bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles
Authors: Das Basanta Kumar , Chakraborty Hirak Jyoti , Kumar Vikash , Rout Ajaya Kumar , Patra Biswanath , Das Sanjoy Kumar , Behera Bijay Kumar 
Published: July 2024

AbstractThe Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world’s largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.
Model based on the automated AI-driven CT quantification is effective for the diagnosis of refractory Mycoplasma pneumoniae pneumonia
Authors: Qian Yali , Tao Yunxi , Wu Lihui , Zhou Changsheng , Liu Feng , Xu Shenglong , Miao Hongjun , Gao Xiucheng , Ge Xuhua 
Published: July 2024

AbstractThe prediction of refractory Mycoplasma pneumoniae pneumonia (RMPP) remains a clinically significant challenge. This study aimed to develop an early predictive model utilizing artificial intelligence (AI)-derived quantitative assessment of lung lesion extent on initial computed tomography (CT) scans and clinical indicators for RMPP in pediatric inpatients. A retrospective cohort study was conducted on patients with M. pneumoniae pneumonia (MP) admitted to the Children’s Hospital of Nanjing Medical University, China from January 2019 to December 2020. An early prediction model was developed by stratifying the patients with Mycoplasma pneumoniae pneumonia (MPP) into two cohorts according to the presence or absence of refractory pneumonia. A retrospective cohort of 126 children diagnosed with Mycoplasma pneumoniae pneumonia (MPP) was utilized as a training set, with 85 cases classified as RMPP. Subsequently, a prospective cohort comprising 54 MPP cases, including 37 instances of RMPP, was assembled as a validation set to assess the performance of the predictive model for RMPP from January to December 2021. We defined a constant Φ which can combine the volume and CT value of pulmonary lesions and be further used to calculate the logarithm of Φ to the base of 2 (Log2Φ). A clinical-imaging prediction model was then constructed utilizing Log2Φ and clinical characteristics. Performance was evaluated by the area under the receiver operating characteristic curve (AUC). The clinical model demonstrated AUC values of 0.810 and 0.782, while the imaging model showed AUC values of 0.764 and 0.769 in the training and test sets, respectively. The clinical-imaging model, incorporating Log2Φ, temperature(T), aspartate aminotransferase (AST), preadmission fever duration (PFD), and preadmission macrolides therapy duration (PMTD), achieved the highest AUC values of 0.897 and 0.895 in the training and test sets, respectively. A prognostic model developed through automated quantification of lung disease on CT scans, in conjunction with clinical data in MPP may be utilized for the early identification of RMPP.
A trajectory similarity computation method based on GAT-based transformer and CNN model
Authors: Dongjiang Liu , Leixiao Li , Jie Li 
Published: July 2024

AbstractTrajectory similarity computation is very important for trajectory data mining. It is applied into many trajectory mining tasks, including trajectory clustering, trajectory classification and trajectory search etc. So efficient trajectory similarity computation method is very useful for improving trajectory mining result. Nowadays many trajectory similarity computation methods have been proposed. But most of them can not be applied into long trajectories similarity calculation efficiently. So a new algorithm called TrajGAT is proposed. This algorithm can calculate similarity for long trajectories. It treats long trajectory as a long sequence. By doing so, long-term dependency of long trajectory is considered by this algorithm while computing similarity value. But, the spatial feature of long trajectories is not considered. As long trajectory can be presented in many different shapes, if two long trajectories are judged as similar trajectories, the outline shape of these two trajectories should be similar as well. To solve this problem, a new trajectory similarity computation method is proposed in this paper. This method not only takes the long-term dependence feature into consideration, but also considers the outline feature of long trajectory. The proposed method employs GAT-based transformer to extract long-term dependence feature from long trajectory. And it applies Convolutional Neural Network to extract outline feature.
The shared mechanism and potential diagnostic markers for premature ovarian failure and dry eye disease
Authors: Long Xi , Wu Zixuan , Jiang Pengfei , Tan Kang , Liu Pei , Peng Qinghua 
Published: July 2024

AbstractPremature ovarian failure (POF), which is often comorbid with dry eye disease (DED) is a key issue affecting female health. Here, we explored the mechanism underlying comorbid POF and DED to further elucidate disease mechanisms and improve treatment. Datasets related to POF (GSE39501) and DED (GSE44101) were identified from the Gene Expression Omnibus (GEO) database and subjected to weighted gene coexpression network (WGCNA) and differentially expressed genes (DEGs) analyses, respectively, with the intersection used to obtain 158 genes comorbid in POF and DED. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses of comorbid genes revealed that identified genes were primarily related to DNA replication and Cell cycle, respectively. Protein–Protein interaction (PPI) network analysis of comorbid genes obtained the 15 hub genes: CDC20, BIRC5, PLK1, TOP2A, MCM5, MCM6, MCM7, MCM2, CENPA, FOXM1, GINS1, TIPIN, MAD2L1, and CDCA3. To validate the analysis results, additional POF- and DED-related datasets (GSE48873 and GSE171043, respectively) were selected. miRNAs-lncRNAs-genes network and machine learning methods were used to further analysis comorbid genes. The DGIdb database identified valdecoxib, amorfrutin A, and kaempferitrin as potential drugs. Herein, the comorbid genes of POF and DED were identified from a bioinformatics perspective, providing a new strategy to explore the comorbidity mechanism, opening up a new direction for the diagnosis and treatment of comorbid POF and DED.
Integrating apaQTL and eQTL analysis identifies a potential causal variant associated with lung adenocarcinoma risk in the Chinese population
Authors: Xu Huiwen , Wu Yutong , Chen Qiong , Yu Yuhui , Meng Qianyao , Qin Na , Zhang Wendi , Tao Xiaobo , Li Siqi , Tian Tian , Zhang Lei , Ma Hongxia , Cui Jiahua , Chu Minjie 
Published: July 2024

AbstractAlternative polyadenylation (APA) plays a crucial role in cancer biology. Here, we used data from the 3′aQTL-atlas, GTEx, and the China Nanjing Lung Cancer GWAS database to explore the association between apaQTL/eQTL-SNPs and the risk of lung adenocarcinoma (LUAD). The variant T allele of rs277646 in NIT2 is associated with an increased risk of LUAD (OR = 1.12, P = 0.015), lower PDUI values, and higher NIT2 expression. The 3′RACE experiment showed multiple poly (A) sites in NIT2, with the rs277646-T allele causing preferential use of the proximal poly (A) site, resulting in a shorter 3′UTR transcript. This leads to the loss of the hsa-miR-650 binding site, thereby affecting LUAD malignant phenotypes by regulating the expression level of NIT2. Our findings may provide new insights into understanding and exploring APA events in LUAD carcinogenesis.
Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV)
Authors: Hu Tao , Ji Quanquan , Ke Xinxin , Zhou Hufeng , Zhang Senfeng , Ma Shengsheng , Yu Chenlin , Ju Wenjun , Lu Meiling , Lin Yu , Ou Yangjing , Zhou Yingsi , Xiao Yibei , Xu Chunlong , Hu Chunyi 
Published: July 2024

AbstractR-loop-triggered collateral single-stranded DNA (ssDNA) nuclease activity within Class 1 Type I CRISPR-Cas systems holds immense potential for nucleic acid detection. However, the hyperactive ssDNase activity of Cas3 introduces unwanted noise and false-positive results. In this study, we identified a novel Type I-A Cas3 variant derived from Thermococcus siculi, which remains in an auto-inhibited state until it is triggered by Cascade complex and R-loop formation. This Type I-A CRISPR-Cas3 system not only exhibits an expanded protospacer adjacent motif (PAM) recognition capability but also demonstrates remarkable intolerance towards mismatched sequences. Furthermore, it exhibits dual activation modes—responding to both DNA and RNA targets. The culmination of our research efforts has led to the development of the Hyper-Active-Verification Establishment (HAVE, 惠父). This innovation enables swift and precise human papillomavirus (HPV) diagnosis in clinical samples, providing a robust molecular diagnostic tool based on the Type I-A CRISPR-Cas3 system. Our findings contribute to understanding type I-A CRISPR-Cas3 system regulation and facilitate the creation of advanced diagnostic solutions with broad clinical applicability.
CRISPR screens in 3D tumourspheres identified miR-4787-3p as a transcriptional start site miRNA essential for breast tumour-initiating cell growth
Authors: Stiff Tom , Bayraktar Salih , Dama Paola , Stebbing Justin , Castellano Leandro 
Published: July 2024

AbstractOur study employs pooled CRISPR screens, integrating 2D and 3D culture models, to identify miRNAs critical in Breast Cancer (BC) tumoursphere formation. These screens combine with RNA-seq experiments allowing identification of miRNA signatures and targets essential for tumoursphere growth. miR-4787-3p exhibits significant up-regulation in BC, particularly in basal-like BCs, suggesting its association with aggressive disease. Surprisingly, despite its location within the 5’UTR of a protein coding gene, which defines DROSHA-independent transcription start site (TSS)-miRNAs, we find it dependant on both DROSHA and DICER1 for maturation. Inhibition of miR-4787-3p hinders tumoursphere formation, highlighting its potential as a therapeutic target in BC. Our study proposes elevated miR-4787-3p expression as a potential prognostic biomarker for adverse outcomes in BC. We find that protein-coding genes positively selected in the CRISPR screens are enriched of miR-4787-3p targets. Of these targets, we select ARHGAP17, FOXO3A, and PDCD4 as known tumour suppressors in cancer and experimentally validate the interaction of miR-4787-3p with their 3’UTRs. Our work illuminates the molecular mechanisms underpinning miR-4787-3p’s oncogenic role in BC. These findings advocate for clinical investigations targeting miR-4787-3p and underscore its prognostic significance, offering promising avenues for tailored therapeutic interventions and prognostic assessments in BC.
Exploring bat-inspired cyclic tryptophan diketopiperazines as ABCB1 Inhibitors
Authors: Koh Javier Yu Peng , Itahana Yoko , Krah Alexander , Mostafa Habib , Ong Mingmin , Iwamura Sahana , Vincent Dona Mariya , Radha Krishnan Sabhashina , Ye Weiying , Yim Pierre Wing Chi , Khopade Tushar M. , Chen Kunihiko , Kong Pui San , Wang Lin-Fa , Bates Roderick W. , Kimura Yasuhisa , Viswanathan Rajesh , Bond Peter J. , Itahana Koji 
Published: July 2024

AbstractChemotherapy-induced drug resistance remains a major cause of cancer recurrence and patient mortality. ATP binding cassette subfamily B member 1 (ABCB1) transporter overexpression in tumors contributes to resistance, yet current ABCB1 inhibitors have been unsuccessful in clinical trials. To address this challenge, we propose a new strategy using tryptophan as a lead molecule for developing ABCB1 inhibitors. Our idea stems from our studies on bat cells, as bats have low cancer incidences and high ABCB1 expression. We hypothesized that potential ABCB1 substrates in bats could act as competitive inhibitors in humans. By molecular simulations of ABCB1-substrate interactions, we generated a benzylated Cyclo-tryptophan (C3N-Dbn-Trp2) that inhibits ABCB1 activity with efficacy comparable to or better than the classical inhibitor, verapamil. C3N-Dbn-Trp2 restored chemotherapy sensitivity in drug-resistant human cancer cells with no adverse effect on cell proliferation. Our unique approach presents a promising lead toward developing effective ABCB1 inhibitors to treat drug-resistant cancers.
Heterogeneous changes in global glacial lakes under coupled climate warming and glacier thinning
Authors: Zhang Taigang , Wang Weicai , An Baosheng 
Published: July 2024

AbstractGlobal glacial lakes have expanded markedly in recent decades, accompanied by many catastrophic glacial lake outburst floods. However, our understanding of glacial lake evolution and connections with global warming and glacier thinning remains insufficient due to fragmented studies and a lack of standardized mapping. Here we evaluated the glacial lake changes and their drivers, taking care to accurately map glacial lakes while excluding non-glacier fed lakes in the same geographic area. In 2020, a total of 71,508 glacial lakes were identified worldwide, covering an area of 21,770.9$$\pm$$
±
544.2 km2. The total volume of 1280.6$$\pm$$
±
354.1 km3 is equivalent to a sea-level rise of 3.45 mm. Since the 1990s, glacial lake numbers, areas, and volumes increased by 54%, 11%, and 9%, respectively. The spatial evolution patterns align well with resolved large-scale, decadal glacier mass changes. Glacier-fed lakes extensively expanded due to glacier retreat and melting, while ice-dammed lakes were primarily affected by thinning ice dams, resulting in heterogeneous changes and underestimated outburst potential. Under the sustained glacier degradation scenario, the results of this study have implications for further evaluation of glacial lake water resources and outburst risks on a global scale.
The mediating role of systemic inflammation and moderating role of racialization in disparities in incident dementia
Authors: Higgins Tejera César , Ware Erin B. , Hicken Margaret T. , Kobayashi Lindsay C. , Wang Herong , Blostein Freida , Zawistowski Matthew , Mukherjee Bhramar , Bakulski Kelly M. 
Published: July 2024

Abstract
Background
Exposure to systemic racism is linked to increased dementia burden. To assess systemic inflammation as a potential pathway linking exposure to racism and dementia disparities, we investigated the mediating role of C-reactive protein (CRP), a systemic inflammation marker, and the moderating role of the racialization process in incident dementia.

Methods
In the US Health and Retirement Study (n = 6,908), serum CRP was measured at baseline (2006, 2008 waves). Incident dementia was classified by cognitive tests over a six-year follow-up. Self-reported racialized categories were a proxy for exposure to the racialization process. We decomposed racialized disparities in dementia incidence (non-Hispanic Black and/or Hispanic vs. non-Hispanic white) into 1) the mediated effect of CRP, 2) the moderated portion attributable to the interaction between racialized group membership and CRP, and 3) the controlled direct effect (other pathways through which racism operates).

Results
The 6-year cumulative incidence of dementia is 12%. Among minoritized participants (i.e., non-Hispanic Black and/or Hispanic), high CRP levels ( ≥ 75th percentile or 4.73μg/mL) are associated with 1.26 (95%CI: 0.98, 1.62) times greater risk of incident dementia than low CRP ( < 4.73μg/mL). Decomposition analysis comparing minoritized versus non-Hispanic white participants shows that the mediating effect of CRP accounts for 3% (95% CI: 0%, 6%) of the racial disparity, while the interaction effect between minoritized group status and high CRP accounts for 14% (95% CI: 1%, 27%) of the disparity. Findings are robust to potential violations of causal mediation assumptions.

Conclusions
Minoritized group membership modifies the relationship between systemic inflammation and incident dementia.
Channel swapping of EEG signals for deep learning‐based seizure detection
Authors: Pan Yayan , Dong Fangying , Yao Wei , Meng Xiaoqin , Xu Yongan 
Published: July 2024

AbstractThe purpose of epilepsy detection is to determine whether epilepsy has occurred by analysing the patient's electroencephalogram (EEG) signals. Compared to traditional methods, epilepsy detection methods based on deep learning have achieved significant improvements in detection accuracy. However, when the number of training samples is limited, the model's detection performance often significantly declines. To address this issue, here a sample enhancement method based on electroencephalogram signal channel swapping is proposed. This method generates new electroencephalogram samples by exchanging electroencephalogram sequences from different channels, thereby expanding the training set and improving epilepsy detection accuracy in few‐shot scenarios. Experiments using the Children's Hospital Boston and the Massachusetts Institute of Technology (CHB‐MIT) dataset show that for training sets with 100, 500, and 1000 samples, detection accuracy improves from 0.6797 to 0.7789, 0.6952 to 0.8210, and 0.7273 to 0.8517, respectively. Compared to the sliding window method, the proposed method demonstrates higher accuracy in extreme low sample sizes. Combining both methods can further enhances detection performance, showing an improvement of approximately 8% across various configurations.
Evaluation of comfort zone boundary based automated emergency braking algorithms for car‐to‐powered‐two‐wheeler crashes in China
Authors: Yang Xiaomi , Lubbe Nils , Bärgman Jonas 
Published: July 2024

AbstractCrashes between cars and powered two‐wheelers (PTWs: motorcycles, scooters, and e‐bikes) are a safety concern; as a result, developing car safety systems that protect PTW riders is essential. While the pre‐crash protection system automated emergency braking (AEB) has been shown to avoid and mitigate injuries for car‐to‐car, car‐to‐cyclist, and car‐to‐pedestrian crashes, much is still unknown about its effectiveness in car‐to‐PTW crashes. Further, the characteristics of the crashes that remain after the introduction of such systems in traffic are also largely unknown. This study estimates the crash avoidance and injury risk reduction performance of six different PTW‐AEB algorithms that were virtually applied to reconstructed car‐to‐PTW pre‐crash kinematics extracted from a Chinese in‐depth crash database. Five of the algorithms include combinations of drivers’ and PTW riders’ comfort zone boundaries for braking and steering, while the sixth is a traditional AEB. Results show that the average safety performance of the algorithms using only the driver's comfort zone boundaries is higher than that of the traditional AEB algorithm. All algorithms resulted in similar distributions of impact speed and impact locations, which means that in‐crash protection systems likely can be made less complex, not having to consider differences in AEB algorithm design among car manufacturers.
A two‐stage optimization method of power supply scheme of on‐board supercapacitor‐powered tram
Authors: Zhang Huazhi , Fu Chengcheng , Wang Qingyuan , Sun Pengfei , Feng Xiaoyun , He Bin 
Published: July 2024

AbstractAiming at the power supply scheme (PSS) of the on‐board supercapacitor‐powered tram, considering the cost and margin of the PSS, a two‐stage method is designed to optimize the layout of the charging stations and the configuration of the supercapacitor (SC). First, the SC‐powered tram model and stable cycle operation model are established, and a two‐stage optimization problem model with the lowest PSS cost and the largest SC margin is established. Then, an improved dual‐population differential evolution algorithm is designed, and the layout of charging stations and the configuration of SC are co‐optimized in the first stage, and then the layout of charging stations is optimized again in the second stage. The simulation results show that co‐optimization can obtain a lower cost of PSS, and furthermore, the layout of charging stations can be optimized again to effectively improve the margin of SC, thereby improving the matching degree between the layout of charging stations and the connection scheme of SC.
Classical channel bandwidth requirements in continuous variable quantum key distribution systems
Authors: Almeida Margarida , Pereira Daniel , Pinto Armando N. , Silva Nuno A. 
Published: July 2024

AbstractThe reconciliation method for continuous variable quantum key distribution systems is usually chosen based on its reconciliation efficiency. Nonetheless, one must also consider the requirements of each reconciliation method in terms of the amount of information transmitted on the classical channel. Such may limit the achievable key rates. For instance, multidimensional reconciliation of dimension 8 demands a classical channel bandwidth 43 times greater than that of the quantum channel baud rate. Decreasing the dimension to 4 halves the required bandwidth, allowing for higher quantum channel baud rates and higher key rates for shorter transmission distances, despite the lesser reconciliation performance.
Measuring attitudes towards historic gardens: development and validation of the Garden Heritage Scale
Authors: Emge Daniel , Kleespies Matthias Winfried , Wenzel Volker 
Published: July 2024

AbstractHistoric gardens and parks are special parts of cultural heritage. On the one hand, such areas can be seen as historic monuments. On the other hand, they can play a crucial role for environmental protection. However, previous environmental education research did not pay much attention to historic greenery. One reason may be the lack of suitable measurement tools. The purpose of the current study was to develop and validate the Garden Heritage Scale (GHS). This novel psychometric instrument may be used for measuring attitudes towards historic gardens. It shows sufficient internal validity, confirmed by two factor analyses with different samples (n = 233;183). Convergent and discriminant validity proved to be adequate as well as retest-reliability and internal consistency. Since the scale showed sufficient quality, it can be recommended for further research.