bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duhuo Jisheng decoction alleviates neuroinflammation and neuropathic pain by suppressing microglial M1 polarization: a network pharmacology research
Authors: Gao Chengcan , Zhao Yulong , Yang Tao , Gao Xu , Meng Chunyang 
Published: August 2023

Abstract
Background
Neuropathic pain (NP) is the most prevalent form of chronic pain resulting from nerve damage or injury. Despite the widespread use of Duhuo Jisheng decoction (DHJSD) in traditional Chinese medicine (TCM) to treat chronic pain, the mechanism underlying its analgesic action remains unclear.

Methods
Using network pharmacology, we obtained DHJSD and NP-related target information from public databases to construct protein–protein interactions (PPI) and compound-target networks based on common target genes. These networks were further analyzed using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG). The interaction between molecules was verified through molecular docking using AutoDock Tools software. Additionally, we treated a chronic constriction injury (CCI) rat model with DHJSD and determined the mechanical withdrawal threshold (MWT). We used an enzyme-linked immunosorbent assay kit to determine the levels of inflammatory cytokines. Furthermore, qRT-PCR was employed to analyze ACHE, NOS2, MAPK3, PTGS2, AKT1, and PPARG mRNA expression, and immunofluorescence was used to evaluate changes in microglia.

Results
Our screening of compounds and targets identified 252 potential targets of DHJSD associated with NP. PPI analysis, along with GO and KEGG analyses, revealed that the potential mechanism of DHJSD in NP treatment may be related to inflammatory reactions, the IL-17 signaling pathway, MAP kinase activity, and endocrine activity. Based on molecular docking, the core target showed significant affinity for DHJSD's active components. Moreover, DHJSD treatment repaired the CCI-induced inflammatory reaction in the spinal cord while regulating the expression of ACHE, NOS2, MAPK3, PTGS2, AKT1, and PPARG mRNA. Immunofluorescence results indicated that the active components of DHJSD may regulate microglial M1 polarization to improve neuroinflammation, PPARG may have been involved in the process.

Conclusion
The multi-component, multi-target, and multi-pathway actions of DHJSD provide new insights into its therapeutic mechanism in NP.
Delayed surgery after hip fracture affects the incidence of venous thromboembolism
Authors: Taoka Takuya , Ohmori Takao , Kanazawa Tomoko , Toda Kazukiyo , Ishihara Takeshi , Ito Yasuo 
Published: August 2023

Abstract
Background
Venous thromboembolism (VTE) is one of the most common complications of hip fracture surgeries, and it is unclear whether delayed surgery affects the incidence of VTE. This study aimed to examine the association between delayed surgery and VTE incidence by statistically adjusting for factors that may influence VTE incidence.

Methods
We included 862 patients ≥ 65 years with hip fractures who underwent surgery between October 2010 and December 2020. We examined the effect of surgical delay 48 h after injury on postoperative VTE. Patients with and without VTE were assigned to groups V and NV, respectively. Those with and without proximal deep venous thrombosis (DVT) were assigned to PD and NPD groups, respectively. Univariate analysis was performed to identify factors that might influence DVT development. Risk factors for developing VTE and proximal DVT were analyzed using logistic regression analysis to determine whether delayed surgery was a risk factor.

Results
VTE was observed in 436 patients (40%) and proximal DVT in 48 patients (5.6%). Univariate analysis showed significant differences in the time from trauma to surgery between the V and NV groups and between the PD and NPD groups. In multivariate analysis, surgery 48 h later was also a risk factor for developing VTE and proximal DVT.

Conclusion
A delay in surgery beyond 48 h after a hip fracture injury is a risk factor for developing VTE and proximal DVT.
A review of anti-tumour effects of Ganoderma lucidum in gastrointestinal cancer
Authors: Ye Ting , Ge Yang , Jiang Xiaoying , Song Hang , Peng Can , Liu Bin 
Published: August 2023

AbstractGastrointestinal (GI) cancer is the most common cancer in the world and one of the main causes of cancer-related death. Clinically, surgical excision and chemotherapy are the main treatment methods for GI cancer, which is unfortunately accompanied with serious adverse reactions and drug toxicity, bringing irreversible damage to patients and seriously affecting the quality of life. Ganoderma lucidum (G. lucidum) has a long history of medicinal and edible use in China. Its bioactive compounds mainly include polysaccharides, triterpenes, and proteins, which have potential anti-tumor activities by inhibiting proliferation, inducing apoptosis, inhibiting metastasis, and regulating autophagy. Currently, there is no in-depth review on the anti-tumor effect of G. lucidum in GI cancer. Therefore, this review is an attempt to compile the basic characteristics, anti-GI caner mechanisms, and clinical application of G. lucidum, aiming to provide a reference for further research on the role of G. lucidum in the prevention and treatment of GI cancer from the perspective of traditional Chinese and western medicine.
Graphical Abstract
Global comparative transcriptomes uncover novel and population-specific gene expression in esophageal squamous cell carcinoma
Authors: Alotaibi Amal , Gadekar Veerendra P. , Gundla Pranav Swaroop , Mandarthi Sumana , Jayendra Nidhi , Tungekar Asna , Lavanya B. V. , Bhagavath Ashok Kumar , Cordero Mary Anne Wong , Pitkaniemi Janne , Niazi Shaik Kalimulla , Upadhya Raghavendra , Bepari Asmatanzeem , Hebbar Prashantha 
Published: August 2023

Abstract
Background
Esophageal squamous cell carcinoma (ESCC) has a poor prognosis and is one of the deadliest gastrointestinal malignancies. Despite numerous transcriptomics studies to understand its molecular basis, the impact of population-specific differences on this disease remains unexplored.

Aims
This study aimed to investigate the population-specific differences in gene expression patterns among ESCC samples obtained from six distinct global populations, identify differentially expressed genes (DEGs) and their associated pathways, and identify potential biomarkers for ESCC diagnosis and prognosis. In addition, this study deciphers population specific microbial and chemical risk factors in ESCC.

Methods
We compared the gene expression patterns of ESCC samples from six different global populations by analyzing microarray datasets. To identify DEGs, we conducted stringent quality control and employed linear modeling. We cross-compared the resulting DEG lists of each populations along with ESCC ATLAS to identify known and novel DEGs. We performed a survival analysis using The Cancer Genome Atlas Program (TCGA) data to identify potential biomarkers for ESCC diagnosis and prognosis among the novel DEGs. Finally, we performed comparative functional enrichment and toxicogenomic analysis.

Results
Here we report 19 genes with distinct expression patterns among populations, indicating population-specific variations in ESCC. Additionally, we discovered 166 novel DEGs, such as ENDOU, SLCO1B3, KCNS3, IFI35, among others. The survival analysis identified three novel genes (CHRM3, CREG2, H2AC6) critical for ESCC survival. Notably, our findings showed that ECM-related gene ontology terms and pathways were significantly enriched among the DEGs in ESCC. We also found population-specific variations in immune response and microbial infection-related pathways which included genes enriched for HPV, Ameobiosis, Leishmaniosis, and Human Cytomegaloviruses. Our toxicogenomic analysis identified tobacco smoking as the primary risk factor and cisplatin as the main drug chemical interacting with the maximum number of DEGs across populations.

Conclusion
This study provides new insights into population-specific differences in gene expression patterns and their associated pathways in ESCC. Our findings suggest that changes in extracellular matrix (ECM) organization may be crucial to the development and progression of this cancer, and that environmental and genetic factors play important roles in the disease. The novel DEGs identified may serve as potential biomarkers for diagnosis, prognosis and treatment.
Recent advances in targeted strategies for triple-negative breast cancer
Authors: Zhu Shuangli , Wu Yuze , Song Bin , Yi Ming , Yan Yuheng , Mei Qi , Wu Kongming 
Published: August 2023

AbstractTriple-negative breast cancer (TNBC), a highly aggressive subtype of breast cancer, negatively expresses estrogen receptor, progesterone receptor, and the human epidermal growth factor receptor 2 (HER2). Although chemotherapy is the main form of treatment for patients with TNBC, the effectiveness of chemotherapy for TNBC is still limited. The search for more effective therapies is urgent. Multiple targeted therapeutic strategies have emerged according to the specific molecules and signaling pathways expressed in TNBC. These include PI3K/AKT/mTOR inhibitors, epidermal growth factor receptor inhibitors, Notch inhibitors, poly ADP-ribose polymerase inhibitors, and antibody–drug conjugates. Moreover, immune checkpoint inhibitors, for example, pembrolizumab, atezolizumab, and durvalumab, are widely explored in the clinic. We summarize recent advances in targeted therapy and immunotherapy in TNBC, with the aim of serving as a reference for the development of individualized treatment of patients with TNBC in the future.
Ariadne: synthetic long read deconvolution using assembly graphs
Authors: Mak Lauren , Meleshko Dmitry , Danko David C. , Barakzai Waris N. , Maharjan Salil , Belchikov Natan , Hajirasouliha Iman 
Published: August 2023

AbstractSynthetic long read sequencing techniques such as UST’s TELL-Seq and Loop Genomics’ LoopSeq combine 3$$'$$

′

barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3$$'$$

′

unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read datasets to improve the taxonomic classification and de novo assembly of complex populations, such as metagenomes.
A high-resolution melting approach for the simultaneous differentiation of five human babesiosis–causing Babesia species
Authors: Wang Yanbo , Zhang Shangdi , Li Xiaoyun , Nian Yueli , Liu Xinyue , Liu Junlong , Yin Hong , Guan Guiquan , Wang Jinming 
Published: August 2023

Abstract
Background
Six species of apicomplexan parasites of the genus Babesia, namely B. microti, B. divergens, B. duncani, B. motasi, B. crassa–like and B. venatorum, are considered to be the primary causal agents of human babesiosis in endemic areas. These six species possess variable degrees of virulence for their primary hosts. Therefore, the accurate identification of these species is critical for the adoption of appropriate therapeutic strategies.

Methods
We developed a real-time PCR–high-resolution melting (qPCR-HRM) approach targeting 18S ribosomal RNA gene of five Babesia spp. based on melting temperature (Tm) and genotype confidence percentage values. This approach was then evaluated using 429 blood samples collected from patients with a history of tick bites, 120 DNA samples mixed with plasmids and 80 laboratory-infected animal samples.

Results
The sensitivity and specificity of the proposed qPCR-HRM method were 95% and 100%, respectively, and the detection limit was 1–100 copies of the plasmid with the cloned target gene. The detection level depended on the species of Babesia analyzed. The primers designed in this study ensured not only the high interspecific specificity of our proposed method but also a high versatility for different isolates from the same species worldwide. Additionally, the Tm obtained from the prepared plasmid standard is theoretically suitable for identifying isolates of all known sequences of the five Babesia species.

Conclusions
The developed detection method provides a useful tool for the epidemiological investigation of human babesiosis and pre-transfusion screening.

Graphical Abstract
Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples
Authors: Nishitani Shota , Fujisawa Takashi X. , Yao Akiko , Takiguchi Shinichiro , Tomoda Akemi 
Published: August 2023

AbstractBackgroundThe pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K array are lacking. A previous study demonstrated that the methylation levels obtained from individual samples were accurately replicated using pooled samples but did not address epigenome-wide association study (EWAS) statistics. The DNA quantification method, which is important for the homogeneous mixing of DNA in the pooled sample method, has since become fluorescence-based, and additional factors need to be considered including the resolution of batch effects of microarray chips and the heterogeneity of the cellular proportions from which the DNA samples are derived. In this study, four pooled samples were created from 44 individual samples, and EWAS statistics for differentially methylated positions (DMPs) and regions (DMRs) were conducted for individual samples and compared with the statistics obtained from the pooled samples.ResultsThe methylation levels could be reproduced fairly well in the pooled samples. This was the case for the entire dataset and when limited to the top 100 CpG sites, consistent with a previous study using the 450K BeadChip array. However, the statistical results of the EWAS for the DMP by individual samples were not replicated in pooled samples. Qualitative analyses highlighting methylation within an arbitrary candidate gene were replicable. Focusing on chr 20, the statistical results of EWAS for DMR from individual samples showed replicability in the pooled samples as long as they were limited to regions with a sufficient effect size.ConclusionsThe pooled sample method replicated the methylation values well and can be used for EWAS in DMR. This method is sample amount-effective and cost-effective and can be utilized for screening by carefully understanding the effective features and disadvantages of the pooled sample method and combining it with candidate gene analyses.
Practical guidelines for the use of gradient boosting for molecular property prediction
Authors: Boldini Davide , Grisoni Francesca , Kuhn Daniel , Friedrich Lukas , Sieber Stephan A. 
Published: August 2023

AbstractDecision tree ensembles are among the most robust, high-performing and computationally efficient machine learning approaches for quantitative structure–activity relationship (QSAR) modeling. Among them, gradient boosting has recently garnered particular attention, for its performance in data science competitions, virtual screening campaigns, and bioactivity prediction. However, different variants of gradient boosting exist, the most popular being XGBoost, LightGBM and CatBoost. Our study provides the first comprehensive comparison of these approaches for QSAR. To this end, we trained 157,590 gradient boosting models, which were evaluated on 16 datasets and 94 endpoints, comprising 1.4 million compounds in total. Our results show that XGBoost generally achieves the best predictive performance, while LightGBM requires the least training time, especially for larger datasets. In terms of feature importance, the models surprisingly rank molecular features differently, reflecting differences in regularization techniques and decision tree structures. Thus, expert knowledge must always be employed when evaluating data-driven explanations of bioactivity. Furthermore, our results show that the relevance of each hyperparameter varies greatly across datasets and that it is crucial to optimize as many hyperparameters as possible to maximize the predictive performance. In conclusion, our study provides the first set of guidelines for cheminformatics practitioners to effectively train, optimize and evaluate gradient boosting models for virtual screening and QSAR applications.
Graphical abstract
Partial response continuous phase modulation with a prolate spheroidal wave function for compass system in the S-band
Authors: Xue Rui , Xie Mingming 
Published: August 2023

AbstractContinuous phase modulation (CPM) has the characteristics of high power efficiency, spectral efficiency, and less out-of-band radiation, which is very suitable for the Compass S-band (2483.5–2500 MHz) with limited power and bandwidth. However, as more and more navigation systems share the S-band, the mutual interference between different systems is gradually increasing, and the compatibility of CPM signals with rectangular or raised cosine pulses needs to be further improved. To enhance the navigation performance and compatibility of current CPM candidate signals, we propose to apply continuous phase modulation with prolate spheroidal wave function (CPM-PSWF) to S-band navigation. The proposed modulation scheme selects PSWF with excellent time-frequency energy aggregation and flexible time-bandwidth product as the frequency pulse function of CPM. Then, the influence of key modulation parameters such as M, L, h, and C on CPM-PSWF power spectral density is analyzed, and a specific partial-response CPM-PSWF signal is proposed as the S-band candidate navigation signal. Finally, the navigation performance evaluation criteria are derived, and the proposed signal scheme and existing candidate schemes are comprehensively evaluated. Theoretical analysis and simulation results indicate that compared with CPM with BM2RC(8), cos-phase binary offset carrier (BOCc(4,4)), sin-phase binary offset carrier (BOCs(4,4)), minimum shift keying-BOCs (MSK-BOCs(4,4)) and binary offset carrier (BPSK(8)), the proposed signal scheme not only delivers exceptional spectral performance but also exhibits superior performance in code tracking accuracy and multipath suppression. In addition, in the acquisition and tracking phase, compared with other candidate signals except for BOCc(4,4), the mutual interference between the proposed signal scheme and most S-band signals is the lowest, which is easier to realize the compatibility of the Compass system with IRNSS, Galileo, and Globalstar systems.
Microscopic weathering mechanisms of subflorescence and crust patterns in the Nankan Grotto, northern Sichuan, China
Authors: Zhang Xuening , Ling Sixiang , Wu Xiyong , Xie Jiawen 
Published: August 2023

Abstract
The mineralogy, geochemical mass balance, sulfur isotope, and micro-structure of the sandstone in the Nankan Grotto were analyzed to explore the weathering mechanisms of the subflorescence and crust patterns. The results revealed that the mineralogical compositions of the rock samples from the subflorescence and crust sites were quartz, feldspar, calcite, and clay minerals. The calcite content was much higher in the crust site than that in the subflorescence site. Based on the microscopic petrographic evidence, the crystallization stress of the thenardite and calcite and the swelling/shrinking stress of the clay minerals led to the detachment of the outer rock layer, after which subflorescence became visible on the newly exposed surface. Solution migration carried Ca2+ from the interior of the rock to the surface, where it combined with CO3
2− and SO4
2− to produce gypsum and calcite on the surface during the drying process, resulting in the formation of the crust. Therefore, the mineralogical composition (especially the calcite content) laid the foundation for the distinct development of the subflorescence and crust. In addition, the microstructure and external environment influenced the amount and location of salt crystallization, eventually leading to thenardite crystallizing within the rock in the subflorescence site while the gypsum precipitated on the surface as a crust. The sulfur isotope analysis revealed that the sulfur in the subflorescence and crust sites was most likely derived from detergents and from the combustion of oil and natural gas. Our research revealed the microscopic weathering mechanisms of the subflorescence and crust patterns in the Nankan Grotto, providing insights on salt weathering mechanisms for stone heritage sites around the world.
Postharvest application of Aloe vera gel and thymol enhances shelf-life of duke cherries via altering physiochemical parameters
Authors: ValizadehKaji Babak , Fakhri Narges 
Published: August 2023

Abstract
Background
Duke cherry is a non-climacteric fruit but deteriorates quickly during storage due to thin pericarp and succulent fruit tissue. The application of edible coatings, essential oils, or their combination is an appropriate technique to maintain the quality characteristics and reduce the deterioration of fruits during storage. This research assessed the effect of Aloe vera gel (AVG), thymol, and their combined use on the physicochemical and qualitative properties of duke cherries kept at 5 °C and 80% relative humidity for 28 d.

Results
Compared to the uncoated fruits, duke cherries coated with a combination of AVG and thymol, showed more values of firmness (12.76–100.32%), total phenol (9.99–45.09%), antioxidant activity (7.90–84.56%), and sensory scores(50.15–100.00%), as well as the activity of guaiacol peroxidase (GPX) (12.03–185.11%) and catalase (CAT) (10.20–243.66%) enzymes during cold storage. Moreover, duke cherries coated with a combination of AVG and thymol had remarkably lower values of weight loss (32.57–42.67%), respiration rate (34.96–49.78%), stem browning (24.50–50.53%), spoilage percentage (84.55–100%), anthocyanin (14.21–23.16%), and total soluble solids/titratable acidity (TSS/TA) (35.64–50.15%), as well as hydrogen peroxide (H2O2) (16.66–32.35%) and malondialdehyde (MDA) (15.23–31.05%).

Conclusion
The application of AVG and thymol, particularly their combination, can have a high practical potential to extend shelf-life and preserve the quality of duke cherries during cold storage. This treatment has various advantages including natural, edible, cost-effective, and efficient.

Graphical Abstract