bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Neural Regeneration Mechanisms for Self-Organized Structural Adaptation in Large Language Models
Authors: Embury Stuart , Belmonte Eduardo , MacDonagh Cillian , Villaverde Ignatius 
Published: November 2024

Abstract

The rapid expansion of data-driven applications has demonstrated the limitations inherent in traditional neural network architectures, where static configurations constrain adaptability and impede long-term functionality. The Dynamic Neural Regeneration (DNR) mechanism introduces a groundbreaking approach to structural adaptability, enabling autonomous reconfiguration of neural architectures through a data-responsive regenerative process that recalibrates layers and nodes in real time. Through comprehensive integration within a large language model (LLM), DNR facilitates adaptive structural evolution that aligns model architecture with shifting data distributions, effectively bridging gaps in scalability, robustness, and accuracy. Experimental results demonstrate that the DNR-enabled LLM significantly outperforms conventional static models in metrics such as adaptability, computational efficiency, and accuracy, highlighting its capacity to maintain high performance across diverse and dynamic datasets. This innovation offers notable improvements in computational sustainability, as the model selectively regenerates only those neural components affected by data-driven relevance, thereby optimizing resource allocation without sacrificing model integrity or predictive precision. The findings demonstrate the DNR mechanism as a transformative advancement, offering a scalable, efficient, and self-organizing approach with broad implications for real-world applications that demand long-term adaptability and resilience in evolving data environments.
The Risk Genes SIRP5, CMC1, and ASAH1 as Potential Targets for the Diagnosis, Immunotherapy, and Treatment of Colon Adenocarcinoma by Single-Cell and Bulk RNA Sequencing Analysis
Authors: Xu Zipeng , Gong Jiantao , Hu Weidong , Ge Chen , Tong Genxi , Cai Fengjun , Zhu Zhenghai , Yuan Yihang , Chen Chaobo 
Published: November 2024

Objective:
Globally, one of the main causes of cancer-related mortality is Colon
Adenocarcinoma (COAD). In this study, a new special Immune Cell Functions (ICF) risk
model was constructed using single-cell and bulk RNA sequencing data to develop a new understanding
and clinical applications for COAD.

Methods:
The immune function gene sets were downloaded from a literature reference, and the
COAD single-cell dataset GSE146771 was downloaded from the Tumour Immune Single Cell
Hub database. Using Lasso analysis, a multiple gene signature was made from the enrichment
scores of immune function gene sets that were enriched in different ways. Robust validation of
the signature was then performed in multiple independent cohorts. After that, we built the model
using a 10-fold cross-test and evaluated its independence for clinical usage using a nomogram.
We also investigated the connection between signature and immune function, genetic variation,
immunotherapy, and the cancer immunological microenvironment. Lastly, we used qPCR and
immunohistochemistry to examine the expression of the unreported model genes. To find the
regulatory functions of unreported model genes, an EdU assay was employed.

Results:
First, 20 differentially enriched immune function gene sets were identified. Ten genes
can be used as a risk profile to assess the prognosis of colon cancer, according to Lasso regression
analysis. Signature performance was stable in both the training cohort and two independent
GEO external cohorts, and risk scores were confirmed as independent prognostic factors.
At the same time, our risk model continued to be highly predictive across various clinical clusters
and clinical characteristics, such as immune checkpoints, tumour genome mutations, and
chemotherapeutic drug resistance. Patients in the low-risk group have exhibited a higher
chance of benefiting from immunotherapy, according to immunotherapy response research.
qPCR and immunohistochemistry analysis have revealed SIRP5 expression as high in COAD
tissues, while CMC1 and ASAH1 expression has been found to be low. According to the findings
of the functional experiment, SIRP5, CMC1, and ASAH1 may control the ability of CRC
cells to proliferate.

Conclusion:
In this study, using scRNA-seq and bulk RNA-seq data, we created a risk model
to predict the prognosis and effectiveness of immunotherapy in patients with COAD. In addition,
we have discovered three model genes (SIRP5, CMC1, and ASAH1) that have not been
reported before. These genes have the potential to be novel therapeutic targets in Colorectal
Cancer (CRC). These findings suggest that this model could be used to evaluate the prognostic
risk and identify potential targets for COAD patient treatment.
NEDD4 Knockdown Suppresses Human Endometrial Stromal Cell Growth and Invasion by Regulating PTGS2-Mediated Ferroptosis in Endometriosis
Authors: Lao Jianting , Hu Panwei , Wan Yiting , Shu Mengmeng , Chen Jing , Yang Hong 
Published: November 2024

Background:
Endometriosis (EM) is a gynecological disease characterized
by the benign growth of endometrial tissue outside the uterus. Upregulation of
neuronally expressed developmentally downregulated 4 (NEDD4) has been reported
to accelerate endometrial cancer progression.

Objectives:
We explored whether abnormal expression of NEDD4 is correlated with
EM.

Methods:
Endometrial tissue in patients without endometriosis was used to develop
the original generation of endometrial stromal cells (ESCs). Different types of
endometrial tissue of patients with endometriosis were used to measure the
expression of NEDD4 by immunohistochemistry (IHC) and western blotting. Its
biological functions in ESCs were investigated using a cell counting kit-8 assay,
fluorescein diacetate (FDA) staining, and Transwell invasion assays. Additionally, its
involvement in ferroptosis was assessed by measuring Fe2+, malondialdehyde (MDA),
glutathione (GSH), and reactive oxygen species (ROS) levels and the expression of
ferroptosis markers.

Results:
Compared with normal controls, NEDD4 levels were significantly elevated in
the endometrial tissue of patients with EM. Furthermore, NEDD4 expression was
higher in the ectopic endometrium than in the eutopic endometrium. NEDD4
knockdown reduced the viability and invasive capacity of ESCs, increased Fe2+, MDA,
and ROS levels, and decreased GSH content. Further analysis revealed that NEDD4
knockdown promoted ferroptosis in ESCs by increasing the expression of
prostaglandin-endoperoxide synthase 2 (PTGS2). As an E3 ubiquitin ligase, NEDD4
reduced PTGS2 protein levels by accelerating its ubiquitination and subsequent
proteasomal degradation.

Conclusion:
These findings suggest that inhibiting NEDD4 reduces ESC growth and
invasion in EM by regulating PTGS2-dependent ferroptosis.
Innovative Nanocomposites for Drug Delivery: A Novel Approach for Diabetic Foot Ulcer
Authors: Parveen Rubi , Ali Faraat , Singh Shiv Dev 
Published: November 2024

Abstract:
Diabetic Foot Ulcer (DFU) is a chronic wound, and a person with diabetes has an increased
lifetime risk of foot ulcers (19%-34%) and high morbidity (65% recurrence in 3-5 years,
20% lifetime amputation). Recent data have shown rising amputation rates, especially in the younger
and minority populations. This abstract discusses innovative approaches for addressing this issue.
This highlights the use of nanotechnology-based drug nanocomposite systems for natural wound
healing therapies, with a focus on nanoparticles, nano-emulsions, and nanogels. This review also
emphasizes the potential of hydrogels for drug delivery, highlighting their versatility in various medical
applications. Furthermore, it delves into the use of silver nanoparticles (AgNP’s) for treating
diabetic wounds while acknowledging the need to address potential toxicity concerns. Finally, the
abstract discusses the utilization of traditional herbal medicine and the integration of modern science
to advance wound care, particularly focusing on wound microbiome, immune response, and controlled
herbal medicine delivery. This study also highlights clinical trials conducted on DFU. Overall,
these abstracts highlight the importance of exploring diverse and innovative solutions to chronic
wound management.
Investigating Biomarkers and Molecular Mechanisms in COPD: Perspectives from In-vivo Models
Authors: Singh Aarti , Arora Swamita , Singh Vivek , Alam Sanjar , Akram Wasim , Dhillon Anjali , Kumar Shivendra , Kumar Arun , Saha Sunam 
Published: November 2024

Purpose:
This review examines COPD pathogenesis, biomarkers, and treatment.
COPD, a progressive respiratory illness that blocks airflow, causes high morbidity and death. The
complicated pathophysiology of COPD involves genetic predisposition, environmental variables
(particularly tobacco smoke), and inflammatory pathways. COPD diagnosis, prognosis, and monitoring
depend on biomarkers in clinical and preclinical investigations. COPD care should include
pharmaceutical and non-pharmacological therapies to improve symptoms, lung function, and outcomes.

Materials and Method:
This review examines COPD pathogenesis, cytokines, and risk factors.
This review article discusses how immune system signalling molecules called cytokines contribute
to COPD's persistent inflammation. Smoking and environmental contaminants are also examined
as COPD risk factors. The analysis also covers biomarkers needed to diagnose and track
the condition.

Results:
The review paper on COPD highlights the critical role of cytokines in the disease's pathophysiology,
emphasizing their contribution to chronic inflammation. Various cytokines, particularly
interleukins, are implicated in driving the inflammatory processes within the airways and lungs,
resulting in tissue damage and airflow limitation, which are hallmark features of COPD. The paper
also identifies smoking and exposure to environmental pollutants as major risk factors for the
development of COPD.

Conclusion:
This review illuminates COPD's complex pathogenesis, highlighting cytokines' involvement
in chronic inflammation. To create targeted therapeutics, cytokine-mediated pathways
must be understood. The review emphasizes biomarkers' use in preclinical and clinical investigations
to diagnose and monitor COPD and provide disease progression insights.
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome
Authors: Wang Linjuan , Li Yujia , Zhang Zhepei , Song Fengcheng , Zan Yufei , Zheng Ranxi , Yuan Zhengrong 
Published: November 2024

Abstract:
With the development of third-generation sequencing technology, genome assembly has
entered a new era. The combination of multiple sequencing methods can combine the strengths of
each, resulting in higher-quality assembly results. Telomere-to-Telomere (T2T) genome refers to a
zero gap genome that is assembled at the T2T level of one or more chromosomes through the combination
of multiple sequencing technologies, such as Pacific Biosciences High-Fidelity (PacBio
HiFi), Oxford Nanopore Technologies (ONT) Ultra-long, High-throughput Chromosome Conformation
Capture (Hi-C), and others. High-quality reference genomes are the basis for genomics research,
and the T2T genome has enabled the exploration of unknown areas of the genome, such as
telomeres and centromeres, which has provided a more in-depth direction for research. This review
provides a comprehensive overview of the T2T genome, reviewing the development of sequencing
technologies and then outlining sequencing strategies, assembly methods, quality assessment processes,
and analysis software for the T2T genome with practical examples. Representative T2T genomic
species of plants, animals, and microorganisms (e.g., human, Arabidopsis, brewer's yeast, and
so on) are presented separately. A summary of the potential and challenges of current T2T genomic
applications is provided, along with an outlook for future developments.
Identification and Analysis of Plant miRNAs: Evolution of In-silico Resources and Future Challenges
Authors: Kushwaha Abhishek , Singh Hausila Prasad , Singh Noopur 
Published: November 2024

Abstract:
Endogenous small RNAs (miRNA) are the key regulators of numerous eukaryotic lineages
playing an important role in a broad range of plant development. Computational analysis of
miRNAs facilitates the understanding of miRNA-based regulations in plants. The discovery of small
non-coding RNAs has led to a greater understanding of gene regulation, and the development of bioinformatic
tools has enabled the identification of microRNAs (miRNAs) and their targets. The need
for comprehensive miRNA analysis is being accomplished by the development of advanced computational
tools/algorithms and databases. Each resource has its own specificity and limitations for the
analysis. This review provides a comprehensive overview of various algorithms used by computational
tools, software, and databases for plant miRNA analysis. However, over a period of about two
decades, a lot of knowledge has been added to our understanding of the biogenesis and functioning
of miRNAs in other plants. Several parameters were already integrated and others need to be incorporated
in order to give more accurate and efficient results. The reassessment of computational recourses
(based on old algorithms) is required on the basis of new miRNA research and development.
Generally, computational methods, including ab-initio and homology search-based methods, are
used for miRNA identification and target prediction. This review presents the new challenges faced
by the existing computational methods and the need to develop new tools and advanced algorithms
and highlight the limitations of existing computational tools and methods, and emphasizing the need
for a comprehensive platform for miRNA gene exploration.
Antidepressant Potential of Hispidulin Present in S. barbata D. Don: Mechanistic Insights through Neurochemical and Behavioral Assessments
Authors: Pannu Arzoo , Goyal Ramesh K. , Goswami Shikha 
Published: November 2024

Background and Aim:
This study aims to investigate the antidepressant properties of
Hispidulin, a flavonoid present in Scutellaria barbata D. Don. The selection of Hispidulin
stems from its notable inhibitory activity against Xanthine Oxidase (XO), a parameter in the
pathophysiology of depression.

Material and Methods:
Mice were subjected to a rigorous evaluation using a murine model of
Chronic Unpredictable Mild Stress (CUMS) to induce depression for 21 days and antidepressant
properties were rigorously assessed using the Tail Suspension Test (TST), Forced Swim
Test (FST), and Open Field Test (OFT). Imipramine and fluoxetine were used as standard
drugs. Additionally, neurochemical analyses were conducted to quantify serotonin (5-HT),
norepinephrine (NE), and dopamine (DA) levels in the cortex, hippocampus, and hypothalamus.
Further mechanistic insights were sought through the estimation of monoamine oxidase (MAO)
activity and assessment of antioxidant enzyme levels in the brain. Plasma nitrite and corticosterone
levels were also measured to delineate the underlying mechanism of action.

Results:
Hispidulin demonstrated significant antidepressant effects, as evidenced by reduced
immobility time in TST and FST and increased exploratory behavior in OFT. Neurochemical
analysis revealed restoration of 5-HT, NE, and DA levels in key brain regions. Furthermore,
Hispidulin modulated MAO activity and enhanced antioxidant enzyme levels in the brain.
Plasma nitrite levels were elevated, indicating enhanced nitric oxide synthesis, while corticosterone
levels were reduced.

Conclusion:
Our findings indicate that Hispidulin exerts potent antidepressant effects, potentially
mediated through its influence on monoaminergic neurotransmitters, MAO activity, and
antioxidant defenses. These results provide valuable mechanistic insights into the antidepressant
action of Hispidulin, supporting its potential therapeutic application in depressive disorders.

result:
Hispidulin demonstrated significant antidepressant effects, as evidenced by reduced immobility time in TST and FST, and increased exploratory behavior in OFT. Neurochemical analysis revealed restoration of 5-HT, NE, and DA levels in key brain regions. Furthermore, Hispidulin modulated MAO activity and enhanced antioxidant enzyme levels in the brain. Plasma nitrite levels were elevated, indicating enhanced nitric oxide synthesis, while corticosterone levels were reduced.
Green Synthesis, Structural Insights, and Antimicrobial Potential of Zinc Oxide Nanoparticles Synthesized via Sustainable Method
Authors: Kumar Vishnu K. , Francis Shebin , P. R Shehsadi , M. V Manjusha , Varghese Princy 
Published: November 2024

Background:
Green synthesized nanoparticles have gained wide interest in
today’s world due to their inherent features like rapidity, eco-friendliness, and costeffectiveness
[4].In this study, zinc oxide (ZnO) nanoparticles were synthesized using an
aqueous extract of Ixora coccinea leaves. X-ray diffraction (XRD) and Transmission
Electron Microscopy (TEM) studies were used to analyze the structural and morphological
properties of prepared Zinc Oxide nanoparticles.

Methods:
The sol-gel method of synthesis via the green route was introduced to synthesize
pure Zinc oxide nanoparticles. Silver-doped Zinc Oxide nanoparticles were also prepared
using the same method

Result:
The XRD studies showed the crystalline nature and revealed the purity of Zinc
Oxide nanoparticles. The specific functional groups responsible for reduction, stabilization,
and capping agents present in the nanoparticles were examined using Fourier Transform
Infrared Spectroscopy (FTIR) spectroscopy. The bacterial destruction was better for
ZnO nanoparticles than reported for plant extracts and standard drugs.

Conclusion:
This study proves that Zinc Oxide nanoparticles contain natural antimicrobial
agents through green synthesis, which may serve to produce drugs for antimicrobial
therapeutics.
Biological Evaluation of Cucumis trigonus (Roxb.) for Memory Enhancing Activity in Scopolamine-induced Amnesia in Mice
Authors: Bharti Abhishek , Bora Kundan Singh 
Published: November 2024

Introduction:
Plants have been employed for centuries to enhance human health due to
their cost-effectiveness and minimal adverse effects. Numerous plants exhibit a wide spectrum of
pharmacological activities, and various herbal medicines are currently being investigated for their
memory-enhancing properties.

Method:
Cucumis trigonus (Roxb.), commonly known as Kachari or Bitter gourd, is one such plant
with diverse pharmacological attributes. Historically, the fruits of C. trigonus have been utilized for
addressing various conditions like leprosy, pyrexia, icterus, hyperglycemia, chronic cough, bronchitis,
abdominal fluid accumulation, anemia, obstipation, diverse gastrointestinal disease, and cognitive
impairment. The current investigation aims to explore the memory enhancement properties of C.
trigonus, rooted in its traditional applications, particularly against scopolamine-induced amnesia in
mice. Morris water maze and elevated plus maze paradigms were employed to evaluate cognitive
performance. Furthermore, the research examined acetylcholine neurotransmission, oxidative stress
markers, and cerebral histopathology.

Result:
The results showed that C. trigonus ethanol extract (dose- 150 or 300 mg/kg., p.o.), markedly
(p<0.05) improved memory in scopolamine-induced amnesia in mice and significantly (p<0.05)
elevated hippocampus acetylcholine concentration. These findings revealed that the ethanol extract
of C. trigonus fruits mitigates memory deficits and demonstrates neuroprotective efficacy analogous
to the reference drug Piracetam. Additionally, the extract showed notable in vivo antioxidant activity.
The occurrence of flavonoids and phenols is likely to be responsible for its memory-enhancing effects
due to their antioxidant properties, which help to prevent the loss of neurons.

Conclusion:
These results support the efficacy and potential of C. trigonus ethanol extract as an
affordable alternative form of herbal medicine for the treatment of Amnesia.
Soluplus-Stabilized Nimodipine-Entrapped Spanlastic Formulations
Prepared with Edge Activator (Tween20): Comparative Physicochemical
Evaluation
Authors: Alkufi Hussein K. , Kassab Hanan J. 
Published: November 2024

Background:
Nimodipine (ND) is a vasodilator drug that is used for acute subarachnoid
hemorrhage. It has a predominant hydrophobic property, causing low solubility and low bioavailability.
Spanlastics are elastic nanovesicular systems based on non-ionic surfactants and edge activators
as major components. The goal of this work is to formulate ND as spanlastic nanovesicles to
improve the drug's bioavailability.

Methods:
Spanlastic formulations containing ND were prepared by using the ethanol injection
method. The composition of the ND formulation includes Span60 as a nonionic surfactant and
Tween 20 as edge activators in different ratios. Stabilizers like Soluplus (SP) are used in some formulations
and then compared with other formulations without that stabilizer. The evaluation study
involved Vesicle Size (VS), PolyDispersity Index (PDI), and Entrapment Efficiency (%EE). Then,
the optimized formula was subjected to an in vitro release study and zeta potential, additionally
comparing the optimized formula with the formula without soluplus in the same concentration in
Scanning Electron Microscopy (SEM), solubility study, Deformability Index (DI), and stability
study.

Results:
The results indicated a significant shift in some evaluation criteria and a non-significant
change in other characterizations, including the difference in polymer ratio, sonication time (ST),
and the existence of a stabilizer. The best formula, F27, was found to have VS, PDI, %EE, and zeta
potential of 125.7±0.29 nm, 0.4744±0.002, and 85.43±0.17% and -20.01 ± 0.89 mV, respectively.
The photomicrographs of the prepared spanlastic revealed a more uniform and spherical spanlastic,
indicating a greater capacity for continuous release. With the addition of Soluplus, the formula became
more stable in one month and had a higher deformability index.

Discussion:
A significant shift was observed in both VS and PDI. As the stabilizer concentration
increases, VS and PDI will decrease. The non-significant shift was noted in the %EE with the presence
of a stabilizer. Soluplus has the ability to spontaneously self-assemble into spherical particles.
Additionally, PEG 6000, as a component of Soluplus's structure, has a tendency to form strong or
tightly bound bilayers and prevent aggregation and formulation of large vesicles.

Conclusion:
This study explains the accessibility of the formulation of ND as spanlastic nanovesicles
by using the ethanol injection method. This spanlastic formulation contains non-ionic surfactants
and edge activators (Span 40 and Tween 20) in varying ratios. To get a stable formula, Soluplus
is added to prevent the development of crystals and agglomeration.