bluuebunny/crossref_metadata_2025_split huggingface dataset:
Four-color ImmunoSpot® assays requiring only 1-3 mL of blood permit precise frequency measurements of antigen-specific B cells secreting immunoglobulins of all four classes and subclasses
Authors: Yao Lingling , Becza Noémi , Maul-Pavicic Andrea , Chekpe Jack , Kirchenbaum Greg A. , Lehmann Paul V. 
Published: October 2023

Abstract
The B lymphocyte response can encompass four immunoglobulin (Ig) classes and four IgG subclasses, each contributing fundamentally different effector functions. Production of the appropriate Ig class/subclass is critical for both successful host defense and avoidance of immunopathology. The assessment of an antigen-specific B cell response, including its magnitude and Ig class/subclass composition, is most often confined to the antibodies present in serum and other biological fluids, and neglects the monitoring of the memory B cell (Bmem) compartment capable of mounting a faster and more efficient antibody response following antigen reencounter. Here, we describe how the frequency and Ig class and IgG subclass use of an antigen-specific Bmem repertoire can be determined with relatively little labor and cost, requiring only 8 x 105 freshly isolated peripheral blood mononuclear cells (PBMC), or if additional cryopreservation and polyclonal stimulation is necessary, 3 million PBMC per antigen. To experimentally validate such cell-saving assays, we have documented that frequency measurements of antibody-secreting cells (ASC) yield results indistinguishable from those of enzymatic (ELISPOT) or fluorescent (FluoroSpot) versions of the ImmunoSpot® assay, including when the latter are detected in alternative fluorescent channels. Moreover, we have shown that frequency calculations that are based on linear regression analysis of serial PBMC dilutions using a single well per dilation step are as accurate as those performed using replicate wells. Collectively, our data highlight the capacity of multiplexed B cell FluoroSpot assays in conjunction with serial dilutions to significantly reduce the PBMC requirement for detailed assessment of antigen-specific B cells. The protocols presented here allow GLP-compliant high-throughput measurements which should help to introduce high-dimensional Bmem characterization into the standard immune monitoring repertoire.
Distributed Muskingum model with a Whale Optimization Algorithm for river flood routing
Authors: Atashi Vida , Barati Reza , Lim Yeo Howe 
Published: October 2023

Abstract
This research introduces a novel nonlinear Muskingum model for river flood routing, aiming to enhance accuracy in modeling. It integrates lateral inflows using the Whale Optimization Algorithm (WOA) and employs a distributed Muskingum model, dividing river reaches into smaller intervals for precise calculations. The primary goal is to minimize the Sum of Square Errors (SSE) between the observed and modeled outflows. Our methodology is applied to six distinct flood hydrographs, revealing its versatility and efficacy. For Lawler's and Dinavar's flood data, the single-reach Muskingum model outperforms multi-reach versions, demonstrating its effectiveness in handling lateral inflows. For Lawler's data, the single-reach model (NR = 1) yields optimal parameters of K = 0.392, x = 0.027, m = 1.511, and β = 0.010, delivering superior results. Conversely, when fitting flood data from Wilson, Wye, Linsley, and Viessman and Lewis, the multi-reach Muskingum model exhibits better overall performance. Remarkably, the model excels with the Viessman and Lewis flood data, especially with two reaches (NR = 2), achieving a 21.6% SSE improvement while employing the same parameter set. This research represents a significant advancement in flood modeling, offering heightened accuracy and adaptability in river flood routing.
The Mechanisms of miRNAs on Target Regulation and their Recent Advances in Atherosclerosis
Authors: Yin Runting , Lu Hongyu , Cao Yixin , Zhang Jia , Liu Geng , Guo Qian , Kai Xinyu , Zhao Jiemin , Wei Yuan 
Published: October 2023

:
miRNAs are crucial regulators in a variety of physiological and pathological
processes, while their regulation mechanisms were usually described as negatively regulating
gene expression by targeting the 3’-untranslated region(3’-UTR) of target gene
miRNAs through seed sequence in tremendous studies. However, recent evidence indicated
the existence of non-canonical mechanisms mediated by binding other molecules
besides mRNAs. Additionally, accumulating evidence showed that functions of intracellular
and intercellular miRNAs exhibited spatiotemporal patterns. Considering that detailed
knowledge of the miRNA regulating mechanism is essential for understanding the
roles and further clinical applications associated with their dysfunction and dysregulation,
which is complicated and not fully clarified. Based on that, we summarized the recently
reported regulation mechanisms of miRNAs, including recognitions, patterns of
actions, and chemical modifications. And we also highlight the novel findings of miRNAs
in atherosclerosis progression researches to provide new insights for non-coding
RNA-based therapy in intractable diseases.
Integrating Network Pharmacology and Experimental Verification to Explore the
Targets and Mechanism for Panax Notoginseng Saponins against Coronary In-stent
Restenosis
Authors: Li Yuanchao , Gao Shenghan , Zhu Hongying , Wang Jianbo 
Published: October 2023

Background:
Despite widespread application of drug-eluting stents in coronary intervention,
in-stent restenosis (ISR) is still a daunting complication in clinical practice. Panax notoginseng saponins
(PNS) are considered to be effective herb compounds for preventing ISR.

Objective:
This study aimed to elucidate the targets and mechanisms of PNS in ISR prevention using network
pharmacology approaches and experimental verification.

Methods:
Relevant targets of PNS active compounds were collected from the HERB database and PharmMapper.
The ISR-related targets were obtained from the GeneCards database and the Comparative Toxicogenomics
Database. The GO and KEGG enrichment analysis was performed using R software. The String
database and Cytoscape software were employed to build the PPI and compounds-targets-pathways-disease
networks. Finally, Molecular docking performed by Autodock Vina and cellular experiments were used to validate
network pharmacology results.

Results:
There were 40 common targets between PNS targets and ISR targets. GO analysis revealed that these
targets focused on multiple ISR-related biological processes, including cell proliferation and migration, cell
adhesion, inflammatory response, and anti-thrombosis and so on. The KEGG enrichment results suggested
that PNS could regulate multiple signaling pathways to inhibit or delay the development and occurrence of
ISR. The molecular docking and cellular experiments results verified the network pharmacology results.

Conclusion:
This study demonstrated that the potential molecular mechanisms of PNS for ISR prevention
involved multiple compounds, targets, and pathways. These findings provide a theoretical reference and
experimental basis for the clinical application and product development of PNS for the prevention of ISR.
Morusin Inhibits RANKL-induced Osteoclastogenesis and Ovariectomized
Osteoporosis
Authors: Jin Cong , Zheng Jiewen , Yang Qichang , Jia Yewei , Li Haibo , Liu Xuewen , Xu Yangjun , Chen Zhuolin , He Lei 
Published: October 2023

Background::
Postmenopausal osteoporosis (PMOP) is a classic type of osteoporosis
that has gradually become a significant health problem worldwide. There is an urgent need for a
safe alternative therapeutic agent considering the poor therapeutic strategies currently available
for this disease. The roots and bark of the Morus australis tree (Moraceae) are used to make a
traditional Chinese medicine known as "Morusin", and accumulating evidence has demonstrated
its multiple activities, such as anti-inflammatory and anti-tumor effects.

Objective::
In this study, we aim to explore the effect of Morusin on mouse osteoclasts and its
mechanism.

Methods::
In this study, we explored the inhibitory effects of Morusin on murine osteoclasts in
vitro and its mechanism, and the protective effect of Morusin on an ovariectomy (OVX)-induced
osteoporosis model in vivo.

Results::
The results showed that Morusin prevented OVX-induced bone loss and dramatically
decreased RANKL-induced osteoclastogenesis. Morusin interfered with RANKL-activated NF-
κB, MAPK, and PI3K/AKT signaling pathways. The expression of three master factors that control
osteoclast differentiation, c-Fos, NFATc1, and c-Jun, was reduced by Morusin treatment.
Collectively, in vitro results indicated that Morusin has a protective effect on OVX-induced bone
loss in a mouse model.

Conclusion::
Our data provide encouraging evidence that Morusin may be an effective treatment
for PMOP.
Yantiao Formula Intervention in Rats with Sepsis: Network Pharmacology
and Experimental Analysis
Authors: Zhu Leilei , Liu Deng , Xu Menghan , Wang Wenqing , Xiong Xudong , Zhou Qianmei , Shi Rong 
Published: October 2023

Aim and Objective::
Traditional Chinese Medicine prescribes Yantiao Formula
(YTF; peach kernel, mirabilite, Angelica sinensis, Radix Scrophulariae, raw rhubarb, Radix
Paeoniae, Flos Lonicerae, Forsythia, and Ophiopogon japonicus) to treat sepsis. Clinically, it
reduced the inflammatory response of sepsis. It also reduced lung damage by decreasing the
level of TNF-α in septic rats' serum. Using network pharmacology analysis, we investigated the
efficacy network and mechanism of YTF in treating sepsis.

Materials and Methods::
We used the Traditional Chinese Medicine Systems Pharmacology
Database and Analysis Platform (TCMSP) and a Bioinformatics Analysis Tool for Molecular
Mechanisms of Traditional Chinese Medicine (BATMAN-TCM) combined with literature to
collect the main components in YTF and their targets. DisGeNET and GENECARDS databases
were used for sepsis-related targets. Cytoscape 3.7.1 software was used to construct the herbcomponent-
target and ingredient-target-disease interaction protein-protein interaction networks
of YTF. The jvenn was used to perform the intersection of YTF targets and sepsis targets. Gene
Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed．
We also created a sepsis rat model using cecal ligation and perforation and stimulated
alveolar macrophages (NR8383) with endotoxin to investigate the mechanisms of YTF.

Results::
GO, and KEGG enrichment analysis revealed that these targets involved mineralocorticoid
secretion, aldosterone secretion, active regulation of chronic inflammatory response, the
exogenous coagulation pathway, and other pathophysiology. It was linked to various inflammatory
factors and the MAPK pathway. YTF inhibits the p38MAPK pathway and decreases TNF-
α, IL-6, and CXCL8 levels.

Conclusion::
YTF has a multi-component, multi-target, and multi-channel role in treating sepsis.
The primary mechanisms may involve inhibiting the p38MAPK pathway to reduce the inflammatory
response.
A Lower IL-34 Expression Is Associated with Non-Healing Diabetic Foot
Ulcers
Authors: Zheng Aitian , Xu Yuanyuan , Cen Nimiao , Wu Biaoliang 
Published: October 2023

Background:
The non-healing of diabetic foot ulcers (DFU) is a major cause of high
disability, morbidity, and mortality. Thus, new therapeutic targets and methods to help healing
in patients with DFUs are major research hotspots

Objective:
This study examined the molecular differences between healing and non-healing
DFUs to identify genes associated with DFU healing.

Method:
Differentially expressed genes (DEGs) were identified by bioinformatics. Samples
were collected from patients with healing (n=10) and non-healing (n=10) DFUs from September
2021 to September 2022. Interleukin (IL)-34 expression was measured by ELISA and qRT-PCT.
The fibroblasts from healing and non-healing DFU were divided according to their gene signatures
and subdivided based on their gene expression profile differences.

Result:
A comparison of fibroblast subpopulation characteristics revealed that the proportion of
subpopulation 4 was significantly higher in non-healing DFUs than in healing DFUs. Subpopulation
4 had 254 upregulated genes and 2402 downregulated genes in the non-healing compared
with the healing DFUs. The DEGs were involved in several biological functions, including cytokine
activity, receptor-ligand activity, signaling receptor activator activity, and receptor regulator
activity. IL-34 was downregulated in non-healing compared with healing DFUs, suggesting
a possible role of IL-34 in DFU healing. In the clinical specimens, IL-34 was significantly
downregulated in non-healing DFUs, consistent with the bioinformatics results.

Conclusion:
IL-34 expression is downregulated in non-healing DFU. IL-34 appears to be
involved in DFU healing, but the exact causal relationship remains to be explored.
Natural and Synthetic Phosphodiesterase Inhibitors in 2023: an Update on
the Impact on Neurological and Psychiatric Conditions
Authors: Ribaudo Giovanni , Gianoncelli Alessandra 
Published: October 2023

Abstract:
This Perspective provides an updated overview on the involvement of phosphodiesterase (PDE)
isoforms and of the corresponding inhibitors in neurological disorders, including dementia, Parkinson’s
disease, multiple sclerosis, neuropsychiatric conditions and cerebral ischemia. Particular
attention has been dedicated to natural and semi-synthetic compounds. Translation into the clinic
of preclinical results, toxicity profile and bioavailability represent the challenging aspects in the
development of PDE inhibitors. With the aim of providing the latest updates to the reader, the
2023 contributions in the field were considered for the preparation of this Perspective.
Untargeted Metabolomic Analyses of Body Fluids to Differentiate
TBI DOC and NTBI DOC
Authors: Xiao Xiaoping , Xu Long , Lu Hezhen , Liu Xiaoyan , Sun Haidan , Guo Zhengguang , Sun Jiameng , Qi Feng , Niu Xia , Wang Aiwei , Ge Qianqian , Zhuang Yutong , Geng Xiaoli , Chen Xueling , Lan Ying , He Jianghong , Sun Wei 
Published: October 2023

Objective:
To investigate the metabolomic differences between Traumatic
brain injury (TBI) disorder of consciousness (DOC) patients and non-traumatic brain
injury (NTBI) DOC patients by using cerebrospinal fluid (CSF), serum and urine
samples beneficial to understand the pathological mechanism differences between the
two etiologies, provide potential clues for the subsequent treatment and prognosis, and
investigate the metabolome differences and similarities between TBI and NTBI among
three different body fluids.

Methods:
In total, 24 TBI DOC subjects and 29 NTBI DOC subjects were enrolled.
CSF, serum and urine samples from TBI DOC and NTBI DOC patients were collected
and analyzed by performing UPLC-MS. The statistical methods and pathway analyses
were applied to discover potential biomarkers and altered metabolic functions.

Results:
When comparing TBI DOC and NTBI DOC, 36, 31 and 52 differential
metabolites were obtained in CSF, serum and urine, respectively. The functional
analysis of differential metabolites obtained in CSF, serum and urine were all related to
amino acid metabolism. Except for amino acid metabolism, metabolic biomarkers in
CSF, serum and urine mainly focus on central function, cognitive function, necrosis
and apoptosis and neurological function, respectively. In CSF, the highest AUC was
0.864 (Isoproturon) and 0.816 (Proline betaine). Then, the AUC of NFurfurylformamide
in serum was 0.941, while the AUC of Dihydronepetalactone and
Doxepin N-oxide glucuronide were 1.0 in urine.

Conclusion:
CSF, serum and urine metabolomic analyses could differentiate TBI
DOC from NTBI DOC and functional analyses showed a metabolic change difference
between TBI DOC and NTBI DOC.
Observation on the Effect of Sequentially Combined Multi-modal
Artificial Liver Treatment on HBV-related Acute-on-chronic Liver
Failure
Authors: Zhou Xueshi , Miu Youhan , Guo Xiaoye , Wang Jun , Su Tingting , Du Hejuan , Wang Sen , Zhang Ying , Qiu Yuanwang , Zhao Weifeng 
Published: October 2023

Objective:
To observe the short-term effect of sequentially combined multimodal
artificial liver treatment (SCMALT) on HBV-related acute-on-chronic liver failure
(HBV-ACLF).

Methods:
HBV-ACLF patients 155 cases undergoing artificial liver treatment were
analyzed, and they were sorted into the SCMALT group and the conventional-modal
artificial liver treatment (CALT) group. The clinical data of all patients were recorded
and the serum levels of interleukin-8 (IL-8), chemokine interferon-inducible protein-10
(IP-10), and interleukin-6 (IL-6) were detected. The changes in the 30-day survival
rate, cytokine level, model for end-stage liver disease (MELD) score, and
complications of artificial liver treatment were analyzed.

Results:
After being followed up for 30 days, 104 patients survived and 51 died. At the
end of the whole-course treatment, the decreases in IL-6, IP-10, and IL-8 levels and
MELD scores in the SCMALT group were greater than in the CALT group. Cox
regression suggested WBC (OR=1.066, 95% CI 1.012-1.123, P=0.017), AT-III
activity (OR=0.935, 95% CI 0.907-0.964, p=0.000) at baseline, artificial liver
treatment mode (OR=0.362, 95% CI 0.164-0.800, p=0.012), number of artificial liver
treatments (OR=0.656 95% CI 0.436-0.986, p=0.043), spontaneous peritonitis
(OR=0.337, 95% CI 0.165-0.689, p=0.003), and hepatic encephalopathy (OR=0.104,
95% CI 0.028-0.388, p=0.001) were independent influencing factors of 30-day
survival rate. SCMALT can significantly prolong the survival period of the patient. No
obvious difference was shown in the proportions of bleeding and circulation instability
between the two groups (p>0.05).

Conclusion:
Compared with the CALT, SCMALT can more effectively remove
inflammatory mediators and reduce the MELD score in HBV-ACLF patients, which can
obviously ameliorate the prognosis, with less effect on the platelet count.
Targeting the AKT/mTOR/p70S6K Pathway for Oligodendrocyte Differentiation and Myelin Regeneration in Neurological Disorders
Authors: Ge Chen , Li Changwei 
Published: October 2023

Background:
The AKT/mTOR/p70S6K pathway has been shown to potentially promote
spinal cord injury (SCI) repair in rats. However, its exact mechanism and beyond needs to
be further explored.

Objective:
This study aims to explore the AKT/mTOR/p70S6K pathway in oligodendrocyte precursor
cell (OPC) differentiation, microglial polarization differentiation, and the role of these in
myelin regeneration in vitro.

Methods:
The isolation, induction and characterization of rat primary neuronal stem cells, OPCs
and oligodendrocytes were investigated with immunofluorescence and RT-qPCR. Then, the role
of AKT/mTOR/p70S6K signaling was explored using western blotting and immunofluorescence,
the effect on myelination was examined with OPC-dorsal root ganglion (DRG) neurons
co-culture, and the influence of M1/M2 polarization status of microglia on myelin formation was
also observed by adding M1/M2 supernatants into OPC-DRG neurons co-culture.

Results:
Activation of the AKT/mTOR/p70S6K pathway elevated the expression of oligodendrocyte
differentiation markers, including MBP, PLP and MOG, which also promoted the colocalization
of MBP and NFH in OPC-DRG neurons co-culture. More interestingly, stimulation
of the AKT/mTOR/p70S6K pathway facilitated M2 polarization of rat microglia. M2 polarization
of microglia enhanced OPC differentiation to oligodendrocytes and myelin formation.

Conclusion:
Our findings highlight the potential of targeting the AKT/mTOR/p70S6K pathway
in promoting oligodendrocyte differentiation and myelin regeneration in neurological disorders
such as SCI.
Method Validation and Monitoring of N-nitrosodimethylamine in Metformin Hydrochloride Products in China by GC-MS/MS
Authors: Zou Jia-jia , Yang Lin , Xu Xiao-li , Li Yan , He Dan 
Published: October 2023

Background:
N-nitrosodimethylamine (NDMA) are a sort of genotoxic impurities
(GTIs) having strong carcinogenic effects and obvious hepatotoxicity. To monitor the NDMA
content of metformin hydrochloride sustained-release tablets and enteric capsules in China
from 2018 to 2022, a GC-MS/MS method was established and validated.

Materials and Methods:
The chromatographic column was Agilent VF-WAXms capillary column
(30 m×0.25 mm, 0.25 μm). The GC-MS/MS method was equipped with multiple reaction
monitoring (MRM) modes. To assess the quantity of NDMA, the molecular ion at mass-tocharge
(m/z) of 74-44 was monitored under the 6 V collision energy, and to assess the quality
of NDMA monitoring, the molecular ions at m/z 74-42 were determined. A total of 143 batches
of metformin hydrochloride-finished products from 35 enterprises were determined by
this method

Results:
The linear range of the method was 0.25 ~ 50.00 ng/mL, r = 0.9998, S/N > 10, and the
limit of detection and quantitation were 0.06 ng/mL and 0.21 ng/mL, respectively. The average
recovery was 98.62%, and the RSD was 4.31%. All batches of enteric capsules met the requirements;
38.21% of the 123 batches sustained-release tablets still exceeded the acceptable daily
intake.

Conclusion:
The presented method is sensitive, accurate, precise, and available for both enteric
capsules and sustained-release tablets of metformin hydrochloride, which can provide a reference
for their quality control. The over-limit phenomenon of NDMA in metformin hydrochloride
products poses new challenges and requirements for both the State Drug Administration
and enterprises.
Impact of Mesenchymal Stem Cells on the Gut Microbiota and Microbiota
Associated Functions in Inflammatory Bowel Disease: A Systematic
Review of Preclinical Evidence on Animal Models
Authors: Liu Airu , Li Chenyang , Wang Chen , Liang Xiaonan , Zhang Xiaolan 
Published: October 2023

Background:
Inflammatory bowel disease (IBD) is a global health problem in which
gut microbiota dysbiosis plays a pivotal pathogenic role. Mesenchymal stem cells (MSCs) therapy
has shown promising application prospects for its powerful immune regulation and tissue repair
ability. Recent experimental data suggest that MSCs also regulate the composition of gut microbiota.
The current review analyzed, for the first time, the research data linking MSCs and gut microbiota
modulation in IBD models aiming at assessing the role of gut microbiota in MSCs repair
of IBD.

Methods:
A comprehensive and structured literature search was performed up to January 2023 on
the PubMed, Web of Science, and Scopus databases. The quality and risk of bias assessment followed
the PRISMA guidelines and SYRCLE's tool.

Results:
A total of nine pre-clinical studies on animal models were included. Although the dose
and route of MSCs applied were quite heterogeneous, results showed that MSCs displayed protective
effects on intestinal inflammation, including mice general assessment, immunoregulation,
and intestinal barrier integrity. Meanwhile, studies showed positive effects on the composition of
gut flora with MSCs administration, which had been characterized by restoration of Firmicutes/
Bacteroides balance and reduction of Proteobacteria. The beneficial bacteria Akkermansia,
Bifidobacterium, and Lactobacillus were also distinctly enriched, and the pathogenic bacteria
Escherichia-Shigella was conversely decreased. The alpha and beta diversity were also regulated
to resemble those of healthy mice. Microbial metabolic functions, such as biosynthesis of secondary
bile acid and sphingolipid metabolism, and some biological behaviors related to cell regeneration
were also up-regulated, while cancer function and poorly characterized cellular function
were down-regulated.

Conclusion:
Current data support the remodeling effect on gut microbiota with MSC administration,
which provides a potential therapeutic mechanism for MSCs in the treatment of IBD. Additional
studies in humans and animal models are warranted to further confirm the role of gut microflora
in MSCs repairing IBD.