bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurovirulent and non-neurovirulent strains of HIV-1 and their Tat proteins induce differential cytokine-chemokine profiles
Authors: Rao Vasudev R. , Rodriguez Milka , Byrareddy Siddappa N. , Ranga Udaykumar , Prasad Vinayaka R. 
Published: February 2025

Abstract

Objectives
HIV-1 enters the central nervous system (CNS) early in infection, and a significant proportion of people with HIV experience CNS complications despite anti-retroviral therapy. Chronic immune dysfunction, inflammatory cytokines and chemokines, and viral proteins like Tat and gp120 released by HIV-1-infected immune cells are implicated in the pathogenesis of HIV-1-associated neurocognitive disorders (HAND).

Methods
To elucidate the contribution of non-viral factors to CNS complications in people with HIV-1, a comparative analysis of neurovirulent subtype B (HIV-1ADA) and non-neurovirulent subtype C (HIV-1Indie-C1) isolates was performed. Culture supernatants from HIV-1-infected PBMCs, either with or without immunodepletion of Tat and gp120, were used to treat SH-SY5Y neuroblastoma cells.

Results
HIV-1ADA-infected PBMC media showed significantly higher neurotoxicity than HIV-1IndieC1-infected PBMC media, notwithstanding the depletion of Tat and gp120, highlighting the role of non-viral factors (e.g., cytokines) contributing to neurotoxicity. A comparison of inflammatory profiles revealed that HIV-1ADA media contained elevated levels of cytokines (IL-1α, IL-1β, IL-6 and TNFα) and chemokines (CCL2, CCL3, CCL4 and IP-10). Given the involvement of Tat in upregulating immune mediators, we tested the role of purified Tat proteins from HIV-1 subtypes B and C in inducing an inflammatory phenotype in PBMCs. PBMCs from healthy subjects were treated with recombinant purified Tat from subtype B or C. Subtype B Tat induced a stronger inflammatory response than subtype C Tat.

Conclusions
These results confirm that both viral and non-viral immune factors mediate neuronal damage in people with HIV.
The Institutional Role of Charity Regulators in Bringing Charities to Account: An International Comparative Study of Charity Regulators in New Zealand, Australia, Canada and England and Wales
Authors: Dimitrov Dara 
Published: February 2025

Abstract
Accountability in the charity sector continues to be important, especially since charity numbers continue to grow regardless of the economic cycle. Charity regulators play a critical role in managing the charity sector as its primary task is ensuring compliance with the regulatory framework. However, it is also important to evaluate whether the practices and procedures of charity regulators are effective within the broader context of charity accountability. This paper aims to explore charity accountability from the perspective of charity regulators. In common law countries, the charity regulator has oversight over the charity sector and, therefore, has the opportunity to enhance charity accountability. Through the lens of institutional theory, this paper provides an international comparative study of New Zealand, Australia, Canada and England and Wales, all of which share a common law heritage. This study demonstrates how the state regulators in each country have applied different mechanisms of charity accountability by institutionalising the norms and standards required from charities. By identifying and comparing the countries, this paper reveals whether some institutional practices by some regulators have been more effective than others in bringing charities to account.
Experimental study of mortar incorporating nano-magnetite on engineering performance and radiation shielding
Authors: Kunchariyakun Kittipong , Sinyoung Suthatip , MacKenzie Kenneth J. D. , Pungkun Vithit , Raknarong Pakkamai , Teh Musofpar , Jekabaso Afham , Sittichan Narumol 
Published: February 2025

Abstract
Here, this study reports the effect of nano-magnetite (nano-Fe3O4) on the γ and neutron-radiation shielding properties of mortar using 1–10 wt% additions of nano-Fe3O4. The results indicate that nano-Fe3O4 additions enhance the radiation-shielding properties of the mortar as a result of pore filling and nucleation effects. The mortar incorporating nano-Fe3O4 exhibited relatively high compressive strength values at 28 and 90 days compared to the control mixture (NFC0). A 5 wt% addition of nano-Fe3O4 provided the best physical (1,847 ± 19.1 kg m−3), compressive strength (216.79 ± 6.19 ksc at 28 days), and radiation shielding properties, increasing the photon linear attenuation coefficient to 0.155 cm−1 from 0.144 cm−1 in the material without nano-Fe3O4. This 5 wt% addition of nano-Fe3O4 also increased fast neutron removal cross-section (ΣR) of neutrons from 0.1109 cm−1 in the control sample to 0.1192 cm−1. These results indicate that the addition of nano-Fe3O4 to radiation-shielding mortar can potentially attenuate gamma rays rather than neutrons and lead to the development of materials for shielding radiation from radioactive storage facilities, thereby reducing the impact of this hazardous waste on humans and the environment.
The evaluation of the relationship between anti angiotensin type I antibodies in hypertensive patients undergoing kidney transplantation
Authors: Senturk Ciftci Hayriye , Eksioglu Demiralp Emel , Gorcin Serpil , Kivanc Demet , Yalcin Funda , Turkmen Aydın , Savran Oguz Fatma 
Published: February 2025

Abstract

Objectives
We aimed to compare the anti-angiotensin II type I receptor (AT1R) antibody levels considering the development of anti-HLA antibodies after transplantation, pathologically confirmed humoral or vascular rejection reactions and late complications.

Methods
Forty-nine hypertensive patients who had presented to the Division of Nephrology, Transplantation Outpatient Clinic of Memorial Health Group Hospitals Transplant Units and Istanbul Medical Faculty for live kidney transplantation and underwent transplantation between 2015 and 2019, were included in our study. Among our patients (29 males/20 females), 76 % had primary hypertension, and 24 % had secondary hypertension. In this study, serum AT1R antibody levels before and after transplantation were measured using the Enzyme-Linked ImmunoSorbent Assay (ELISA) method. The anti-HLA antibody was detected with the Luminex method using the single antigen bead (SAB) assay.

Results
The AT1R antibody was found positive in 7 (18.9 %) of 37 patients who had primary hypertension and in 4 (33.3 %) of 12 patients who had secondary hypertension (p=0.426). The examination of the frequencies of development of post-transplant anti-HLA antibodies showed that the frequency of AT1R antibody positivity was found higher in the group with positive anti-HLA antibodies compared to the levels in the group with negative anti-HLA antibodies (p=0.002). The comparison of the pre-transplant and post-transplant values showed that the AT1R antibody level was statistically significantly decreased after transplantation [7.3/6.6 (3.2–21.1) vs. 6.2/4.7 (1.5–24.5), p=0.001].

Conclusions
The findings of our study suggest that the evaluation of the AT1R antibody levels among non-HLA antibodies may be important for predicting the immunological risk before transplantation.
Propuestas de intervención para la disminución de la violencia psicológica en el contexto escolar: una revisión bibliográfica
Authors: Herrera Navas Cristopher David , López Rodríguez Yanelin , Del Pino Calderón Jorge Luis 
Published: February 2025

La violencia psicológica en el ámbito escolar se ha extendido como una de las principales problemáticas educativas que transversaliza horizontalmente todas las formas de violencia existentes, esto la ha posicionado como un fenómeno cultural, multicausal y de interés común. El propósito de esta investigación fue analizar las propuestas de intervención que aparecen documentadas para la disminución de la violencia psicológica en contextos educativos. Como metodología, se emplea un paradigma interpretativo de tipología documental para generar una revisión bibliográfica a través del protocolo PRISMA. Como resultados, se analizan 15 propuestas generadas para la prevención de violencia psicológica, resaltando sus objetivos, contextos, muestras, principales resultados y conclusiones. Se concluye que la mayoría de propuestas de intervención para el abordaje de la violencia psicológica en contextos educativos coinciden en la consideración de ciertos componentes específicos para su desarrollo, tales como: 1) el nivel de comprensión del problema específico; 2) la transversalización curricular de la propuesta; 3) la evaluación y monitoreo permanente; 4) la participación asertiva de la comunidad educativa; 5) la actitud de perfeccionamiento de la comunidad educativa en materia socio-emocional; 6) la cultura de intervención social de la comunidad para la búsqueda del bien común; la sostenibilidad; y 7) la sostenibilidad de la intervención a largo plazo. Por lo tanto, se podría decir que la prevención de la violencia psicológica demanda un cambio cultural, integral, continuo, permanente e integrador.
Chemical Quality of Irrigation Waters in Hamilton, Kearny, Finney, and Northern Gray Counties
Authors: Hathaway L.R. , Carr B.L. , Galle O.K. , Magnuson L.M. , Waugh T.C. , Dickey H.P. 
Published: February 2025

One-hundred-ninety-nine pumping irrigation wells were sampled in Hamilton, Kearny, Finney, and northern Gray counties and adjoining portions of Wichita, Scott, Grant, Stanton, and Haskell counties during late July 1975. Saline water of a SO4 type is found in the western three-fourths of the Arkansas River valley and a zone north of the river in Finney County. A better quality water of a Ca-HCO3 type exists in the sandy regions south of the river. Localized variations exist in the Scott-Finney Depression area.
Compiled chemical quality data and chemical quality maps are presented for the study area.
Factors influencing the development of speaking skills among Ecuadorian EFL learners: Teachers’ perspectives
Authors: Alvarez Carlos Lenin , Tamayo Monica R. , Santos Jardel Coutinho dos 
Published: February 2025

Secondary school students in Ecuador face significant challenges in developing English speaking skills, which are crucial for effective communication. This study explores the factors affecting the development of speaking skills and identifies teachers’ suggestions for addressing these challenges. The literature indicates factors on performance, methodology, linguistics, affective, and contextual factors. Employing an explanatory sequential mixed-method design, quantitative data were first collected through a survey of 142 EFL experienced teachers across various Ecuadorian regions, followed by qualitative insights from semi-structured interviews with seven experienced teachers. Findings reveal that large class sizes, limited instructional time, and insufficient speaking-focused activities in course materials impede effective practice. Methodological issues, such as inadequate English exposure outside the classroom, further hinder proficiency. Linguistic challenges include reliance on native language and pronunciation difficulties, while affective factors like anxiety and low confidence also impact students' speaking willingness. Recommendations include reducing class sizes, increasing instructional time, and including more speaking activities in curricula. These recommendations are not just theoretical but practical and feasible, emphasizing their potential impact on students' oral proficiency. Emphasis is also placed on fostering a supportive classroom environment, enhancing teacher professional development, and integrating authentic language use into lessons. These findings have broader implications for EFL education globally, highlighting the need for curriculum reforms, improved classroom management, and targeted teacher training. The study provides valuable insights into the complexities of teaching and learning speaking skills and offers practical recommendations for enhancing students' oral proficiency.
On Rainbow Vertex Antimagic Coloring of Related Prism Graphs and Its Operations
Authors: Prihandini Rafiantika , Wulandari Evi Tri , Dafik  , Kristiana Arika Indah , Adawiyah Robiatul , Alfarisi Ridho 
Published: February 2025

Let $G=(V,E)$ be a simple, connected and un-directed graph, for $f:E(G)\rightarrow\{1,2,\dots, |E(G)|\}$, the weight of a vertex $v\in V(G)$ under $f$ is $w_f(v)=\Sigma_{e \in E(v)} f(e)$, where $E(v)$ is the set of vertices incident to $v$. The function $f$ is called vertex antimagic edge labeling if every vertex has distinct weight. While, rainbow vertex coloring is a coloring of graph vertices where each vertex on the graph is connected by a path that all internal vertices on the $u-v$ path have different colors. We introduce a new notion, namely a rainbow vertex antimagic coloring, which is a combination of antimagic labeling and rainbow vertex coloring. The rainbow vertex antimagic connection number of $G$, denoted by $rvac(G)$, is the smallest number of colors taken over all rainbow colorings induced by rainbow vertex antimagic labelings of $G$. In this paper we aim to discover some new lemmas or theorems regarding to $rvac(G)$.
Prediction and History Matching of Observed Production Rate and Bottomhole Pressure Data Sets from In-Situ Crosslinked Polymer Gel Conformance Treatments Using Machine Learning Methods
Authors: Chen Yuhao , Onur Mustafa , Kuzu Nihal , Narin Onur 
Published: February 2025

Summary
We present a computationally efficient methodology based on the use of machine learning (ML) for predicting and history matching oil rate, water rate, and injection bottomhole pressure (BHP) data recorded during an in-situ polymer gel treatment. Using this methodology, we can estimate rock/fluid parameters affecting the in-situ gel process that impact reservoir conformance. The use of two ML methods is investigated for this purpose. One of the ML methods used is the least-squares support vector regression (LS-SVR), a kernel-based ML method, and the other is the long short-term memory (LSTM) network, a deep learning method. The LS-SVR and LSTM proxy models are built on training sets of BHP and rate data generated with a commercial high-fidelity reservoir simulator (HFRS) based on compositional flow simulation using a double-permeability model. The reservoir models are calibrated using synthetically generated, random noise added BHP, oil, and/or water production rate data sets with small and large window sizes before and after polymer gel treatment. The ensemble smoother with multiple data assimilation (ES-MDA) is used for history matching the observed well outputs and assessing the uncertainty in the estimated parameters. When a compositional HFRS is replaced with any of the ML-based methods for performing history matching, we show that the LS-SVR and LSTM methods provide significant computational savings (more than an order of magnitude) in history matching including their training times over the conventional history matching based on a direct use of an HFRS. LSTM provides better predictions than LS-SVR for the same sizes of training sets and observed well outputs. However, for larger training sets, LSTM provides a significant computational gain over LS-SVR if clustering is not used for training LS-SVR surrogates for well outputs. In addition, we also identify the key parameters that have a significant impact on the performance of in-situ polymer gel treatment. The relative permeability curves of oil and water, absolute fracture permeability, polymer and crosslinked concentrations, and residual resistance factors (RRFTs) are the key parameters in the performance of in-situ polymer gel treatment. Although we have shown the application of our proposed methodology for a simple synthetic compositional reservoir model, the methodology is general in that it can be used for a real field case in a similar way for generating computationally efficient history-matched LS-SVR and LSTM surrogates that can be used to perform computationally efficient reservoir robust production optimization for in-situ gel operation.
Thermodynamic Characteristics and Impact Mechanisms of Core Barrels in Pressure-Preserved Coring Retrieval
Authors: Lin Tiejun , Yu Chengxiu , Zeng Dezhi , Sun Shaoliang , Su Yang , Han Hao , Shen Ruiqi , Zhu Zelin , Zhang Caigong , Xiao Huan 
Published: February 2025

Summary
During pressure-preserved coring (PPC) retrieval, the core barrel’s pressure preservation performance is crucial for accurately assessing deep oil and gas resources. By accounting for the thermodynamic properties of the core, drilling fluid, and the variation in the core barrel’s working volume, we developed a thermodynamic model to predict temperature and pressure changes and to investigate the variation of thermodynamic parameters within the core barrel. A digital solution framework for the model was established using a fully implicit difference algorithm. Introducing the pressure preservation performance coefficient allowed us to evaluate the influence of key parameters—such as core length, drilling fluid density, and the core barrel’s height/diameter ratio—on pressure preservation. The model accurately predicts the thermal evolution during core retrieval and assesses the core barrel’s pressure preservation performance. Model predictions showed a relative error of less than 2.79% compared with laboratory measurements and less than 4.03% compared with field-collected data. During coring, the volumes of the core, drilling fluid, and core barrel increased by maximum values of 0.21%, 1.95%, and 1.00%, respectively. When ambient temperatures were high, adjusting the core length could improve pressure preservation. Given that various parameters affect core barrel design, it is recommended to increase the drilling fluid density, increase the height/diameter ratio of the core barrel, and keep the core barrel’s working volume below 20 L.
Plastome phylogenomics of the Diverse Neotropical Orchid Genus Lepanthes with Emphasis on Subgenus Marsipanthes (Pleurothallidinae: Orchidaceae)
Authors: Arias Tatiana , Moreno Juan Sebastian , Reyes Sebastian , Almario Martin Llano , Serna-Sánchez Alejandra , Iturralde Gabriel A. , Valencia Janice , Baquero Luis , Zuluaga Alejandro 
Published: February 2025

Abstract

The first successful resolution of phylogenetic relationships within main lineages in the diverse Neotropical orchid genus Lepanthes Sw. is presented here. Genome skimming produced ten newly sequenced chloroplast genomes, with additional plastome coding genes (17–86) retrieved from GenBank, alongside 26 amplified matK and rITS genes, enabling phylogenetic reconstruction. The Lepanthes plastomes (157,185 − 158,260 bp, 37.15% GC content) contained 136 annotated genes, including 86 protein-coding, 42 tRNA, and 8 rRNA genes. Six hypervariable regions, including parts of the ycf1 gene, were identified as potential DNA barcodes. Phylogenetic analyses revealed that Carl Luer’s subgeneric classifications are non-monophyletic, reflecting significant morphological homoplasy. PCA and correlation analyses confirmed widespread homoplasy in continuous morphological characters. Six major clades were identified, though backbone resolution remains unresolved at two nodes of the phylogeny, requiring the use of nuclear markers or expanded sampling. Subgenus Marsipanthes species are non-monophyletic and constitute an East Andean early divergent clade with species from subgenus Lepanthes, while some derived Biogeographic Choco Marsipanthes clades were recovered, forming a polytomy with species from subgenus Lepanthes. The genus likely originated in southern Ecuador or northern Peru, dispersing across the Andes into the broader Neotropics. Although only a subset of Lepanthes diversity was sampled, the study captures significant taxonomic, geographic, and morphological variation. It provides foundational insights into the genus’s evolution, along with tools and hypotheses that can be expanded upon in future research to further refine our understanding of its evolutionary history.
XA-Novo: an accurate and high-throughput mass spectrometry-based de novo sequencing technology for monoclonal antibodies and antibody mixtures
Authors: Xiong Yueting , Jiang Wenbin , Xiao Jin , Bu Qingfang , Wang Jingyi , Jiang Zhenjian , Luo Ling , Chen Xiaoqing , Qiu Yijie , Wu Yangtao , Liu Fan , Yu Rongshan , Xia Ning-Shao , Yuan Quan 
Published: February 2025

Abstract

Elucidating antibody sequences by mass spectrometry (MS)-based de novo sequencing is essential but challenging. Herein, we propose XA-Novo, an accurate, robust, high-throughput de novo sequencing solution that integrates a single-pot multi-enzymatic gradient digestion method with a beam search-based Fusion assembler to accurately decipher complete antibody sequences at both the sample preparation stage and the data analysis phase. We first benchmark XA-Novo using data from multiple known antibodies across various species, demonstrating that it outperforms commercial solutions in identification capacity, data completeness, and antibody reconstruction accuracy. Furthermore, XA-Novo successfully reconstructs three immunotherapeutic antibodies with unknown sequences, and in vitro assays validating that the generated antibodies exhibit equivalent functionality to their commercial counterparts. Furthermore, XA-Novo excels in discriminating mixtures of COVID-19 neutralizing antibodies, achieving over 99% sequence coverage accuracy, further validating the effectiveness and flexibility of our solution. We anticipate that XA-Novo will be a powerful tool for future antibody research applications.
Regularized win ratio regression for variable selection and risk prediction, with an application to a cardiovascular trial
Authors: Mao Lu 
Published: February 2025

Abstract

Background: The win ratio has been widely used in the analysis of hierarchical composite endpoints, which prioritize critical outcomes such as mortality over nonfatal, secondary events. Although a regression framework exists to incorporate covariates, it is limited to low-dimensional datasets and may struggle with numerous predictors.This gap necessitates a robust variable selection method tailored to the win ratio framework.

Methods: We propose an elastic net-type regularization approach for win ratio regression, extending the proportional win-fractions (PW) model in low-dimensional settings. The method addresses key challenges, including adapting pairwise comparisons to penalized regression, optimizing model selection through subject-level cross-validation, and defining performance metrics via a generalized concordance index. The procedures are implemented in the wrnet R-package, publicly available at https://lmaowisc.github.io/wrnet/.

Results: Simulation studies demonstrate that wrnet outperforms traditional (regularized) Cox regression for time-to-first-event analysis, particularly in scenarios with differing covariate effects on mortality and nonfatal events. When applied to data from the HF-ACTION trial, the method identified prognostic variables and achieved superior predictive accuracy compared to regularized Cox models, as measured by overall and component-specific concordance indices.

Conclusion: The wrnet approach combines the interpretability and clinical relevance of the win ratio with the scalability and robustness of elastic net regularization. The accompanying R-package provides a user-friendly interface for routine application of the procedures, whenever appropriate. Future research could explore additional applications or refine the methodology to address non-proportionalities in win-loss risks and nonlinearities in covariate effects.