bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico Analysis of Maize Spermidine Synthase: Detailed Insights from
Substrate Docking Studies
Authors: Eftekhari Fatemeh , Sarcheshmehpour Mehdi , Lohrasbi-Nejad Azadeh , Boroomand Naser 
Published: January 2025

Introduction::
Polyamines are vital in regulating stress signaling pathways, inhibiting reactive
oxygen species, and stabilizing the photosynthetic apparatus in plants, with their levels fluctuating
under stress conditions. Among the key enzymes in polyamine biosynthesis is spermidine
synthase, which synthesizes spermidine in the presence of putrescine and S-adenosyl 3-
(methylsulfanyl) propylamine.

Methods::
This study focused on the structural analysis of the maize spermidine synthase enzyme
(SPDS-Maiz), highlighting its significance in plant stress tolerance. The enzyme's threedimensional
structure was modeled using the amino acid sequence and SWISS-MODEL, followed
by refinement with the GalaxyRefine2 web server. Molecular docking studies were performed for
its cofactor and substrate. Molecular dynamics simulations performed for 100 ns using Gromacs
software confirmed the conformational stability of the apo and holoenzyme’s structure.

Results::
The structural model showed 90.3% of its amino acids in favored areas of the Ramachandran
plot and obtained a notable score of 95.528% ERRAT. Molecular dynamics simulation confirmed
the stability of the SPDS-Maiz structure by analyzing the physical movements of atoms and
molecules. The docking studies showed that Asp226 is crucial in the interaction of putrescine and
dc-SAM with the active site of the enzyme. Additional amino acids, including Gln122, Asp207,
Ser227, Ser228, Glu236, Gln122, Asp226, Ser227, and Gln259, played a role in supporting the enzyme-
dc-SAM-putrescine complex. Putrescine (PUT) exhibited stronger van der Waals interactions
(-48.23 kcal/mol) and nonpolar solvation energy (-7.46 kcal/mol) compared to Sadenosylmethionine
(dc-SAM). However, PUT incurred higher polar solvation penalties (+134.68
kcal/mol) due to its +2 charge, whereas dc-SAM benefited from slightly lower desolvation costs.

Conclusion::
The study successfully modeled and refined the three-dimensional structure of the
SPDS-Maiz enzyme, highlighting the critical role of Asp226 and other amino acids in substrate
binding. Although dc-SAM had better electrostatic complementarity (-60.27 kcal/mol), the overall
binding free energy (-20.58 kcal/mol for PUT vs. -11.22 kcal/mol for dc-SAM) indicated that PUT
achieved stronger binding affinity, driven by its hydrophobic interactions. These findings provide
insights into how the enzyme and substrate interact and the underlying molecular mechanisms in
spermidine synthesis in plants.
Investigating the Risk Factors Associated with Type 1 Diabetes (T1D) in the South of Iran: A Casecontrol Study
Authors: Mirrashidi Fatemeh Sadat , Kiani Amin , Hushmandi Kiavash , Raesi Rasoul , daneshi salman 
Published: January 2025

Background:
Type 1 diabetes (T1D) is an autoimmune disorder characterized by a complex
interplay of genetic and environmental factors.

Aim:
The objective of this study was to identify the risk factors associated with T1D in the southern
region of Iran during the year 2022.

Methods:
This research employed a case-control design involving two groups (79 individuals in
each group) of healthy children and adolescents diagnosed with T1D. The study assessed and compared
the groups regarding various potential risk factors that may influence the development of
T1D. Data analysis was performed using SPSS-22 software.

Results:
Significant differences were observed between the two groups concerning several factors,
including the age at which children began kindergarten, their weight at one year and 18
months, maternal weight gain during pregnancy, delivery method, age of introduction to complementary
feeding, duration of breastfeeding, use of cow's milk and vitamin D supplements before
one year of age, as well as family history of T1D and other autoimmune diseases among fathers
and siblings.

Conclusion:
The findings indicate that, in addition to genetic predispositions, numerous environmental
factors contribute to the risk of developing T1D. Consequently, it is recommended that
health managers and policymakers investigate these risk factors more broadly across various regions
to implement effective strategies aimed at reducing the incidence of T1D nationwide.
Soxhlet Extraction and FT-IR Spectroscopy Coupled to Chemometrics:
Authenticating Beef, Pork and Wild boar Rendang
Authors: Syofyan Syofyan , Fadillah Rismah , Zehanna Detta , Hamidi Dachriyanus , Syafri Suryati 
Published: January 2025

Background:
Rendang is one of the traditional foods of West Sumatra made from processed beef, which is vulnerable to adulteration with non-halal meats such as pork.

Objective:
This research aimed to develop the method for discriminating beef fat and lard (pig and
wild boar) of rendang using a Fourier Transform Infra-Red (FTIR) combined with chemometric
analysis.

Material and Methods:
The training data set was rendang made of the binary mixture of beef and
pork (pig and wild boar) with 11 concentrations. The testing data set was rendang obtained from
several food stalls in Padang, West Sumatra Indonesia. Fat was extracted using the soxhlet
method and then analyzed using ATR-FTIR spectroscopy at 4000-400 cm-1 wave numbers. The
discriminant analysis (DA) was used to discriminate fat, while the Principle Component Regression (PCR) and Partial Least Square (PLS) models were used for quantification analysis.

Results:
The result showed DA could classify rendang without misclassification at wave numbers
of 1400-1000 cm-1 (pig) and 2800-1000 cm-1 (wild boar). About seven of ten commercial rendang
were identified as beef, but three of them failed using the Beef-Pork-DA model. Meanwhile, five
commercial rendang were classified as mixture and wild boar using the Beef-Wild boar DA model. In quantitative analysis, the best PCR model for pig was at a wave number of 1500-1000 cm-1
with a calibration R2
value of 0.9946, predicted R2
0.9926, RMSEC 0.0327, and RMSEP 0.0464.
The best PLS model for wild boars was at wave numbers 1400-1000 cm-1 with the R2
calibration
value of 0.9974, R2
prediction 0.9875, RMSEC 0.0229, RMSEP 0.0572.

Conclusion:
FTIR spectroscopy combined with chemometrics successfully classified and quantified beef fat pork, and wild boar fat in rendang. However, further validation of the five rendang
testing datasets using the DNA-based method that failed to identify as beef using the FT-IR
method is necessary.

conclusion:
FTIR spectroscopy combined with chemometrics successfully classified and quantified beef fat and lard (pig and wild boar) in rendang. However, further validation of the three rendang testing datasets using the DNA-based method that failed to identify as beef using the FT-IR method is necessary.
Identifying Biomarkers for Atherosclerosis via Gene Expression and Biological Networking
Authors: Chhotaray Sangeeta , Jal Soumya 
Published: January 2025

Background:
Atherosclerosis is a chronic disease caused by the accumulation of lipids,
inflammatory cells, and fibrous elements in arterial walls, leading to plaque formation and
cardiovascular conditions like coronary artery disease, stroke, and peripheral arterial disease.
Factors like hyperlipidemia, hypertension, smoking, and diabetes contribute to its development.
Diagnosis relies on imaging and biomarkers, while management includes lifestyle modifications,
pharmacotherapy, and surgical interventions. Computational biology is transforming biological
knowledge into clinical practice by identifying biomarkers that can predict clinical outcomes.
This involves omics data, predictive modeling, and data integration. Statistical analysis-based
methods are also being developed to develop and integrate methods for screening, diagnosing,
and prognosing atherosclerosis.

Methodology:
The present work aimed to uncover critical genes and pathways to enhance the
understanding of the mechanism of atherosclerosis. GSE23746 was analyzed to find differentially
expressed genes (DEGs) using 19 control samples and 76 atherosclerotic samples.

Result:
A total of 76 DEGs were identified. Analysed DEGs using Gene Ontology (GO) and
Kyoto Encyclopaedia of Genes and Genomes (KEGG) to generate enrichment datasets. A Protein-
Protein Interaction (PPI) network of DEGs was created utilizing the Search Tool for the Retrieval
of Interacting Genes (STRING).

Conclusion:
Ten hub genes, namely EGR1, PTGS2, TNF, NFKBIA, CXCL8, TNFAIP3, CCL3,
IL1B, PTPRC, and CD83, were found to be significantly linked to atherosclerosis. Furthermore,
the metabolic pathway analysis through KEGG and STRING provides potential targets for therapeutic
interventions through HUB genes to diagnose the illness at an early stage, which aids in
the reduction of cardiovascular risk. From risk factor profiling to the discovery of novel biomarkers,
several components such as phospholipids, ANGPTL3, LCAT, and the proteinencoded
OCT-1 gene, play a vital role in crucial processes. These compounds are potential therapeutic
targets for early diagnosis of atherosclerotic lesions and future novel biomarkers.
Leptomeningeal Masses or Masquerades: A Spectrum of Diseases with Leptomeningeal Enhancement and their Mimics
Authors: Yogendra Praveen M , Nickalls Oliver James , Ho Chi Long 
Published: January 2025

Background:
Leptomeningeal enhancement, visible on MRI, can indicate a variety of diseases, both neoplastic and non-neoplastic.

Objective:
This comprehensive pictorial review aims to equip radiologists and trainees with a thorough understanding of the diverse imaging presentations of
leptomeningeal disease.

Methods:
Drawing from a retrospective analysis of MRI scans conducted between 1 January 2008 and 30 September 2022, at two tertiary teaching hospitals
in Singapore, this review covers a wide range of conditions.

Case Collection:
The main neoplastic conditions discussed include leptomeningeal carcinomatosis, myelomatosis, schwannoma, CNS lymphoma, and pineal region
tumors. Additionally, the review addresses non-neoplastic enhancements such as meningoencephalitis, intracranial hypotension, cerebral
ischemia/infarction, epidural lipomatosis, syringomyelia, Sturge-Weber syndrome, and subarachnoid hemorrhage.

Conclusion:
By highlighting the imaging features and patterns associated with these conditions, the review underscores the critical role of accurate diagnosis
and timely management in improving patient outcomes. Enhanced understanding of these conditions can significantly improve patient outcomes
through timely and effective therapeutic interventions
SVMVGGNet-16: A Novel Machine and Deep Learning Based Approaches for Lung Cancer Detection Using Combined SVM and VGGNet-16
Authors: Ansari Mohd Munazzer , Kumar Shailendra , Heyat Md Belal Bin , Ullah Hadaate , Bin Hayat Mohd Ammar , Sumbul  , Parveen Saba , Ali Ahmad , Zhang Tao 
Published: January 2025

Background and Objective:
Lung cancer remains a leading cause of cancer-related mortality worldwide, necessitating early and accurate detection methods. Our study aims to
enhance lung cancer detection by integrating VGGNet-16 form of Convolutional Neural Networks (CNNs) and Support Vector Machines (SVM)
into a hybrid model (SVMVGGNet-16), leveraging the strengths of both models for high accuracy and reliability in classifying lung cancer types
in different 4 classes such as adenocarcinoma (ADC), large cell carcinoma (LCC), Normal, and squamous cell carcinoma (SCC).

Methods:
Using the LIDC-IDRI dataset, we pre-processed images with a median filter and histogram equalization, segmented lung tumors through
thresholding and edge detection, and extracted geometric features such as area, perimeter, eccentricity, compactness, and circularity. VGGNet-16
and SVM employed for feature extraction and classification, respectively. Performance matrices were evaluated using accuracy, AUC, recall,
precision, and F1-score. Both VGGNet-16 and SVM underwent comparative analysis during the training, validation, and testing phases.

Results:
The SVMVGGNet-16 model outperformed both, with a training accuracy (97.22%), AUC (99.42%), recall (94.22%), precision (95.28%), and F1-
score (94.68%). In testing, our SVMVGGNet-16 model maintained high accuracy (96.72%), with an AUC (96.87%), recall (84.67%), precision
(87.40%), and F1-score (85.73%).

Conclusion:
Our experimental results demonstrate the potential of SVMVGGNet-16 in improving diagnostic performance, leading to earlier detection and
better treatment outcomes. Future work includes refining the model, expanding datasets, conducting clinical trials, and integrating the system into
clinical practice to ensure practical usability.
HIV Infection Complicated with Cytomegalovirus Colitis: A Case Report of 18FFDG PET/CT Imaging
Authors: Fang Shengwei , Zhang Peipei 
Published: January 2025

Background:
Cytomegalovirus (CMV) infection is common in the digestive and central nervous systems and can infect the entire digestive tract from the mouth
to the rectum. In immunocompromised patients, CMV infection is prone to develop into CMV disease, especially in Acquired Immune Deficiency
Syndrome (AIDS) patients. Severe cases may accelerate the progression of AIDS patients and form systemic CMV infection. Timely diagnosis and
treatment are very important for the prognosis of patients.

Case Presentation:
In this paper, we report a 36-year-old man with a Human Immunodeficiency Virus (HIV) infection complicated with CMV colitis. Three weeks
ago, he developed abdominal pain with fresh blood in the stool, accompanied by anal pain. He was found to be HIV positive 8 years ago. An
enhanced CT scan showed edema and irregular thickening of the rectal wall, obvious enhancement of the mucosa, and multiple enlarged lymph
nodes around. 18F-FDG PET/CT imaging displayed diffuse rectum wall thickening and increased glucose metabolism, and the SUV max was 12.7.
There were multiple enlarged lymph nodes around the rectum, glucose metabolism was increased, and the SUVmax was 4.6.

Conclusion:
18F-FDG-PET imaging technology has potential value in the diagnosis of CMV colitis, especially in immunocompromised patients. Detection of
FDG concentrations in the colon wall can help diagnose CMV infection and understand the extent of the lesion, which is essential for the timely
initiation of antiviral therapy.
Targeting PD-1 in Squamous Cell Carcinoma: Flavonoid-based Therapeutics Unveiled through in silico and in vitro Approaches
Authors: Sharma Neha , Mazumder Rupa , Rai Pallavi , Debnath Abhijit 
Published: January 2025

Introduction:
Squamous cell carcinoma is a major public health concern, with traditional
treatments such as surgery, chemotherapy, and radiation therapy frequently resulting in
significant side effects. Immunotherapy targeting checkpoints such as PD-1, CTLA-4, and B7-
H3 provides a more specific approach but incurs high costs due to monoclonal antibodies.

Aim and Objective:
This study aims to investigate the potential of natural flavonoids as lowtoxicity,
small molecule-based alternatives targeting the PD-1 immunological checkpoint for
SCC treatment. It aims to identify and evaluate flavonoid compounds from the NPACT database
for their efficacy through in silico and in vitro screenings.

Method:
Employing a comprehensive in silico approach, including SBVS, Drug Likeness, Toxicity
Prediction, Consensus Molecular Docking, DFT, and 300 ns MD simulations, this study
screened for flavonoids with high affinity to PD-1. Identified lead molecules were further validated
through in-vitro assays, such as NRU, to assess their anticancer activities.

Result:
The flavonoid NPACT01407 showed high affinity for PD-1, favorable drug-like properties,
low toxicity, and effective stability at the active site, along with an optimal IC50 value,
highlighting its potential as an effective immunotherapeutic agent for SCC.

Conclusion:
The study highlights the potential of the flavonoid molecule NPACT01407 as a
promising candidate for the immunotherapeutic treatment of Squamous cell carcinoma. These
findings provide a solid basis for further experimental validation and drug development efforts,
suggesting a novel, less toxic, and cost-effective approach to cancer treatment.
Determination of Flavonoid Content in Brazilian Propolis Extracts by UV-Vis Spectroscopy and PLS Regression
Authors: Araujo Assimos Ariane , Donizeti Bernardes Cristina , Gabriela Aleme Helga , Jorge Sanches Barbeira Paulo 
Published: January 2025

Background:
The determination of flavonoid content in propolis is very important because
these substances are assigned various biological properties present in propolis and their content
is regulated by Brazilian legislation. The spectrophotometric method, based on the formation of a
yellow complex between Al(III) and carbonyl and hydroxyl groups of flavonoids, is the most used to
determine flavonoid content but is time-consuming (only after one hour the absorbance of the solutions
can be read) and reagents.

Objective:
This work proposes a simple method to determine flavonoid content using UV-Vis and
Partial Least Squares (PLS) regression.

Methods:
A robust PLS spectrophotometric method for the quantification of flavonoids in propolis,
based on spectra of ethanol-diluted samples, was developed and a complete validation was done in
this model, estimating several figures of merit.

Results:
The model built proved to be very effective, showing good results for flavonoid content,
with a range of 0.06 to 1.50 %mass, providing root mean square error of prediction (RMSEP) of 0.05
%mass.

Conclusion:
This proposed model has the advantage of being less laborious and faster, involves a
small amount of solvents, is an alternative to routine analysis, and can be used as a screening method.
Fabrication of a PVC Membrane Sensor Based on a HKUST-1
Metal-organic Framework for Direct Determination of Cysteamine in
Pharmaceutical Formulation
Authors: Kaya Lutfi , Coldur Fatih , Kanberoglu Gulsah Saydan 
Published: January 2025

Background:
The most common use of cysteamine is the treatment of cystinosis. Excessive intake of cysteamine can lead to serious side effects and health complications. Therefore, the
monitoring of cysteamine levels is highly significant.

Objective:
Several techniques have been developed to measure cysteamine accurately. Many of these
methods are constrained by various limitations, including labor-intensive pre-treatment procedures,
sophisticated equipment, skilled operators, and costly consumables. The present study aims to fabricate a cysteamine-selective potentiometric sensor based on HKUST-1 metal-organic framework
exhibiting a wider linear range and more sensitive potentiometric responses compared to the ion pairbased cysteamine-selective sensor that was developed previously

Methods:
A novel PVC membrane cysteamine-selective sensor was fabricated by coating the membrane cocktail consisting of poly(vinyl chloride), HKUST-1 metal-organic framework, plasticizer (onitrophenyloctylether), and ionic additive (potassium tetrakis (4-chlorophenyl) borate) onto the conductive solid contact surface. The potentiometric performance characteristics of the sensor were
evaluated in detail

Results:
The sensor exhibits a linear response to cysteamine concentration in the range of 1.0×10−6
M -1.0×10−2 M (R2
=0.9958) with a slope of 51.5 mV/decade and a detection limit of 8.0×10-7 M. It
operates effectively within a pH range of 3.9-5.7 and displays a rapid response time.

Conclusion:
Compared to the cysteamine-selective sensor available in the literature, the current sensor stands out with its wider linear operating range and lower detection limit. The sensor consistently
yields reproducible and stable potentiometric responses towards cysteamine. The fabricated cysteamine-selective sensor effectively quantifies cysteamine content in pharmaceutical formulations.
A Single-Arm, Open-Label, Phase Ib Clinical Study Evaluating the Efficacy and Safety of Durvalumab in Combination with Albumin-Bound Paclitaxel
and Carboplatin as Neoadjuvant Therapy for Resectable Stage III Non-Small Cell Lung Cancer
Authors: Zhong Yuejiao , Li Tao , Bai Zhaoshi , Qiu Ninglei , Liu Siwen , Xia Wenjia , Wei Qiang , Chen Lingxiang 
Published: January 2025

Objective:
This study aimed to explore the clinical efficacy and safety of durvalumab
combined with albumin-bound paclitaxel and carboplatin as neoadjuvant therapy for resectable
stage III Non-small Cell Lung Cancer (NSCLC).

Methods:
A single-arm open-label phase Ib study was conducted. A total of 40 patients with driver
gene-negative resectable stage III NSCLC were enrolled. All patients received neoadjuvant
treatment with durvalumab in combination with albumin-bound paclitaxel and carboplatin. The
clinical efficacy, Major Pathological Response (MPR), Complete Pathological Response (pCR),
and safety were assessed. Flow cytometry was used to detect the expression of programmed cell
death receptor 1 (PD-1) on total T, helper T, and cytotoxic T lymphocytes in peripheral blood before
and after neoadjuvant treatment. Adverse reactions during the treatment were recorded. Disease-
free Survival (DFS) and Overall Survival (OS) curves were constructed.

Results:
After the neoadjuvant treatment, the overall Objective Response Rate (ORR) in the 40 patients
with NSCLC was 65.00%. MPR was achieved in 27 patients (67.50%), and pCR was
achieved in nine patients (22.50%). The expression levels of PD-1 on total T, helper T, and cytotoxic
T lymphocytes in patients with NSCLC significantly decreased after treatment (all p < 0.05).
The most common adverse events were hair loss (47.50%), nausea and vomiting (42.50%), and fatigue
(40.00%). The majority of adverse events were grades 1 and 2, with a small number of
events being grades 3 and 4. At the end of the follow-up period, the average DFS was 21.49 ±
0.99 months, and the average OS was 24.79 ± 0.53 months.

Conclusion:
Neoadjuvant treatment with durvalumab combined with albumin-bound paclitaxel
and carboplatin as first-line therapy for driver gene-negative stage III NSCLC achieved a high
pathological response rate and improved immune function. It is expected to extend patient survival
with good tolerability.
Differential Expression and Distribution of Slco4a1 and Slco1b2 in an
Internal Environment Disorder-induced Hepatocellular Carcinoma Mouse
Model
Authors: Luo Haoxuan , Xie Yang , Huang Shan , Zhang Yu 
Published: January 2025

Objective:
This study aims to enhance the understanding of underlying mechanisms and potential therapies of the solute carrier organic anion (SLCO) transporter family in internal environment
disorder (IED)-induced hepatocellular carcinoma (HCC). This could lead to new therapeutic strategies
and offer new directions for the creation of new patents for HCC treatment products.

Methods:
The orthotopic transplantation (OT), IED and IED-based OT (IED-OT) mouse models were
established. Expression patterns of Slco4a1 and Slco1b2 were determined using reverse transcriptionquantitative polymerase chain reaction (RT-qPCR), western blotting (WB) and immunohistochemistry
(IHC) in various tissues, including lung, stomach, liver, spleen, kidney, colon, small intestine, HCC tissues and adjacent non-cancerous tissues.

Results:
Animals exhibited symptoms, including weight loss, lethargy, chills, dyspnea, altered hair texture, and gastrointestinal disturbances, confirming the successful establishment of the IED model. The
analysis demonstrated differential expression and tissue-specific distribution of Slco4a1 and Slco1b2,
which are associated with IED-induced changes. These alterations potentially disrupt organ transport
functions, thereby promoting the development of HCC. Additionally, they suggest a role in rebalancing
the tumor microenvironment and mitigating damage resulting from abnormal substance accumulation.

Conclusions:
Changes in SLCO expression and distribution induced by IED may play pivotal roles in
the development of HCC. These findings contribute insights that could inform novel therapeutic strategies against HCC.