bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Cytotoxicity and Antimicrobial Activity of Experimental
Composites Containing Chitosan-Silver Oxide Particles Against Two Main
Pathogenic Bacteria in Periodontal Disease
Authors: Nasrabadi Nahid , Ramezanian Navid , Ghorbanian Parisa , Forouzanfar Ali , Mohammadipour Hamideh Sadat 
Published: November 2023

Introduction:
Bacterial biofilm is known as the main cause of periodontal disease.
Generally, the anaerobic Gram-negative, such as Porphyromonas gingivalis and Fusobacterium
nucleatum, are considered the most identified bacteria.

Objective:
This study aimed to investigate the antimicrobial effect and cytotoxicity of two
experimental composites containing chitosan-silver oxide (CH-Ag2O) particles.

Materials and methods:
Four experimental groups, including Ag2O and CH, along with two
composites of CH-Ag2O 20 and CH-Ag2O 60 mg, were prepared. Antimicrobial activity was
performed against Porphyromonas gingivalis (ATCC#33277) and Fusobacterium nucleatum
(ATCC#25586) using the agar dilution method. Moreover, the cytotoxicity assay was performed on
human gingival fibroblasts (HGF) by the use of the MTT method. The obtained data were analyzed
with descriptive methods, one-way ANOVA, and Tukey’s LSD tests.

Results:
The antibacterial activity of both composites was higher than both CH and Ag2O, and the
greatest antibacterial properties were presented in CH-Ag2O 60. In all three measurements (24, 48,
and 72h), the greatest cytotoxicity was seen in Ag2O, followed by CH, CH-Ag2O 20, and CH-Ag2O
60 in descending order, respectively. The cytotoxicity of these components was related to the
concentration and not to the time of exposure. The results showed that Ag2O in 3.7 and 7.5 μg/ml
concentrations and CH-containing groups in 250 and 500 μg/ml were toxic to the cultured HGF.

Conclusion:
The experimental composite containing CH-Ag2O 60 showed the greatest antibacterial
properties against two periodontal pathogens evaluated. In order to clarify the clinical significance
of composite cytotoxicity, further clinical studies are necessary.
Association of PD-L1 Expression with Clinicopathologic Characters
in Gastric Cancer: A Comprehensive Meta-analysis
Authors: Han Zhuo , Wang Nan , Qiao Qing , He Xianli , Wang Nan 
Published: November 2023

Purpose::
The expression level of programmed death ligand-1(PD-L1) in patients
with gastric cancer is the key to determining the use of immune drugs. The relationship
between PD-L1 expression level and clinical characteristics is worth exploring.

Methods::
By setting the search terms correlated to PD-L1 and gastric cancer, a nearly
comprehensive search was carried out in four major databases, and the deadline for
searching was September 1, 2022. The retrieved documents were further screened by
strict inclusion and exclusion criteria after removing the duplication. Next, the quality of
the included studies was evaluated with the Newcastle-Ottawa Scale (NOS) scale. Finally,
the STATA15.1 software was used to process data and draw plots, and the odds ratios
(ORs) were adopted to assess the pooled effect size.

Results::
A total of 85 works of literature were included in this study through screening
strictly, and detailed data were extracted after evaluating the quality of the literature.
The process of analysis was conducted in the whole population, Asia-Africa population,
European and American population, and Asian population with CPS≥1, amd all found
that the expression of PD-L1 in gastric cancer was correlated with age, tumor size, EBV
infection, Her-2 expression and microsatellite status. However, the subgroup of the region
also found some differences in Asian and Western regions, which was interesting
and worth studying further. The included research of this study did not have significant
publish bias.

Conclusion::
After careful analysis, this study found that age (>60 years), tumor size
(>5cm), EBV infection (+), Her-2 expression (+), microsatellite status (MSI), and mismatch
repair status (dMMR) were risk factors for positive expression of PD-L1 in gastric
cancer.
Impact of Breaking up of Sitting Time on Anti-inflammatory Response Induced by Extracellular Vesicles
Authors: Padilha Camila S. , Antunes Bárbara M. , Jiménez-Maldonado Alberto , St-Pierre David H. , Lira Fabio S. 
Published: November 2023

Abstract:Physical inactivity and sedentary behaviors (SB) have promoted a dramatic increase in the incidence of a host of chronic disorders over the last century. The breaking up of sitting time (i.e., sitting to standing up transition) has been proposed as a promising solution in several epidemiological and clinical studies. In parallel to the large interest it initially created, there is a growing body of evidence indicating that breaking up prolonged sedentary time (i.e., > 7 h in sitting time) could reduce overall mortality risks by normalizing the inflammatory profile and cardiometabolic functions. Recent advances suggest that the latter health benefits, may be mediated through the immunomodulatory properties of extracellular vesicles. Primarily composed of miRNA, lipids, mRNA and proteins, these vesicles would influence metabolism and immune system functions by promoting M1 to M2 macrophage polarization (i.e., from a pro-inflammatory to anti-inflammatory phenotype) and improving endothelial function. The outcomes of interrupting prolonged sitting time may be attributed to molecular mechanisms induced by circulating angiogenic cells. Functionally, circulating angiogenic cells contribute to repair and remodel the vasculature. This effect is proposed to be mediated through the secretion of paracrine factors. The present review article intends to clarify the beneficial contributions of breaking up sitting time on extracellular vesicles formation and macrophage polarization (M1 and M2 phenotypes). Hence, it will highlight key mechanistic information regarding how breaking up sitting time protocols improves endothelial health by promoting antioxidant and anti-inflammatory responses in human organs and tissues.
Insight into Early Diagnosis of Multiple Sclerosis by Targeting Prognostic Biomarkers
Authors: Puranik Nidhi , Yadav Dhananjay , Song Minseok 
Published: November 2023

Abstract:Multiple sclerosis (MS) is a central nervous system (CNS) immune-mediated disease that mainly strikes young adults and leaves them disabled. MS is an autoimmune illness that causes the immune system to attack the brain and spinal cord. The myelin sheaths, which insulate the nerve fibers, are harmed by our own immune cells, and this interferes with brain signal transmission. Numbness, tingling, mood swings, memory problems, exhaustion, agony, vision problems, and/or paralysis are just a few of the symptoms. Despite technological advancements and significant research efforts in recent years, diagnosing MS can still be difficult. Each patient's MS is distinct due to a heterogeneous and complex pathophysiology with diverse types of disease courses. There is a pressing need to identify markers that will allow for more rapid and accurate diagnosis and prognosis assessments to choose the best course of treatment for each MS patient. The cerebrospinal fluid (CSF) is an excellent source of particular indicators associated with MS pathology. CSF contains molecules that represent pathological processes such as inflammation, cellular damage, and loss of blood-brain barrier integrity. Oligoclonal bands, neurofilaments, MS-specific miRNA, lncRNA, IgG-index, and anti-aquaporin 4 antibodies are all clinically utilised indicators for CSF in MS diagnosis. In recent years, a slew of new possible biomarkers have been presented. In this review, we look at what we know about CSF molecular markers and how they can aid in the diagnosis and differentiation of different MS forms and treatment options, and monitoring and predicting disease progression, therapy response, and consequences during such opportunistic infections.
Cysteine-coated Magnetite Nanoparticles for the Removal of Carmoisine Edible Dye from Aqueous Medium
Authors: Nikzad Shalkouhi Somaye , Kefayati Hassan , Shariati Shahab 
Published: November 2023

Background:
In this study, cysteine-coated magnetite nanoparticles (Fe3O4@Cys
MNPs) were synthesized by chemical method and applied as a recoverable and efficient adsorbent
for the removal of carmoisine dye from aqueous solutions. The synthesized MNPs were
characterized by FT-IR, XRD, SEM, and TEM studies.

Methods:
The effect of various experimental parameters on the dye removal efficiency was studied
using Taguchi orthogonal array design (L16 array). Under the optimum conditions (pH = 2,
stirring time = 30 min, adsorbent amount = 0.1 g and without salt addition), more than 92% of
carmoisine was removed from the aqueous solutions.

Results:
The kinetic studies showed rapid adsorption dynamics by a pseudo second-order kinetic
model, confirming that diffusion controls the adsorption process. Dye adsorption equilibrium data
were fitted well to the Freundlich isotherm, and the synthesized adsorbent showed high
removal efficiency.

Conclusion:
The obtained results showed that the synthesized MNPs act as a reusable adsorbent
for carmoisine removal with an easy procedure.
Shoutai Pill Enhances Endometrial Receptivity in Controlled Ovarian Hyperstimulation Mice by Improving the In-Vivo Immune Environment
Authors: Liu Ziping , Zhang Jizhong , Li Liming , Zhang Tiane , Huang Li , Yin Qiaozhi 
Published: November 2023

Background:
The Shoutai pill (STP) is a classic formulation in traditional Chinese
medicine. Preliminary experimental observations from our study suggest that it is effective in
enhancing endometrial receptivity. However, the underlying mechanisms by which STP influences
endometrial receptivity remain to be elucidated.

Objective:
The objective of this study is to investigate the effects and mechanisms of the STP formulation
in enhancing endometrial receptivity in controlled ovarian hyperstimulation (COH) model mice.

Methods:
The network pharmacology analysis identified target proteins associated with the reduction
of endometrial receptivity by STP. The COH mouse model was established using the
GnRHa+PMSG+HCG protocol. The levels of MHC-1 and MHC-2 in mouse serum were measured
using the ELISA method, while the levels of IL-1β, IL-4, IL-10, IP-10, IL-1a, IL-2, IL-17,
TNF-a, and IFN-y were measured using liquid chip technology.

Results:
STP exhibited a significant improvement in the immune environment of COH model
mice. The major active components of STP were identified as beta-sitosterol and quercetin,
among others. Furthermore, AKT1, VEGFA, and several immune factors, such as TNF, IFN, IL-
1β, and IL-10, were identified as key targets for regulating endometrial receptivity. STP enhanced
the expression of IL-10, IL-4, and IP-10 in the mice while reducing the expression levels
of IL-2, IL-17, TNF-α, and IFN-γ in COH mice. These effects led to the modulation of early
high expression of IL-1β and an improvement in endometrial receptivity.

Conclusion:
This study demonstrates that STP can modulate in-vivo immune factors throughout
the COH process, subsequently restoring the immune equilibrium within the endometrium,
thereby enhancing the endometrial receptivity in the COH model mice.
Evaluation of Supervised Machine Learning Algorithms and Computational Structural
Validation of Single Nucleotide Polymorphisms Related to Acute Liver Injury
with Paracetamol
Authors: Sridharan Kannan , Balasundaram Ambritha , D Thirumal Kumar , C George Priya Doss 
Published: November 2023

Aims:
To identify single nucleotide polymorphisms (SNPs) of paracetamol-metabolizing enzymes that
can predict acute liver injury.

Background:
Paracetamol is a commonly administered analgesic/antipyretic in critically ill and chronic renal
failure patients and several SNPs influence the therapeutic and toxic effects.

Objective:
To evaluate the role of machine learning algorithms (MLAs) and bioinformatics tools to delineate the
predictor SNPs as well as to understand their molecular dynamics.

Methods:
A cross-sectional study was undertaken by recruiting critically ill patients with chronic renal failure and
administering intravenous paracetamol as a standard of care. Serum concentrations of paracetamol and the principal
metabolites were estimated. Following SNPs were evaluated: CYP2E1*2, CYP2E1_-1295G>C, CYP2D6*10,
CYP3A4*1B, CYP3A4*2, CYP1A2*1K, CYP1A2*6, CYP3A4*3, and CYP3A5*7. MLAs were used to identify the
predictor genetic variable for acute liver failure. Bioinformatics tools such as Predict SNP2 and molecular docking
(MD) were undertaken to evaluate the impact of the above SNPs with binding affinity to paracetamol

Results:
CYP2E1*2 and CYP1A2*1C genotypes were identified by MLAs to significantly predict hepatotoxicity.
The predictSNP2 revealed that CYP1A2*3 was highly deleterious in all the tools. MD revealed binding energy of
-5.5 Kcal/mol, -6.9 Kcal/mol, and -6.8 Kcal/mol for CYP1A2, CYP1A2*3, and CYP1A2*6 against paracetamol.
MD simulations revealed that CYP1A2*3 and CYP1A2*6 missense variants in CYP1A2 affect the binding ability
with paracetamol. In-silico techniques found that CYP1A2*2 and CYP1A2*6 are highly harmful. MD simulations
revealed CYP3A4*2 (A>G) had decreased binding energy with paracetamol than CYP3A4, and CYP3A4*2 (A>T)
and CYP3A4*3 both have greater binding energy with paracetamol.

Conclusion:
Polymorphisms in CYP2E1, CYP1A2, CYP3A4, and CYP3A5 significantly influence paracetamol's
clinical outcomes or binding affinity. Robust clinical studies are needed to identify these polymorphisms' clinical
impact on the pharmacokinetics or pharmacodynamics of paracetamol.
Pharmacodynamics Research on Danggui-Shaoyao-San through Body
Fluid Indexes of Spleen Deficiency-water Dampness Rats using
Bio-impedance Technology
Authors: Chen Ran , Yang Mo , Peng Can , Yin Dengke , Zhang Yunjing , Xu Fan 
Published: November 2023

Background::
Spleen deficiency-water dampness symptom is closely related to body
fluid-mediated organism metabolism and circulation. However, previous clinical evaluation of
spleen deficiency-water dampness model was based only on body weight, D-xylose excretion
rate, serum gastrin content, etc. Therefore, we established a large sample of normal rats and
model rats experiment to verify the scientific nature of bio-impedance measuring body fluid
indexes for evaluation of the modeling state. Pharmacodynamics research on Danggui-Shaoyao-
San (DSS) was conducted through body fluid index changes of rats using bio-impedance technology.

Methods::
A spleen deficiency-water dampness symptom rat model was established through an
inappropriate diet combined with excess fatigue. Experimental rats were divided into a normal
control group, a model control group, a positive drug control group (hydrochlorothiazide), a
blood-activating group, a water-disinhibiting group, and a DSS group. Total Body Water/Body
Weight (TBW%), extracellular fluid/total body water content (ECF%), intracellular fluid/total
body water content (ICF%), extracellular fluid/intracellular fluid (ECF/ICF), fat mass/body
weight (FM%), fat-free mass/body weight (FFM%), and fat mass/fat-free mass (FM/FFM) of
150 rats were detected by a Bio-Imp Vet Body analyzer.

Results::
The TBW% of the model control group increased significantly, and the FM/FFM was
significantly reduced compared with the normal group (P < 0.05) (P < 0.01), showing symptoms
of spleen deficiency and diarrhea; the TBW% of the blood-activating group, and the waterdisinhibiting
group decreased significantly, and the FM/FFM increased significantly (P < 0.05)
(P < 0.01). The TBW% and FM/FFM in the water-disinhibiting group had returned to nearnormal
values compared with the model control group. The blood-activating and waterdisinhibiting
split prescriptions in DSS are both effective in treating spleen deficiency-water
dampness rats. Comparatively, the fluid-regulating effect of split prescriptions in DSS was
even stronger than that of DSS as shown in the present study.

Conclusions::
These findings suggest that using bio-impedance technology to measure body fluid
indexes can pave a road for further exploring the molecular mechanism of the reason why the
blood-activating and disinhibit-water split prescriptions in DSS are both effective in treating
spleen deficiency-water dampness rats.
N-acetylcysteine Attenuates Cigarette Smoke-induced Alveolar Epithelial
Cell Apoptosis through Reactive Oxygen Species Depletion and
Glutathione Replenish In vivo and In vitro
Authors: Zhao Jie , Han Mi , Tian Yange , Zhao Peng , Liu Xuefang , Dong Haoran , Feng Suxiang , Li Jiansheng 
Published: November 2023

Background::
Chronic obstructive pulmonary disease (COPD) is the third leading
cause of death worldwide. N-acetylcysteine (NAC) is well known for its antioxidant properties,
along with potential protective effects on COPD. However, the molecular mechanism of NAC
against the apoptosis of alveolar epithelial cells (AECs) in COPD remains unclear.

Objective::
This study aimed to explore the anti-apoptosis effect of NAC in COPD mice and alveolar
epithelial cells.

Methods::
In the present study, the mouse model of COPD was established by cigarette smoke
(CS), and mouse alveolar epithelial (MLE-12) cells were treated with cigarette smoke extract
(CSE). TdT-mediated dUTP nick-end labeling (TUNEL) assay, reverse transcription polymerase
chain reaction (RT-PCR), and western blot were performed to evaluate the effects of NAC on
apoptosis, endoplasmic reticulum (ER) stress, and mitochondrial dysfunction. Meanwhile, LButhionine-
sulfoximine (BSO), a glutathione (GSH) inhibitor, was used to uncover the mechanism
of COPD treatment by NAC.

Results::
We found that NAC pretreatment could attenuate the protein levels of apoptosis, ER
stress, and mitochondrial dysfunction-related genes caused by CS in vivo. Meanwhile, CSE could
decrease MLE-12 cell viability, which was prevented by apoptosis inhibitor ZVAD-FMK but not
necroptosis inhibitor necrostatin-1. Pretreatment of MLE-12 cells with NAC increased cellular
GSH levels, inhibited cellular and mitochondrial reactive oxygen species (ROS) accumulation,
and decreased protein level of apoptosis, ER stress, and mitochondrial dysfunction-related genes.
Moreover, experiment results showed that BSO could completely reverse the beneficial effects of
NAC.

Conclusion::
Our study confirmed that NAC can attenuate CS-induced AEC apoptosis via alleviating
ROS-mediated ER stress and mitochondrial dysfunction pathway, and the mechanism was
found to be related to replenishing the cellular GSH content.
Complete Chloroplast Genomes of Pterodon emarginatus Vogel and
Pterodon pubescens Benth: Comparative and Phylogenetic Analyses
Authors: Brito Juliana Borges Pereira , Maria Antunes Adriana , dos Santos Braga  Ferreira Ramilla , de Campos Telles Mariana Pires , Pelegrineti Targueta Cíntia , Soares Thannya Nascimento 
Published: November 2023

Background:
The species Pterodon emarginatus and P. pubescens, popularly known as
white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use
and reforestation. They are sister species with evolutionary proximity.

Objective:
Considering that the chloroplast genome exhibits a conserved structure and genes, the
analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity
issues.

Methods:
The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina
MiSeq platform. The genomes were assembled based on the de novo strategy. We performed
the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity
and phylogenetic relationships were analyzed using the gene sequences of these species and
others of the Leguminosae family, whose genomes are available in databases.

Results:
The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens
is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127
genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the
inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens.
The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family
were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the
proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of
primers with potential for the development of molecular markers were designed.

Conclusion:
The genetic information obtained on the chloroplast genomes of P. emarginatus and P.
pubescens presented here reinforces the similarity and evolutionary proximity between these species,
with a similarity percentage of 99.8%.
Genome Sequencing and Organization of Three Geographically Different
Isolates of Nucleopolyhedrovirus from the Gypsy Moth Reveal Significant
Genomic Differences
Authors: Gencer Donus , Inan Cihan , Bayramoglu Zeynep , Nalcacioglu Remziye , Yin Feifei , Zhu Zheng , Wang Jun , Hu Zhihong , Pavlik Lillian , Arif Basil , Demirbag Zihni , Demir Ismail 
Published: November 2023

Background:
The gypsy moth (Lymantria dispar L., Lepidoptera: Erebidae) is a worldwide
pest of trees and forests. Lymantria dispar nucleopolyhedrovirus (LdMNPV) belongs to the
Baculoviridae family and is an insect virus specific to gypsy moth larvae. In this study, we describe
the complete genome sequences of three geographically diverse isolates, H2 (China), J2 (Japan),
and T3 (Turkey), of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV).

Methods:
The genomes of isolates H2, J2, and T3 were subjected to shotgun pyrosequencing using
Roche 454 FLX and assembled using Roche GS De Novo Assembler. Comparative analysis of all
isolates was performed using bioinformatics methods.

Results:
The genomes of LdMNPV-H2, J2, and T3 were 164,746, 162,249, and 162,614 bp in size,
had GC content of 57.25%, 57.30%, and 57.46%, and contained 162, 165, and 164 putative open
reading frames (ORFs ≥ 150 nt), respectively. Comparison between the reference genome
LdMNPV-5/6 (AF081810) and the genomes of LdMNPV-H2, J2, and T3 revealed differences in
gene content. Compared with LdMNPV-5/6, ORF5, 6, 8, 10, 31, and 67 were absent in LdMNPVH2,
ORF5, 13, and 66 were absent in LdMNPV-J2, and ORF10, 13, 31, and 67 were absent in
LdMNPV-T3. In addition, the gene encoding the mucin-like protein (ORF4) was split into two parts
in isolates H2 and T3 and designated ORF4a and ORF4b. Phylogenetic analysis grouped isolates
H2 and J2 in a different cluster than isolate T3, which is more closely related to the Turkish and
Polish isolates. In addition, H2 was found to be closely related to a South Korean LdMNPV isolate.

Conclusion:
This study provided a more detailed overview of the relationships between different
geographic LdMNPV isolates. The results showed remarkable differences between groups at the
genome level.