bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weakly supervised semantic segmentation for MRI: exploring the advantages and disadvantages of class activation maps for biological image segmentation with soft boundaries
Authors: Syed Shaheen , Anderssen Kathryn E. , Stormo Svein Kristian , Kranz Mathias 
Published: February 2023

AbstractFully supervised semantic segmentation models require pixel-level annotations that are costly to obtain. As a remedy, weakly supervised semantic segmentation has been proposed, where image-level labels and class activation maps (CAM) can detect discriminative regions for specific class objects. In this paper, we evaluated several CAM methods applied to different convolutional neural networks (CNN) to highlight tissue damage of cod fillets with soft boundaries in MRI. Our results show that different CAM methods produce very different CAM regions, even when applying them to the same CNN model. CAM methods that claim to highlight more of the class object do not necessarily highlight more damaged regions or originate from the same high discriminatory regions, nor do these damaged regions show high agreement across the different CAM methods. Additionally, CAM methods produce damaged regions that do not align with external reference metrics, and even show correlations contrary to what can be expected.
Generalizability and performance of methods to detect non-wear with free-living accelerometer recordings
Authors: Skovgaard Esben Lykke , Roswall Malthe Andreas , Pedersen Natascha Holbæk , Larsen Kristian Traberg , Grøntved Anders , Brønd Jan Christian 
Published: February 2023

AbstractWearable physical activity sensors are widely used in research and practice as they provide objective measures of human behavior at a low cost. An important challenge for accurate assessment of physical activity behavior in free-living is the detection non-wear. Traditionally, heuristic algorithms that rely on specific interval lengths have been employed to detect non-wear time; however, machine learned models are emerging. We explore the potential of detecting non-wear using decision trees that combine raw acceleration and skin temperature, and we investigate the generalizability of our models, traditional heuristic algorithms, and recently developed machine learned models by external validation. The Decision tree models were trained using one week of data from thigh- and hip-worn accelerometers from 64 children. External validation was performed using data from wrist-worn accelerometers of 42 adolescents. For non-wear episodes longer than 60 min, the heuristic algorithms performed the best with F1-scores above 0.96. However, regarding episodes shorter than 60 min, the best performing method was the decision tree model including the six most important predictors with F1 scores above 0.74 for all sensor locations. We conclude that for classifying non-wear time, researchers should carefully select an appropriate method and we encourage the use of external validation when reporting on machine learned non-wear models.
Attention-assisted hybrid 1D CNN-BiLSTM model for predicting electric field induced by transcranial magnetic stimulation coil
Authors: Sathi Khaleda Akhter , Hosain Md Kamal , Hossain Md. Azad , Kouzani Abbas Z. 
Published: February 2023

AbstractDeep learning-based models such as deep neural network (DNN) and convolutional neural network (CNN) have recently been established as state-of-the-art for enumerating electric fields from transcranial magnetic stimulation coil. One of the main challenges related to this electric field enumeration is the prediction time and accuracy. Despite the low computational cost, the performance of the existing prediction models for electric field enumeration is quite inefficient. This study proposes a 1D CNN-based bi-directional long short-term memory (BiLSTM) model with an attention mechanism to predict electric field induced by a transcranial magnetic stimulation coil. The model employs three consecutive 1D CNN layers followed by the BiLSTM layer for extracting deep features. After that, the weights of the deep features are redistributed and integrated by the attention mechanism and a fully connected layer is utilized for the prediction. For the prediction purpose, six input features including coil turns of single wing, coil thickness, coil diameter, distance between two wings, distance between head and coil position, and angle between two wings of coil are mapped with the output of the electric field. The performance evaluation is conducted based on four verification metrics (e.g. R2, MSE, MAE, and RMSE) between the simulated data and predicted data. The results indicate that the proposed model outperforms existing DNN and CNN models in predicting the induced electrical field with R2 = 0.9992, MSE = 0.0005, MAE = 0.0188, and RMSE = 0.0228 in the testing stage.
Identification of a hypoxia-related gene prognostic signature in colorectal cancer based on bulk and single-cell RNA-seq
Authors: Qiao Yihuan , Jiang Xunliang , Li Yaoting , Wang Ke , Chen Rujie , Liu Jun , Du Yongtao , Sun Li , Li Jipeng 
Published: February 2023

AbstractColorectal cancer (CRC) is the most common and fatal tumor in the gastrointestinal system. Its incidence and mortality rate have increased in recent years. Hypoxia, a persistent physiological tumor feature, plays a vital role in CRC tumorigenesis, metastasis, and tumor microenvironment (TME). Therefore, we constructed a hypoxia-related gene (HRG) nomogram to predict overall survival (OS) and explored the role of HRGs in the CRC TME. The Cancer Genome Atlas (TCGA) dataset was used as the training set, and two Gene Expression Omnibus datasets (GSE39582 and GSE103479) were used as the testing sets. HRGs were identified using the Gene Set Enrichment Analysis (GSEA) database. An HRG prognostic model was constructed in the training set using the least absolute shrinkage and selection operator regression algorithm and validated in the testing sets. Then, we analyzed tumor-infiltrating cells (TICs) using the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm. Furthermore, single-cell next-generation RNA sequencing (RNA-seq) was used to investigate HRG expression in different TICs in the GSE139555 dataset. Finally, reverse transcription polymerase chain reactions (RT-PCR) were used to validate HRG mRNA expression in ten pairs of CRC normal and cancer tissue samples. A six HRG prognostic signature was constructed, with a superior OS prediction ability in CRC patients (area under the receiver operating characteristic curve (AUC) at one year: 0.693, AUC at three years: 0.712, and AUC at five years: 0.780). GSEA enrichment analysis identified six pathways enriched in the high-risk group. The TIC analysis indicated that the high-risk group had lower T-cell expression and higher neutrophil expression than the low-risk group. Furthermore, immune-related genes had an inseparable relationship with the HRG prognostic signature. Based on single-cell RNA-seq data, we found elevated hexokinase 1 (HK1) and glucose-6-phosphate isomerase (GPI) gene expression in natural killer (NK) and CD8+ T cells. RT-PCR in ten CRC normal-tumor tissue pairs showed that expression of the signature’s six HRGs varied differently in cancerous and paracancerous tissues. The constructed HRG signature successfully predicted the OS of whole-stage CRC patients. In addition, we showed that the signature’s six HRGs were closely associated with the TME in CRC, where hypoxia inhibits the antitumor function of T cells.
Precision dual-comb spectroscopy using wavelength-converted frequency combs with low repetition rates
Authors: Sugiyama Yohei , Kashimura Tsubasa , Kashimoto Keiju , Akamatsu Daisuke , Hong Feng-Lei 
Published: February 2023

AbstractPrecision spectroscopy contributed significantly to the development of quantum mechanics in its early stages. In the twenty-first century, precision spectroscopy has played an important role in several fields, including fundamental physics, precision measurement, environmental monitoring, and medical diagnostics. An optical frequency comb is indispensable in determining the frequency axis in precision spectroscopy and it is useful as a light source for spectroscopy. Dual-comb spectroscopy uses two frequency combs with slightly different repetition rates and has the potential to surpass conventional Fourier-transform infrared spectrometers. The resolution of dual-comb spectroscopy is limited by the frequency spacing of the comb components, that is, the repetition rate of the comb. We demonstrate dual-comb spectroscopy in the visible-wavelength region using wavelength-converted frequency combs from Er-doped fiber combs. The repetition rates of the combs are relatively low at 19.8 MHz, resulting in relatively high resolution in the dual-comb spectroscopy. The observed spectral shape in dual-comb spectroscopy agrees well with the fitting result based on the hyperfine structure of molecular iodine. The realized dual-comb spectroscopy using wavelength-converted Er-doped fiber combs is reliable (maintenance free) and applicable in other experiments at visible wavelengths.
Effect of contact vector direction on achieving cavotricuspid isthmus block
Authors: Sumi Hitoshi , Hoshiyama Tadashi , Morihisa Kenji , Noda Katsuo , Kaneko Shozo , Kanazawa Hisanori , Ishii Masanobu , Fujisue Koichiro , Sueta Daisuke , Takashio Seiji , Usuku Hiroki , Matsushita Kenichi , Tsujita Kenichi 
Published: February 2023

AbstractCavotricuspid isthmus (CTI) ablation is an important treatment strategy for CTI-dependent atrial flutter (AFL). The location of the catheter contact area is confirmed by the contact vector direction (CVD) through three-dimensional mapping during the procedure. However, the relationship between CVD during radiofrequency ablation and its efficacy in achieving CTI block has not been clarified. This study aimed to investigate the relationship between CVD and efficacy in achieving CTI block. CVDs during radiofrequency ablation were divided into proximal vectors against the distal tip (P-vector) and other vectors (normal-vector). In 39 patients who underwent CTI linear ablation, the CTIs were divided into two segments: the tricuspid valve area (anterior) and inferior vena cava area (posterior). The frequency of the residual conduction gap was compared between segments in which the P- and normal-vectors were observed. P-vectors were observed in 13 of the 78 segments. The median ablation index was not significantly different between segments in which the P-vector and normal-vector were observed (398.2 [384.2–402.2] vs. 393.3 [378.3–400.1], p = 0.15). However, residual conduction gaps were significantly more frequently observed in the segment in which the P-vector was observed than those in which only the normal-vector was observed (6/13, 46.2% vs. 3/65, 4.6%; p < 0.01). During a 6-month follow-up, two patients required a second session of ablation due to AFL recurrence. A residual conduction gap was observed in one patient at the site where the P-vector was observed in the first session. Avoiding the P-vector might be an important factor in improving CTI block and reducing AFL recurrence.
Muscle fat replacement and contractility in patients with skeletal muscle sodium channel disorders
Authors: Pedersen Jonas Jalili , Stemmerik Mads Godtfeldt , Jacobsen Laura Nørager , Skriver Sofie Vinther , Wilms Gustav Rhode , Duno Morten , Vissing John 
Published: February 2023

AbstractSkeletal muscle sodium channel disorders give rise to episodic symptoms such as myotonia and/or periodic paralysis. Chronic symptoms with permanent weakness are not considered characteristic of the phenotypes. Muscle fat replacement represents irreversible damage that inevitably will impact on muscle strength. This study investigates muscle fat replacement and contractility in patients with pathogenic SCN4A variants compared to healthy controls. T1-weighted and 2-point Dixon MRI of the legs were conducted to assess fat replacement. Stationary dynamometry was used to assess muscle strength. Contractility was determined by maximal muscle contraction divided by cross-sectional muscle area. The average cross-sectional intramuscular fat fraction was greater in patients compared with controls by 2.5% in the calves (95% CI 0.74–4.29%, p = 0.007) and by 2.0% in the thighs (95% CI 0.75–3.2%, p = 0.003). Muscle contractility was less in patients vs. controls by 14–27% (p < 0.05). Despite greater fat fraction and less contractility, absolute strength was not significantly less. This study quantitatively documents greater fat fraction and additionally describes difference in muscle contractility in a large cohort of patients with skeletal muscle sodium channel disorders. The clinical impact of these abnormal findings is likely limited as muscle hypertrophy in the patients served to preserve absolute muscle strength. Subgroup analysis indicated significant difference in phenotype by genotype, however these findings lack statistical significance and serve as inspiration for future researchers to probe into the geno- phenotype relationship in these disorders.Trial registration: The study was registered at http://clinicaltrials.gov (identifier: NCT04808388).
Static friction coefficient depends on the external pressure and block shape due to precursor slip
Authors: Iwashita Wataru , Matsukawa Hiroshi , Otsuki Michio 
Published: February 2023

AbstractAmontons’ law states that the maximum static friction force on a solid object is proportional to the loading force and is independent of the apparent contact area. This law indicates that the static friction coefficient does not depend on the external pressure or object shape. Here, we numerically investigate the sliding motion of a 3D viscoelastic block on a rigid substrate using the finite element method (FEM). The macroscopic static friction coefficient decreases with an increase in the external pressure, length, or width of the object, which contradicts Amontons’ law. Precursor slip occurs in the 2D interface between the block and substrate before bulk sliding. The decrease in the macroscopic static friction coefficient is scaled by the critical area of the precursor slip. A theoretical analysis of the simplified models reveals that bulk sliding results from the instability of the quasi-static precursor slip caused by velocity-weakening local friction. We also show that the critical slip area determines the macroscopic static friction coefficient, which explains the results of the FEM simulation.
Acquisition of new function through gene duplication in the metallocarboxypeptidase family
Authors: Fajardo Daniel , Saint Jean Ritchie , Lyons Peter J. 
Published: February 2023

AbstractGene duplication is a key first step in the process of expanding the functionality of a multigene family. In order to better understand the process of gene duplication and its role in the formation of new enzymes, we investigated recent duplication events in the M14 family of proteolytic enzymes. Within vertebrates, four of 23 M14 genes were frequently found in duplicate form. While AEBP1, CPXM1, and CPZ genes were duplicated once through a large-scale, likely whole-genome duplication event, the CPO gene underwent many duplication events within fish and Xenopus lineages. Bioinformatic analyses of enzyme specificity and conservation suggested a greater amount of neofunctionalization and purifying selection in CPO paralogs compared with other CPA/B enzymes. To examine the functional consequences of evolutionary changes on CPO paralogs, the four CPO paralogs fromXenopus tropicaliswere expressed in Sf9 and HEK293T cells. Immunocytochemistry showed subcellular distribution of Xenopus CPO paralogs to be similar to that of human CPO. Upon activation with trypsin, the enzymes demonstrated differential activity against three substrates, suggesting an acquisition of new function following duplication and subsequent mutagenesis. Characteristics such as gene size and enzyme activation mechanisms are possible contributors to the evolutionary capacity of the CPO gene.
Federated blockchain system (FBS) for the healthcare industry
Authors: Mohey Eldin Ashraf , Hossny Eman , Wassif Khaled , Omara Fatma A. 
Published: February 2023

AbstractBlockchain is a distributed technology that introduced the well known Bitcoin cryptocurrency into action. Blockchain has been considered for research by many countries and industries. It is being applied in many fields such as the healthcare domain. Many companies started using Blockchain to increase the security and privacy of the Electronic Healthcare Records for their patients. The work in this paper discusses some existing healthcare problems and challenges. In addition, the paper reviews some related work models and provides a comparison that shows their objectives and limitations. Also, a proposed Federated Blockchain System (FBS) is introduced to provide solutions for these healthcare problems and elaborates the technical details of the system architecture. Moreover, the effectiveness of the system has been validated which showed an average of 68–100 ms for performing query operations and average of 0.944–19.041 s for performing writing operations on the system. Finally, a discussion of the system validation and future work are presented.
A physics-informed neural network based on mixed data sampling for solving modified diffusion equations
Authors: Fang Qian , Mou Xuankang , Li Shiben 
Published: February 2023

AbstractWe developed a physics-informed neural network based on a mixture of Cartesian grid sampling and Latin hypercube sampling to solve forward and backward modified diffusion equations. We optimized the parameters in the neural networks and the mixed data sampling by considering the squeeze boundary condition and the mixture coefficient, respectively. Then, we used a given modified diffusion equation as an example to demonstrate the efficiency of the neural network solver for forward and backward problems. The neural network results were compared with the numerical solutions, and good agreement with high accuracy was observed. This neural network solver can be generalized to other partial differential equations.
A hybrid multi-objective optimization of functional ink composition for aerosol jet 3D printing via mixture design and response surface methodology
Authors: Zhang Haining , Liu Zhixin , Yin Shuai , Xu Haifeng 
Published: February 2023

AbstractThe limited electrical performance of microelectronic devices caused by low inter-particle connectivity and inferior printing quality is still the greatest hurdle to overcome for Aerosol jet printing (AJP) technology. Despite the incorporation of carbon nanotubes (CNTs) and specified solvents into functional inks can improve inter-particle connectivity and ink printability respectively, it is still challenging to consider multiple conflicting properties in mixture design simultaneously. This research proposes a novel hybrid multi-objective optimization method to determine the optimal functional ink composition to achieve low electrical resistivity and high printed line quality. In the proposed approach, silver ink, CNTs ink and ethanol are blended according to mixture design, and two response surface models (ReSMs) are developed based on the Analysis of Variance. Then a desirability function method is employed to identify a 2D optimal operating material window to balance the conflicting responses. Following that, the conflicting objectives are optimized in a more robust manner in the 3D mixture design space through the integration of a non-dominated sorting genetic algorithm III (NSGA-III) with the developed ReSMs and the corresponding statistical uncertainty. Experiments are conducted to validate the effectiveness of the proposed approach, which extends the methodology of designing materials with multi-component and multi-property in AJP technology.
Survival improvement for patients with metastatic colorectal cancer over twenty years
Authors: Zeineddine Fadl A. , Zeineddine Mohammad A. , Yousef Abdelrahman , Gu Yue , Chowdhury Saikat , Dasari Arvind , Huey Ryan W. , Johnson Benny , Kee Bryan , Lee Michael S. , Morelli Maria Pia , Morris Van K. , Overman Michael J. , Parseghian Christine , Raghav Kanwal , Willis Jason , Wolff Robert A. , Kawaguchi Yoshikuni , Vauthey Jean-Nicolas , Sun Ryan , Kopetz Scott , Shen John Paul 
Published: February 2023

AbstractOver the past two decades of successive clinical trials in metastatic colorectal cancer (CRC), the median overall survival of both control and experimental arms has steadily improved. However, the incremental change in survival for metastatic CRC patients not treated on trial has not yet been quantified. We performed a retrospective review of 1420 patients with de novo metastatic CRC who received their primary treatment at the University of Texas M.D. Anderson Cancer Center (UTMDACC) from 2004 through 2019. Median OS was roughly stable for patients diagnosed between 2004 and 2012 (22.6 months) but since has steadily improved for those diagnosed in 2013 to 2015 (28.8 months), and 2016 to 2019 (32.4 months). Likewise, 5-year survival rate has increased from 15.7% for patients diagnosed from 2004 to 2006 to 26% for those diagnosed from 2013 to 2015. Notably, survival improved for patients with BRAFV600E mutant as well as microsatellite unstable (MSI-H) tumors. Multivariate regression analysis identified surgical resection of liver metastasis (HR = 0.26, 95% CI, 0.19–0.37), use of immunotherapy (HR = 0.44, 95% CI, 0.29–0.67) and use of third line chemotherapy (regorafenib or trifluridine/tipiracil, HR = 0.74, 95% CI, 0.58–0.95), but not year of diagnosis (HR = 0.99, 95% CI, 0.98–1), as associated with better survival, suggesting that increased use of these therapies are the drivers of the observed improvement in survival.
Important factors for the reliable and reproducible preparation of non-aqueous electrolyte solutions for lithium batteries
Authors: Cao Xia 
Published: February 2023

AbstractElectrolyte solutions play a crucial role in rechargeable lithium batteries. Driven by an ever-increasing demand for better batteries, more and more stringent performance requirements are being asked of electrolytes. This demand to achieve electrolytes beyond the state-of-the-art has driven an increasing number of publications over the past decade. Nevertheless, a detailed description of electrolyte preparation is frequently missing when reporting new electrolytes for batteries, creating a barrier for others to reproduce important findings. In addition, false or misleading information in a paper may result from unintentional inaccuracies during the electrolyte preparation process. This article highlights important factors for the reliable and reproducible preparation of non-aqueous electrolyte solutions for lithium batteries, with the aim of encouraging researchers to follow more rigorous reporting standards.