bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Review of High Impact CpG Sites and Regions for MGMT Methylation in Glioblastoma [A Systematic Review of MGMT Methylation in GBM]
Authors: Gibson David , Lambing Hannah , Bhattacharya Prithanjan , Vo Anh Huan , Tahir Peggy , Chehab Farid , Butowski Nicholas 
Published: October 2023

Abstract
Background
MGMT (O 6 -methylguanine-DNA methyltransferase) promoter methylation is a commonly assessed prognostic marker in glioblastoma (GBM). Epigenetic silencing of the MGMT gene by promoter methylation is associated with greater overall and progression free survival with alkylating agent regimens. To date, there is marked heterogeneity in how MGMT promoter methylation is tested and which CpG sites are interrogated.
Methods
To further elucidate which MGMT promoter CpG sites are of greatest interest, we performed comprehensive searches in PubMed, Web of Science, and Embase and reviewed 2,365 article abstracts. We followed the GRADE scoring system to Assess risk of bias and the quality of the studies we included.
Results
We included articles on adult glioblastoma that examined significant sites or regions within MGMT promoter for the outcomes: overall survival, progression free survival, and/or MGMT expression. We excluded systemic reviews and articles on lower grade glioma. Nine articles met inclusion criteria with variable overlap in laboratory and statistical methods employed, as well as CpG sites interrogated. Pyrosequencing or BeadChip arrays were the most popular methods utilized, and CpG sites between CpG’s 70–90 were most frequently investigated. Overall, there was moderate concordance between the CpG sites that the studies reported to be highly predictive of prognosis. Combinations or means of sites between CpG’s 73–89 were associated with improved OS and PFS. Four studies identified CpG sites associated with prognosis that were closer to the transcription start site: CpG’s 8, 19, 22, 25, 27, 32, and 38.
Conclusion
The following systematic review details a comprehensive investigation of the current literature and highlights several potential key CpG sites that demonstrate significant association with OS, PFS, and MGMT expression. However, there were several limitations within the studies such as smaller sample sizes, variance between methylation testing methods, and differences in the various statistical methods to test for association to outcome.
Pilot implementation of group-based psychotherapy led by nonspecialists for lung cancer patients with depression at Vietnam National Cancer Hospital
Authors: Do Mai Tuyet , Linh Linh Thi Thuy , Nguyen Tam Thanh , Tran Huong Thi Thanh 
Published: October 2023

Abstract
Aim: The prevalence of non-small cell lung cancer (NSCLC) is high, with an increasing global disease burden. This is the first study to evaluate the effectiveness of group-based psychotherapy in patients with NSCLC and depression in Vietnam during the COVID-19 pandemic.
Methods: A non-randomized controlled intervention study was conducted on 40 depressed adult patients with NSCLC at the Vietnam National Cancer Hospital (VNCH) from August 2021 to August 2022. Depression was screened for and followed up using the Patient Health Questionnaire, nine items (PHQ-9) with a cutoff 8. The virtual group intervention consisted of eight weekly sessions with the facilitation of two trained non-specialists under the supervision of a specialist. Quantitative data from 16 participants in each arm were analyzed using proper statistics, with a statistical significance 0.05.
Results: Depression remission was observed in both groups. The decrease in the median PHQ-9 score of the intervention group (from 10.5 to 7) was higher than that of the control group (from 10.5 to 9 score). However, this difference was not statistically significant (p>0.05). The intervention reduced the risk of depression by 29% compared with the control group (RR=0.71, p<0.05). In the intervention group, five subjects who remained depressed participated in fewer sessions than the control group’s figure (1.4 vs 5.1 average) with p < 0.05.
Conclusion: The group psychological intervention led by non-specialists is a promising approach to managing mental health problems in cancer patients, especially in online formats with low cost to adapt to limited-resource contexts.
Attention-based Multimodal learning framework for Generalized Audio- Visual Deepfake Detection
Authors: Masood Momina , Javed Ali , Irtaza Aun 
Published: October 2023

Abstract
Deepfake media proliferated on the internet has major societal consequences for politicians, celebrities, and even common people. Recent advancements in deepfake videos include the creation of realistic talking faces and the usage of synthetic human voices. Numerous deepfake detection approaches have been proposed in response to the potential harm caused by deepfakes. However, the majority of deepfake detection methods process audio and video modality independently and have low identification accuracy. In this work, we propose an ensemble multimodal deepfake detection method that can identify both auditory and facial manipulations by exploiting correspondence between audio-visual modalities. The proposed framework comprises unimodal and cross-modal learning networks to exploit intra- and inter-modality inconsistencies introduced as a result of manipulation. The suggested multimodal approach employs an ensemble of deep convolutional neural-network based on an attention mechanism that extracts representative features and effectively determines if a video is fake or real. We evaluated the proposed approach on several benchmark multimodal deepfake datasets including FakeAVCeleb, DFDC-p, and DF-TIMIT. Experimental results demonstrate that an ensemble of deep learners based on unimodal and cross-modal network mechanisms exploit highly semantic information between audio and visual signals and outperforms independently trained audio and visual classifiers. Moreover, it can effectively identify different unseen types of deepfakes as well as robust under various post-processing attacks. The results confirm that our approach outperforms existing unimodal/multimodal classifiers for audio-visual manipulated video identification.
Mining Analysis of the Spatiotemporal Evolution Characteristics of Rapeseed Production Layout Based on Big Data Visualization
Authors: Keyi Liu , Yunpeng Cui 
Published: October 2023

Abstract
As one of China's important oilseed crops, the optimization of rapeseed production layout holds significant importance for the restructuring of the country's agricultural industry. This study employs a large-scale data mining and analysis model to quantify the evolution of rapeseed production centroid in both the entire nation and Hubei Province. Leveraging the visualization tool Qlik Sense for thematic design, two themes emerge: "Spatiotemporal Evolution Characteristics of National Rapeseed Production Layout" and "Spatiotemporal Evolution Characteristics of Rapeseed Production Layout in Hubei Province". These visualization themes feature robust interactive effects, enabling a flexible presentation of the spatiotemporal evolution characteristics of the rapeseed production layout. By examining the migration paths, magnitudes, and directions of production centroids, a quantitative exploration of the dynamic spatiotemporal evolution patterns of rapeseed production on both national and provincial scales is conducted, providing foundational support for decision-making concerning the spatial layout of rapeseed production.
Performance evaluation of seasonal precipitation forecasting using NMME over West Africa
Authors: Tchinda Armand Feudjio , Tanessong Roméo Stève , Nonki Rodric Mérimé , Mamadou Ossénatou , Yepdo Zephirin Djomou 
Published: October 2023

Abstract
In West Africa (WA) in recent years, users in agriculture, hydrology, disaster risk management, health and many other sectors have expressed a growing demand for high-resolution seasonal forecasts with a sufficient lead time for response planning. We present a regional evaluation of precipitation forecasts from 14 North American Multi-Model Ensemble (NMME) seasonal forecast models, using Global precipitation Climatology Centre (GPCC) and Africain Rainfall Climatology Version 2 (ARC2) as a reference over the June-September (JJAS) season. We first assessed the quality of the forecasts in reproducing the climatology, then the quality of each individual model as well as the ensemble model in predicting the quality of forecasts in WA at a 0–5 month lead time. The results show that NMME models capture the seasonal rainfall climatology of the JJAS season over the central, and southeastern parts of WA around 11 mm/day. We found that, in most cases, precipitation skill was highest during the first lead time (i.e. the initialization month's forecasts) and declined rapidly thereafter. The performance of each model in forecasting seasonal precipitation for the JJAS season shows a high ability to predict normal conditions, and appears not to predict below- and above-normal seasons well (Probability of Detection (POD) of less than 40%). Overall, the performance of the NMME ensemble mean (MME) was not consistently better than that of a single individual model, underlining the need for more advanced weight-based averaging schemes. The NMME forecasting system offers a promising skill set for forecasting seasonal precipitation over WA during the JJAS season at first lead time.
Wildlife target detection based on improved YOLOX-s network
Authors: XiaoAn Bao , LinQing Zhou , XiaoMei Tu , Biao Wu , QingQi Zhang , YuTing Jin , Na Zhang 
Published: October 2023

Abstract
Addresses the problem of poor detection accuracy or even false detection of wildlife caused by rainy environment at night. In this paper, a wildlife target detection algorithm based on improved YOLOX-s network is proposed. The algorithm improves the accuracy of wildlife detection at night, rainy day and reduces the probability of false detection of wildlife in this complex environment. Firstly, the MobileViT-Pooling module is proposed based on the MobileViT attention mechanism, which uses a spatial pooling operator with no parameters as a token mixer module to reduce the number of network parameters. This module performs feature extraction on three feature layers of the backbone network output respectively, senses the global information and strengthens the weight of the effective information. Secondly, the Dynamic Head module is used on the downstream task of network detection, which fuses the information of scale sensing, spatial sensing, and task sensing and improves the representation ability of the target detection head. Finally, the Focal idea is utilized to improve the IoU loss function, which balances the learning of high and low quality IoU for the network. The wildlife dataset used in this paper is from a provincial nature reserve in Zhejiang Province。Experimental results show that the improved YOLOX-s network achieves an mAP@0.5 of 87.8%, an increase of 7.9%, and an mAP@0.5:0.95 of 62.0%, a 5.3% improvement.
Single Cell Multiome Atlas of the Human Developing Retina
Authors: Chen Rui , Zuo Zhen , Cheng Xuesen , Ferdous Salma , Shao Jianming , Li Jin , Liu Jiaxiong , Jacobo Antonio , Li Yumei , Moshiri Ala 
Published: October 2023

Abstract

Development of retina is under tight temporal and spatial control. To gain insights of the molecular underpinning of this process, we generated a single-nuclei multiome atlas of the human developing retina with approximately 300,000 nuclei from 12 donors aged between 10 and 23 weeks post-conception with matched macula and peripheral regions from each donor. This atlas captures all major cell classes and over 50 cell types in the retina along with a large proportion of progenitors and cell-type-specific precursors. Cell trajectory analysis reveals a transition from continuous progression in early progenitor cells to a hierarchical development during the later stages of cell type specification. Both known and novel candidate transcription factors, along with gene regulatory networks that drive the transitions of various cell fates, are identified. Comparisons between macular and peripheral retina indicate a largely consistent yet distinct developmental pattern. In particular, the retinoic acid pathway emerges as a potential key driver for retinal patterning. This multiome developing retina atlas offers unparalleled resolution into the transcriptional and chromatin accessibility landscape during development, presenting an invaluable resource for deeper insights into retinal development and associated diseases.
Macrophages reside in the muscle spindle to control sensorimotor function at millisecond timescale
Authors: Giovanni Simone Di , Yan Yuyang , Vargas Irene , Xu Luyang , Antolin Nuria , Kong Guiping , Palmisano Ilaria , Yi Yang , Chadwick Jessica , Mueller Franziska , Bull Anthony , Celso Cristina Lo , Primiano Guido , Servidei Serenella , Bellardita Carmelo 
Published: October 2023

Abstract

The stretch reflex is a fundamental component of the motor system that orchestrates the coordinated muscle contractions underlying movement. At the heart of this process lie the muscle spindles (MS), specialized receptors finely attuned to fluctuations in tension within intrafusal muscle fibers. The tension variation in the MS triggers a series of neuronal events; an initial depolarization of sensory type Ia afferents that subsequently causes the activation of a motoneurons within the spinal cord. This neuronal cascade culminates in the execution of muscle contraction, underscoring a presumed closed-loop mechanism between the musculoskeletal and nervous systems.
In contrast, surprisingly here we report the discovery of a new population of macrophages with exclusive molecular and functional signatures within the muscle spindle that express the machinery for synthesizing and releasing glutamate. Using mouse intersectional genetics with optogenetics and electrophysiology, we show that activation of muscle spindle macrophages (MSMP) drives proprioceptive sensory neuron firing at a millisecond timescale. This subsequently activates spinal circuits, motor neurons, and muscles via a glutamate-dependent mechanism. Additionally, we found that MSMP can also respond to the activation of the stretch reflex circuitry by increasing the expression of glutaminase, enabling them to convert the glutamine released by myocytes during muscle contraction into glutamate.
Our results have identified a new cellular component, the MSMP, that directly regulates neural activity and muscle contraction. The glutamate-mediated signalling of MSMP and their dynamic response to sensory cues introduces a novel dimension to our understanding of sensation and motor action, potentially offering innovative therapeutic approaches in conditions that affect sensorimotor function.
Identification of Immune-related Core Genes Based on Immune Signatures of Age-related Macular Degeneration
Authors: Ge Panpan , Cao Guoping , Zhou Kun 
Published: October 2023

Abstract
Background
Age-related macular degeneration (AMD) is a disease that affects the retina and choroid and is the leading cause of blindness in older adults. Despite the prevalence of this disease, its etiology and pathogenesis are unknown, and many studies have shown that the immune system plays an important role in the development and progression of age-related macular degeneration. Here, we aimed to explore the immune profile of different stages of age-related retinopathy and to identify immune-related biomarkers that could improve the treatment of patients with age-related retinopathy.
Methods
Publicly available gene expression profiles of AMD samples at different stages of the disease were downloaded from the GEO database (GSE115828 dataset). The activity of 19 immune signatures in AMD retinal samples was assessed using ssGSEA, and the changes in immune levels at different stages of AMD were compared. Differential expression analysis was performed on advanced AMD samples, and the screened immune-related differentially expressed genes (DEGs) were used as a candidate gene set. We constructed an AMD-related model based on AMD immune-related DEGs by logistic regression and least absolute shrinkage and selection operator (LASSO), which was also verified by ROC curve. Finally, protein-protein interaction (PPI) networks were mapped using STRING and further analyzed using Cytoscape software.
Results
As AMD progresses to advanced stages, the activity of 13 immune signatures gradually increases. A total of 91 immune-related DEGs were identified by differential expression analysis and further submitted to LASSO regression model for screening, and a total of 12 core genes were identified (AUC = 0.827). Three important clusters with a high degree of intermolecular interactions were identified in the PPI network, revealing three major molecular mechanisms, including MHC class II antigen processing and presentation, microglia activation and complement activation.
Conclusion
Multiple immune signatures play an important role in the development of age-related macular degeneration. Twelve core immune-related genes were identified that warrant investigation in experimental and clinical studies. PPI network analysis revealed three immune-related molecular mechanisms of AMD.
Effects of Xenorhabdus and Photorhabdus bacterial metabolites on the ovipositional activity of Aedes albopictus
Authors: Touray Mustapha , Cimen Harun , Bode Edna , Bode Helge B. , Hazir Selcuk 
Published: October 2023

Abstract
Viral diseases like yellow fever, dengue, zika have an alarming impact on public health affecting millions of people around the globe. These diseases can be transmitted by Aedes albopictus – a species originally endemic to South Asia but now widely distributed in several countries outside Asia. Xenorhabdus and Photorhabdus spp., are enteric Gram-negative bacterial symbionts of insect-preying nematodes and are known to produce an array of natural products (NP) with various activities including larvicidal activity. This study demonstrated that supernatants of different Xenorhabdus and Photorhabdus bacteria effectively deterred Ae. albopictus mosquito oviposition in a concentration dependent manner. Xenorhabdus cabanillasii displayed deterrent effects at 50-5% concentrations with oviposition activity index values ranging between -0.87 and -0.35, whereas the index values for X. nematophila were between -0.82 and -0.52 at concentrations of 50-10%. The other bacteria (X. szentirmaii, X. doucetiae, and P. kayaii) were effective at concentrations ≥20%. Using promoter exchange mutants of selected biosynthetic gene clusters in a Δhfq background generated by the easyPACId approach, fabclavine from X. szentirmaii was identified as the bioactive compound with evident deterrent effects. Such compounds with deterrence effects could be useful in mosquito control programs as preventing breeding site in specific habitats can greatly influence mosquito species establishment, population densities, and dispersion in conducive areas.
GC-MS Analysis, Antioxidant, and Antidiabetic Properties of Methanol Extract of
Annona muricata L. Leaves - An In vitro and In silico Study
Authors: Mishra Abhay Prakash , Nigam Manisha , Nambooze Jennifer , Salau Veronica F. , Olofinsan Kolawole A. , Iriti Marcello , Matsabisa Motlalepula G. 
Published: October 2023

Abstract:
The Annona muricata L. leaves have been long employed in the traditional remedy of
diabetes mellitus (DM) and its comorbidities. Different analytical techniques were used to evaluate
the methanol extract of this plant part. In vitro antidiabetic assays of A. muricata extract were analysed
using α-glucosidase and α-amylase inhibition tests. Employing gas chromatography-mass
spectrometry (GC-MS), the primary bioactive components of the methanol extract were identified.
Additionally, molecular docking experiments regarding the identified compounds were performed
by silicification of UCFS Chimera, Autodock Vina, and BIOVIA Discovery Studio software. The
total phenolic content of the A. muricata leaf extract was 14.83 mg GAE/g and the total flavonoids
34.22 mg QE/g. The plant extract showed concentration-dependent ferric reducing antioxidant power (FRAP)
when compared with the standard ascorbic acid whereas significant radical scavenging activity was exhibited
through the 2,2-Diphenyl-1-picrylhydrazyl (DPPH•) assay with IC50 of 0.202 μg/mL. Ten compounds were revealed
by GC-MS analysis, and they exhibited a favourable quantity (area %). The extract inhibited α-amylase
enzymes with a range of 36.52% - 67.30% as well as α-glucosidase enzymes with a range of 42.68 - 72.80% at
different doses (15 μg/mL - 240 μg/mL) and performed well compared to the conventional drug acarbose. The
high binding affinity of plant phytochemicals to α-amylase and α-glucosidase and their acceptable pharmacokinetic
characteristics further suggested a prospective therapeutic relevance. According to our investigations, the
leaves of A. muricata can be used to develop drugs with high antioxidant potential. However, adequate scientific
data is needed for A. muricata's therapeutic use, as well as further clinical and in vivo research both for toxicological
and pharmacological evaluation.
Supported Ionic Liquid Phase for Biocatalysis: The Current Applications, Synthesis
and Prospects
Authors: Wolny Anna , Chrobok Anna 
Published: October 2023

Abstract:
In this work, the potential of supported ionic liquids-based biocatalysts was presented. Efforts are
underway to identify suitable carrier matrices for biocatalytic reactions, considering the crucial role of surface
morphology. Factors such as mechanical and thermal properties, surface area, pore volume, density, and functionalization
potential are being carefully considered during selection. The correlation between carrier, enzyme,
and il structures highlights the importance of constructing biocatalysts with exceptional catalytic activity. Enzymes
immobilized on silp/sillp carriers generally exhibit enhanced activity compared to the native protein.
Silp-type carriers improve process efficiency, enable easy separation and recycling of biocatalysts, and prolong
the protein's lifespan.