bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research on the Anti-tumor Activity of Novel Histone Deacetylase Inhibitors based on 3D QSAR Model
Authors: Meng Liqiang , Yang Yanhong Ou , Yao Jianxin , Lv Fuyin , huo yuehong 
Published: October 2023

Abstract
Background
Histone deacetylases (HDACs) pertain to the category of Zn2+ or nicotinamide adenine dinucleotide (NAD+)-dependent proteolytic enzymes. While the antitumor effect of HDAC inhibitors alone has been demonstrated and the effect of HDAC inhibitors on solid tumors is not ideal, which considerably limits their clinical use. Therefore, the search for novel HDAC inhibitors equipped with specific inhibitors is extremely urgent and necessary.
Methods
3D-QSAR was employed to investigate insights into the crucial structural element that effect the activity of novel HDAC small molecule inhibitors. The best saliency CoMFA and CoMSIA models are obtained using 55 molecules in the training set and 16 molecules in the test set.
Results
The statistical quality of the generated model is demonstrated by internal and external cross-validations. The CoMFA model obtained satisfactory values (q2 = 0.664, r2 = 0.917, SEE = 0.217) while optimized CoMSIA model exceed with (q2 = 0.672, r2 = 0.948, SEE = 0.175).
Conclusion
The statistical parameters from 3D-QSAR models reveal that the results are reliable and significant with strong predictive ability. These theoretical results may contribute to the design of novel HDAC small molecule inhibitors with enhanced activity for the treatment of cancer.
From beauty to belief: The aesthetic and diversity values of plants and pets in shaping biodiversity loss belief among urban residents
Authors: Vuong Quan-Hoang , Duong Minh-Phuong Thi , Sari Ni Putu Wulan Purnama , La Viet-Phuong , Nguyen Minh-Hoang 
Published: October 2023

Abstract

Aesthetics is a crucial ecosystem service provided by biodiversity, which is believed to help improve humans’ quality of life and is linked to environmental consciousness and pro-environmental behaviors. However, how aesthetic experience induced by plants/animals influences the belief in the occurrence and significance of biodiversity loss among urban residents remains understudied. Thus, the current study aimed to examine how the diversity of pets and in-house plants affect urban residents’ belief in biodiversity loss in different scenarios of aesthetic experiences (positive and negative aesthetic experiences at home due to plants/animals). Using the Bayesian Mindsponge Framework (BMF) analytics on a dataset of 535 Vietnamese urban residents, we found that the people’s aesthetic feeling about their house induced by plants/animals positively affects their belief in the occurrence and significance of biodiversity loss. The diversity of plants and pets also positively influences the level of biodiversity loss belief, but the effect is conditional on the aesthetic experience of the urban residents. Specifically, the positive impact of species diversity on the belief only exists when urban residents feel that their houses’ aesthetics are negatively affected by plants/animals. Moreover, the effect of pet diversity on biodiversity loss belief is less significant and reliable than that of plant diversity. These findings suggest that raising the houses’ aesthetics through in-house planting or pet ownership can potentially enhance biodiversity loss belief and subsequently build an eco-surplus culture among urban residents.
Aerodynamic Characteristics of the Retro Propulsion Landing Burn of Vertically Landing Launchers
Authors: Marwege Ansgar , Gülhan Ali 
Published: October 2023

Abstract

In the frame of the European funded H2020 project RETALT (Retro Propulsion Assisted Landing Technologies) the unsteady aerodynamics of vertically descending and landing launchers have been investigated. In this paper experimental data of the landing burn tested in the Vertical Free-Jet Facility Cologne (VMK) at DLR in Cologne is presented. The landing burn was simulated with a cold gas jet of pressurized air opposing the wind tunnel free stream. Tests with several jet conditions were compared to results without active jet. Proper Orthogonal Decomposition of Schlieren recordings and spectral analyses of their time histories are performed and are compared to frequencies in pressure measurements. Dominant frequencies were found, which are strongest at Mach 0.8. Especially a Strouhal number of 0.2 was found to be most dominant. The intensity of the dominant frequencies, can be lowered if the engine is active. The normalized root mean square pressure fluctuations are between 0.1 and 0.3 during the landing maneuver. Additionally, the steady flow features scale well with the ambient pressure ratio and the momentum flux ratio.
The challenges of delivery in Pre-hospital Emergency Medical Services ambulances in Iran: a qualitative study
Authors: Sheikhi Rahim Ali , Heidari Mohammad 
Published: October 2023

Abstract

Background: Although encountering with unplanned births in the ambulance is uncommon, but the Emergency Medical Service (EMS) providers may face with it before arrival to hospital, that can accompany with problems and challenges for ambulance staff, pregnant women and neonates. This research was done to explain the experiences of EMS providers and pregnant women.
Methods: A qualitative study was conducted, and 28 Emergency Medical Technicians (EMTs), midwives and pregnant women who had experience of prehospital births in ambulance were interviewed. Data were analyzed with thematic content analysis also MAXQDA/10 software was used for data analysis and code extraction.
Results: The analysis of the interviews revealed two main categories. Factors that cause delivery in ambulance and its challenges. The factors include cultural problems, weak managers and inaccessibility to facilities and the challenges consist of fear and anxiety, native culture and lack of resources.
Conclusions: Several approaches should be taken to reduce birth in ambulances and Pre-hospital Emergency Medical Services (PEMS), including long-term cultural activities with community participation, public education and awareness-raising activities, education and follow-up of pregnant women with simultaneous increase accessibility to health facilities. Also, EMTs should be educated and trained about delivery in ambulance. Services improvement by providing proper and equipped ambulance as well as support EMTs against litigation claims are other important activities.
Plant and gastropod diversity across fragmented urban landscapes: patterns and environmental drivers
Authors: Čejka Tomáš , Jarolímek Ivan , Michalková Michaela , Šibíková Mária 
Published: October 2023

Abstract

Context.
Understanding biota distribution patterns and diversity within fragmented urban environments is essential for effective conservation and management.
Objectives.
The objective is to explore the impacts of fragmentation on plant and mollusc communities by examining their diversity and community composition in isolated urban forests and continuous forest stands along urban-rural gradients. The study aimed to explore plant and mollusc diversity variation across the urban-rural gradient in various landscape categories such as forest islands, peninsulas, and contiguous (control) stands and determine the responsible environmental drivers.
Methods.
The study surveyed 30 plots in Bratislava City, Slovakia, to evaluate the species richness and density of vascular plants and terrestrial gastropods in different landscape categories (see above); we also utilised microclimate data from selected plots.
Results.
The islands exhibited the highest number of non-native gastropod and plant species, whereas the control plots showed the lowest. Additionally, the forest islands were identified by an increased soil pH, coarse woody debris and litter content, enhancing the species richness of plants and molluscs. GLMs demonstrate that the landscape category had the most notable impact on the diversity of plants and molluscs. While fragmentation characteristics had an impact on the composition of plant species, they did not have a significant effect on the composition of molluscan communities.
Conclusions.
The research underlines the significance of landscape categories, environmental factors, and fragmentation characteristics when assessing biodiversity in urban forests. This finding can be used to formulate effective strategies for protecting native biota in fragmented urban forests.
Nomogram model for predicting early recurrence for resectable pancreatic cancer：A multicenter study
Authors: Man Quan , Pang Huifang , Liang Yuexiang , Chang Shaofei , Wang Junjin , Gao Song 
Published: October 2023

Abstract
This study aimed toestablish an accurate preoperative nomogram model for predicting early recurrence (ER) for resectable pancreatic adenocarcinoma.
We retrospectively analyzed patients who underwent pancreatectomy for pancreatic ductal adenocarcinoma between January 2011 and December 2020. The training set consisted of 604 patients, while the validation set included 222 patients.Survival was estimated using Kaplan–Meier curves. The factors influencing early recurrence of resectable pancreatic cancer after surgery were investigated, then the predictive model for early recurrence was established, and subsequently the predictive model was validated based on the data of the validation group.
The preoperative risk factors for ER included a Charlson age-comorbidity index ≥4 (odds ratio [OR]: 0.628), tumor size >3.0 cm on computed tomography (OR: 0.628), presence of clinical symptoms (OR: 0.515), carbohydrate antigen 19-9 >181.3 U/mL (OR 0.396), and carcinoembryonic antigen >6.01 (OR: 0.440). The area under the curve (AUC) of the predictive model in the training group was 0.711 (95% confidence interval: 0.669–0.752), while it reached 0.730 (95% CI: 0.663–0.797) in the validation group. The predictive model may enable the prediction of the risk of postoperative ER in patients with resectable pancreatic ductal adenocarcinoma, thereby optimizing preoperative decision-making for effective treatment.
WEAP Model Based Evaluation of Future Scenarios and Strategies for Sustainable Water Management in the Chennai Basin, India
Authors: RaziSadath Puthan Veettil , RinishaKartheeshwari Mariappan , Elango Lakshmanan 
Published: October 2023

Abstract

The gap between water supply and demand is increasing in several urban clusters of the world. This study uses the water evaluation and planning model to assess the water supply and demand dynamics in one of the large metropolitan regions of the Chennai hydrological basin. The primary water supply sources, including reservoirs, groundwater, inter-basin transfer, and desalination plants, were integrated into the model to simulate the current and future water demand and supply scenario. Three rainfall scenarios (excess, normal, and deficit) were utilized to assess their impacts on water supply. The study highlights the increase in unmet demand for normal and deficit rainfall scenarios. In response, various mitigation options were explored, including increasing groundwater recharge, reservoir capacity enhancement, water treatment plant expansion, additional storage, and utilization of water stored in rock quarries. The findings provide valuable insights for policymakers and stakeholders to develop sustainable water management strategies in the Chennai Basin.
Potential impacts of climate change on ecologically relevant flows: a case study in the Himalayan River basin
Authors: Pradhan Pragya , Shrestha Sangam , Shanmugam Mohana Sundaram 
Published: October 2023

Abstract

Understanding the potential impact of anthropogenic climate change on the hydrological regime of the Koshi River Basin (KRB) is very important for sustainable water resources and ecosystem management. The hydrological studies are mainly focused on the annual, seasonal, and peak flows of the hydrological regime; however, the ecologically relevant flows of the hydrological regime are less explored. In this study, we analyzed the different flow characteristics based on the magnitude, intensity, and duration using the Indicator of Hydrologic Alterations (IHA) under the influence of shared socio-economic pathway (SSP) scenarios. We found that the KRB will experience a shift in hydro-climatic events, an increase in rise and fall rates of flow, increase in monthly low flows of the hydrological regime, eventually affecting the livelihoods and ecosystem of the basin. This study highlights the importance of environmental flow components (EFCs) in a hydrological regime to better understand the flow characteristics during the future hydro-climatic variability.
Nucleoside Scaffolds and Carborane Clusters for Boron Neutron Capture Therapy: Developments and Future Perspective
Authors: Khalil Ahmed , Adam Mohamed Shaker S. 
Published: October 2023

:
Nucleosides containing carboranes are one of the most important boron delivery
agents for boron neutron capture therapy, BNCT, which are good substrates of hTK1.
The development of several nucleosides containing carboranes at early stages led to the
discovery of the first generation of 3CTAs by incorporating a hydrocarbon spacer between
the thymidine scaffold and carborane cluster and attaching dihydroxylpropyl group on the
second carbon (C2) atom of the carborane cluster (e.g., N5 and N5-2OH). Phosphorylation
rate, tumor cellular uptake, and retention have been evaluated in parallel to change
the length of the tether arm of spacers in these compounds. Many attempts were reported
and discussed to overcome the disadvantage of the first generation of 3CTAs by a) incorporating
modified spacers between thymidine and carborane clusters, such as ethyleneoxide,
polyhydroxyl, triazole, and tetrazole units, b) attaching hydrophilic groups at C2 of
the carborane cluster, c) transforming lipophilic closo-carboranes to hydrophilic nidocarborane.
The previous modifications represented the second generation of 3CTAs to
improve the hydrogen bond formation with the hTK1 active site. Moreover, amino acid
prodrugs were developed to enhance biological and physicochemical properties. The
structure-activity relationship (SAR) of carboranyl thymidine analogues led to the
roadmap for the development of the 3rd generation of the 3CTAs for BNCT.
Quantitative Structure-activity Relationship (QSAR) Modelling of Indomethacin Derivatives using Regression Analysis
Authors: Shukla Neerja , Sharma Bechan 
Published: October 2023

Background:
Indomethacin is a non-steroidal anti-inflammatory drug (NSAID)
used for medication to reduce fever, spondylitis, or shoulder pain. It mainly
works by the inhibition of prostaglandins, the endogenous signaling molecules.

Methods:
Fifteen indomethacin derivatives have been analyzed in relation to their physicochemical
and molecular properties. Two-dimensional (2D) structures of fifteen indomethacin
derivatives were drawn using the ACD Lab Chem Sketch version. Most of
the topological parameters, such as wiener index (W), mean wiener index (Wa), Balaban
indices (J), Balaban centric index (BAC), and molecular connectivity (χ), were calculated
by using E Dragon software. The most common molecular file formats accepted in EDragon
software were SMILES notations created online by Babel software and 2D structures
of various derivatives, which were converted into 3D optimized structures using online
CORINA, provided by Molecular Networks GMBH. 3D structures of compounds
were also drawn on Gauss View software for calculations of various density functional
theory (DFT) based quantum chemical descriptors, such as total energy (TE), softness
(S), hardness (η), chemical potential (μ), highest occupied molecular orbital energy (HOMO),
and lowest unoccupied molecular orbital energy (LUMO). All species were fully
optimized in the gas phase with a 6-31+G* basis set. The harmonic vibrational frequency
calculations were used to confirm that the optimized structures were minima, as characterized
by positive vibrational frequencies.

Results:
Combinations of various descriptors, such as D, ID, IOR, Log P, Mr, Mv, Mw,
Pc, BAC, Pz, St, W, Wa, 0χ, 1χ, 2χ,3χ,4χ, 5χ, and Xeq have been found to be significant
for modeling of activity. QSAR model no. 2: pIC50= -20.605 (±6.600) IOR - 0.747
(±0.454) I1 -5.083 (±3.478) Xeq + 51.647 optimized with empirical parameters with
high statistical quality (R= 0.921, R2=0.848) was found to be the best model obtained.

Conclusion:
The QSAR model obtained suggests that substituents with a lesser value of
the index of refraction and less electronegative groups were favourable for the activity,
whereas indomethacin derivatives with a CH2CH2NHCONH(CH2)3ONO2 group at R1 position
were unfavourable for the activity. The results were critically discussed based on
regression data and cross-validation techniques. Pogliani factor Q and the results of the
LOO (leave-one-out) method confirmed the reliability and predictability of the proposed
models that could be highly beneficial for the future designing of new analogues with
higher potency.
The Biological Significance of AFF4: Promoting Transcription Elongation,
Osteogenic Differentiation and Tumor Progression
Authors: Long Qian , Xiang Mingli , Xiao Linlin , Wang Jiajia , Guan Xiaoyan , Liu Jianguo , Liao Chengcheng 
Published: October 2023

Abstract:
As a member of the AF4/FMR2 (AFF) family, AFF4 is a scaffold protein in the superelongation
complex (SEC). In this mini-view, we discuss the role of AFF4 as a transcription
elongation factor that mediates HIV activation and replication and stem cell osteogenic differentiation.
AFF4 also promotes the progression of head and neck squamous cell carcinoma, leukemia,
breast cancer, bladder cancer and other malignant tumors. The biological function of AFF4
is largely achieved through SEC assembly, regulates SRY-box transcription factor 2 (SOX2),
MYC, estrogen receptor alpha (ESR1), inhibitor of differentiation 1 (ID1), c-Jun and noncanonical
nuclear factor-κB (NF-κB) transcription and combines with fusion in sarcoma (FUS), unique
regulatory cyclins (CycT1), or mixed lineage leukemia (MLL). We explore the prospects of using
AFF4 as a therapeutic in Acquired immunodeficiency syndrome (AIDS) and malignant tumors
and its potential as a stemness regulator.
Investigation of the Molecular Mechanisms Underlying the Therapeutic
Effect of Perilla frutescens L. Essential Oil on Acute Lung Injury Using
Gas Chromatography-Mass Spectrometry and Network Pharmacology
Authors: Chen Hou , Bai Lu , Shi Yanqiong , Zhang Xiaofei , Wang Xuan , Wang Yujiao , Hu Jiadong , Zhou Peijie 
Published: October 2023

Objective:
The present study aimed to investigate the molecular mechanism through
which Perilla essential oil treats acute lung injury (ALI) through network pharmacology, molecular
docking, and in vitro assays.

Methods:
Relevant ALI targets of the active ingredients of Perilla essential oil were predicted
using the SwissTargetPrediction database and meta TarFisher database. These ALI targets were
then screened using GeneCards and DisGeNET, and differentially expressed ALI target genes
were identified using the Gene Expression Omnibus (GEO) database. Next, key targets were enriched
using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).
Protein-protein interaction network analysis was performed to obtain targets with the highest
degree values for molecular docking with Perilla essential oil active ingredients. For in vitro experiments,
lipopolysaccharide (LPS) was used to induce an ALI inflammation model using
RAW264.7 cells. The model cells were then treated with Perilla essential oil to detect the protein
expression levels of vascular endothelial factor (NO), tumor necrosis factor (TNF-α), and
p65 nuclear transcription factor in them.

Results:
Sixty-eight key targets of Perilla oil were identified for the treatment of ALI. These targets
were found to be involved in biological processes related to peptides, response to lipopolysaccharides,
the positive regulation of cytokine production, etc., using GO. The signaling pathways
found to be associated with the targets included the AGE-RAGE signaling pathway in diabetic
complications, the NF-kappa B signaling pathway, and small cell lung cancer and other inflammatory
signaling pathways. The five key targets that showed good binding activity with Perilla oil active
ingredients included TNF, RELA, PARP1, PTGS2, and IRAK4. In vitro assays showed that
Perilla essential oil could significantly reduce NO and TNF-α levels and inhibit the phosphorylation
of nuclear transcription factor P65, thus inhibiting the activation of NF-κB signaling pathway.

Conclusion:
Perilla essential oil can play a role in the treatment of ALI by inhibiting the activation
of the NF-κB signaling pathway and preventing an excessive inflammatory response. This
study thus provides a reference for the in-depth study of the mechanisms through which Perilla
essential oil treats ALI.
Exploration of the Potential Mechanism of Yujin Powder Treating
Dampness-heat Diarrhea by Integrating UPLC-MS/MS and Network
Pharmacology Prediction
Authors: Jiang Li-dong , Zhang Wang-dong , Wang Bao-shan , Cai Yan-zi , Qin Xue , Zhao Wen-bo , Ji Peng , Yuan Zi-wen , Wei Yan-ming , Yao Wan-ling 
Published: October 2023

Background:
Yujin powder (YJP) is a classic prescription for treating dampness-heat
diarrhea (DHD) in Traditional Chinese Medicine (TCM), but the main functional active ingredients
and the exact mechanisms have not been systematically studied.

Objective:
This study aimed to preliminarily explore the potential mechanisms of YJP for treating
DHD by integrating UPLC-MS/MS and network pharmacology methods.

Method:
Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
technology was used to determine the ingredients of YJP. And then, the targets of these components
were predicted and screened from TCMSP, SwissTargetPrediction databases. The disease
targets related to DHD were obtained by using the databases of GeneCards, OMIM, DisGeNET,
TTD, and DrugBank. The protein-protein interaction networks (PPI) of YJP-DHD were constructed
using the STRING database and Origin 2022 software to identify the cross-targets by
screening the core-acting targets and a network diagram by Cytoscape 3.8.2 software was also
constructed. Metascape database was used for performing GO and KEGG enrichment anlysis on
the core genes. Finally, molecular docking was used to verify the results with AutoDock 4.2.6,
AutoDock Tools 1.5.6, PyMOL 2.4.0, and Open Babel 2.3.2 software.

Result:
597 components in YJP were detected, and 153 active components were obtained
through database screening, among them the key active ingredients include coptisine, berberine,
baicalein, etc. There were 362 targets treating DHD, among them the core targets included TNF,
IL-6, ALB, etc. The enriched KEGG pathways mainly involve PI3K-Akt, TNF, MAPK, etc. Molecular
docking results showed that coptisine, berberine, baicalein, etc., had a strong affinity with
TNF, IL-6, and MAPK14. Therefore, TNF, IL-6, MAPK14, ALB, etc., are the key targets of the
active ingredients of YJP coptisine, baicalein, and berberine, etc. They have the potential to regulate
PI3K-Akt, MAPK, and TNF signalling pathways. The component-target-disease network
diagram revealed that YJP treated DHD through the effects of anti-inflammation, anti-diarrhea,
immunoregulation, and improving intestinal mucosal injury.

Conclusion:
It is demonstrated that YJP treats DHD mainly through the main active ingredients
coptisine, berberine, baicalein, etc. comprehensively exerting the effects of anti-inflammation,
anti-diarrhea, immunoregulation, and improving intestinal mucosal injury, which will provide
evidence for further in-depth studying the mechanism of YJP treating DHD.