bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shape-based Methods in Mobility Data Analysis: Effectiveness and Limitations
Authors: Landi Cristiano , Guidotti Riccardo 
Published: November 2024

Abstract

Although Mobility Data Analysis (MDA) has been explored for a long time, it still lags behind advancements in other fields.A common issue in MDA is the lack of methods' standardization and reusability. On the other hand, for instance, in time series analysis, the existing methods are typically general-purpose, and it is possible to apply them across diverse datasets and applications without extensive customization. Still, in MDA, most contributions are ad-hoc and designed to address specific research questions, which limits their generalizability and reusability.
Recently, some researchers explored the application of shapelet transform to trajectory data, i.e., extracting discriminatory sub-trajectories from training data to be used as classification features. Unlike current MDA methods, this line of research eliminates the need for feature engineering, greatly improving its ability to generalize. While shapelets on mobility data have shown state-of-the-art performance on public classification datasets, it is still not clear why they work. Are these subtrajectories merely proxies for geographic location, or do they also capture motion dynamics? We empirically show that shapelet-based approaches are a viable alternative to classical methods and flexible enough to solve MDA tasks related solely to trajectory shape, solely to movement dynamics, and those related to both. Additionally, we investigate the problem of Geographic Transferability, showing that such approaches offer a promising starting point for tackling this challenge.
Different Varieties of Rice (Oryza sativa) Affect Cadmium Accumulation by Reshaping Rhizosphere Bacterial Community
Authors: Zhang Shangdu , Luo Zhengliang , Peng Ju , Wu Xiang , Shi Bangzhi , Meng Xiufei , Qin Yuanyi , Zhou Leliang , Zhu Feiying , Bai Liangyang 
Published: November 2024

Abstract

Cadmium rice is a serious danger to human health due to its ability to enrich cadmium from soil to rice plants. Previously, we have identified two self-bred late-season high quality rice varieties, which are "Yuzhenxiang" and "Xiangwanxian 12". However, the mechanism on the distribution and tolerance of their significant differences in cadmium accumulation have barely been studied so far. Therefore, in this study, we comparatively analyze the relationships between the rhizosphere bacterial community and Cd accumulation in these two rice varieties under three different Cd stress conditions during the maturity period. Our results firstly showed that significant differences in physicochemical properties affect the Cd content in rice roots, which increased with increasing Cd content in the soil. Notably, the spearman correlation analysis suggested that the differed enrichment of Variibacter, Nitrospira, Galella, Mycobacterium, and Desulfobacca affected by rice variety, which play key roles in root Cd accumulation. In general, our research indicate that the different rice varieties can altered the structure soil bacterial communities to affect Cd concentration in rice. This provides theoretical support to better control the Cd pollution problem through agricultural ecology protection.
Salinity-driven transmembrane transport of free nitrous acid to enhance inhibition on nitrite-oxidizing bacteria for robust nitritation
Authors: Lv Xue-Er , Tang Rui , Ma Zi-Hang , Chen Rui-Xue , Wang Yu , An Ying , Jiang Lu-Man , Zhou Zhen 
Published: November 2024

Abstract

Stable and selective suppression of nitrite-oxidizing bacteria (NOB) remains a bottleneck for nitritation. Here, we present an efficient NOB suppression strategy relying on synergistic effects of free nitrous acid (FNA) and salinity, i.e., the intrinsic substances during wastewater treatment. The co-presence of over 0.06 mg N/L FNA and 3.3 g Na+/L salinity achieved stable NOB inhibition, maintaining a nitrite accumulation ratio over 90% with negligible nitrite oxidation rate and NOB abundance. This strategy overcame the adaptation of NOB to FNA or salinity alone. Due to the synergistic effect, the permeability of cell membrane increased obviously. Driven by salinity, especially at 3.3 g Na+/L, the inward transport of both FNA and protons was accelerated, thereby raising intracellular FNA concentration and enhancing its lysis to reactive antibacterial species. In response to this synergistic inhibition, ammonia-oxidizing bacteria (AOB) activity increased progressively with Nitrosomonas as the dominating genus. The persistence of Nitrosomonas was mainly ascribed to denitrification by itself. This differential evolution of AOB and NOB caused by FNA and salinity provides a valuable reference for promoting the application of nitritation-based wastewater treatment processes.
Harnessing Pre-trained Models for Accurate Prediction of Protein-Ligand Binding Affinity
Authors: Li Jiashan , Gong Xinqi 
Published: November 2024

Abstract

Background: The binding between proteins and ligands plays a crucial role in the field of drug discovery. However, this area currently faces numerous challenges. On one hand, existing methods are constrained by the limited availability of labeled data, often performing inadequately when addressing complex protein-ligand interactions. On the other hand, many models struggle to effectively capture the flexible variations and relative spatial relationships between proteins and ligands. These issues not only significantly hinder the advancement of protein-ligand binding research but also adversely affect the accuracy and efficiency of drug discovery. Therefore, in response to these challenges, our study aims to enhance predictive capabilities through innovative approaches, providing more reliable support for drug discovery efforts.
Methods: This study leverages a pre-trained model with spatial awareness to enhance the prediction of protein-ligand binding affinity. By perturbing protein structures in a manner consistent with physical constraints and employing self-supervised tasks, we improve the representation of small molecule structures, allowing for better adaptation to affinity predictions. Meanwhile, our approach enables the identification of potential binding sites on proteins.
Results: Our model achieves a significantly higher correlation coefficient in binding affinity predictions, with a classification ROC exceeding 95% for binding site identification.
Conclusion: This research presents a novel approach that not only enhances the accuracy of binding affinity predictions but also facilitates the identification of binding sites, showcasing the potential of pre-trained models in computational 1 drug design. Data and code are available at https://anonymous.4open.science/r/ SableBind-1B53.
Balanced Group Convolution: An Improved Group Convolution Based on Approximability Estimates
Authors: Lee Youngkyu , Park Jongho , Lee Chang-Ock 
Published: November 2024

Abstract

The performance of neural networks has been significantly improved by increasing the number of channels in convolutional layers.
However, this increase in performance comes with a higher computational cost, resulting in numerous studies focused on reducing it.
One promising approach to address this issue is group convolution, which effectively reduces the computational cost by grouping channels.
However, to the best of our knowledge, there has been no theoretical analysis on how well the group convolution approximates the standard convolution.
In this paper, we mathematically analyze the approximation of the group convolution to the standard convolution with respect to the number of groups.
Furthermore, we propose a novel variant of the group convolution called \textit{balanced group convolution}, which shows a higher approximation with a small additional computational cost.
We provide experimental results that validate our theoretical findings and demonstrate the superior performance of the balanced group convolution over other variants of group convolution.
SINE Retrotransposons Import Polyadenylation Signals to 3’UTRs in Dog (Canis familiaris)
Authors: Choi Jessica , Pinto Lelani Del , Sutter Nathan 
Published: November 2024

Abstract

Background
Messenger RNA 3’ untranslated regions (3’UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA (AATAAA in DNA) is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3’UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy numbers. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands of Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may terminate transcript in some dog genes.
Results
The dog’s nine Can-SINE consensus sequences carry an average of three AATAAA PASs on their sense strands but zero on their antisense strands. Consistent with the idea that Can-SINEs can terminate transcripts, we find that sense-oriented Can-SINEs are approximately ten times more frequent at 3’ ends of 3’UTRs compared to further upstream within 3’UTRs. Furthermore, the count of AATAAA PASs on head-to-tail SINE sequence differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3’UTR ends are likely to carry AATAAA on the mRNA sense strand while those further upstream are not. We identified loci where Can-SINE insertion has truncated or altered a dog 3’UTR compared to the human ortholog. Dog 3’UTRs have peaks of AATAAA PAS frequency at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp length for target site duplications (TSDs). All dog Can-SINE types favor integration at TSDs beginning with A(4).
Conclusion
Dog Can-SINE activity has imported AATAAA PASs into gene transcripts and led to alteration of 3’UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3’UTR regions but are retained at the far downstream end of 3’UTRs, which we infer reflects their role as termination sequences for these transcripts.
IGFBP1 facilitates tumor proliferation, invasion and migration by modulating the MAPK- ERK signaling pathway in lung adenocarcinoma
Authors: Xiao Zengtuan , Zhang Mengzhe , Di Yiying , Liu Zuo , Zhang Zhenfa 
Published: November 2024

Abstract

Objective
Lung adenocarcinoma (LUAD) is the most prevalent histological subtype of lung cancer, and lymph node metastasis serves as a significant prognostic risk factor. The identification of molecular biomarkers associated with lymph node metastasis holds paramount importance in the prevention and treatment strategies for this condition.
Methods
We identified the GFBP1 as the biomarker with the highest risk for lymph node metastasis by bioinformatical analysis. And we conducted the cell proliferation, invasion, and migration assays in H1975 and H1299 cells by overexpressing IGFBP1. The single-cell-RNA-sequence data indicated that IGFBP1 facilitates the progression of LUAD cells through the MAPK signaling pathway. Subsequently, western blot analysis was performed to validate these findings, while the ERK inhibitor U0126 was employed for cellular experiments and in vivo verification to elucidate the precise biological function of IGFBP1.
Results
IGFBP1 emerged as the most prominent biomarker for lymph node metastasis risk. Difference was shown in immunohistochemistry, univariate and multivariate Cox regression analyses. The vitro experiments confirmed that the overexpression of IGFBP1 in H1299 and H1975 cells can significantly promote proliferation, migration and invasion capacities. Western blot analysis validated that IGFBP1 overexpression substantially increased p-ERK expression levels. The use of the ERK inhibitor U0126 in subcutaneous tumor formation demonstrated that U0126 effectively suppressed both proliferation and invasion in animal model.
Conclusions
IGFBP1 indicates the promotion of lymph node metastasis in LUAD by facilitating tumor proliferation, invasion, and migration through modulation of the MAPK-ERK signaling pathway. Targeting this pathway exhibits significant potential for inhibiting tumor progression.
Leveraging lactate transporters for superior 3-hydroxypropionic (3-HP) acid production from methanol in Komagataella phaffii
Authors: Àvila-Cabré Sílvia , Albiol Joan , Ferrer Pau 
Published: November 2024

Abstract

Background
Bioconversion of methanol derived from CO2 reduction into value-added chemicals is crucial for mitigating global warming and reducing fossil fuels dependence within a circular economy. Production of 3-hydroxypropionic (3-HP) acid, a key building block for the development of biobased products such as acrylates and 1,3-propanediol, has been successfully achieved using methanol as the sole carbon and energy source in the methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris). However, challenges remain in meeting commercially relevant concentrations, yields and productivities of 3-HP, prompting further strain optimization. In the present study, we have combined metabolic engineering strategies aiming at increasing metabolic precursors supply and redirecting carbon flux towards 3-HP production.
Results
A combinatorial metabolic engineering strategy targeted to increase precursor supply and 3-HP export was applied to the original 3-HP producing K. phaffii strain harboring the synthetic b-alanine pathway and a heterologous NADP-dependent formate dehydrogenase. To do so, several genes encoding for enzymes catalyzing reactions immediately upstream of the β-alanine pathway were overexpressed to enhance the pathway’s precursors supply. However, only the overexpression of the pyruvate carboxylase PYC2 gene significantly increased the 3-HP yield on biomass (YP/X) in small-scale cultivations. Co-overexpression of PYC2 and the lactate permeases ESBP6 and JEN1 genes led to a 55% improvement in titer (1.5 g l− 1) and product yield (0.13 g g− 1) compared to the reference strain, mostly due to Esbp6 activity, proving its effectiveness as a 3-HP transporter. Deletion of the native formate dehydrogenase gene FDH1 did not increase methanol flux entering the assimilatory pathway. Instead, knockout strains showed severe growth defects due to toxic intermediates accumulation. Co-expression of a gene encoding for a mutated NADP-dependent formate dehydrogenase in these strains failed to compensate for the loss of native FDH. The strain combining PYC2, ESBP6 and JEN1 overexpression was further tested in fed-batch cultures at pH 5, achieving a final 3-HP concentration of 27.0 g l− 1 in 39.3 h, with a product yield of 0.19 g g− 1 and a volumetric productivity of 0.56 g l− 1 h− 1. These results represent a 42% increase in final concentration and over 20% improvement in volumetric productivity compared to the original 3-HP producing strain. Furthermore, bioreactor-scale cultivations at pH 3.5 revealed increased robustness of the strains overproducing monocarboxylate transporters.
Conclusions
Our results point out the potential of lactate transporters to efficiently drive 3-HP export in K. phaffii, leading to higher titers, yields, and productivities, even at lower pH conditions.
CFD study and Experimental Verification of droplet formation characteristics in a flow-focusing microfluidic device
Authors: Sani Hajar Mohamadzade , Hosseinalipour Seyed Mostafa 
Published: November 2024

Abstract

Droplet-based microfluidics has received much attention today due to the precise control of droplet size and the uniform and integrated droplet production. In this paper, the droplet formation process in a three-dimensional geometry of a flow-focusing microfluidic device has been simulated by developing a code with the finite element method (FEM) and the two-phase level set method (LSM). Effective physical factors, including the continuous phase viscosity, two-phase flow velocities, interfacial tension and injection angle have been investigated on different parameters including the droplet generation mechanism, two-phase flow regimes, droplet size, droplet formation frequency and droplet breakup time to clarify the best conditions for the droplet formation with the desired shape and size. Based on the numerical model results, a flow-focusing microfluidic device has been fabricated with the same simulation dimensions under injection angle of \(\:\theta\:={90}^{^\circ\:}\) connection and evaluated using the lithography process. The simulation results accuracy has been validated by comparing with the experimental results. The relative error was less than \(\:4\%\) which shows that the experimental results and numerical model are in good agreement. Repeatability tests have been conducted as well and the standard deviation value and the coefficient of variation showed good repeatability and homogeneity in the produced droplets.
Diagnosis of Current Transformers Based on Symmetrized Dot Pattern and Horizontal Enhanced Convolution
Authors: Zhao Pinzhang , Zhang Zhongyu , Wei Jian , Wang Lihui 
Published: November 2024

Abstract

The stability of fibre optic current transformers (FOCTs), crucial for power metering systems, is paramount. This paper introduces an innovative fault diagnosis method to enhance FOCT diagnostic capabilities. Firstly, utilizing advanced AI and neural networks, the method employs Symmetric Point Pattern (SDP) for complex data fusion, alongside Principal Component Analysis (PCA) for feature reduction. Secondly, Horizontal Enhanced Convolution (HEC) identifies key characteristics, while residual architecture tackles gradient descent issues in traditional CNNs. Then, inspired by Feature Pyramid Networks (FPNs), a new architecture efficiently extracts multiscale features, preventing overfitting with Selective Pooling Prevention Filtering (SPPF). The developed SDP-MSFCNN model achieved a high diagnostic accuracy of 98.82%, surpassing the 90.72% of conventional SDP-CNN and the 96.61% of MA1-DCNN. This approach significantly enhances power system reliability and efficiency, and is ready for integration into high-voltage network fault diagnosis systems, improving the intelligence and safety of 110kV to 1000kV AC/DC transformers.
An Exploration of the Application of Item Response Theory to the Measurement of Child Abuse in Canada
Authors: Goodwin Shane W. , Bader Danielle , Arim Rubab , Frank Kristyn , Shields Margot , Tanaka Masako , Gonzalez Andrea , Campeau Aimée , McKinnon Britt , Afifi Tracie O. , MacMillan Harriet L. , Tonmyr Lil 
Published: November 2024

Abstract

PURPOSE
There is a longstanding need for a consistent approach to estimate the prevalence of child abuse to inform programs, policies, and research. A key step in achieving a consistent approach is to examine current differences in the application of cut-offs in the public health reporting of child abuse.
METHODS
To address this issue, this exploratory study applied item response theory (IRT) to determine standard cut-points for two types of child abuse, namely physical and sexual abuse, using nationally representative data from the 2018 Survey of Safety in Public and Private Spaces. Two different cut-offs from the literature were considered in the IRT models. The first cut-off (i.e., cut-off 1) estimated the proportion of individuals who experienced abuse in childhood (before age 15 years) using a frequency of one or more times. In contrast, a second cut-off (i.e., cut-off 2) was more conservative, requiring experiencing a higher frequency of abuse across all items.
RESULTS
Model fit statistics and option characteristic curves suggested a good fit for physical abuse using cut-off 2. In contrast, a good fit was obtained for sexual abuse using cut-off 1.
CONCLUSION
This study provides support towards using cut-off 2 for physical abuse and cut-off 1 for sexual abuse. Consistent approaches to measuring child abuse is important to improve our understanding of the epidemiology of child abuse, as well as approaches to its assessment, treatment, and prevention. Future research should explore the feasibility of using IRT methods to establish cut-offs for other types of maltreatment.
Enhancing ward rounds for older patients with frailty: A modified Delphi process
Authors: Andersen Lene Holst , Løfgren Bo , Skipper Mads , Krogh Kristian , Jensen Rune Dall 
Published: November 2024

Abstract

Background
Despite their prevalence, ward round practices are not well described, particularly within the CanMEDS competency framework, leading to challenges in achieving proficiency. We aimed to identify consensus-based content items for conducting ward rounds with older patients with frailty to provide clearer guidelines and enhanced understanding of best practices for medical professionals.
Methods
A nationwide Danish five-round Delphi study conducted during 2023. Geriatric medicine (30) and medical communication (5) experts were invited to participate. The participants’ comments and an iterative thematic approach were used to identify and refine content items and themes, after which participants assessed items for consensus. Consensus was defined as 75% of participants voting 7-9 on a 1-9 Likert scale. Items without consensus returned to the next Delphi round with elimination if no consensus was reached after the second assessment.
Results
Delphi study response rates were 26(74%), 21(81%), 18(86%), 13(72%), and 11(85%) in Delphi rounds 1-5, respectively. Experts reached consensus on 108 content items on conducting ward rounds with older patients with frailty. Items were organized into four themes: 1) preparing ward rounds, 2) conducting ward rounds, 3) competencies, 4) circumstances related to the patient group. Ward round preparation and the conduction of ward round detailed the process of managing older inpatients living with frailty, including conducting a holistic review of patient history and functional status, as well as improving the environment, such as by reducing noise. Competencies and patient circumstances related to the patient group included knowledge, skills, and attitudes to improve ward round quality, including flexibility in terms of reading patient cues and adjusting content to changes in cognition and alertness and knowledge on how to communicate with patients living with cognitive impairment.
Conclusions
Geriatric medicine and medical communication experts reached consensus on 108 content items for conducting ward rounds with older patients with frailty. The items were grouped into four themes: preparing for ward rounds, conducting ward rounds, required competencies, and patient-related circumstances. The authors believe that this study serves as a valuable resource for medical training and future research.