bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying the potential transcriptional regulatory network in Hirschsprung disease by integrated analysis of microarray datasets
Authors: Xu Wenyao , Yu Hui , Chen Dian , Pan Weikang , Yang Weili , Miao Jing , Jia Wanying , Zheng Baijun , Liu Yong , Chen Xinlin , Gao Ya , Tian Donghao
Published: April 2023

Objective

Hirschsprung disease (HSCR) is one of the common neurocristopathies in children, which is associated with at least 20 genes and involves a complex regulatory mechanism. Transcriptional regulatory network (TRN) has been commonly reported in regulating gene expression and enteric nervous system development but remains to be investigated in HSCR. This study aimed to identify the potential TRN implicated in the pathogenesis and diagnosis of HSCR.

Methods

Based on three microarray datasets from the Gene Expression Omnibus database, the multiMiR package was used to investigate the microRNA (miRNA)–target interactions, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Then, we collected transcription factors (TFs) from the TransmiR database to construct the TF–miRNA–mRNA regulatory network and used cytoHubba to identify the key modules. Finally, the receiver operating characteristic (ROC) curve was determined and the integrated diagnostic models were established based on machine learning by the support vector machine method.

Results

We identified 58 hub differentially expressed microRNAs (DEMis) and 16 differentially expressed mRNAs (DEMs). The robust target genes of DEMis and DEMs mainly enriched in several GO/KEGG terms, including neurogenesis, cell–substrate adhesion, PI3K–Akt, Ras/mitogen-activated protein kinase and Rho/ROCK signaling. Moreover, 2 TFs (TP53andTWIST1), 4 miRNAs (has-miR-107,has-miR-10b-5p,has-miR-659-3p, andhas-miR-371a-5p), and 4 mRNAs (PIM3,CHUK,F2RL1, andCA1) were identified to construct the TF–miRNA–mRNA regulatory network. ROC analysis revealed a strong diagnostic value of the key TRN regulons (all area under the curve values were more than 0.8).

Conclusion

This study suggests a potential role of the TF–miRNA–mRNA network that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment.
A relation between undrained CPTu results and the state parameter for liquefiable soils
Authors: Monforte Lluís , Arroyo Marcos , Gens Antonio
Published: April 2023

This paper presents a new interpretation procedure to estimate the initial state parameter from cone penetration testing (CPTu) in undrained conditions based on the results from a comprehensive set of numerical simulations of CPTu in low permeability liquefiable soil. CPTu simulations are performed using the Particle Finite Element Method, whereas the material response is modelled with the Clay and Sand Model. The effects of soil constitutive parameters and roughness of the soil–steel interface are examined. It turns out that the numerical results are correctly summarized by an analytical relation derived from undrained cavity expansion results in critical state soils, as long as the constraints resulting from cone geometry are taken into account. The resulting adapted analytical formulation is notable for its simplicity and ease of use, comparing favorably with existing alternatives.
Axial response of resin-encapsulated cable bolts in monotonic and cyclic loading
Authors: Rastegarmanesh Ashkan , Mirzaghorbanali Ali , McDougall Kevin , Aziz Naj , Anzanpour Sina , Nourizadeh Hadi , Moosavi Mahdi
Published: April 2023

The ease of use and the design flexibility of cable bolts have made them a popular choice for rock support. Cable bolts can be encapsulated with cementitious grout or resin. There is a need to better understand the impact of resins on the behaviour of cable bolts under varying load and stress regimes over their long service life. This study reports on 18 large-scale resin pull-out tests. The testing apparatus minimised the rotational movement of the cable at the exit point by using a fully grouted anchor tube. Six cable bolts, ranging from 50 to 100 tonnes in capacity, anchored using a fast-curing urea silica resin, were tested under monotonic and cyclic loading. Each cable type was tested twice in monotonic loading, and then the average initial peak load was used to generate a cyclic loading pattern. The study found that the resin product had a relatively low load capacity regardless of the cable type, and that loading type had a minimal impact on the results. The cable diameter had a minor influence on the pull-out results. The resin provided a stiff behaviour and an excellent response to repeated loading.
Stability of tracked vehicles on soft grounds under multidirectional loading conditions
Authors: Dong Youkou , Yan Dingtao , Feng Xiaowei
Published: April 2023

Tracked vehicles are widely deployed for heavy lifting and transportation on inaccessible terrains such as swamps, bogs, and peatlands. The stability of a tracked vehicle is traditionally assessed only under uniaxial loading conditions and the impact of combined loading from different directions is ignored. This makes the conventional design framework somewhat unreliable. The failure envelope approach has been widely employed to assess the load-carrying capacity of shallow foundations. However, the failure envelopes available in public domain mainly focused on single isolated foundations, ignoring the interference effect between the tracks due to the rigid connection of the vehicle. This paper aims to develop an integrated framework to assess the stability of a tracked vehicle on a soft soil under fully three-dimensional loading conditions. The finite element method is adopted to simulate the soil–vehicle interactions, with the tracks idealised as two shallow foundations in parallel. The stability of the foundation system is described in terms of failure envelopes considering various track configurations and load combinations. Failure envelopes are represented by expressions and ultimately integrated into a multiple-nested function to determine the overall stability factor. The framework is demonstrated by a case study of designing a tracked vehicle under combined loading conditions.
Genomic description of critical cannabinoid biosynthesis genes
Authors: Innes Peter A. , Vergara Daniela
Published: April 2023

Cannabinoid production is a key attribute of the plant Can nabis sativa and characterizing the genes involved is an essential first step to develop tools for their optimization. We used bioinformatic approaches to annotate and explore variation in the genes coding for enzymes comprising the cannabinoid pathway: olivetol synthase (OLS), olivetolic acid cyclase (OAC), cannabigerolic acid synthase (CBGAS), and the cannabinoid oxidocyclases (THCAS, CBDAS, CBCAS) in multiple C. sativa genome assemblies from diverse lineages. The former three enzymes generate the precursor molecules for the oxidocyclases to produce cannabinoids tetrahydrocannabinol (THC) and cannabidiol (CBD). We show that duplications of OLS and OAC are consistent across varieties, and that OAC has the least amount of sequence diversity based on phylogenetic comparisons. We also found that one CBGAS-like gene exhibits copy number variation among varieties. We discuss implications of these genes existing on separate chromosomes (with homologs of each found in close proximity), and the significance of CBGAS being located on the X chromosome for cannabinoid production in female plants. This study provides valuable insight on the genomic identity and variation of cannabinoid biosynthesis genes that will benefit future research on the origin and evolution of this pathway, a driver of economic, social, and medicinal value.
Cluster of electric thrusters for astronautic and robotic INPPS flagship space flights to Mars and Europa moon
Authors: Jansen Frank , Andreussi Tommaso , Cesarretti Giovanni , Ehresmann Manfred , Grill Julia , Herdrich Georg , Funaki Ikkoh , Girard Nathalie , Grundmann Jan Thimo , Krejci David , Leiter Hans , Masson Frederic , Maiwald Volker , Misuri Tommaso , Oriol Stephane , Piragino Antonio , Reissner Alexander , Schanz Lars
Published: April 2023

This review deals with the selection of the electric propulsion system (EPS) for the internationally developed and designed, primary nuclear-electric space tug International Nuclear Power and Propulsion System (INPPS). INPPS is scheduled for interplanetary missions to Mars and Jupiter moon Europa missions by the end of decade 2020. Regarding specific technical and mission parameters preselected electric thruster (ET) types, developed by international companies and institutions, are analysed, evaluated and investigated for a possible application as propulsion system (PS), the so-called CET (Cluster of Electric Thrusters). It is analysed whether solely electric thrusters, combined in an adequate CET, enable the envisaged interplanetary missions—robotic and astronautic/crewed with the INPPS flagship.

Thruster clusters with strategic consortium considerations are analysed as a feasible PS of the INPPS. The studied CET consists of the following: (a) only European ETs, (b) combination of German and European ETs, (c) Japanese and European ETs or at least (d) Japanese, European and US thrusters. The main results are (1) Robotic and crewed INPPS mission to Mars/Europa are realizable with EPS only (no chemical propulsion is needed), (2) that every CET, except (c) of only Japanese and part of European thrusters, is capable to perform the main part of envisaged INPPS flagship mission orbit to Mars, back to Earth and to Jupiter/Europa moon.
A Framework for Distributed Feature Selection
Authors: Sharifnezhad Mona , Rahmani Mohsen , Ghaffarian Hossein
Published: April 2023

Many current multivariate filter feature selection approaches consider redundancy and relevance between features and class vectors simultaneously. However, these multivariate filter algorithms calculate the suitability of features by only the intrinsic characteristics of the data. In this paper, we suggest a new distributed framework to offset the multivariate feature selection problem. We propose the interaction with classifiers in multivariate filter feature selection. Our proposed framework calculates the relevance of each feature to class labels by embedded algorithms. Then, this technique examines redundancy among features through multivariate filter algorithms. In addition, in the proposed framework, we use horizontal distribution of data instead of using all them once. This approach reduces the runtime of the process in datasets with many samples and environments without centralized data. The results of the evaluation show that the proposed framework can improve classification accuracy compared with the methods just based on multivariate filters. In addition, the experimental results demonstrate that our algorithm outperforms compared approaches in precision, recall, and runtime.
MULTI-SOURCE AND HETEROGENEOUS ONLINE MUSIC EDUCATION MECHANISM: AN ARTIFICIAL INTELLIGENCE-DRIVEN APPROACH
Authors: YANG YUANYUAN , DOLLY RAVEENA JUDIE , ALASSAFI MADINI O. , SLOWIK ADAM , ALSAADI FAWAZ E.
Published: April 2023

In order to solve the challenges brought by multi-source and cross-domain scenarios to online music education, this paper designs an online music education system based on advanced artificial intelligence technology, which can provide personalized learning course resource recommendations for music online learners. The system includes four layers, consisting of user interface layer, application module layer, function module layer and data storage layer. At the application module level, this paper proposes a music recommendation algorithm based on a personalized multimodal network model. The recommendation algorithm performs music information retrieval (MIR) based on the similarity judgment of the contour of music pitch and the overall change, and constructs a multimodal network model based on the user’s preference for resources to achieve personalized music recommendation. This paper crawls more than one million music score data from a well-known music platform database in China to establish a dataset to evaluate the performance of this method. The comparison results with three existing works show that the method proposed in this paper has good performance and can provide users with suitable music recommendations. The artificial intelligence technology-driven online music education mechanism proposed in this paper has good prospects.
COMPLEXITY-BASED ANALYSIS OF MUSCLE ACTIVATION DURING WALKING AT DIFFERENT SPEEDS
Authors: SRIRAM SRIDEVI , RAJAGOPAL KARTHIKEYAN , KREJCAR ONDREJ , FRISCHER ROBERT , NAMAZI HAMIDREZA
Published: April 2023

In this research, we investigated the effect of changes in walking speed on variations of the complexity of electromyogram (EMG) signals recorded from the right and left legs of subjects. We specifically employed fractal theory and approximate entropy to analyze the changes in the complexity of EMG signals recorded from 13 subjects walked at 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, and 4.0 km/h on a flat surface. The results showed that by increasing of walking speed, the complexity of EMG signals decreases. The statistical analysis also indicated the significant effect of variations in walking speed on the variations of the complexity of EMG signals. This method analysis can be applied to other physiological signals of humans (e.g. electroencephalogram (EEG) signals) to investigate the effect of walking speed on other organs’ activations (e.g. brain).
DATA COLLECTION AND PERFORMANCE EVALUATION OF RUNNING TRAINING SPORT USING DIFFERENT NEURAL NETWORK TECHNIQUES
Authors: YANG CAIRU , CHANG YU-TENG
Published: April 2023

With the increasing engagement of human beings in the pursuit of healthcare, running as a sport has become a fashionable and healthcare first choice. This research uses artificial intelligence technology to carry out intelligent analysis when conducting running training. Artificial intelligence technology can accurately analyze and predict the application requirements of sports training postures. We proposed an analysis of sports posture and a prediction system, which uses running training data in the form of a heart rate, recorded on a GPS smart sports watch, as well as using the recurrent neural network (RNN), long and short-term memory (LSTM) and the gate recursive unit (GRU). These three types of neural network methods can predict which method is best suited for a road race and can confirm that it will be completed within the scheduled finish time; these models will also perform an intelligent analysis of physical fitness (heart rate, pace) and running technology (cadence, pace). The training and test data are collected from the running training records (running distance, time, heart rate, stride frequency, stride length, pace, calories, altitude and other characteristic values) as input parameters, to test and compare the running completion time trends of the RNN, LSTM and GRU neural network methods in the exercise table, so as to evaluate their predictive abilities. The results show that the GRU method has the best predictive accuracy, and the least accurate is the LSTM method. After the hidden layers are added to the three predictive methods, the RNN is slightly regressive, the LSTM indicates a trend of significant improvement and the GRU exhibits less obvious changes.
Resonance phenomena in dielectric media: A review and comparison of acoustic and electromagnetic modes
Authors: Gidion Gunnar , Aftab Taimur , Reindl Leonhard M. , Rupitsch Stefan J.
Published: April 2023

The theory and application of resonances and vibrational modes are part of the foundation of science. In this contribution, examples of acoustical resonators are highlighted, and compared to electromagnetic modes. As an example from architecture, we describe the phenomenon of whispering galleries; such modes are nowadays known in dielectric and optical resonators. A specimen of a semicircular whispering bench in Park Sanssouci in Potsdam is acoustically investigated and demonstrated to show low losses for sound propagation. A special acoustical bug is discussed which was used for the espionage of the U.S. ambassador in Moscow. The Sovyets could interrogate this passive device by radio waves. Its working principle was based on the electromagnetic resonance of the cavity that the sound-sensitive membrane was part of. The underlying relation between excitation and resonance is compared to the sound production in flue organ pipes. A stopped flue organ pipe was investigated using a piezoelectric film sensor inside the pipe body. The results show that even-numbered modes, which are usually suppressed in the radiated sound of a stopped pipe, are still present in the vibrations inside the resonator.
Patents as Real Options: A Sensitivity Analysis of Option Valuation Using the Binomial Model
Authors: Thoma Grid
Published: April 2023

Using the real option approach and the binomial decision tree model, patent value is discussed in terms of how patent protection gives firms flexibility in making investment decisions on whether or how to continue exploiting the underlying invention in the commercialisation phase. The results of this paper, in agreement with predictions of current financial theory, indicate that patent real option value increases when the following input factor conditions exist: increased patent asset value, longer time to the expiration of patent protection, higher interest rates, larger variability of future values of the patent asset, decreased patent commercialisation investment, and lower cost of delay in commercialisation investment decisions. Furthermore, patent real option value sensitivities are estimated for each of these input factors of the binomial decision tree model. More broadly, the paper provides a novel valuation tool for the monetary appraisal of patents and contributes to the IP literature on devising timely indicators of innovative activities.
Optimal Incentives in a Limit Order Book: A SPDE Control Approach
Authors: Baldacci Bastien , Bergault Philippe
Published: April 2023

With the fragmentation of electronic markets, exchanges are now competing in order to attract trading activity on their platform. Consequently, they developed several regulatory tools to control liquidity provision/consumption on their liquidity pool. In this paper, we study the problem of an exchange using incentives in order to increase market liquidity. We model the limit order book as the solution of a stochastic partial differential equation (SPDE) as in [R. Cont and M. S. Müller, 2021, A stochastic partial differential equation model for limit order book dynamics, SIAM Journal on Financial Mathematics 12(2), 744–787]. The incentives proposed to the market participants are functions of the time and the distance of their limit order to the mid-price. We formulate the control problem of the exchange who wishes to modify the shape of the order book by increasing the volume at specific limits. Due to the particular nature of the SPDE control problem, we are able to characterize the solution with a classic Feynman–Kac representation theorem. Moreover, when studying the asymptotic behavior of the solution, a specific penalty function enables the exchange to obtain closed-form incentives at each limit of the order book. We study numerically the form of the incentives and their impact on the shape of the order book, and analyze the sensitivity of the incentives to the market parameters.
QUANTITATIVE ASSESSMENT OF THE EFFECT OF GOVERNMENT EXPENDITURE ON POVERTY INCIDENCE IN NIGERIA
Authors: OBELE TOLULOPE ELORHOR , ADEBIYI OYEYEMI OMODADEPO
Published: April 2023

The allocation and level of government spending is meant to be one major factor that can reduce poverty in a country. This study uniquely conducts the assessment of the effect of government expenditure on poverty incidence in Nigeria over the period of 1986 — 2020. Stationary features of the series were tested by the Augmented Dickey — Fuller (ADF) unit root test. The ADF result indicates that the series are stationary at I(1). The result of the Johansen cointegration test indicates that there exists an equilibrium relationship among the variables in the study. The Johansen normalization cointegration result presented gave a proof by indicating that in the long-run government expenditure on building and construction, and government expenditure on health (GH) has positive impacts on poverty incidence while, government expenditure on security has a negative impact on poverty incidence in Nigeria. The vector error correction model (VECM) result of about 2.77% also indicates that there is an existing positive relationship between government spending on education and poverty incidence in Nigeria. GH has an inappropriate sign; thus, is an indication that GH do not have the desired impact relating to poverty reduction in Nigeria. Hence, the study recommends that the Nigerian government should raise her spending on health by promoting excellent health care and health facilities that will enhance health and economic provisioning of the poor. Also, the government should stretch more of its spending on education such as the finance of teachers’ training, research and development in order to reduce poverty level in Nigeria. The study further suggests a cross-country analysis on public spending, and poverty reduction in order to generalize these findings in a wider perspective.
Textured Mesh Quality Assessment: Large-scale Dataset and Deep Learning-based Quality Metric
Authors: Nehmé Yana , Delanoy Johanna , Dupont Florent , Farrugia Jean-Philippe , Le Callet Patrick , Lavoué Guillaume
Published: April 2023

Over the past decade, three-dimensional (3D) graphics have become highly detailed to mimic the real world, exploding their size and complexity. Certain applications and device constraints necessitate their simplification and/or lossy compression, which can degrade their visual quality. Thus, to ensure the best Quality of Experience, it is important to evaluate the visual quality to accurately drive the compression and find the right compromise between visual quality and data size. In this work, we focus on subjective and objective quality assessment of textured 3D meshes. We first establish a large-scale dataset, which includes 55 source models quantitatively characterized in terms of geometric, color, and semantic complexity, and corrupted by combinations of five types of compression-based distortions applied on the geometry, texture mapping, and texture image of the meshes. This dataset contains over 343k distorted stimuli. We propose an approach to select a challenging subset of 3,000 stimuli for which we collected 148,929 quality judgments from over 4,500 participants in a large-scale crowdsourced subjective experiment. Leveraging our subject-rated dataset, a learning-based quality metric for 3D graphics was proposed. Our metric demonstrates state-of-the-art results on our dataset of textured meshes and on a dataset of distorted meshes with vertex colors. Finally, we present an application of our metric and dataset to explore the influence of distortion interactions and content characteristics on the perceived quality of compressed textured meshes.
Association between Interactions among ACE Gene Polymorphisms and Essential Hypertension in Patients in the Hefei Region, Anhui, China
Authors: Wang Li , Song Ting-ting , Dong Chang-wu
Published: April 2023

Objective. Essential hypertension (EH) is a common cardiovascular disease that endangers human health. Its pathogenesis is complex and has not been fully elucidated. We explore the association between EH and interactions among polymorphisms of the angiotensin converting enzyme (ACE) gene in the Hefei region, Anhui, China. Methods. A total of 500 participants (400 hypertensive and 100 normotensive) were included in this study. The polymorphisms were detected via improved multiple ligase detection reaction (iMLDR). To improve the accuracy of prediction, multifactor dimensionality reduction (MDR) was used to analyze the overall effect of interactions among seven loci on the incidence of EH. Results. The frequencies of polymorphisms in the ACE genes rs12709426, rs4291, rs4309, rs4331, rs4343, rs4459609, and rs4461142 in the EH group were not statistically significantly different from those in the control group. We also found that the single nucleotide polymorphism (SNP) rs12709426 only had a homozygous AA genotype and no polymorphisms. There were no differences in the frequency of genetic polymorphisms between the EH and control groups. The best model explaining the EH group was the combined effect of ACE genes rs4291, rs4309, and rs4461142. Conclusion. There is an interaction effect among ACE gene loci in EH patients in Hefei region, Anhui, China. Also, the ACE gene SNP rs12709426 only has a homozygous AA genotype and does not show an association with EH.
Genetic Variation of New Purple-Fleshed Sweet Potato (Ipomoea batatas L.) Genotypes in Indonesia by Multivariate Analysis
Authors: Ustari Debby , Wicaksono Arif Affan , Concibido Vergel , Suganda Tarkus , Ruswandi Dedi , Ruminta  , Karuniawan Agung
Published: April 2023

Purple-fleshed sweet potato (PFSP) is a major staple food and feed material in tropical countries. The pandemic of COVID-19 that encouraged healthy lifestyles worldwide further increases the importance of PFSP. Despite its importance, the investment in research to improve PFSP in Indonesia was left behind. The objective of the research was to estimate the genetic variation and genetic distance of new PFSP genotypes prior to variety release. The research trials were arranged in a randomized block design, with nine new PFSP genotypes from polycrosses breeding as treatments and three check varieties in four growing environments in West Java, i.e., Cilembu, Jatinangor, Maja, and Karangpawitan during one season. Agronomic traits data were analyzed by the multivariate analysis. The principal component analysis (PCA) showed high genetic variation of PFSP in four environments. The eigenvalue ranges from 1.92 to 5.29 in Cilembu which contributed to 80.958% variability, 0.543–6.177 which contributed variability to 92.135% in Jatinangor, 0.824–5.695 in Karangpawitan which contributed to 92.117%, and 0.822–4.797 in Maja which contributed to 86.133%. Storage root length, storage root diameter, number of roots per plant, total root weight per plant, number of marketable/commercial roots, marketable/commercial root weight, number of roots per plot, and total storage root weight have a discriminant value of more than 0.7 in PC 1. Agglomerative hierarchical clustering (AHC) showed a wide distribution obtaining two clusters in Cilembu with euclidean distance 1.92–5.29, Jatinangor 1.72–6.09, Karangpawitan 1.28–6.38, and Maja 2.05–5.09. High genetic variation in the four environments greatly supports to the development of PFSP new varieties.
Roof Water Damage Prediction and Evaluation of Sand-Mud Sedimentary Tectonic Strata
Authors: Jiang Pengfei , Zhuge Fumin , Jing Suolin , Li Zongkai , Xiao Peng , Lv Yuguang
Published: April 2023

The prediction and control of roof water disaster has been one of the key problems in the mining process of coal resources. With the increase of mining depth in the western mining area, the roof caving and communicating to the overlying water-bearing strata have led to an increasing number of roof water inrush accidents and deterioration of production environment of the working face. Aiming at the problem of roof water disaster prediction of sandy-argillaceous structural strata in Shanghaimiao mining area in China, firstly, the mechanical structure model of roof water inrush was built according to the parameters in the advance of the working face, and the thickness of the sandstone was used as the main controlling geological factor; the formula was derived for calculating the water-rich intensity

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of the overlying strata in the mining area. Secondly, starting from the height of the “Breakage-arch” development disturbance by combining the mechanical structure model of roof water inrush, the relative positional relation of the “Breakage-arch” and the water-bearing strata was analyzed, and a new method for judging the risk coefficient

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of roof water inrush was proposed. Finally, according to the geological drilling histogram and the field conditions of #111084 working face of the no. 1 mine in Shanghaimiao mine area, the water-rich index and water inrush risk coefficient of overlying water-bearing strata were obtained by means of discriminant analysis, and the water inrush risk of #111084 working face was evaluated and predicted quantitatively. The water-rich property evaluation of water-bearing strata under the condition of low degree of hydrogeological exploration was evaluated accurately and reasonably, and a new evaluation method of the water disaster during mining was proposed.
Dynamic Pressure Manifestation Mechanism and Control Techniques for Roadways with Large Mining Heights and Intense Mining: A Case Study
Authors: Xu Dong , Gao Mingshi , Yu Xin
Published: April 2023

Responding to severe surrounding rock deformation failures and other problems in roadways in western China with large mining heights and intense mining, the work presented in this paper studied the mechanism of surrounding rock deformation failures in roadways with dynamic pressure through field investigations, theoretical analysis, and numerical simulation. According to the research findings, mining roadway deformation failures are affected by roadway layout orientation, working face mining intensity, and dynamic load disturbances from roof breakage. Coal pillars, as bridges connecting the roof and floor, constitute the energy transfer path near roadways surrounding rock, and an unreasonable coal pillar size and lateral overhanging roof structure may aggravate static load energy accumulation in the roadway surrounding rock. Roadway protection with small or large coal pillars may increase elastic energy loss in the energy transfer path; a reasonable size of small and large coal pillars is 15 m and 35 m, respectively. Using roof cutting for pressure relief may reduce the elastic energy of roadway surrounding rock by 14.35-26.33% during primary mining and 21.57-29.31% during secondary mining, thereby reducing the static load elastic energy in the surrounding rock and improving the stability of roadway surrounding rock.
The Indirect Effect of Depression between Nightmares and Well‐Being in Lebanese Patients with Schizophrenia
Authors: Mahfoud Daniella , El Ahdab Jad , Helwe Sami , Topalian Michael , Tarabay Christina , Rifi Karim , Haddad Georges , Obeid Sahar , Hallit Souheil
Published: April 2023

Background. Because nightmares seem to be associated with depression in schizophrenia, detecting them early in therapeutic practice might be critical to ensuring effective avoidance of the development of depressive symptomatology. This helps promote well‐being and improve the patient’s quality of life and illness prognosis. Therefore, the aim of this study was to examine the indirect effect of depression between nightmares and well‐being in a Lebanese sample of patients with schizophrenia. Method. This monocentric cross‐sectional study, conducted in July 2022, enrolled patients with chronic schizophrenia admitted to the Psychiatric Hospital of the Cross. Data were collected from a total of 148 participants through face‐to‐face interviews. The questionnaire included a nightmares measure, PSYRATS, Calgary depression scale for schizophrenia, PTSD checklist for DSM‐5, the digit span subset, and WHO‐5Well‐Being Index. Results. The presence of nightmares was significantly associated with more depression, whereas higher depression was significantly associated with lower well‐being. It is noteworthy that the presence of nightmares was not directly associated with well‐being. Conclusion. Nightmares lead indirectly to lower well‐being in schizophrenia patients, with depression serving as a mediating factor in this association. This suggests that interventions aiming at improving dream content may also have a beneficial effect in reducing depression in schizophrenia leading therefore to better well‐being of the patients.
Drug Discovery in Canine Pyometra Disease Identified by Text Mining and Microarray Data Analysis
Authors: Wang Xin , Yu Guohua
Published: April 2023

Canine pyometra, which is accompanied by bacterial contamination of the dog uterus, is defined as a complex disease associated with the activation of several systems, including the immune system. This study uses text mining and microarray data analysis methods to discover some existing targeted gene drugs and expand potential new drug indications. Text mining (“canine pyometra”) and microarray data analysis (GSE99877) were used to obtain a common set of genes. These genes and protein‐protein interaction (PPI) networks were analyzed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. Then, the important genes clustered in the PPI network were selected for gene‐drug interaction analysis to provide evidence for potential drug discovery. Through text mining and data analysis, we obtained 17,544 text mining genes (TMGs) and 399 differentially expressed genes (DEGs), respectively. There were 256 repeat genes between TMGs and DEGs, including 70 upregulated genes and 186 downregulated genes. Thirty‐seven genes clustered in three significant gene modules. Eight of the 37 genes can target 23 existing drugs. In conclusion, the discovery of 8 immune response‐related genes (BTK, CSF2RA, CSF2RB, ITGAL, NCF4, PLCG2, PTPRC, and TOP2A) targeting 23 existing drugs may expand the drug indications for pyometra‐related diseases in dogs.
Application of Fiber Grating Sensing in Similar Model Impact Tests of Underground Engineering
Authors: Gao Lei , Li Zhihao , Li Jie , Wang Zhen , Jiang Haiming , Wang Mingyang
Published: April 2023

To clarify damage or degradation mechanisms of underground shock disturbance of deep caverns, a customized model of a deep cavern to subjected ground shock was employed to simulate the following properties and processes: crustal stress loading, cavern excavation, and ground-shock disturbance loading. The similar model specimen was a cube of 1.3 m length and a size similarity ratio of 1 : 50. A fiber Bragg grating (FBG) strain sensor with multipoint distributions was developed to monitor the distribution of internal strains in the model. Sensors were appropriately arranged and packaged in the similar model of deep rock to determine strain variation in the model under hydrostatic confining pressure, construction dynamic load, and shock dynamic load. This investigation involved high crustal stress simulation, tunnel boring machine (TBM) construction simulation, and deep explosive shock simulation, respectively. The results suggest that the sensors can accurately monitor the strain during the entire process comprising loading, excavation, and shock generation and obtain the distribution of cave strain during excavation and shock generation. The cave strain indicated that the left and right sides of the tunnel both experienced a rapid increase in tensile strain from the top plane shock wave, proportional to the shock force. The mechanism of surrounding rock failure and the occurrence of the V-shaped blasting pit were clarified. In the model test, the following phenomena related to deep tunnel failure were simulated: particle ejection, block collapse, slabbing, and tunnel face collapse. The oscillatory wave was also monitored with FBG sensors. The results demonstrated that FBG strain sensor had good repeatability and could accurately monitor strain change in the different blocks, thus demonstrating considerable potential for use in similar model tests. The model tests conducted in this study can provide important technical reference and support for the construction and protective design of deep caverns.
Supplementary File 1 from Bayesian Machine Learning Enables Identification of Transcriptional Network Disruptions Associated with Drug-Resistant Prostate Cancer
Authors: Blatti Charles , de la Fuente Jesús , Gao Huanyao , Marín-Goñi Irene , Chen Zikun , Zhao Sihai D. , Tan Winston , Weinshilboum Richard , Kalari Krishna R. , Wang Liewei , Hernaez Mikel
Published: April 2023

Supplementary Notes (S1-S5)Supplementary Tables (S1 - S5; S10 - S11)Supplementary Figures (S1 - S12)
Supplementary Data from DNA Methylation Landscapes of Prostate Cancer Brain Metastasis Are Shaped by Early Driver Genetic Alterations
Authors: Gallon John , Rodriguez-Calero Antonio , Benjak Andrej , Akhoundova Dilara , Maletti Sina , Amstutz Ursula , Hewer Ekkehard , Genitsch Vera , Fleischmann Achim , Rushing Elisabeth J. , Grobholz Rainer , Fischer Ingeborg , Jochum Wolfram , Cathomas Gieri , Osunkoya Adeboye O. , Bubendorf Lukas , Moch Holger , Thalmann George , Feng Felix Y. , Gillessen Silke , Ng Charlotte K.Y. , Rubin Mark A. , Piscuoglio Salvatore
Published: April 2023

Supplementary Figures
Supplementary Data from DNA Methylation Landscapes of Prostate Cancer Brain Metastasis Are Shaped by Early Driver Genetic Alterations
Authors: Gallon John , Rodriguez-Calero Antonio , Benjak Andrej , Akhoundova Dilara , Maletti Sina , Amstutz Ursula , Hewer Ekkehard , Genitsch Vera , Fleischmann Achim , Rushing Elisabeth J. , Grobholz Rainer , Fischer Ingeborg , Jochum Wolfram , Cathomas Gieri , Osunkoya Adeboye O. , Bubendorf Lukas , Moch Holger , Thalmann George , Feng Felix Y. , Gillessen Silke , Ng Charlotte K.Y. , Rubin Mark A. , Piscuoglio Salvatore
Published: April 2023

Supplementary Tables
Table S6 from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Authors: Yao Lijun , Wang Julia T. , Jayasinghe Reyka G. , O'Neal Julie , Tsai Chia-Feng , Rettig Michael P. , Song Yizhe , Liu Ruiyang , Zhao Yanyan , Ibrahim Omar M. , Fiala Mark A. , Fortier Julie M. , Chen Siqi , Gehrs Leah , Rodrigues Fernanda Martins , Wendl Michael C. , Kohnen Daniel , Shinkle Andrew , Cao Song , Foltz Steven M. , Zhou Daniel Cui , Storrs Erik , Wyczalkowski Matthew A. , Mani Smrithi , Goldsmith Scott R. , Zhu Ying , Hamilton Mark , Liu Tao , Chen Feng , Vij Ravi , Ding Li , DiPersio John F.
Published: April 2023

Pearson R correlation values between bulk RNA expression and scRNA expression in PCs for target genes.
Table S5 from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Authors: Yao Lijun , Wang Julia T. , Jayasinghe Reyka G. , O'Neal Julie , Tsai Chia-Feng , Rettig Michael P. , Song Yizhe , Liu Ruiyang , Zhao Yanyan , Ibrahim Omar M. , Fiala Mark A. , Fortier Julie M. , Chen Siqi , Gehrs Leah , Rodrigues Fernanda Martins , Wendl Michael C. , Kohnen Daniel , Shinkle Andrew , Cao Song , Foltz Steven M. , Zhou Daniel Cui , Storrs Erik , Wyczalkowski Matthew A. , Mani Smrithi , Goldsmith Scott R. , Zhu Ying , Hamilton Mark , Liu Tao , Chen Feng , Vij Ravi , Ding Li , DiPersio John F.
Published: April 2023

List of recurrent mutations with potential utility as neoantigens
Table S4. from Dysregulation of Mitochondrial Translation Caused by CBFB Deficiency Cooperates with Mutant PIK3CA and Is a Vulnerability in Breast Cancer
Authors: Malik Navdeep , Kim Young-Im , Yan Hualong , Tseng Yu-Chou , du Bois Wendy , Ayaz Gamze , Tran Andy D. , Vera-Ramirez Laura , Yang Howard , Michalowski Aleksandra M. , Kruhlak Michael , Lee Maxwell , Hunter Kent W. , Huang Jing
Published: April 2023

This is supplementary Table 4.
Table S8 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S8: Multivariable analysis for overall (N=469) and progression-free (N=453) survival NOT including HER2. Overall and Progression-Free survival data of patients with ER+ breast cancer and treated with endocrine therapy are also shown.
Table S1 from Dysregulation of Mitochondrial Translation Caused by CBFB Deficiency Cooperates with Mutant PIK3CA and Is a Vulnerability in Breast Cancer
Authors: Malik Navdeep , Kim Young-Im , Yan Hualong , Tseng Yu-Chou , du Bois Wendy , Ayaz Gamze , Tran Andy D. , Vera-Ramirez Laura , Yang Howard , Michalowski Aleksandra M. , Kruhlak Michael , Lee Maxwell , Hunter Kent W. , Huang Jing
Published: April 2023

This is supplementary Table 1.
Table S6 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S6: Bivariate analysis of TONSL H-score with other tumor markers
Table S3 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S3: DepMap analysis reveals gene essentiality for survival of select genes upregulated in immortalized cells compared to primary cells.
Table S14 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S14: Genes differentially expressed in TMD-436pLKO and TMD-436shTONSL cells. Fold changes in gene expression are indicated.
Table S12 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S12: List of interactors and antagonists of BRCA1-BRAD1 complex. Fold changes in gene expression are indicated.
Table S11 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S11: The effects of TONSL overexpression on proliferation signature of breast tumors.
Supplementary Table S2 from G-Quadruplex Structures Are Key Modulators of Somatic Structural Variants in Cancers
Authors: Zhang Rongxin , Shu Huiling , Wang Yuqi , Tao Tiantong , Tu Jing , Wang Cheng , Mergny Jean-Louis , Sun Xiao
Published: April 2023

Epigenetic data used in this study
Supplementary Data from G-Quadruplex Structures Are Key Modulators of Somatic Structural Variants in Cancers
Authors: Zhang Rongxin , Shu Huiling , Wang Yuqi , Tao Tiantong , Tu Jing , Wang Cheng , Mergny Jean-Louis , Sun Xiao
Published: April 2023

Supplementary Figures and Supplementary Methods
Supplementary Data from Active Remodeling of Capillary Endothelium via Cancer Cell–Derived MMP9 Promotes Metastatic Brain Colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Movie 5
Data from Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases
Authors: Wood Colin S. , Pennel Kathryn A.F. , Leslie Holly , Legrini Assya , Cameron Andrew J. , Melissourgou-Syka Lydia , Quinn Jean A. , van Wyk Hester C. , Hay Jennifer , Roseweir Antonia K. , Nixon Colin , Roxburgh Campbell S.D. , McMillan Donald C. , Biankin Andrew V. , Sansom Owen J. , Horgan Paul G. , Edwards Joanne , Steele Colin W. , Jamieson Nigel B.
Published: April 2023

Abstract
Strong immune responses in primary colorectal cancer correspond with better patient survival following surgery compared with tumors with predominantly stromal microenvironments. However, biomarkers to identify patients with colorectal cancer liver metastases (CRLM) with good prognosis following surgery for oligometastatic disease remain elusive. The aim of this study was to determine the practical application of a simple histological assessment of immune cell infiltration and stromal content in predicting outcome following synchronous resection of primary colorectal cancer and CRLM and to interrogate the underlying functional biology that drives disease progression. Samples from patients undergoing synchronous resection of primary colorectal cancer and CRLM were evaluated in detail through histological assessment, panel genomic and bulk transcriptomic assessment, IHC, and GeoMx spatial transcriptomics (ST) analysis. High immune infiltration of metastases was associated with improved cancer-specific survival. Bulk transcriptomic analysis was confounded by stromal content, but ST demonstrated that the invasive edge of the metastases of long-term survivors was characterized by adaptive immune cell populations enriched for type II IFN signaling and MHC-class II antigen presentation. In contrast, patients with poor prognosis demonstrated increased abundance of regulatory T cells and neutrophils with enrichment of Notch and TGFβ signaling pathways at the metastatic tumor center. In summary, histological assessment can stratify outcomes in patients undergoing synchronous resection of CRLM, suggesting that it has potential as a prognostic biomarker. Furthermore, ST analysis has revealed significant intratumoral and interlesional heterogeneity and identified the underlying transcriptomic programs driving each phenotype.
Significance:
Spatial transcriptomics uncovers heterogeneity between patients, between matched lesions in the same patient, and within individual lesions and identifies drivers of metastatic progression in colorectal cancer with reactive and suppressed immune microenvironments.
Supplementary Table S2 from Phase I Study of the Liposomal Formulation of Eribulin (E7389-LF): Results from the Advanced Gastric Cancer Expansion Cohort
Authors: Shitara Kohei , Hirao Motohiro , Iwasa Satoru , Oshima Takashi , Komatsu Yoshito , Kawazoe Akihito , Sato Yasuyoshi , Hamakawa Takuya , Yonemori Kan , Machida Nozomu , Yuki Satoshi , Suzuki Takuya , Okumura Shiori , Takase Takao , Semba Taro , Zimmermann Bob , Teng Angela , Yamaguchi Kensei
Published: April 2023

Supplementary Table S2 outlines the representativeness of study patients.