bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pseudogenes and the associated ceRNA network as potential prognostic biomarkers for colorectal cancer
Authors: Li Zhuoqi , Zhou Jing , Gu Liankun , Zhang Baozhen 
Published: October 2022

AbstractColorectal cancer (CRC) is one of the most common and malignant carcinomas. Many long noncoding RNAs (lncRNAs) have been reported to play important roles in the tumorigenesis of CRC by influencing the expression of some mRNAs via competing endogenous RNA (ceRNA) networks and interacting with miRNAs. Pseudogene is one kind of lncRNA and can act as RNA sponges for miRNAs and regulate gene expression via ceRNA networks. However, there are few studies about pseudogenes in CRC. In this study, 31 differentially expressed (DE) pseudogenes, 17 DE miRNAs and 152 DE mRNAs were identified by analyzing the expression profiles of colon adenocarcinoma obtained from The Cancer Genome Atlas. A ceRNA network was constructed based on these RNAs. Kaplan–Meier analysis showed that 7 pseudogenes, 4 miRNAs and 30 mRNAs were significantly associated with overall survival. Then multivariate Cox regression analysis of the ceRNA-related DE pseudogenes was performed and a 5-pseudogene signature with the greatest prognostic value for CRC was identified. Moreover, the results were validated by the Gene Expression Omnibus database, and quantitative real-time PCR in 113 pairs of CRC tissues and colon cancer cell lines. This study provides a pseudogene-associated ceRNA network, 7 prognostic pseudogene biomarkers, and a 5-pseudogene prognostic risk signature that may be useful for predicting the survival of CRC patients.
DFT calculations of 1H- and 13C-NMR chemical shifts of 3-methyl-1-phenyl-4-(phenyldiazenyl)-1H-pyrazol-5-amine in solution
Authors: Safi Zaki S. , Wazzan Nuha 
Published: October 2022

AbstractGeometries of the 3-methyl-1-phenyl-4-(phenyldiazenyl)-1H-pyrazol-5-amine azo-dye compound and its tautomer were optimized using B3LYP and M06-2X functionals in coupling with TZVP and 6–311 + G(d,p) basis sets. The 1H- and 13C-NMR chemical shifts of all species were predicted using 13 density functional theory (DFT) approaches in coupling with TZVP and 6–311 + G(d,p) basis sets at the different optimized geometries by applying the using GIAO method using the eight geometries. The selected functionals are characterized by having different amount of Hartree–Fock exchange. The selected DFT methods were B3LYP, M06-2X, BP86, B97XD, TPSSTPSS, PBE1PBE, CAM-B3LYP, wB97XD, LSDA, HSEH1PBE, PW91PW91, LC-WPBE, and B3PW91. The results obtained were compared with the available experimental data using different statistical descriptors such as root mean square error (RMSE) and maximum absolute error (MAE). Results revealed that the prediction of the 1H-NMR chemical shifts has more significant dependence on the applied geometry than that of the prediction of the 13C-NMR chemical shifts. Among all the examined functionals, B97D and TPSSTPSS functionals were found to be the most accurate ones, while the M06-2X functional is the least accurate one. Results also revealed that the prediction of NMR chemical shifts using TZVP basis sets results is more accurate results than 6–311 + G(2d,p) basis set.
Chiral topographic instability in shrinking spheres
Authors: Xu Fan , Huang Yangchao , Zhao Shichen , Feng Xi-Qiao 
Published: October 2022

AbstractMany biological structures exhibit intriguing morphological patterns adapted to environmental cues, which contribute to their important biological functions and also inspire material designs. Here, we report a chiral wrinkling topography in shrinking core–shell spheres, as observed in excessively dehydrated passion fruit and experimentally demonstrated in silicon core–shells under air extraction. Upon shrinkage deformation, the surface initially buckles into a buckyball pattern (periodic hexagons and pentagons) and then transforms into a chiral mode. The neighbouring chiral cellular patterns can further interact with each other, resulting in secondary symmetry breaking and the formation of two types of topological network. We develop a core–shell model and derive a universal scaling law to understand the underlying morphoelastic mechanism and to effectively describe and predict such chiral symmetry breaking far beyond the critical instability threshold. Moreover, we show experimentally that the chiral characteristic adapted to local perturbation can be harnessed to effectively and stably grasp small-sized objects of various shapes and made of different stiff and soft materials. Our results not only reveal chiral instability topographies, providing fundamental insights into the surface morphogenesis of the deformed core–shell spheres that are ubiquitous in the real world, but also demonstrate potential applications of adaptive grasping based on delicate chiral localization.
Distributed remote antenna unit with selection‐based of (RoF‐IoT) paradigm: Performance improvement
Authors: Ahmad Shakir Salman , Al‐Raweshidy Hamed , Alkhayyat Ahmed 
Published: October 2022

AbstractMixing the wireless medium with fiber optics can form a new communication system called a radio‐over‐fiber (RoF) network; it is a promising solution that can provide high bandwidth and a reliable connection between numerous sensors in wireless sensor networks (WSN) and the central office (base station) within a particular area. This paper first design and discusses new paradigms of fire detection in the IoT environment using RoF technology. Second, this paper covers the distribution of remote antenna unit (DRAU) architecture within RoF‐IoT. Finally, best remote antennas unit selection (BRAUS) of distributed RAUs architecture protocols utilizing new selection metrics is proposed. Two important metrics have been analysed and mathematically modelled, outage probability and bandwidth efficiency, respectively. Both metrics have been analysed as a function of the distance, number of RAUs, fiber optic attenuation, and path loss factor. Based on the simulation and numerical analysis, the outage probability of proposed protocols is reduced by 65% compared to recent work; in addition, the bandwidth efficiency of the proposed protocol is increased by 34% compared to recent work.
Distributed massive UAV jamming optimization algorithm with artificial bee colony
Authors: Chen Peilin , Li Haobo , Ma Lejing 
Published: October 2022

AbstractWith the massive application of unmanned aerial vehicles (UAVs) in disaster relief, fire protection, security and other fields, jamming countermeasures to UAVs in airports and competition venues have become the core link of security in high‐level matches and important places. The existing jamming sources are mainly single point jamming. Due to the shielding of buildings, it is impossible to fully cover the venue, and the existing suppressed jamming will affect the communication broadcasting. Here, a distributed optimal jamming method for massive UAVs is proposed. Through the identification and positioning of massive UAVs, using the location information of distributed jamming sources, the UAV jamming architecture based on satellite navigation is constructed. Combined with tabu search artificial bee colony theory, the distributed optimal jamming of UAVs is realized, which solves the problems of few jamming targets, slow speed and low success rate of the existing optimal jamming methods. The proposed method is compared with the existing methods in three aspects: communication frequency, jamming trajectory deviation and optimization speed. The simulation results show that the proposed method effectively improves the jamming success rate and jamming speed and can meet the application requirements of massive UAV jamming in the region.
Pose‐driven human activity anomaly detection in a CCTV‐like environment
Authors: Yang Yuxing , Angelini Federico , Naqvi Syed Mohsen 
Published: October 2022

AbstractHuman activity anomaly detection plays a crucial role in the next generation of surveillance and assisted living systems. Most anomaly detection algorithms are generative models and learn features from raw images. This work shows that popular state‐of‐the‐art autoencoder‐based anomaly detection systems are not capable of effectively detecting human‐posture and object‐positions related anomalies. Therefore, a human pose‐driven and object‐detector‐based deep learning architecture is proposed, which simultaneously leverages human poses and raw RGB data to perform human activity anomaly detection. It is demonstrated that pose‐driven learning overcomes the raw RGB based counterpart limitations in different human activities classification. Extensive validation is provided by using popular datasets. Then, it is demonstrated that with the aid of object detection, the human activities classification can be effectively used in human activity anomaly detection. Moreover, novel challenging datasets, that is, BMbD, M‐BMbD and JBMOPbD, are proposed for single and multi‐target human posture anomaly detection and joint human posture and object position anomaly detection evaluations.
Spatio‐temporal adaptive graph convolutional networks for traffic flow forecasting
Authors: Ma Qiwei , Sun Wei , Gao Junbo , Ma Pengwei , Shi Mengjie 
Published: October 2022

AbstractAccurate forecasting of traffic flow is crucial for intelligent traffic control and guidance. It is very challenging to forecast the traffic flow due to the high non‐linearity, complexity and dynamicity of the data. Most existing forecasting methods focus on designing complicated graph neural network architectures to capture the spatio‐temporal features of traffic data with the help of predefined graphs. However, traffic data exhibit a strong spatial dependency, which means that there are often complex correlations between nodes in a road network topology graph. Moreover, the spatial correlations of the road network change over time. To capture the properties of the road network topology graph, a novel spatio‐temporal adaptive graph convolutional networks model (STAGCN) based on deep learning is proposed. Utilize adaptive graph generation block to capture the static and dynamic structures of the traffic road network respectively, and they are integrated to construct an adaptive road network topology graph. Then the spatio‐temporal features of the traffic data are captured using spatio‐temporal convolution blocks. Experiments were conducted on publicly available traffic datasets for freeway traffic in California, USA, and the results showed that the prediction accuracy of the STAGCN model outperformed multiple baseline methods.
Microfluidically fabricated fibers containing pancreatic islets and mesenchymal stromal cells improve longevity and sustained normoglycemia in diabetic rats
Authors: Navaei-Nigjeh Mona , Mirzababaei Soheyl , Ghiass Mohammad Adel , Roshanbinfar Kaveh , Gholami Mahdi , Abdollahi Mohammad 
Published: October 2022

Abstract
Type 1 diabetes mellitus is an autoimmune disease characterized by the loss of pancreatic islet β cells. Insulin injections and pancreas transplants are currently available therapies. The former requires daily insulin injections, while the latter is constrained by donor organ availability. Islet transplantation is a promising alternative treatment for type 1 diabetes mellitus that may overcome the limitations of previous techniques. Two challenges, however, must be addressed: limited cell retention as a result of the immune response and limited function of the transplanted cells that survive. To address these problems, we developed a microfluidic technology for a one-step generation of islet-laden fibers to protect them from the immune response. This approach enables continuous generation of microfibers with a diameter suitable for islet encapsulation (275 µm). We, then, transplanted islet-laden fibers into diabetic Wistar rats. While islet-laden fibers alone were unable to restore normoglycemia in diabetic rats, adding mesenchymal stromal cells (MSCs) restored normoglycemia for an extended time. It increased the animals’ lifespan by up to 75 d. Additionally, it improved the glucose-stimulated response of islets to the point where there was no significant difference between the treatment group and the healthy animals. Additionally, the presence of MSCs suppressed the immune response, as seen by decreased levels of pro-inflammatory cytokines such as tumor necrosis factor-α. Taken together, these fibers including islet and MSCs provide a versatile platform for concurrently improving cell preservation and functioning following in vivo transplantation.
Facile molten salt synthesis of carbon-anchored TiN nanoparticles for durable high-rate lithium-ion battery anodes
Authors: Liu Ruijia , Li Na , Zhao Enyue , Zhao Jinkui , Yang Lingxu , Wang Wenjun , Liu Huijun , Zeng Chaoliu 
Published: October 2022

Abstract
Transition metal nitrides (TMNs), including titanium nitride (TiN), exhibit remarkable application prospects as anodes for durable high-rate lithium-ion batteries (LIBs). Regrettably, the absence of simple synthesis methods restricts their further development. Herein, a facile and low-cost molten salt synthesis strategy was proposed to prepare carbon-anchored TiN nanoparticles as an advanced anode material for LIBs with high rate capabilities. This nanosized TiN obtained is ∼5 nm in size and well-distributed onto carbon plates, which could release a reversible capacity of ∼381.5 mAh g−1 at 0.1 A g−1 after 250 cycles and ∼141.5 mAh g−1 at 1.0 A g−1 after 1000 cycles. Furthermore, it was confirmed that the conversion reaction between TiN and Li-ions happened during the electrochemical reaction process, resulting in the formation of Li3N and Ti. This unique microstructure attributed from TiN nanoparticles anchored by carbon could support the structural volume during cycling. This work highlights the method superiority of TiN prepared via a molten salt synthesis strategy as an anode for LIBs with impressive rate performances.
OmicsEV: a tool for comprehensive quality evaluation of omics data tables
Authors: Wen Bo , Jaehnig Eric J , Zhang Bing 
Published: October 2022

Abstract

Summary
RNA-Seq and mass spectrometry-based studies generate omics data tables with measurements for tens of thousands of genes across all samples in a study. The success of a study relies on the quality of these data tables, which is determined by both experimental data generation and computational methods used to process raw experimental data into quantitative data tables. We present OmicsEV, an R package for the quality evaluation of omics data tables. For each data table, OmicsEV uses a series of methods to evaluate data depth, data normalization, batch effect, biological signal, platform reproducibility and multi-omics concordance, producing comprehensive visual and quantitative evaluation results that help assess the data quality of individual data tables and facilitate the identification of the optimal data processing method and parameters for the omics study under investigation.

Availability and implementation
The source code and the user manual of OmicsEV are available at https://github.com/bzhanglab/OmicsEV, and the source code is released under the GPL-3 license.
A phylogenetic analysis of two preludes from &#x2028;J. S. Bach’s Well-Tempered Clavier II
Authors: Windram Heather F , Charlston Terence , Tomita Yo , Howe Christopher J 
Published: October 2022

Abstract
J. S. Bach’s Well-Tempered Clavier II is well known for the complexity of its source situation, and its vast array of variant readings. The current article uses techniques of phylogenetic analysis, developed in the biological sciences, to deepen our understanding of the complex relationships between the primary sources. The computer algorithm NeighborNet is used to analyse data comprising the textual variants for the Prelude in A, bwv888 and the Prelude in C, bwv870. The resultant grouping of sources reflects the differences in revision practice between the two preludes. While Bach saw little need to revise the Prelude in A, the Prelude in C underwent a process of continued revision that can be discerned in the results of the phylogenetic analysis. The analyses also highlight the uncertain relationship of the manuscript DD70 with the other sources of the Prelude in C and the implications for 18th-century performance practice.
Echoes behaving badly? Rhetorical and acoustic experimentalism in the echo fantasias of Jan Pieterszoon Sweelinck and his contemporaries
Authors: Ferraguto Mark 
Published: October 2022

Abstract
The 17th-century ‘echo fantasia’ for keyboard has long posed problems of classification and attribution. This article focuses on a particularly problematic example of the genre, the Echo Fantasia in d attributed to Jan Pieterszoon Sweelinck (d4). Once expurgated from the Sweelinck canon, d4 differs substantially from its compatriots, most notably in its erratic echo scheme in which some echoes are marked louder than their antecedents, and others take the shape of improvisatory variants. Viewing d4 from a wider perspective, this article positions the echo fantasia at the intersection of early 17th-century rhetorical and acoustic experimentalism. On the one hand, literary portrayals of the figure of Echo relied on rhetorical devices—such as anadiplosis—that also characterize d4. On the other hand, d4’s misbehaving echoes evoke the playful experimentalism of early scientists investigating echoes, including Francis Bacon, Isaac Beeckman and Marin Mersenne. Akin to a miniature musical laboratory, the echo fantasia was a genre in which the strangest echo effects could be replicated at the organ.
A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation
Authors: Shen Dongxu , He Xiaoli , Weng Peifang , Liu Yanan , Wu Zufang 
Published: October 2022

Abstract
Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.
Creation of an Inflammatory Bowel Disease Referral Pathway for Identifying Patients Who Would Benefit From Inflammatory Bowel Disease Specialist Consultation
Authors: Scott Frank I , Ehrlich Orna , Wood Dallas , Viator Catherine , Rains Carrie , DiMartino Lisa , McArdle Jill , Adams Gabrielle , Barkoff Lara , Caudle Jennifer , Cheng Jianfeng , Kinnucan Jami , Persley Kimberly , Sariego Jennifer , Shah Samir , Heller Caren , Rubin David T 
Published: October 2022

Abstract

Background
Recommendations regarding signs and symptoms that should prompt referral of patients with inflammatory bowel disease (IBD) to an IBD specialist for a consultation could serve to improve the quality of care for these patients. Our aim was to develop a consult care pathway consisting of clinical features related to IBD that should prompt appropriate consultation.

Methods
A scoping literature review was performed to identify clinical features that should prompt consultation with an IBD specialist. A panel of 11 experts was convened over 4 meetings to develop a consult care pathway using the RAND/UCLA Appropriateness Method. Items identified via scoping review were ranked and were divided into major and minor criteria. Additionally, a literature and panel review was conducted assessing potential barriers and facilitators to implementing the consult care pathway.

Results
Of 43 features assessed, 13 were included in the care pathway as major criteria and 15 were included as minor criteria. Experts agreed that stratification into major criteria and minor criteria was appropriate and that 1 major or 2 or more minor criteria should be required to consider consultation. The greatest barrier to implementation was considered to be organizational resource allocation, while endorsements by national gastroenterology and general medicine societies were considered to be the strongest facilitator.

Conclusions
This novel referral care pathway identifies key criteria that could be used to triage patients with IBD who would benefit from IBD specialist consultation. Future research will be required to validate these findings and assess the impact of implementing this pathway in routine IBD-related care.
Laboratory signatures differentiate the tolerance to hypothermic circulatory arrest in acute type A aortic dissection surgery
Authors: Liu Hong , Qian Si-Chong , Han Lu , Dong Zhi-Qiang , Shao Yong-Feng , Li Hai-Yang , Zhang Wei , Zhang Hong-Jia 
Published: October 2022

AbstractOBJECTIVESOur goal was to investigate whether laboratory signatures on admission could be used to identify risk stratification and different tolerance to hypothermic circulatory arrest in acute type A aortic dissection surgery.METHODSPatients from 10 Chinese hospitals participating in the Additive Anti-inflammatory Action for Aortopathy & Arteriopathy (5A) study were randomly divided into derivation and validation cohorts at a ratio of 7:3 to develop and validate a simple risk score model using preoperative variables associated with in-hospital mortality using multivariable logistic regression. The performance of the model was assessed using the area under the receiver operating characteristic curve. Subgroup analyses were performed to investigate whether the laboratory signature-based risk stratification could differentiate the tolerance to hypothermic circulatory arrest.RESULTSThere were 1443 patients and 954 patients in the derivation and validation cohorts, respectively. Multivariable analysis showed the associations of older age, larger body mass index, lower platelet–neutrophile ratio, higher lymphocyte–monocyte ratio, higher D-dimer, lower fibrinogen and lower estimated glomerular filtration rate with in-hospital death, incorporated to develop a simple risk model (5A laboratory risk score), with an area under the receiver operating characteristic of 0.736 (95% confidence interval 0.700–0.771) and 0.715 (95% CI 0.681–0.750) in the derivation and validation cohorts, respectively. Patients at low risk were more tolerant to hypothermic circulatory arrest than those at middle to high risk in terms of in-hospital mortality [odds ratio 1.814 (0.222–14.846); odds ratio 1.824 (1.137–2.926) (P = 0.996)].CONCLUSIONSThe 5A laboratory-based risk score model reflecting inflammatory, immune, coagulation and metabolic pathways provided adequate discrimination performances in in-hospital mortality prediction, which contributed to differentiating the tolerance to hypothermic circulatory arrest in acute type A aortic dissection surgery.Clinical Trials. gov number NCT04918108