bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of prognostic features of amino acid metabolism-related lncRNAs in hepatocellular carcinoma
Authors: CHENG LVE , Cai Dong , Li Shengwei 
Published: January 2023

Abstract
Background

As an important part of cellular energy metabolism, amino acid metabolism provides energy support for tumor progression. In recent years, it has been found that in addition to traditional proteins, long-stranded non-coding RNAs (lncRNAs) are also involved in amino acid metabolism in tumors. However, potential lncRNA biomarkers that potentially regulate amino acid metabolism and affect the prognosis of HCC patients remain to be further explored.

Materials and Methods

Genomic and clinical data were obtained from The Cancer Genome Atlas (TCGA) database, and amino acid metabolism-related genes were obtained from the Molecular Signature Database v5.1 (MSigDB). Prognostic features were constructed by co-expression analysis and Cox regression analysis. Patients were divided into high-risk and low-risk groups, and then independent prognostic analysis and ROC curve plotting were performed to assess the prognostic value of the features. Subsequently, immune-related functions of lncRNA and tumor mutational burden (TMB) were analyzed. Finally, we analyzed amino acid metabolism-related lncRNAs using the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm to determine their sensitivity to potential drugs for hepatocellular carcinoma.

Results

A total of 6 lncRNAs related to amino acid metabolism were obtained as LINC02870, AL031985.3, AC011476.3, AC012640.1, AL365361.1, LUCAT1, and prognostic features were established. We found that high-risk patients had poorer overall survival (OS) and progression-free survival (PFS) and higher mortality. Independent prognostic analysis, ROC, C-index and column line plot showed that amino acid metabolism-related lncRNAs could accurately predict the prognosis of patients. Column line plots and heat maps showed a significant difference in the distribution of amino acid metabolism-related lncRNAs between high- and low-risk groups. We also found that patients with high TMB had poorer OS, and the TIDE algorithm showed that high-risk patients had a greater likelihood of immune escape and poorer immunotherapy outcomes.

Conclusion

In conclusion, six lncRNAs associated with amino acid metabolism can accurately predict the prognosis of patients with hepatocellular carcinoma and may provide new insights for clinical application and treatment.
Reliability of routine and standardized in-center blood pressure measurement in chronic hemodialysis patients in Dakar: a case control study
Authors: Faye Moustapha , Ouanekpone Cedric Patrick , Ba Baro , Diop Mariama , Ba Bacary , Faye Gnagna , Keita Niakhaleen , Ndongo Modou , Sy Abou , Faye Maria , Lemrabott Ahmed Tall , Niang Abdou , Ka Elhadji Fary 
Published: January 2023

Abstract
Background
Blood pressure (BP) measurement in the diagnosis and monitoring of hypertension continues to be a topic of debate. The objectives of this study were 1) to evaluate the performance of hemodialysis center BP measurements (routine and standardized BP measurements) in the diagnosis of ambulatory BP in chronic hemodialysis patients using 44h ambulatory BP monitoring (44h-ABPM) as the reference measurement; 2) to compare the performance of standardized and routine BP measurement; and 3) to evaluate the concordance between the values measured at the hemodialysis center and the BP values at 44h-ABPM.
Methods
In this 23-month case control study including 56 patients followed in the hemodialysis units of Aristide Le Dantec Hospital (HALD) and Idrissa Pouye General Hospital (HOGIP), BP was measured by 3 methods: i) an automated measurement (OMRON®) carried out by health professional called routine BP measurement (RBPM) in pre and post dialysis; ii) the mean of five automated measurements in a patient isolated in a quiet room called standardized BP measurement (SBPM) before and after dialysis; iii) 44h-ABPM with the CONTEC® device. The hypertension was defined as BP ≥ 130/80 mmHg at 44h-ABPM.
Results
Fifty-six (56) patients including 31 men (55%) with a mean age of 45.20 ± 13.64 years were included. Thirty-one patients (55%) were hypertensive at the 44h-ABPM. Pre-dialysis SBPM was significantly better than pre-dialysis RBPM (AUC [IC 95%], 0.881 [0.778-0.984]/0.785 [0.664-0.907], p=0.02) in detecting 44h ambulatory systolic BP (SBP) ≥ 130 mmHg. Post-dialysis SBPM was also outperformed post-dialysis RBPM (0.916 [0.843-0.988]/0.874 [0.782-0.965]) in detecting 44h ambulatory SBP ≥ 130 mmHg without statistically significant difference. Pre-dialysis SBPM outperformed pre-dialysis RBPM (0.882 [0.776-0.988]/0.878 [0.781-0.975] in detecting 44h ambulatory DBP ≥ 80 mmHg without statistically significant difference. Post-dialysis SBPM also outperformed post-dialysis RBPM (0.914 [0.832-0.996]/0.848 [0.743-0.952]) in detecting 44h ambulatory DBP ≥ 80 mmHg without statistically significant difference. Hemodialysis center measurements overestimate ambulatory BP at 44h-ABPM.
Conclusion
Hemodialysis center measurements overestimate ambulatory BP despite excellent performance on ROC curve analysis. SBPM performs better than RBPM and in particular in the detection of a SBP ≥ 130 mmHg in the ambulatory setting. SBPM overestimates SBP less than RBPM.
Signature methods for brain-computer interfaces
Authors: Xu Xiaoqi , Lee Darrick , Drougard Nicolas , Roy Raphaëlle N. 
Published: January 2023

Abstract
Brain-computer interfaces (BCIs) allow direct communication between one’s central nervous system and a computer without any muscle movement hence by-passing the peripheral nervous system. They can restore disabled people’s ability to interact with their environment, e.g. communication and wheelchair control. However, to this day their performance is still hindered by the non-stationarity of electroencephalography (EEG) signals, as well as their susceptibility to noise from the users’ environment and from their own physiological activity. Moreover, a non-negligible amount of users struggle to use BCI systems based on motor imagery. In this paper, a new method based on the path signature is introduced to tackle this problem by using features which are different from the usual power-based ones. The path signature is a series of iterated integrals computed from a multidimensional path. It is invariant under translation and time reparametrization, which makes it a robust feature for multichannel EEG time series. The performance can be further boosted by combining the path signature with the gold standard Riemannian classifier in the BCI field exploiting the geometric structure of symmetric positive definite (SPD) matrices. The results obtained on publicly available datasets show that the signature method is more robust to inter-user variability than classical ones, especially on noisy and low-quality data. Hence, this study paves the way towards the use of mathematical tools that until now have been neglected, in order to tackle the EEG-based BCI variability issue. It also sheds light on the lead-lag relationship captured by path signature which seems relevant to assess the underlying neural mechanisms.
An Analytical Local Tool Path Smoothing Method with Curvature Control
Authors: Zhao Gang , Wei Zixuan , Jing Xishuang , Shen Boyan , Xie Fubao , Zhang Chengyang , Chen Siyu 
Published: January 2023

Abstract
In traditional multi-axis machining, the linear tool path generated by computer-aided manufacturing systems is still in a broad tool path format, resulting in discontinuities at the corners, which slow down tool motion, and also trigger tool vibration, reducing machining accuracy and surface quality. In order to ensure the C3 continuity of the tool during the multi-axis machining process, this paper proposes an analytical B-spline local smoothing method with curvature control. The tool position trajectory and tool orientation are both smoothed by a 5th spline curve with 9 control points. Optimal control points are determined for position and orientation splines to achieve C3 continuity at the junctions between the spline and linear segment while preserving the predefined geometric tolerance limits and minimizing the maximum curvature of the inserted B-spline curve. The smoothed tool path is expected to have less curvature fluctuation, which can significantly improve both the kinematic performance of the machine tool and the machining efficiency. Both computer simulations and physical printing experiments are carried out to demonstrate the improvements of our proposed method in motion smoothness and tracking accuracy in multi-axis machining tasks.
Textbook Outcome in Colon Carcinoma: Implications for Overall Survival and Disease-free Survival.
Authors: Rubio-García J.J , Barberá Francisco Mauri , Tudela Celia Villodre , Morote Silvia Carbonell , Olea Ana Isabel Fábregues , López Cándido Alcázar , Torremocha Clara Llopis , López Joaquín Ruiz , Martín Álvaro Gomis , Simo Manuel Romero , Ramia-Ángel José Manuel 
Published: January 2023

Abstract
BACKGROUND:
Textbook outcome (TO) is a multidimensional quality management tool that uses a set of traditional surgical measures to reflect an "ideal" surgical result for a particular pathology. The aim of the present study is to record the rate of TO in patients undergoing elective surgery for colon cancer.
MATERIAL AND METHODS:
Retrospective study of all patients undergoing scheduled colon cancer surgery at a Spanish university hospital from September 2012 to August 2016. Patients with rectal cancer were excluded. The variables included in the definition of TO were: R0 resection, number of isolated nodes ≥12, no Clavien-Dindo ≥IIIa complications, no prolonged stay, no readmissions, and no mortality in the first 30 days.
RESULTS:
Five hundred and sixty-four patients were included in the study. TO was achieved in 49.8%. The sample had a mean age of 69 ± 11 years, and 60% were male. Female sex (OR 1.61; 95% CI 2.30-1.13), T3 and T4 classification (OR 2.50, 95% CI 4.59-1.36, and OR 2.55, 95% CI 5.21-1.24 respectively) and laparoscopic approach (OR 1.53, 95% CI 2.33-1.00) were independent factors that were significantly associated with achieving a TO. Patients who achieved TO had higher overall survival (p=0.008) than those who did not. However, with regard to disease-free survival, no statistically significant differences were found (p=0.303).
CONCLUSION:
TO is a useful, easy-to-interpret management tool for measuring oncological results and for predicting patient survival.
The study was registered in the public accessible database clinicaltrials.gov with the ClinicalTrials.gov ID: NCT05675904. Public release date: 01/05/2023.
Investigation on cutting damage mechanism of carbon fiber reinforced polymer based on macro/microscopic simulation
Authors: Zhu Zhaoju , Kang Rongqing , Huang Jianwei , Zhu Yunqi , Sun Xinhui 
Published: January 2023

Abstract
Carbon fiber reinforced polymer (CFRP) is widely used in the aerospace field due to its excellent physical and mechanical properties such as high specific strength, high specific modulus and good corrosion resistance. However, it is prone to bring burrs, tears, matrix, and fiber debonding during the cutting process due to its non-homogeneity and anisotropy, which seriously affects the service life of the material. To explore the damage failure mechanism of the CFRP cutting process, 2D and 3D finite element simulation models were established based on Abaqus in this paper. Furthermore, the influence law of fiber direction on cutting damage failure and chip forming was analyzed from micro and macro levels. Finally, the effectiveness of the simulation model was verified by experiments. The results show that the cutting surface of CFRP with a 45° fiber angle is serrated, and the local failure is not obvious; the main defect of CFRP with 90° fiber angle cutting is a matrix and fiber debonding, and some fibers will be crushed and cut off; Serious degumming phenomenon occurred in the cutting process of CFRP with 135° fiber angle, and the bending and fracture of fiber also occur below the cutting depth; It is noteworthy that the stress distribution diverges along the fiber direction.
Association of RNF213 polymorphism and cortical hyperintensity sign on fluid-attenuated inversion recovery images after direct revascularization surgery for moyamoya disease: possible involvement of intrinsic vascular vulnerability
Authors: Uchino Haruto , Ito Masaki , Tokairin Kikutaro , Tatezawa Ryota , Sugiyama Taku , Kazumata Ken , Fujimura Miki 
Published: January 2023

Abstract
A cortical hyperintensity on fluid-attenuated inversion recovery images (FLAIR cortical hyperintensity, FCH) is an abnormal finding after direct revascularization surgery for moyamoya disease. This study aimed to investigate the pathophysiology of FCH through genetic analyses of RNF213 p.R4810K polymorphism and perioperative hemodynamic studies using single photon emission computed tomography. We studied 96 hemispheres in 65 adults and 47 hemispheres in 27 children, who underwent combined direct and indirect revascularization. Early or late FCH was defined when it was observed on postoperative days 0–2 or 6–9, respectively. FCH scores (range: 0–6) were evaluated according to the extent of FCH in the operated hemisphere. FCHs were significantly more prevalent in adult patients than pediatric patients (early: 94% vs. 78%; late: 97% vs. 59%). In pediatric patients, FCH scores were significantly improved from the early to late phase regardless of the RNF213 genotype (mutant median: 2 vs. 1; wild-type median: 4 vs. 0.5). In adults, FCH scores were significantly improved in patients with the wild-type RNF213 allele (median: 4 vs. 2); however, they showed no significant improvement in patients with the RNF213 mutation. FCH scores were significantly higher in patients with symptomatic cerebral hyperperfusion than those without it (early median: 4 vs. 3; late median: 5 vs. 4). In conclusion, the RNF213 p.R4810K polymorphism was associated with prolonged FCH, and extensive FCH was associated with symptomatic cerebral hyperperfusion in patients with moyamoya disease.
Cell reprogramming via direct somatic embryogenesis in an Atlantic Forest species vulnerable to extinction: polarity of Euterpe edulis stem segments induced with pyridinecarboxylic acid
Authors: de Mello Tamyris , Correia Ludmila Nayara Freitas , Hegedus Clovis Eduardo Nunes , Schmildt Edilson Romais , Ferreira Adésio , Lopes José Carlos , Otoni Wagner Campos , Alexandre Rodrigo Sobreira 
Published: January 2023

Abstract
Euterpe edulis Martius, commonly known as juçara, has high economic value because its palm heart is considered a delicacy and its fruit, which is rich in antioxidants, is considered a “super fruit.” Because this endangered species can only be propagated via the seminiferous route, we aimed to analyze somatic embryogenesis of stem explants from E. edulis seedlings in response to their polarity and the type and concentration of growth regulators. Immature seeds were collected from a selected matrix in Pedra Menina (ES/MG, Brazil) and germinated in vitro. Six-month-old seedlings were segmented into four explants based on their polarity, and placed in culture medium supplemented with 50, 100, 150, 200, 250, 300, 450 or 600 µM picloram (PIC). After induction, the explants were transferred to maturation medium supplemented with 1-naphthaleneacetic acid (0.53 µM) and 2-isopentenyladenine (12.3 µM) and two maturation times (30 and 60 days) were evaluated. After 60 days of induction, proembryos appeared asynchronously directly from the stem segments. Upon transfer to maturation medium, a large number of somatic embryos and masses were observed at both times. The polarity of the explants did not influence their embryogenic induction, and all four stem segments could be used for somatic embryogenesis following treatment with 150 µM PIC. A large number of somatic embryos were generated during later stages of maturation. It is recommended to remove the explants from the maturation medium after 30 days to avoid oxidation.
CBCT-based synthetic CT generation using a hybrid approach for adaptive radiotherapy of nasopharyngeal carcinoma
Authors: Jihong Chen , Kerun Quan , Kaiqiang Chen , Xiuchun Zhang , Yimin Zhou , penggang Bai 
Published: January 2023

Abstract
Objective:
This study aims to utilize a hybrid approach of phantom correction and deep learning for synthesized CT (sCT) images generation based on cone-beam CT (CBCT) images for nasopharyngeal carcinoma (NPC).
Methods:
A total of 52 CBCT/CT paired images of NPC patients were used for training (41), validation (11) datasets. Hounsfield Units (HU) of the CBCT images was corrected by a commercial CIRS phantom. Then the original CBCT and the corrected CBCT (CBCT_cor) were trained separately with the some cycle generative adversarial network (CycleGAN) to generate SCT1 and SCT2. The mean error (ME) and mean absolute error (MAE) were used to quantify the image quality. For the patients in the validation datasets, the contours and treatment plans in CT images were transferred to original CBCT, CBCT_cor, SCT1 and SCT2 for dosimetric comparison. Finally, dose distribution, dosimetric parameters and 3D gamma pass rate were analyzed.
Results:
Compared with rigidly registered CT (RCT), the MAE of CBCT, CBCT_cor, SCT1 and SCT2 were 346.11 ± 13.58HU, 145.95 ± 17.64HU, 105.62 ± 16.08HU and 83.51 ± 7.71HU, respectively. Moreover, the average dosimetric parameter differences for the CBCT_cor, SCT1 and SCT2 were 2.7% ± 1.4%, 1.2% ± 1.0% and 0.6% ± 0.6%, respectively. Using the dose distribution of RCT images as reference, the 3D gamma pass rate of the hybrid method was significantly better than the other methods.
Conclusion:
A novel hybrid approach based on HU-ED correction and CycleGAN was developed to generate sCT images for CBCT images of NPC patients. The image quality and dose accuracy of the hybrid approach were outperform the simple CycleGAN method. This finding has great significance for the clinical application of adaptive radiotherapy for NPC.
Approximation schemes for McKean-Vlasov and Boltzmann type equations (error analysis in total variation distance)
Authors: Qin Yifeng 
Published: January 2023

Abstract

We deal with Mckean-Vlasov and Boltzmann type jump equations. This means that the coefficients of the stochastic equation depend on the law of the solution, and the equation is driven by a Poisson point measure with intensity measure which depends on the law of the solution as well. In [3], Alfonsi and Bally have proved that under some suitable conditions, the solution $X_t$ of such equation exists and is unique. One also proves that $X_t$ is the probabilistic interpretation of an analytical weak equation. Moreover, the Euler scheme $X_t^{\mathcal{P}}$ of this equation converges to $X_t$ in Wasserstein distance. In this paper, under more restricted assumptions, we show that the Euler scheme $X_t^{\mathcal{P}}$ converges to $X_t$ in total variation distance and $X_t$ has a smooth density (which is a function solution of the analytical weak equation). On the other hand, in view of simulation, we use a truncated Euler scheme $X^{\mathcal{P},M}_t$ which has a finite numbers of jumps in any compact interval. We prove that $X^{\mathcal{P},M}_{t}$ also converges to $X_t$ in total variation distance. Finally, we give an algorithm based on a particle system associated to $X^{\mathcal{P},M}_t$ in order to approximate the density of the law of $X_t$. Complete estimates of the error are obtained.
Origin and evolution of RAS oncoprotein membrane targeting
Authors: Philips Mark , García-España Antonio 
Published: January 2023

Abstract
KRAS, HRAS and NRAS oncogenes belong to a family of 40 highly homologous genes, which in turn are a subset of a superfamily of >160 genes encoding small GTPases. RAS oncoproteins consist of a globular G-domain (aa1-166) and a 22-23aa unstructured hypervariable region (HVR) that mediates membrane targeting. The evolutionarily origins of the RAS isoforms, their HVRs and alternative splicing of the KRAS locus has not been explored. We found that KRAS is basal to the oncogene family and its duplication generated HRAS in the common ancestor of vertebrates. In a second round of duplication HRAS generated NRAS and KRAS generated an additional RAS gene we have designated KRASBL, absent in mammals and birds. KRAS4A arose through a duplication and insertion of the 4th exon of NRAS into the 3rd intron of KRAS. We found evolutionarily conservation of a short polybasic region (PBR1) in HRAS, NRAS and KRAS4A, a second polybasic region (PBR2) in KRAS4A, two neutralized basic residues (NB) and a serine in KRAS4B and KRASBL, and a modification of the CaaX motif in vertebrates with farnesyl rather than geranylgeranyl polyisoprene lipids, suggesting that a less hydrophobic membrane anchor is critical to RAS oncoprotein function. The persistence of four RAS isoforms through >400 MY of evolution argues strongly for differential function.
Accurate Detection of Paroxysmal Atrial Fibrillation with Certified-GAN and Neural Architecture Search
Authors: Asadi Mehdi , Poursalim Fatemeh , Loni Mohammad , Daneshtalab Masoud , Sjödin Mikael , Gharehbaghi Arash 
Published: January 2023

Abstract
This paper presents a novel machine learning framework for detecting Paroxysmal Atrial Fib-rillation (PxAF), a pathological characteristic of Electrocardiogram (ECG) that can lead to fatalconditions such as heart attack. To enhance the learning process, the framework involves a Gen-erative Adversarial Network (GAN) along with a Neural Architecture Search (NAS) in the datapreparation and classifier optimization phases. The GAN is innovatively invoked to overcome theclass imbalance of the training data by producing the synthetic ECG for PxAF class in a certifiedmanner. The effect of the certified GAN is statistically validated. Instead of using a general-purposeclassifier, the NAS automatically designs a highly accurate convolutional neural network architecture customized for the PxAF classification task. Experimental results show that the accuracy of theproposed framework exhibits a high value of 99% which not only enhances state-of-the-art by up to5.1%, but also improves the classification performance of the two widely-accepted baseline methods,ResNet-18, and Auto-Sklearn, by 2.2% and 6.1%
Yield loss in coconut variety East Coast Tall (ECT) owing to rugose spiraling whitefly (RSW), Aleurodicus rugioperculetus M. infestation
Authors: Raghuteja Puvvala Viswanadha , Rao Nagulapati Butchi Venkata Chalapathi , Padma Ede , Kireeti Alwala , Umakrishna Kavuru , Rao Ganta Koteswara 
Published: January 2023

Abstract
Appraisal of nut yield reduction in East Coast Tall (ECT) variety of coconut palms with exotic and invasive rugose spiraling whitefly (RSW) infestation @ low (<10 spirals per leaflet), medium (10 – 20 spirals per leaflet) and high (> 20 spirals per leaflet) incidence was studied out at two experimental locations viz., Horticultural Research Station (HRS), Ambajipeta and Kalavalapalli. The per cent (%) yield loss was estimated to be 6.61 and 22.45 per cent in ECT palms with low and medium RSW incidence, while comparatively greater yield loss of 27.59 per cent was recorded in palms with high incidence at HRS, Ambajipeta. Likewise, at Kalavalapalli village, the per cent (%) yield loss in ECT palms with low, medium and high RSW incidence was recorded to be 6.49, 25.65 and 30.38 per cent respectively. Further, declining trend of button setting was noticed for last 2 years (2019 to 2021) at HRS, Ambajipeta with 45.04 per cent during 2018 (highest before RSW infestation), while the least setting was recorded in the year 2021 with 28.39 per cent. The button setting during the years 2019 and 2020 was 33.41 and 31.19 per cent.