bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urinary CD163: an early biomarker of diabetic nephropathy in type 2 diabetes
Authors: Abo Hashish Tahany Ibrahim , Abdel Ghafar Muhammad Tarek , Eisa Abd Elmoteleb , Okda Hanaa 
Published: February 2025

Abstract

Objectives
This study aimed to evaluate the urinary level of soluble CD163 (sCD163) in patients with type 2 diabetes as a potential early indicator of diabetic nephropathy (DN).

Methods
This cross-sectional study included 60 type 2 diabetic patients and 20 healthy individuals. Patients were divided into three groups according to their albumin/creatinine ratio: normoalbuminuric, microalbuminuric, and macroalbuminuric groups. Urinary levels of sCD163 (usCD163) were measured using ELISA.

Results
The mean CD163 levels showed a significantly increasing trend from the patients without nephropathy to those with nephropathy. The multivariate logistic regression analysis revealed that CD163 was an independent risk factor for DN progression in patients with DM (p = 0.011). According to the ROC curve, at a cutoff value of CD163 > 510.2 pg/mL, the area under the curve was 0.88 for discriminating diabetic patients with DN from those without.

Conclusions
sCD163 can be used as a potential marker for prediction of DN in patients with type 2 diabetes.
Traumatic injury leads to ovarian cell death and reproductive disturbances in Drosophila melanogaster
Authors: Dixon Cameron T. , Yang Pamela , McCall Kimberly 
Published: February 2025

ABSTRACT
Traumatic injury (TI), or global blunt force trauma, can arise from many sources such as car crashes, sports and intimate partner violence. Effects from these injuries impact the whole organism and can lead to many different pathologies, such as inflammation, neurodegeneration, gut dysbiosis, and female reproductive detriments. Drosophila melanogaster has recently emerged as a powerful model to study traumatic injuries due to their high conservation of physiological effects post-trauma and the genetic toolset that they leverage. Previously, we reported female-specific reproductive deficits post mild TI in Drosophila. Here we investigate the effects of more severe trauma on females and found an increased retention of mature eggs and decrease in egg laying. Additionally, severe trauma led to an increase of midstage egg chamber death and formation of melanization, a known marker of immune activation. These studies provide a valuable invertebrate model to understand disturbances to female reproduction post-trauma.
The Impact of Wearable Device Use on Physical Activity Levels in Individuals with Cardiovascular Disease
Authors: Leung Willie , Tiralla Gillian 
Published: February 2025

ABSTRACT

Introduction
Cardiovascular disease (CVD) remains the leading cause of mortality globally despite being widely preventable. Such an epidemic calls for increased prevention efforts and awareness of the modifiable risk factors associated with CVD. Physical activity has the ability to prevent, manage, and treat CVD. With the increasingly popular use of wearable devices, such as fitness trackers, individuals are able to monitor physical activity and may benefit from the additional motivation the devices provide. This study aimed to assess the impact of wearable device use on physical activity levels among individuals with CVD using data from the 2017 Behavioral Risk Factors Surveillance System.

Methods
A cross-sectional secondary analysis was conducted on a sample of 419 individuals with CVD, categorized into wearable device users and non-users. Descriptive analyses, chi-square analysis, and logistic regressions were performed. Physical activity levels, including total minutes of physical activity per week, vigorous activity, and adherence to aerobic physical activity guidelines, were compared between groups.

Results
Regardless of wearable device use status, most individuals with CVD (68.62%; 95% confidence interval, 56.58%–79.18%) met aerobic physical activity guidelines. The analysis resulted in no significant differences in physical activity levels between wearable device users and non-users, with both groups showing similar rates of meeting aerobic physical activity guidelines (P > 0.05).

Conclusion
Wearable devices could have the potential to play a role in managing CVD by encouraging safe monitoring of physical activity. Further research is needed to explore the role of wearable devices in promoting sustained physical activity and addressing barriers specific to CVD populations.
375–395 nm UV generation in Zn-indiffused MgO-doped PPLN waveguides pumped by an Alexandrite laser
Authors: Tawy Goronwy , Palomar Davidson Noelia , Bannerman Rex H. , Churchill Glenn , Smith Peter G. R. , Gates James C. , Gawith Corin B. E. 
Published: February 2025

We present results of wide wavelength coverage in the ultra-violet (UV) from a Zn-indiffused MgO-doped periodically-poled lithium-niobate (PPLN) waveguide. A continuous tuning range of 375–395 nm is obtained via second-harmonic-generation (SHG) in Λ = 6.1 − 6.9 µm poled gratings using a single continuously tunable alexandrite pump laser. Detailed results of the waveguide modes are provided and are shown to match well with the theoretical model. A maximum UV power of 4.1 mW is obtained from 200 mW of throughput pump power from the third-order SHG interaction, providing a route toward a compact and rugged laser source across the 350–400 nm UV range.
Metabolite pathway alterations identified by magnetic resonance metabolomics in a proximal tubular epithelial cell line treated with TGF‐β1
Authors: Humphries Tyrone L. R. , Lee Soobin , Urquhart Aaron J. , Vesey David A. , Micallef Aaron S. , Winterford Clay , Kassianos Andrew J. , Galloway Graham J. , Francis Ross S. , Gobe Glenda C. 
Published: February 2025

AbstractTubulointerstitial fibrosis is a characteristic hallmark of chronic kidney disease (CKD). Metabolic perturbations in cellular energy metabolism contribute to the pathogenesis of CKD, but the chemical contributors remain unclear. The aim of this investigation was to use two dimensional 1H‐nuclear magnetic resonance (2D‐COSY) metabolomics to identify the chemical changes of kidney fibrogenesis. An in vitro transforming growth factor‐β1 (TGF‐β1)‐induced model of kidney fibrogenesis with human kidney‐2 (HK‐2) proximal tubular epithelial cells (PTEC) was used. The model was validated by assaying for various pro‐fibrotic molecules, using quantitative PCR and Western blotting. 2D‐COSY was performed on treated cells. Morphological and functional changes characteristic of tubulointerstitial fibrosis were confirmed in the model; expression of fibronectin, collagen type IV, smooth muscle actin, oxidative stress enzymes increased (p < 0.05). NMR metabolomics provided evidence of altered metabolite signatures associated with glycolysis and glutamine metabolism, with decreased myo‐inositol and choline, and metabolites of the oxidative phase of the pentose phosphate pathway with increased glucose and glucuronic acid. The altered PTEC cellular metabolism likely supports the rapid fibrogenic energy demands. These results, using 2D‐COSY metabolomics, support development of a biomarker panel of fibrosis detectable using clinical magnetic resonance spectroscopy to diagnose and manage CKD.
Research on the variation in the Shields curve of silt initiation
Authors: Qi Qinghui , Dong Peihua , Qu Hongling 
Published: February 2025

Abstract
The sediment particles on muddy coasts are relatively fine, and they are easy to move under the dynamic action of wave power, which can easily cause sedimentation problems in port channels. Therefore, the problem of silt initiation is a key issue for in-depth research in the development process of silt coast harbors. Based on a large amount of experimental data on silt initiation in silty coast conducted by predecessors, the relationship between the incipient Shields number and sediment parameters such as sediment particle size and sediment density was quantitatively analyzed. The explicit calculation formula of the incipient Shields number is established, and the modified distribution map of the incipient curve zone is drawn. The role of particle size and sediment density in sediment incipient motion was elucidated. The modified distribution map of the incipient motion curve was drawn, which promotes the application of the Shields curve in muddy coastal engineering.
Optimization of stirred animal cell bioreactor based on CFD-PBM
Authors: Wang Xuemin , Ma Benchi 
Published: February 2025

Abstract
Stirred bioreactor has been widely used in biopharmaceutical field, and it is particularly important to understand the culture environment of animal cells in stirred bioreactor. This study, utilizing Computational Fluid Dynamics (CFD) in conjunction with the Population Balance Model (PBM), explores the effect of various operational conditions and impeller combinations (downward-pumping elephant ear impeller (EED) combined with a concave disc turbine impeller (CBDT), dual downward-pumping elephant ear impellers (EED-EED), and a combination of downward-pumping (EED) and upward-pumping (EEU) elephant ear impellers) on bioreactor performance, with the goal of developing a stirred bioreactor suited for animal cell culture. The findings reveal that increasing the stirring rate significantly enhances fluid circulation within the bioreactor, leading to an increase in gas holdup. Enhanced stirring rate and aeration not only facilitate bubble dispersion but also result in a significantly higher gas holdup in the lower part of the bioreactor compared to the upper part. Moreover, higher stirring rate also lead to larger bubble diameters. At the highest stirring rate, the maximum hydrodynamic stress in the bioreactor reaches 16 Pa, while the Kolmogorov length scale is smaller at high stirring rate. The EED-EEU demonstrates effective gas dispersion with uniform bubble distribution and minimal hydrodynamic stress; the EED-EED combination, while offering the best bubble dispersion, is associated with larger bubble diameters and higher hydrodynamic stress.
Generalized Hermite process: Tempering, properties and applications
Authors: Araya Héctor 
Published: February 2025

Abstract
In this work, we introduce a new process by modifying the kernel in the time domain representation of the generalized Hermite process. This modification is constructed by means of multiplication of the kernel in the time definition of the process by an exponential tempering factor

λ
>
0

{\lambda>0}

such that this new process is well defined. Several properties of the process are studied.
Metalloporphyrin-mediated oxidative degradation of risperidone under mild conditions: an LC-MS/MS study
Authors: Subash Midhuna , Bijoy Rachel , Chorghade Mukund S. , Thorat Bhaskar N. 
Published: February 2025

Abstract
This study examines the oxidative breakdown of an antipsychotic drug risperidone utilizing a metalloporphyrin catalyst in a controlled, constrained amount of time and moderate reaction conditions. Analyzing products and tracking the oxidative degradation process using LC-MS/MS analysis gave precise information on the reaction products and defined structural changes. The study investigated the fragmentation patterns of risperidone’s oxidative breakdown products, delving into the mechanisms underlying each fragmentation pathway. Our work highlights the creation of site-specific metabolites. Risperidone-N-oxide was identified as a significant oxidative product along with minimal quantities of in vivo metabolite, 9-hydroxyrisperidone.
Eberconazole nitrate–loaded spanlastics: nanocarriers for topical delivery system
Authors: Haldankar Piyusha Pradip , Fernandes Adison , DCruz Cleona Elizabeth Mary , Kumar Lalit , Shirodkar Rupesh Kalidas 
Published: February 2025

Abstract
Eberconazole nitrate (EBN), a broad-spectrum imidazole antifungal agent, is widely used for the topical treatment of fungal mycoses. However, as a BCS class II drug, EBN faces problems such as poor skin permeability and low cutaneous bioavailability. To overcome these problems, a novel surfactant-based nanovesicular delivery system was developed. The aim of this study was to develop and evaluate a nanovesicular spanlastic gel loaded with EBN for sustained topical delivery and improved bioavailability. The EBN spanlastic vesicles were formulated using a modified ethanol injection method. Using a 2³ factorial design and Stat-Ease 360® software, eight formulations were evaluated to optimize particle size and entrapment efficiency. The vesicles exhibited nano size (93.5 nm – 368.6 nm) and high entrapment efficiency (94.14 % – 97.30 %). The optimized formulation had the smallest size and the highest entrapment efficiency. TEM analysis confirmed non-agglomerated circular vesicles. In vitro studies showed an enhanced drug release of 87.2 % within 8 h. The optimized spanlastic formulation was incorporated into a 1 wt% Carbopol 934 gel and tested for parameters such as viscosity, spreadability, drug content, skin irritation and in vitro release. Ex vivo permeation studies showed better drug release (97.3 %), higher flux (0.137 mg cm−2 h−1) and a higher permeability coefficient (0.0137) compared to conventional formulations. The results suggest that the nano spanlastic gel is a promising antifungal delivery system for EBN.
Los autos sacramentales de Calderón y la renovación de la escena española (1927-1939)
Authors: Adillo Rufo Sergio 
Published: February 2025

Este artículo analiza la puesta en escena de los autos sacramentales de Calderón entre 1927 y 1939, distinguiendo tres tendencias principales: los montajes arqueológicos, los espectáculos cercanos al lenguaje de la vanguardia y las obras de propaganda. El repaso a los grandes hitos de cada una de estas aproximaciones al género permitirá extraer conclusiones sobre los rápidos cambios de paradigma en el acercamiento a Calderón de los profesionales, del público y de los agentes del campo de poder.
Cervantes y Venecia: una nota a El licenciado Vidriera sobre las crónicas de Indias
Authors: J. Sáez Adrián 
Published: February 2025

El elogio cervantino a Venecia en El licenciado Vidrieraes una pequeña corografía que abarca una comparación con México, de acuerdo con una semejanza forjada en una cadena de crónicas de Indias. Así, el pasaje constituye un buen ejemplo del interés de Cervantes tanto por América como por su tradición historiográfica, al tiempo que también permite explicar la imagen ofrecida de la ciudad en contraste con otras negativas visiones coetáneas.
Ambientes vulnerables. Aportes conceptuales y definiciones para el análisis de la vulnerabilidad de los sistemas ambientales
Authors: Freitas Scaraffuni Gabriel , Achkar Borrás Marcel 
Published: February 2025

En las últimas décadas, los cambios producidos por las actividades humanas en los ecosistemas se han vuelto más evidentes, pues han causado procesos de degradación ambiental y social.Algunos análisis de esta situación atribuyen parte de la responsabilidad a las formas epistemológicas y teóricas de abordarlos, por lo que han sido propuestos varios modelos conceptuales alternativos. Por su parte, el concepto de vulnerabilidad ha sido utilizado para abordar cuestiones ambientales desde distintas construcciones teóricas y metodológicas, a causa de lo cual no existe un consenso sobre su definición o modelos para su aplicación. Si bien se ha avanzado en perspectivas que, desde el enfoque de sistemas, intentan modelar la vulnerabilidad de un territorio de forma integrada, aún permanecen limitaciones asociadas principalmente a las formas como se han buscado evaluar y representar las relaciones entre las partes que integran el sistema. Más allá de esto, el desarrollo de modelos de vulnerabilidad ofrece el potencial de superar miradas lineales de tipo intervención–impacto y permitir análisis sistémicos, lo cual lo convierte en un área con potencial para la innovación. El presente artículo tiene por objetivo proponer una definición conceptual de vulnerabilidad desde una perspectiva de sistemas ambientales, que permita modelar su variabilidad espacial y temporal. Este proceso implicará no solo reconocer la existencia de múltiples dimensiones y sus interrelaciones, sino, además, integrar elementos como las propiedades emergentes del sistema, la definición específica de la degradación de su funcionamiento y la existencia y consideración de procesos estocásticos, propio de los sistemas abiertos y dinámicos.
Desafíos y perspectivas de la situación ambiental en el Perú: el caso de los bosques
Authors: Dunin Borkowski Ana Sabogal 
Published: February 2025

El artículo revisa la política ambiental actual en relación con la situación de los bosques en el Perú. Se enlaza la situación actual con una revisión de la historia ambiental reciente y los enfoques de la conservación de los bosques en el Perú para, finalmente, orientar la discusión hacia las perspectivas y posibles soluciones para la conservación de los bosques.
Rapid in situ mutation detection in extracellular vesicle DNA
Authors: Rahman Md Mofizur , Wang Lixue , Chen Yundi , Rahman Md Motiar , Islam M Oli Al , Lee Luke P. , Wan Yuan 
Published: February 2025

Aim: A PCR- and sequencing-free mutation detection assay facilitates cancer diagnosis and reduces over-reliance on specialized equipment. This benefit was highlighted during the pandemic when high demand for viral nucleic acid testing often sidelined mutation analysis. This shift led to substantial challenges for patients on targeted therapy in tracking mutations. Here, we report a 30-min DNA mutation detection technique using Cas12a-loaded liposomes in a microplate reader, a fundamental laboratory tool.
Methods: CRISPR-Cas12a complex and fluorescence-quenching (FQ) probes are introduced into tumor-derived extracellular vesicles (EV) through membrane fusion. When CRISPR-RNA hybridizes with the DNA target, activated Cas12a can trans -cleave FQ probes, resulting in fluorescence signals for the quantification of DNA mutation.
Results: This method enables the detection of EGFR L858R mutation in EV DNA within 30 min. Laborious extraction, purification, and other preparation steps for EV DNA are eliminated. The need for advanced data processing is also dispensed with. In a cohort study involving 10 healthy donors and 30 patients with advanced non-small cell lung cancer (NSCLC), the assay achieved a sensitivity of 86.7%, a specificity of 90%, and an accuracy of 87.5%.
Conclusion: The limit of detection of our Cas12 assay was ~ 8 × 105 EVs, corresponding to a mutation allele frequency (MAF) of ~ 10%. The MAF in late-stage cancers varies widely but often falls within 5%-50%. Therefore, without amplification of targets, this Cas12 assay can detect mutations in patients with advanced lung cancer. Future advancements in multiplex and high-throughput mutation detection using this assay will streamline self-diagnosis and treatment monitoring at home.
Comparing macromolecular complexes - a fully automated benchmarking suite
Authors: Schwede Torsten , Studer Gabriel , Robin Xavier , Bienert Stefan , Durairaj Janani , Tauriello Gerardo 
Published: February 2025

Abstract

Protein structure prediction has a long history of benchmarking such as CASP, CAMEO and CAPRI. With the rise of AI-based methods for prediction of macromolecular complexes, benchmarking with large datasets and robust, automated scores to compare predictions against a reference has become essential. Also, the increasing size and complexity of experimentally determined reference structures by crystallography or cryo EM poses challenges for structure comparison methods. In this manuscript, we review the current state of the art in scoring methodologies, identify existing limitations, and present novel approaches for automated scoring of tertiary and quaternary structures, protein-protein interfaces, and protein-ligand complexes. Our methods are designed to scale efficiently, enabling the assessment of large, complex systems. All developments are available in the structure benchmarking framework of OpenStructure. OpenStructure is open source software and available for free at https://openstructure.org/.
Can linguists better understand DNA?
Authors: WANG LIANG 
Published: February 2025

Abstract

Multilingual transfer ability, which reflects how well models fine-tuned on one source language can be applied to other languages, has been well studied in multilingual pre-trained models. However, the existence of such capability transfer between natural language and gene sequences/languages remains under explored. This study addresses this gap by drawing inspiration from the sentence-pair classification task used for evaluating sentence similarity in natural language. We constructed two analogous tasks: DNA-pair classification(DNA sequence similarity) and DNA-protein-pair classification(gene coding determination). These tasks were designed to validate the transferability of capabilities from natural language to gene sequences. Even a small-scale pre-trained model like GPT-2-small, which was pre-trained on English, achieved an accuracy of 78% on the DNA-pair classification task after being fine-tuned on English sentence-pair classification data(XTREME PAWS-X). While training a BERT model on multilingual text, the precision reached 89%. On the more complex DNA-protein-pair classification task, however, the model's output was barely distinguishable from random output. Experimental validation has confirmed that the transfer of capabilities from natural language to biological language is unequivocally present. Building on this foundation, we have also investigated the impact of model parameter scale and pre-training on this capability transfer. We provide recommendations for facilitating the transfer of capabilities from natural language to genetic language, as well as new approaches for conducting biological research based on this capability. This study offers an intriguing new perspective on exploring the relationship between natural language and genetic language.
Machine Learning for Experimental Design of Ultrafast Electron Diffraction
Authors: Shaaban Mohammad , Krishnamoorthy Aravind , El-Borgi Sami 
Published: February 2025

Abstract

Ultrafast Electron Diffraction (UED) experiments can generate several gigabytes of data that must be manually processed and analyzed to extract insights into materials behavior at ultrafast timescales. The lack of real-time data analysis precents in situ tuning of experimental parameters toward desirable outcomes or away from sample damage. Here, we demonstrate that machine learning methods based on Convolutional Neural Networks (CNN) trained on synthetic UED data can perform real-time analysis of diffraction data to resolve dynamical processes in the material and identify signs of material damage. Convolutional Variational Autoencoder (VAE) models showed the ability to track structural phase transformation in a model material system through the time trajectory of UED images in the low-dimensional latent space. By mapping experimental conditions to distinct regions of the latent space, such models enable real-time steering of experimental parameters towards conditions that realize phase transformations or other desirable outcomes. These examples show the ability of machine learning (ML) to design self-correcting diffraction experiments to optimize the use of large-scale user facilities. These methods can readily be extended to other experimental characterization methods, including microscopy and spectroscopy.