
Autosomal dominant CDK13-related disease is characterized by congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (CHDFIDD). Heterozygous pathogenic variants, particularly missense variants in the kinase domain, have previously been described as disease causing. Using the determination of a methylation pattern and comparison with an established episignature, we reveal the first hypomorphic variant in the kinase domain of CDK13, leading to a never before described autosomal recessive form of CHDFIDD in a boy with characteristic features. This highlights the utility of episignatures in variant interpretation, as well as a potential novel diagnostic approach in unsolved cases or for disease prognosis.
Time-varying intensity of ventilatory inefficiency and mortality in patients with acute respiratory distress syndrome
Authors: Jiang Lianlian , Chen Hui , Chang Wei , Sun Qin , Yuan Xueyan , Wu Zongsheng , Xie Jianfeng , Liu Ling , Yang Yi 
Published: January 2025

Abstract

Background
The association between bedside ventilatory parameters—specifically arterial carbon dioxide pressure (PaCO2) and ventilatory ratio (VR)—and mortality in patients with acute respiratory distress syndrome (ARDS) remains a topic of debate. Additionally, the persistence of this association over time is unclear. This study aims to investigate the relationship between 28-day mortality in ARDS patients and their longitudinal exposure to ventilatory inefficiency, as reflected by serial measurements of PaCO2 and VR.

Methods
We conducted a secondary analysis of four randomized controlled trials (FACTT, ALTA, EDEN, and SAILS) from the ARDS Network. All included patients were intubated and received mechanical ventilation. Patients were excluded if they underwent extracorporeal life support or were on mechanical ventilation for less than one day. The primary outcome was 28-day mortality. Bayesian joint models were employed to estimate the strength of associations over time.

Results
A total of 2,851 patients were included in our analysis. The overall 28-day mortality rate was 21.3%, with a median duration of invasive mechanical ventilation of 9 days (IQR: 4–28 days). After adjustment, each daily increment in PaCO2 (HR 1.008, 95% CI 0.997–1.018) was not associated with mortality, while a daily increment in VR (HR 1.548, 95% CI 1.309–1.835) was associated with increased mortality. This association persisted during the prolonged stages (Days 0–23) of mechanical ventilation. Furthermore, a significant increase in the risk of death was related to daily exposure to VR > 2 (HR 1.088 per day, 95% CI 1.034–1.147) and its cumulative effect (HR 1.085 per area, 95% CI 1.050–1.122), whereas PaCO2 was found to be insignificant.

Conclusion
VR, which reflects ventilatory inefficiency, should be closely monitored during invasive mechanical ventilation. Cumulative exposure to high intensities of VR may be associated with increased mortality in patients with ARDS.
In vitro and molecular docking evaluation of black sesame seeds' anti-prostate cancer and antioxidant activity processed by nine steaming nine drying
Authors: Magdamit Glennielyn D. , Hsieh Cheng-Yang , Lee Mon-Juan , De Castro-Cruz Kathlia A. , Austria Samantha Franchette B. , Sipat Beatrice D. , Huang Steven Kuan-Hua , Tsai Po-Wei 
Published: January 2025

Abstract
Black sesame seeds, known for their rich flavor and medicinal properties, hold significant potential as natural therapeutics against prostate cancer, a major health challenge for men today. This study explores the traditional processing technique of nine cycles of steaming and drying, which enhances the bioactive potential of these seeds. The impact of this processing on the antioxidant and anti-prostate cancer properties of black sesame seeds was systematically investigated, focusing on the key lignans, sesamin and sesamolin. HPLC was utilized to analyze the content ratios of sesamin and sesamolin, while DPPH and FRAP assays evaluated antioxidant capabilities, and MTT assays assessed anti-cancer properties against DU145 cells. Findings reveal that three cycles of steaming and drying significantly enhance antioxidant and anti-cancer activities against DU145, achieving peak concentrations of sesamin and sesamolin of 21.583% and 14.991%, respectively, with an optimal ratio of 1.4397:1. The superior antioxidant and anti-prostate cancer activity of this sample is attributed to optimal processing conditions that maximize the stability and extraction of bioactive compounds, particularly non-lignan antioxidants, while minimizing degradation; this is likely enhanced by the interplay between various phytochemicals and the effects of thermal processing on cellular structure. Processed seeds consistently outperformed raw seeds—except for those subjected to a single cycle. Additionally, molecular docking analyses revealed compelling interactions between sesamin and sesamolin and key proteins implicated in prostate cancer (FYN, ITGB3, PDGFRA, PDGFRB, and PIK3R1), demonstrating higher LibDock scores than the standard anti-cancer drug 5-fluorouracil. This research highlights the exceptional antioxidant and anti-cancer potential of black sesame seeds, particularly through the three-steaming and three-drying method, emphasizing the importance of the sesamin to sesamolin ratio in developing future anti-cancer therapeutics.
Recurrence of chronic encapsulated hematoma following cyst formation after stereotactic radiosurgery for brain arteriovenous malformations: a case report
Authors: Sistiaga Iñigo L. , Catalán-Uribarrena Gregorio , Gamba Silvia , Carrasco Alejandro , Zaldumbide Laura , Mosteiro Lorena , Pomposo Iñigo 
Published: January 2025

Abstract

Background
Delayed radiation-induced complications after stereotactic radiosurgery (SRS) for arteriovenous malformations (AVM) have scarcely been described in the literature, and their incidence, pathophysiology, and treatment remain unclear. Additionally, the literature regarding these complications is confusing. The authors present a well-documented case report describing these late complications, adding evidence to the possible common pathophysiological mechanism underlying them, and illustrating an effective treatment modality when they occur.

Case presentation
A case of a 28-year-old male with an increasing cyst formation (CF) appearing 10 years after SRS for AVM is presented. Despite surgical treatment, due to the incomplete resection of the angiomatous nodule, recurrence as a chronic encapsulated expanding hematoma (CEEH) occurred. This relapse required a second treatment, which could have been avoided if aggressive surgical treatment had been performed initially.

Conclusions
This case highlights the continuum between CF and CEEH, challenging existing confusion in the literature. Complete resection of the angiomatous nodule associated with CF is imperative for achieving resolution and preventing recurrence.
Automated characterisation of cerebral microbleeds using their size and spatial distribution on brain MRI
Authors: Sundaresan Vaanathi , Zamboni Giovanna , Dineen Robert A. , Auer Dorothee P. , Sotiropoulos Stamatios N. , Sprigg Nikola , Jenkinson Mark , Griffanti Ludovica 
Published: January 2025

Abstract
Cerebral microbleeds (CMBs) are small, hypointense hemosiderin deposits in the brain measuring 2–10 mm in diameter. As one of the important biomarkers of small vessel disease, they have been associated with various neurodegenerative and cerebrovascular diseases. Hence, automated detection, and subsequent extraction of clinically useful metrics (e.g., size and spatial distribution) from CMBs are essential for investigating their clinical impact, especially in large-scale studies. While some work has been done for CMB segmentation, extraction of clinically relevant information is not yet explored. Herein, we propose the first automated method to characterise CMBs using their size and spatial distribution, i.e., CMB count in three regions (and their substructures) used in Microbleed Anatomical Rating Scale (MARS): infratentorial, deep, and lobar. Our method uses structural atlases of the brain for determining individual regions. On an intracerebral haemorrhage study dataset, we achieved a mean absolute error of 2.5 mm for size estimation and an overall accuracy > 90% for automated rating. The code and the atlas of MARS regions in Montreal Neurological Institute—MNI space are publicly available.

Relevance statement
Our method to automatically characterise cerebral microbleeds (size and location) showed a mean absolute error of 2.5 mm for size estimation and an over 90% accuracy for rating of infratentorial, deep and lobar regions. This is a promising approach to automatically provide clinically relevant cerebral microbleeds metrics.

Key Points

We present a method to automatically characterise cerebral microbleeds according to size and location.

The method achieved a mean absolute error of 2.5 mm for size estimation.

Automated rating for infratentorial, deep, and lobar regions achieved an over 90% overall accuracy.

We made the code and atlas of Microbleed Anatomical Rating Scale regions publicly available.

Graphical Abstract
Joint approximate diagonalization technique for modal identification of the Donghai Bridge
Authors: Li Ben , Chen Lin , Nagarajaiah Satish , Sun Limin 
Published: January 2025

Abstract
The second-order blind identification (SOBI) and its variants have been extensively explored for output-only modal identification of civil structures under varied excitations. At the core of these methods is the matrix joint approximate diagonalization (JAD) technique, while their efficiency and accuracy are largely determined by how the target-matrices for JAD are constructed from multi-channel structural responses. This study first formulates the JAD framework for structural identification, where different techniques in formulating the target-matrices are summarized and mathematical tools to conduct JAD are also presented. Then two novel ways stemming from conventional identification methods are presented as alternatives to construct the target-matrices for ambient identification, to maintain a low-order formulation and even avoiding the formation of covariance matrix. Subsequently, in view of the large number of candidate target-matrices which are analytically usable, a guiding principle is proposed for selecting reliable target-matrices, where the closeness of the eigenvectors of the target-matrices are compared beforehand, therefore eliminating of distorted target-matrices and also improving the efficiency of the subsequent JAD. The proposed techniques are applied to modal identification of the Donghai Bridge from monitoring data and the proposed JAD-based methods are compared in this context. The results suggest the effectiveness of the proposed techniques and also provide a performance evaluation of these methods.
A cardiac transcriptional enhancer is repurposed during regeneration to activate an anti-proliferative program
Authors: Rao Anupama , Russell Andrew , Segura-Bermudez Jose , Franz Charles , Dockery Rejenae , Blatnik Anton , Panten Jacob , Zevallos Mateo , McNulty Carson , Pietrzak Maciej , Goldman Joseph Aaron 
Published: January 2025

ABSTRACT
Zebrafish have a high capacity to regenerate their hearts. Several studies have surveyed transcriptional enhancers to understand how gene expression is controlled during heart regeneration. We have identified REN (the runx1 enhancer) that, during regeneration, regulates the expression of the nearby runx1 gene. We show that runx1 mRNA is reduced with deletion of REN (ΔREN), and cardiomyocyte proliferation is enhanced in ΔREN mutants only during regeneration. Interestingly, in uninjured hearts, ΔREN mutants have reduced expression of adamts1, a nearby gene that encodes a Collagen protease. This results in excess Collagen within cardiac valves of uninjured hearts. The ΔREN Collagen phenotype is rescued by an allele with Δrunx1 mutations, suggesting that in uninjured hearts REN regulates adamts1 independently of runx1. Taken together, this suggests that REN is rewired from adamts1 in uninjured hearts to stimulate runx1 transcription during regeneration. Our data point to a previously unappreciated mechanism for gene regulation during zebrafish heart regeneration. We report that an enhancer is rewired from expression in a distal cardiac domain to activate a different gene in regenerating tissue.
ChatGPT for Textual Analysis? How to Use Generative LLMs in Accounting Research
Authors: de Kok Ties 
Published: January 2025

Generative large language models (GLLMs), such as ChatGPT and GPT-4 by OpenAI, are emerging as powerful tools for textual analysis tasks in accounting research. GLLMs can solve any textual analysis task solvable using nongenerative methods as well as tasks previously only solvable using human coding. Whereas GLLMs are new and powerful, they also come with limitations and present new challenges that require care and due diligence. This paper highlights the applications of GLLMs for accounting research and compares them with existing methods. It also provides a framework on how to effectively use GLLMs by addressing key considerations, such as model selection, prompt engineering, and ensuring construct validity. In a case study, I demonstrate the capabilities of GLLMs by detecting nonanswers in earnings conference calls, a traditionally challenging task to automate. The new GPT method achieves an accuracy of 96% and reduces the nonanswer error rate by 70% relative to the existing Gow et al. (2021) method. Finally, I discuss the importance of addressing bias, replicability, and data sharing concerns when using GLLMs. Taken together, this paper provides researchers, reviewers, and editors with the knowledge and tools to effectively use and evaluate GLLMs for academic research. This paper was accepted by Eric So, accounting. Funding: Supported by the Foster School of Business – University of Washington. Supplemental Material: The online appendix and data files are available at https://doi.org/10.1287/mnsc.2023.03253 .
Educação da Inteligência e da Vontade na Psicologia do Educador Padre Leonel Franca S.J
Authors: Assis Raquel Martins , Massimi Marina 
Published: January 2025

O artigo apresenta pesquisa em História da Psicologia, que analisa relações entre inteligência e vontade na estrutura e funcionamento psicológico do ser humano elaboradas no universo cultural da Companhia de Jesus e sistematizadas pelo jesuíta brasileiro Padre Leonel Franca (1893-1948). Verifica-se em que medida as conceituações sobre Psicologia revelam aspectos de continuidades ou de descontinuidades com as ciências da alma desenvolvidas pela Companhia, principalmente nos Tratados dos Conimbricenses. Foram utilizados os conceitos de intelectual mediador, segundo Gomes e Hansen, e de tradição de pertença elaborado por Massimi. As fontes analisadas foram livros e conferências de Leonel Franca. Evidenciou-se aspectos de continuidade com a Antiga Companhia de Jesus por meio da adoção da matriz aristotélico-tomista. Essa matriz é associada à apropriação de estudos da Pedagogia e da Psicologia da época.
Design considerations of highly sensitive dual resonance metasurface grating biosensor
Authors: Shafaay Amira , Ghanim Abdelrahman M. , Swillam Mohamed A. 
Published: January 2025

This study introduces a highly responsive surface plasmon resonance (SPR) optical sensor and an all-dielectric metasurface for monitoring water salinity and glucose levels in blood. We present optimized low-cost microfluidic sensors capable of measuring water salinity (0%–40%, refractive index 1.333–1.341) and successfully detecting glucose solutions (5%–50%, refractive index 1.32–1.41). The metasurface of both structures, designed for high sensitivity, is proposed and numerically simulated in the visible and near-infrared spectral ranges. The SPR sensor consists of a multilayer grating made of Si3N4 and Al2O3 placed on a silver layer, with a SiO2 substrate. To reduce fabrication costs, the Si3N4 layer was replaced with silicon, and the plasmonic layer was eliminated. The sensor was optimized for sensitivity and accuracy using finite difference time domain simulations via Lumerical software. For water salinity detection, both plasmonic and all-dielectric sensors achieved a maximum sensitivity of 167 nm/RIU and 459 nm/RIU, respectively. The sensors also accurately detected sugar concentrations, with maximum sensitivities of about 157 nm/RIU and 542 nm/RIU for the SPR and all-dielectric structures, respectively.
High-resolution long-distance depth imaging LiDAR with ultra-low timing jitter superconducting nanowire single-photon detectors
Authors: McCarthy Aongus , Taylor Gregor G. , Garcia-Armenta Jorge , Korzh Boris , Morozov Dmitry V. , Beyer Andrew D. , Briggs Ryan M. , Allmaras Jason P. , Bumble Bruce , Colangelo Marco , Zhu Di , Berggren Karl K. , Shaw Matthew D. , Hadfield Robert H. , Buller Gerald S. 
Published: January 2025

Single-photon time-of-flight light detection and ranging (LiDAR) is a versatile technique for the measurement of absolute distances and for depth profiling. It has a wide variety of applications (e.g., land surveying, autonomous car navigation, underwater imaging) with the potential to achieve high-resolution three-dimensional images over long ranges when the key components of the measurement system are of a suitably high specification. In this work, a novel, high-efficiency, and low timing jitter superconducting nanowire single-photon detector, in conjunction with a custom single-pixel scanning transceiver system, and the time-correlated single-photon counting technique, enable the acquisition of millimeter-scale resolution depth images of scenes at standoff distances of hundreds of meters. A 1550 nm wavelength fiber laser was coupled to the monostatic transceiver to provide the illumination. The system was eye-safe with the maximum average optical output power being ≤3.5mW for measurements of a scene at a standoff distance of 1 km. The overall system instrumental response was approximately 13 ps full width half maximum. This enabled 1 mm depth features on a reference board and a human head to be clearly resolved when measured by the system in broad daylight at standoff distances of 45 and 325 m using per-pixel acquisition times of between 0.25 and 1 ms. These high-resolution results demonstrate the enormous potential of such a system to acquire detailed depth and intensity images of scenes from long distances in daylight or darkness conditions. This could lead to step change improvements in applications such as facial and human activity recognition and the imaging of scenes through clutter and atmospheric obscurants.
Interrogating the ballistic regime in liquids with rotational optical tweezers
Authors: Watson Mark L. , Stilgoe Alexander B. , Favre-Bulle Itia A. , Rubinsztein-Dunlop Halina 
Published: January 2025

Accessing the ballistic regime of single particles in liquids remains an experimental challenge that shrouds our understanding of particle–liquid interactions on exceedingly short time scales. We demonstrate rotational ballistic measurements of microspheres in liquids by observing the thermalization of the angular velocity. This study uses sensitive high-bandwidth polarization measurements from light scattered by orientation-locked birefringent probes trapped with rotational optical tweezers. The particle–liquid interactions in the ballistic regime are decoupled from the optical potential allowing direct studies of single-particle rotational dynamics in a previously inaccessible parameter space. This enabled us to observe and validate rotational hydrodynamic effects and perform ultrafast calibration-free viscometry using less than 50 ms of data. This methodology establishes a unique tool for studying microscopic rotational dynamics and probing highly dynamic microenvironments, including systems out of equilibrium.