bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-body physics under dissipative spin–orbit coupling
Authors: Zhao 赵 Xi 茜 
Published: December 2024

Abstract
We study the trimer state in a three-body system, where two of the atoms are subject to Rashba-type spin–orbit coupling and spin-dependent loss while interacting spin-selectively with the third atom. The short-time conditional dynamics of the three-body system is effectively governed by a non-Hermitian Hamiltonian with an imaginary Zeeman field. Remarkably, the interplay of non-Hermitian single particle dispersion and the spin-selective interaction results in a Borromean state and an enlarged trimer phase. The stability of trimer state can be reflected by the imaginary part of trimer energy and the momentum distribution of trimer wave function. We also show the phase diagram of the three-body system under both real and imaginary Zeeman fields. Our results illustrate the interesting consequence of non-Hermitian spectral symmetry on the few-body level, which may be readily observable in current cold-atom experiments.
Nanomedicine in cancer treatment - an overview
Authors: Dhanabalan Dharanidharan , Shanmugam Narkunaraja 
Published: December 2024

Abstract
Cancer remains a formidable global health challenge, with millions of lives lost annually and a projected increase in cases, particularly in regions like South Central Asia, Europe, Eastern Europe, etc, Traditional cancer treatments, including chemotherapy, radiotherapy, and surgery, face limitations in effectively managing the complex tumor microenvironment and addressing the diverse characteristics of cancer cells. Nano-oncology has emerged as a promising frontier in cancer therapy, utilizing nanoscale materials to deliver therapeutic agents with precision and efficacy. The benefits of nanoparticle-based drug delivery systems are the ability to target tumor cells while minimizing adverse effects and overcoming multidrug resistance. Advancements in hybrid nanoparticle development have further enhanced the stability and performance of drug delivery systems, offering new avenues for cancer treatment. Moreover, nanoparticle-based therapies hold the potential to modulate the immunosuppressive tumor microenvironment and improve outcomes in immunotherapy. The review provides a comprehensive overview of nanotherapeutic products currently in various preclinical and clinical study stages, focusing on their success rates in lung and breast cancers compared to conventional chemotherapeutic drugs. By elucidating the landscape of nano-oncology and evaluating its efficacy in specific cancer types, this review aims to shed light on the transformative potential of nanoparticle-based approaches in cancer treatment and diagnosis. They are exploring nano-oncology promises to pave the way for innovative strategies in combating cancer and improving patient outcomes globally.
MnCo2O4 nanorods-based electrochemical sensing platform for ultrasensitive detection of copper (II) ions in drinking water samples
Authors: Nguyen Ngoc Huyen , Ngo Xuan Dinh , Hoang Van Thanh , Mai Vu Thi Huong , Phan Vu Ngoc , Pham Duc Thang , Anh-Tuan Le 
Published: December 2024

Abstract
MnCo2O4 nanorods (MCO) are successfully fabricated by microwave-assisted hydrothermal method. MCO is coated on the commercial screen-printed electrode (SPE), aiming for effective detection of copper (II) ions (Cu2+). The morphological and structural characteristics are investigated through x-ray diffraction (XRD), Raman spectra, and scanning electron microscope (SEM) analysis. Besides, electrochemical properties and performance to detect Cu2+ on the modified electrode (MCO/SPE) are studied in detail using electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), and differential pulse anodic stripping voltammetry (DPASV) measurements. The results show the MCO/SPE display magnificent enhancements in dynamic linear range, sensitivity, limit of detection (LOD), selectivity, and stability. Under optimized conditions, the prepared electrochemical sensor had a linear range of 0.001–100 μM, corresponding to LOD of 0.72 nM. Notably, the achieved results point out the great potential of the developed sensor based on MnCo2O4 nanorods for heavy metal ion detection.
Effect of inlet sub-cooling on heat transfer and flow stability in a hybrid heat sink
Authors: Joshi Vipul , Pratihar A K 
Published: December 2024

Abstract
Inlet sub-cooling of fluid has significant influence on stability and heat transfer process during flow boiling in microchannel heat sinks for devices generating high heat flux. A computational study of a hybrid microchannel-microgap heat sink section has been performed for constant high heat flux condition with varying water inlet sub- cooling. Results of the transient two-phase analysis reveal that at saturated inlet condition (∆Tin = 0 K), heat sink shows better temperature uniformity and hotspot mitigation capabilities but had high pressure fluctuations due to flow reversal resulting in flow boiling instability. By increasing sub-cooling (∆Tin = 5 K and ∆Tin = 10 K), the pressure fluctuations reduced considerably but developed non-uniform, high surface temperatures in heat sink due to delay in onset of boiling, which can cause hotspots. Increasing the subcooling also resulted in increase in heat transfer coefficient (h) in heat sink, particularly in downstream microgap section. The study corroborated the importance and effect of inlet sub-cooling on heat transfer performance and flow stability of a hybrid heat sink with two-phase flow.
GADIFF: a transferable graph attention diffusion model for generating molecular conformations
Authors: Wang Donghan , Dong Xu , Zhang Xueyou , Hu LiHong 
Published: December 2024

Abstract
The diffusion generative model has achieved remarkable performance across various research fields. In this study, we propose a transferable graph attention diffusion model, GADIFF, for a molecular conformation generation task. With adopting multiple equivariant networks in the Markov chain, GADIFF adds GIN (Graph Isomorphism Network) to acquire local information of subgraphs with different edge types (atomic bonds, bond angle interactions, torsion angle interactions, long-range interactions) and applies MSA (Multi-head Self-attention) as noise attention mechanism to capture global molecular information, which improves the representative of features. In addition, we utilize MSA to calculate dynamic noise weights to boost molecular conformation noise prediction. Upon the improvements, GADIFF achieves competitive performance compared with recently reported state-of-the-art models in terms of generation diversity(COV-R, COV-P), accuracy (MAT-R, MAT-P), and property prediction for GEOM-QM9 and GEOM-Drugs datasets. In particular, on the GEOM-Drugs dataset, the average COV-R is improved by 3.75% compared with the best baseline model at a threshold (1.25 Å). Furthermore, a transfer model named GADIFF-NCI based on GADIFF is developed to generate conformations for noncovalent interaction (NCI) molecular systems. It takes GADIFF with GEOM-QM9 dataset as a pre-trained model, and incorporates a graph encoder for learning molecular vectors at the NCI molecular level. The resulting NCI molecular conformations are reasonable, as assessed by the evaluation of conformation and property predictions. This suggests that the proposed transferable model may hold noteworthy value for the study of multi-molecular conformations. The code and data of GADIFF is freely downloaded from https://github.com/WangDHg/GADIFF.
RNA-ModX: a multilabel prediction and interpretation framework for RNA modifications
Authors: Yuge Chelsea Chen , Hang Ee Soon , Mamtha Madasamy Ravi Nadar , Vishwakarma Shashikant , Wang Sijia , Wang Cheng , Le Nguyen Quoc Khanh 
Published: December 2024

Abstract
Accurate prediction of RNA modifications holds profound implications for elucidating RNA function and mechanism, with potential applications in drug development. Here, the RNA-ModX presents a highly precise predictive model designed to forecast post-transcriptional RNA modifications, complemented by a user-friendly web application tailored for seamless utilization by future researchers. To achieve exceptional accuracy, the RNA-ModX systematically explored a range of machine learning models, including Long Short-Term Memory (LSTM), Gated Recurrent Unit, and Transformer-based architectures. The model underwent rigorous testing using a dataset comprising RNA sequences containing the four fundamental nucleotides (A, C, G, U) and spanning 12 prevalent modification classes (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um), with sequences of length 1001 nucleotides. Notably, the LSTM model, augmented with 3-mer encoding, demonstrated the highest level of model accuracy. Furthermore, Local Interpretable Model-Agnostic Explanations were employed to facilitate result interpretation, enhancing the transparency and interpretability of the model’s predictions. In conjunction with the model development, a user-friendly web application was meticulously crafted, featuring an intuitive interface for researchers to effortlessly upload RNA sequences. Upon submission, the model executes in the backend, generating predictions which are seamlessly presented to the user in a coherent manner. This integration of cutting-edge predictive modeling with a user-centric interface signifies a significant step forward in facilitating the exploration and utilization of RNA modification prediction technologies by the broader research community.
Testing for a difference in means of a single feature after clustering
Authors: Chen Yiqun T , Gao Lucy L 
Published: December 2024

Abstract
For many applications, it is critical to interpret and validate groups of observations obtained via clustering. A common interpretation and validation approach involves testing differences in feature means between observations in two estimated clusters. In this setting, classical hypothesis tests lead to an inflated Type I error rate. To overcome this problem, we propose a new test for the difference in means in a single feature between a pair of clusters obtained using hierarchical or k-means clustering. The test controls the selective Type I error rate in finite samples and can be efficiently computed. We further illustrate the validity and power of our proposal in simulation and demonstrate its use on single-cell RNA-sequencing data.
Spatial proteomics reveals sirtuin 1 to be a determinant of T-cell infiltration in human melanoma
Authors: Placke Jan-Malte , Bottek Jenny , Váraljai Renata , Shannan Batool , Scharfenberg Sarah , Krisp Christoph , Spangenberg Philippa , Soun Camille , Siemes Devon , Borgards Lars , Hoffmann Franziska , Zhao Fang , Paschen Anette , Schlueter Hartmut , von Eggeling Ferdinand , Helfrich Iris , Rambow Florian , Ugurel Selma , Tasdogan Alpaslan , Schadendorf Dirk , Engel Daniel R , Roesch Alexander 
Published: December 2024

Abstract

Background
The tumour microenvironment significantly influences the clinical response of patients to therapeutic immune checkpoint inhibition (ICI), but a comprehensive understanding of the underlying immune-regulatory proteome is still lacking.

Objectives
To decipher targetable biologic processes that determine tumour-infiltrating lymphocytes (TiLs) as a cellular equivalent of clinical response to ICI.

Methods
We mapped the spatial distribution of proteins in TiL-enriched vs. TiL-low compartments in melanoma by combining microscopy, matrix-assisted laser desorption mass spectrometry imaging and liquid chromatography–mass spectrometry, as well as computational data mining. Pharmacological modulation of sirtuin 1 (SIRT1) activity in syngeneic mouse models was used to evaluate the efficacy of pharmacological SIRT1 activation in two syngeneic melanoma mouse models, one known to be α-programmed cell death protein 1 (PD-1) sensitive and the other α-PD-1 resistant.

Results
Spatial proteomics and gene ontology-based enrichment analysis identified &gt; 145 proteins enriched in CD8high tumour compartments, including negative regulators of mammalian target of rapamycin signalling such as SIRT1. Multiplexed immunohistochemistry confirmed that SIRT1 protein was expressed more in CD8high than in CD8low compartments. Further analysis of bulk and single-cell RNA sequencing data from melanoma tissue samples suggested the expression of SIRT1 by different lymphocyte subpopulations (CD8+ T cells, CD4+ T cells and B cells). Furthermore, we showed in vivo that pharmacological SIRT1 activation increased the immunological effect of α-PD-1 ICI against melanoma cells in mice, which was accompanied by an increase in T-cell infiltration and T-cell-related cytokines, including interferon (IFN)-γ, CCL4, CXCL9, CXCL10 and tumour necrosis factor-α. In silico analysis of large transcriptional data cohorts showed that SIRT1 was positively associated with the proinflammatory T-cell chemokines CXCL9, CXCL10 and IFN-γ, and prolonged overall survival of patients with melanoma.

Conclusions
Our study deciphers the proteomics landscape in human melanoma, providing important information on the tumour microenvironment and identifying SIRT1 as having important prognostic and therapeutic implications.
Rapid Selection of Human Immunodeficiency Virus-2 Capsid Mutations in Salvage Therapy With Lenacapavir-containing Regimen
Authors: Montrouge Thomas , Bertine Mélanie , Peytavin Gilles , Saint-Joannis Thibault , Bachelard Antoine , De Truchis Pierre , Lariven Sylvie , Morlat Philippe , Pouderoux Cécile , Damond Florence , Sayre Naomi , Tubiana Roland , Valin Nadia , Charpentier Charlotte , Descamps Diane , Ghosn Jade , Le Hingrat Quentin 
Published: December 2024

Abstract
Lenacapavir is the first capsid inhibitor and its use is currently approved for multidrug-resistant human immunodeficiency virus-1 infection. We report that, despite the initial efficacy of a lenacapavir-containing regimen in patients with multidrug-resistant human immunodeficiency virus-2 viruses, virological suppression was not achieved after a year and most patients selected capsid drug resistance–associated mutations.
Associations between iron markers with hemoglobin and outcomes in peritoneal dialysis patients-results from the PDTAP study
Authors: Wang Zi , Liu Guiling , Hao Li , Li Shaomei , Pei Huaying , Zhao Jinghong , Zhang Ying , Xiong Zibo , Liao Yumei , Li Ying , Lin Qiongzhen , Hu Wenbo , Li Yulin , Zheng Zhaoxia , Duan Liping , Fu Gang , Guo Shanshan , Zhang Beiru , Yu Rui , Sun Fuyun , Ma Xiaoying , Zhao Zhanzheng , Xiao Jing , Shen Yulan , Zhang Yong , Du Xuanyi , Ji Tianrong , Wang Caili , Deng Lirong , Yue Yingli , Chen Shanshan , Ma Zhigang , Li Yingping , Zuo Li , Zhao Huiping , Zhang Xianchao , Wang Xuejian , Liu Yirong , Gao Xinying , Chen Xiaoli , Li Hongyi , Du Shutong , Zhao Cui , Xu Zhonggao , Zhang Li , Chen Hongyu , Li Li , Wang Lihua , Yan Yan , Ma Yingchun , Wei Yuanyuan , Zhou Jingwei , Li Yan , Dong Jie 
Published: December 2024

Abstract
Iron metabolism markers, such as Transferrin Saturation (TSAT) and ferritin, are crucial in anemia management in patients with chronic kidney disease (CKD) and those undergoing dialysis, yet optimal levels remain unelucidated. We conducted a prospective multicenter cohort study using data from the nationwide Peritoneal Dialysis Telemedicine-based Management Platform (PDTAP) to analyze TSAT, ferritin, and hemoglobin (Hb) levels, and their associations with mortality in the peritoneal dialysis (PD) population. Our study included 4429 PD patients, analyzing data through restricted cubic splines and Cox regression models, adjusted for multiple confounders. Nonlinear associations between Hb levels and TSAT/ferritin were observed. Hb levels increased with TSAT up to 40%, then plateaued, whereas ferritin levels increased with the decline of Hb. Further, ferritin levels above 200 ng/mL were independently linked to increased mortality risk (hazard ratio [HR] 1.207, 95% confidence interval [CI]: 1.134–1.286), with this effect decreasing as high-sensitivity C-reactive protein (hsCRP) levels rose. This risk was notably significant in patients with a history of cardiovascular disease (CVD). At last, ferritin/Hb ratio more than 2 was associated with increased risk of mortality after adjusting for demographic, nutritional factors and erythropoiesis agents (HR 1.219, 95% CI: 1.144–1.299). The ferritin/Hb ratio demonstrated superior predictive ability for iron responsiveness compared to ferritin alone, monitoring the ferritin/Hb ratio may help assess the relative iron content in the body and provide reference for iron supplementation among patients undergoing PD.
A systematic review of applications, manipulations and manipulation checks of construal level theory in advertising
Authors: Saeed Muhammad Rashid , Khan Hiba , Khan Huda , Lee Richard 
Published: December 2024

Abstract
Advertising research has increasingly applied construal level theory (CLT) to predict advertising effectiveness. This study systematically reviews and synthesizes CLT-based advertising research by focusing on the theoretical tenets of CLT, construal-level manipulations, and construal-level manipulation checks applied in this research domain. This is the first systematic review of CLT-based advertising research involving psychological distance, which is the distance from self, here, and now. The review identified 86 relevant articles published in top-ranked journals between 2009 and 2023, retrieved from seven electronic academic databases. It found that CLT-based advertising studies are primarily anchored on the theoretical tenets of matching effect, categorization effect, and psychological distance. It further identified and classified the construal-level manipulations used in CLT-based advertising research into three categories: psychological-distance dimensions, psychological manipulations, and marketing-related factors. Finally, this review highlights the critical gaps in existing research and offers avenues for future research.
Wolbachia pipientis modulates germline stem cells and gene expression associated with ubiquitination and histone lysine trimethylation to rescue fertility defects in Drosophila
Authors: Kagemann Catherine H , Bubnell Jaclyn E , Colocho Gabriela M , Arana Daniela C , Aquadro Charles F 
Published: December 2024

Abstract
Wolbachia pipientis are maternally transmitted endosymbiotic bacteria commonly found in arthropods and nematodes. These bacteria manipulate reproduction of the host to increase their transmission using mechanisms, such as cytoplasmic incompatibility, that favor infected female offspring. The underlying mechanisms of reproductive manipulation by W. pipientis remain unresolved. Interestingly, W. pipientis infection partially rescues female fertility in flies containing hypomorphic mutations of bag of marbles (bam) in Drosophila melanogaster, which plays a key role in germline stem cell daughter differentiation. Using RNA-seq, we find that W. pipientis infection in bam hypomorphic females results in differential expression of many of bam's genetic and physical interactors and enrichment of ubiquitination and histone lysine methylation genes. We find that W. pipientis also rescues the fertility and germline stem cell functions of a subset of these genes when knocked down with RNAi in a wild-type bam genotype. Our results show that W. pipientis interacts with ubiquitination and histone lysine methylation genes which could be integral to the mechanism by which W. pipientis modulates germline stem cell gene function.
Pharmacists’ perceptions of the impact of Objective Structured Clinical Examination on professional development and competence: a cross-sectional study in Qatar
Authors: Nasr Ziad G , Shehzad Hafsa , Wilby Kyle J 
Published: December 2024

Abstract

Objectives
The Objective Structured Clinical Examination (OSCE) is a key tool in healthcare education, assessing clinical skills and competencies. This study explores OSCE’s impact on pharmacists’ competence, confidence, and practice readiness, focusing on its role in professional development and long-term practice improvement.

Methods
A cross-sectional survey was conducted among Qatar University pharmacy graduates with at least a year of practice experience. The survey included 10 items on a 4-point Likert scale to capture quantitative data, along with open-ended questions for more detailed reflections and qualitative insights. Quantitative data were analyzed using SPSS, and qualitative data were thematically analyzed through an inductive approach, with two researchers independently coded responses and identifying themes.

Key findings
Out of 75 eligible pharmacists, 46 responded (61.3% response rate). Over 85% reported that OSCE improved communication and interprofessional collaboration skills, and 80% felt it helped apply essential professional skills effectively. However, opinions varied on making OSCE a licensure requirement. Six main themes emerged: (i) Enhanced Interprofessional Collaboration Skills, (ii) Application of Professional Skills, (iii) Practical Application of Pharmacy Education, (iv) Adaptability for Evolving Healthcare Challenges, (v) Enhancement of Patient-Facing Communication Skills, and (vi) Identification of Personal Strengths and Weaknesses.

Conclusions
This study demonstrates that OSCEs enhance pharmacists’ clinical skills, communication, and practice readiness. Pharmacy programs should continue integrating OSCEs alongside other assessments for comprehensive evaluation. Policymakers are encouraged to explore OSCEs for licensure, ensuring standardization and evaluator training. Future research should assess OSCE’s long-term impact on pharmacists’ career development and patient outcomes.
A Core Glycolipid Vaccine Elicits Cross-reactive Antibodies Against Salmonella Species and Protects Against Invasive Nontyphoidal Salmonella Disease in Mice
Authors: Baliban Scott M , Shridhar Surekha , Luo Kun , Kolasny Jacqueline , Hyun Sang , Zhao Zhiyong , Tennant Sharon M , Cross Alan S 
Published: December 2024

Abstract

Background
Enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi A in addition to gastroenteritis and invasive disease, predominantly attributable to nontyphoidal Salmonella serovars Typhimurium and Enteritidis, are major causes of death and disability across the globe. A broad-spectrum vaccine that protects against disease caused by typhoidal and nontyphoidal serovars of Salmonella is not available for humans but would prevent a considerable burden of disease worldwide.

Methods
We previously developed a broad-spectrum vaccine for gram-negative bacteria that is based on the inner core domain of detoxified Escherichia coli O111, Rc (J5) mutant lipooligosaccharide, a highly conserved antigen across gram-negative bacteria, complexed with an outer membrane protein of group B Neisseria meningitidis. In this study, mice and rabbits were immunized with the J5 core/outer membrane protein subunit vaccine. We assessed the cross-reactivity of antisera with various Salmonella species lipopolysaccharides and the protective efficacy of passive and active immunization with J5 vaccine against experimental nontyphoidal Salmonella infection in mice.

Results
Vaccination with J5 induced IgG responses that strongly recognized lipopolysaccharide from both typhoidal and nontyphoidal Salmonella and imparted a survival benefit against lethal heterologous challenges with S. Typhimurium and S. Enteritidis. Additionally, passive transfer studies with rabbit hyperimmune sera raised against the J5 vaccine revealed that anti-core antibodies were protective against lipopolysaccharide challenge in D-galactosamine–sensitized mice.

Conclusions
Our findings support the development of core glycolipids as a novel Salmonella vaccine candidate. Further investigation is warranted to determine the efficacy of the J5 core/outer membrane protein vaccine against other Salmonella serovars of concern.