bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genuine multipartite entanglement measures based on multi-party teleportation capability
Authors: Choi Minjin , Bae Eunok , Lee Soojoon 
Published: September 2023

AbstractQuantifying entanglement is vital to understand entanglement as a resource in quantum information processing, and many entanglement measures have been suggested for this purpose. When mathematically defining an entanglement measure, we should consider the distinguishability between entangled and separable states, the invariance under local transformation, the monotonicity under local operations and classical communication, and the convexity. These are reasonable requirements but may be insufficient, in particular when taking into account the usefulness of quantum states in multi-party quantum information processing. Therefore, if we want to investigate multipartite entanglement as a resource, then it can be necessary to consider the usefulness of quantum states in multi-party quantum information processing when we define a multipartite entanglement measure. In this paper, we define new multipartite entanglement measures for three-qubit systems based on the three-party teleportation capability, and show that these entanglement measures satisfy the requirements for being genuine multipartite entanglement measures. We also generalize our entanglement measures forN-qubit systems, where$$N \ge 4$$N≥4, and discuss that these quantities may be good candidates to measure genuine multipartite entanglement.
Study of β1-transferrin and β2-transferrin using microprobe-capture in-emitter elution and high-resolution mass spectrometry
Authors: Luo Ruben Yiqi , Pfaffroth Christopher , Yang Samuel , Hoang Kevin , Yeung Priscilla S.-W. , Zehnder James L. , Shi Run-Zhang 
Published: September 2023

AbstractCerebrospinal fluid (CSF) leak can be diagnosed in clinical laboratories by detecting a diagnostic marker β2-transferrin (β2-Tf) in secretion samples. β2-Tf and the typical transferrin (Tf) proteoform in serum, β1-transferrin (β1-Tf), are Tf glycoforms. An innovative affinity capture technique for sample preparation, called microprobe-capture in-emitter elution (MPIE), was incorporated with high-resolution mass spectrometry (HR-MS) to study the Tf glycoforms and the primary structures of β1-Tf and β2-Tf. To implement MPIE, an analyte is first captured on the surface of a microprobe, and subsequently eluted from the microprobe inside an electrospray emitter. The capture process is monitored in real-time via next-generation biolayer interferometry (BLI). When electrospray is established from the emitter to a mass spectrometer, the analyte is immediately ionized via electrospray ionization (ESI) for HR-MS analysis. Serum, CSF, and secretion samples were analyzed using MPIE-ESI-MS. Based on the MPIE-ESI-MS results, the primary structures of β1-Tf and β2-Tf were elucidated. As Tf glycoforms, β1-Tf and β2-Tf share the amino acid sequence but contain varying N-glycans: (1) β1-Tf, the major serum-type Tf, has two G2S2 N-glycans on Asn413 and Asn611; and (2) β2-Tf, the major brain-type Tf, has an M5 N-glycan on Asn413 and a G0FB N-glycan on Asn611. The resolving power of the innovative MPIE-ESI-MS method was demonstrated in the study of β2-Tf as well as β1-Tf. Knowing the N-glycan structures on β2-Tf allows for the design of more novel test methods for β2-Tf in the future.
Forecasting influenza hemagglutinin mutations through the lens of anomaly detection
Authors: Garjani Ali , Chegini Atoosa Malemir , Salehi Mohammadreza , Tabibzadeh Alireza , Yousefi Parastoo , Razizadeh Mohammad Hossein , Esghaei Moein , Esghaei Maryam , Rohban Mohammad Hossein 
Published: September 2023

AbstractThe influenza virus hemagglutinin is an important part of the virus attachment to the host cells. The hemagglutinin proteins are one of the genetic regions of the virus with a high potential for mutations. Due to the importance of predicting mutations in producing effective and low-cost vaccines, solutions that attempt to approach this problem have recently gained significant attention. A historical record of mutations has been used to train predictive models in such solutions. However, the imbalance between mutations and preserved proteins is a big challenge for the development of such models that need to be addressed. Here, we propose to tackle this challenge through anomaly detection (AD). AD is a well-established field in Machine Learning (ML) that tries to distinguish unseen anomalies from normal patterns using only normal training samples. By considering mutations as anomalous behavior, we could benefit existing rich solutions in this field that have emerged recently. Such methods also fit the problem setup of extreme imbalance between the number of unmutated vs. mutated training samples. Motivated by this formulation, our method tries to find a compact representation for unmutated samples while forcing anomalies to be separated from the normal ones. This helps the model to learn a shared unique representation between normal training samples as much as possible, which improves the discernibility and detectability of mutated samples from the unmutated ones at the test time. We conduct a large number of experiments on four publicly available datasets, consisting of three different hemagglutinin protein datasets, and one SARS-CoV-2 dataset, and show the effectiveness of our method through different standard criteria.
Metabolic and transcriptomic profiling during wheat seed development under progressive drought conditions
Authors: Mega Ryosuke , Kim June-Sik , Tanaka Hiroyuki , Ishii Takayoshi , Abe Fumitaka , Okamoto Masanori 
Published: September 2023

AbstractGlobally, bread wheat (Triticum aestivum) is one of the most important staple foods; when exposed to drought, wheat yields decline. Although much research has been performed to generate higher yield wheat cultivars, there have been few studies on improving end-product quality under drought stress, even though wheat is processed into flour to produce so many foods, such as bread, noodles, pancakes, cakes, and cookies. Recently, wheat cultivation has been affected by severe drought caused by global climate change. In previous studies, seed shrinkage was observed in wheat exposed to continuous drought stress during seed development. In this study, we investigated how progressive drought stress affected seed development by metabolomic and transcriptomic analyses. Metabolite profiling revealed the drought-sensitive line reduced accumulation of proline and sugar compared with the water-saving, drought-tolerant transgenic line overexpressing the abscisic acid receptor TaPYL4 under drought conditions in spikelets with developing seeds. Meanwhile, the expressions of genes involved in translation, starch biosynthesis, and proline and arginine biosynthesis was downregulated in the drought-sensitive line. These findings suggest that seed shrinkage, exemplifying a deficiency in endosperm, arose from the hindered biosynthesis of crucial components including seed storage proteins, starch, amino acids, and sugars, ultimately leading to their inadequate accumulation within spikelets. Water-saving drought tolerant traits of wheat would aid in supporting seed formation under drought conditions.
Spatial perspective and identity in visual awareness of the bodily self-other distinction
Authors: Ciorli Tommaso , Pia Lorenzo 
Published: September 2023

AbstractSpatial perspective and identity of visual bodily stimuli are two key cues for the self-other distinction. However, how they emerge into visual awareness is largely unknown. Here, self- or other-hands presented in first- or third-person perspective were compared in a breaking-Continuous Flash Suppression paradigm (Experiment 1) measuring the time the stimuli need to access visual awareness, and in a Binocular Rivalry paradigm (Experiment 2), measuring predominance in perceptual awareness. Results showed that, irrespectively of identity, first-person perspective speeded up the access, whereas the third-person one increased the dominance. We suggest that the effect of first-person perspective represents an unconscious prioritization of an egocentric body coding important for visuomotor control. On the other hand, the effect of third-person perspective indicates a conscious advantage of an allocentric body representation fundamental for detecting the presence of another intentional agent. Summarizing, the emergence of self-other distinction into visual awareness would strongly depend on the interplay between spatial perspectives, with an inverse prioritization before and after conscious perception. On the other hand, identity features might rely on post-perceptual processes.
EP300 promotes ferroptosis via HSPA5 acetylation in pancreatic cancer
Authors: Wang Yuan , Liu Yang , Wang Cong , Kang Rui , Tang Daolin , Liu Jiao 
Published: September 2023

AbstractFerroptosis is a form of regulated cell death characterized by oxidative injury-induced lipid peroxidation. However, the detailed protein post-translational modification regulatory mechanism of ferroptosis remains largely unknown. Here, we report that E1A binding protein P300 (EP300) acetyltransferase promotes ferroptosis in human pancreatic ductal adenocarcinoma (PDAC) cells via the acetylation of heat shock protein family A (Hsp70) member 5 (HSPA5), also known as GRP78 or BIP) on the site of K353. Acetylated HSPA5 loses its ability to inhibit lipid peroxidation and subsequent ferroptotic cell death. Genetic or pharmacological inhibition of EP300-mediated HSPA5 acetylation on K353 increases PDAC cell resistance to ferroptosis. Moreover, histone deacetylase 6 (HDAC6) limits HSPA5 acetylation and subsequent ferroptosis. Collectively, these findings not only identify regulatory pathways for HSPA5 acetylation during ferroptosis, but also highlight promising strategies to increase ferroptosis sensitivity in PDAC cells.
A thioacetamide-induced liver fibrosis model for pre-clinical studies in microminipig
Authors: Nishi Kotaro , Yagi Hiroshi , Ohtomo Mana , Nagata Shogo , Udagawa Daisuke , Tsuchida Tomonori , Morisaku Toshinori , Kitagawa Yuko 
Published: September 2023

AbstractDrug-induced liver fibrosis models are used in normal and immunosuppressed small animals for transplantation and regenerative medicine to improve liver fibrosis. Although large animal models are needed for pre-clinical studies, they are yet to be established owing to drug sensitivity in animal species and difficulty in setting doses. In this study, we evaluated liver fibrosis by administering thioacetamide (TA) to normal microminipig and thymectomized microminipig; 3 times for 1 week (total duration: 8 weeks). The pigs treated with TA showed elevated blood cytokine levels and a continuous liver injury at 8 weeks. RNA-seq of the liver showed increased expression of fibrosis-related genes after TA treatment. Histopathological examination showed degenerative necrosis of hepatocytes around the central vein, and revealed fibrogenesis and hepatocyte proliferation. TA treatment caused CD3-positive T cells and macrophages scattered within the hepatic lobule to congregate near the center of the lobule and increased αSMA-positive cells. Thymectomized pigs showed liver fibrosis similar to that of normal pigs, although the clinical signs tended to be milder. This model is similar to pathogenesis of liver fibrosis reported in other animal models. Therefore, it is expected to contribute to research as a drug discovery and pre-clinical transplantation models.
Experimental studies of the influence of mobile fan positioning parameters on the ability to transport the air stream into the door opening
Authors: Kaczmarzyk Piotr , Warguła Łukasz , Janik Paweł 
Published: September 2023

AbstractThe article aims to determine the influence of fan positioning parameters, i.e., its distance from a door opening (1–7 m) and the angle of inclination of the impeller axis in relation to the ground (0°–18°) on the amount of air flow pumped through a door opening. The experiment was carried out using a mock-up simulating a door opening, on which a measurement plane was located, without the cubic capacity (building structure) behind the door opening. The volumetric air flow stream was determined based on measuring (at 50 measuring points) the velocity of the air stream blown onto the surface of the door opening mock-up. Four commercial positive pressure ventilators, commonly used in rescue operations, with a power of 0.6–6.3 kW were tested. The tests showed that the value of the air flow stream at the most favourable setting (distance in the range of 3–5 m and the angle of the impeller axis to the ground in the range of 5°–12.2°) is included in the range of 18,304 ± 2460 m3/h to about 45,189 ± 4619 m3/h. Such settings cause the air stream to be aimed at the central area of the door opening. Imprecise mobile fan arrangement may reduce the flow rate from 41 to 76% in relation to the most favourable results.
Risk analysis of fluctuating hypercalcemia after leukapheresis in cellular therapy
Authors: Jo Tomoyasu , Arai Yasuyuki , Kitawaki Toshio , Nishikori Momoko , Mizumoto Chisaki , Kanda Junya , Yamashita Kouhei , Nagao Miki , Takaori-Kondo Akifumi 
Published: September 2023

AbstractOptimized management of citrate-induced hypocalcemia is required to provide safe leukapheresis. We prospectively analyzed subjects who underwent leukapheresis for cytotherapy, and evaluated serum ionized (iCa) concentrations before, at the end of, and 1 h after leukapheresis. During leukapheresis, calcium gluconate solution was continuously supplemented intravenously with hourly measurement of iCa. 76 patients including 49 lymphapheresis for chimeric antigen receptor T-cell therapy and 27 stem cell collections were enrolled. Median processing blood volume was 10 L (range, 6–15 L). Fluctuating hypercalcemia, in which the iCa concentration rose above its upper limit 1 h after leukapheresis, was observed in 58 subjects (76.3%). Multivariate analysis revealed that higher ratios of processing blood volume to body weight, more rapid calcium supplementation, and lower iCa concentration at the end of leukapheresis significantly increased elevation of serum iCa concentration by 1 h after leukapheresis. Based on multivariate analyses, we developed a formula and a diagram that accurately estimates serum iCa concentration 1 h post-leukapheresis. This suggests optimal targets for iCa concentration and calcium supplementation rates. In cases with high ratios of processing blood volume to body weight, slowing the rate of blood processing, rather than increasing calcium supplementation should safely alleviate hypocalcemia during leukapheresis without inducing hypercalcemia thereafter.
A novel reconstruction method combining multi-detector SPECT with an elliptical orbit and computer tomography for cardiac imaging
Authors: Sheng Jinhua , Huang Pu , Zhou Rougang , Li Zhongjin , Yang Xiaofan , Wang Jialei 
Published: September 2023

AbstractThe myocardial single photon emission computed tomography (SPECT) is a good study due to its clinical significance in the diagnosis of myocardial disease and the requirement for improving image quality. However, SPECT imaging faces challenges related to low spatial resolution and significant statistical noise, which concerns patient radiation safety. In this paper, a novel reconstruction system combining multi-detector elliptical SPECT (ME-SPECT) and computer tomography (CT) is proposed to enhance spatial resolution and sensitivity. The hybrid imaging system utilizes a slit-slat collimator and elliptical orbit to improve sensitivity and signal-to-noise ratio (SNR), obtains accurate attenuation mapping matrices, and requires prior information from integrated CT. Collimator parameters are corrected based on CT reconstruction results. The SPECT imaging system employs an iterative reconstruction algorithm that utilizes prior knowledge. An iterative reconstruction algorithm based on prior knowledge is applied to the SPECT imaging system, and a method for prioritizing the reconstruction of regions of interest (ROI) is introduced to deal with severely truncated data from ME-SPECT. Simulation results show that the proposed method can significantly improve the system's spatial resolution, SNR, and image fidelity. The proposed method can effectively suppress distortion and artifacts with the higher spatial resolution ordered subsets expectation maximization (OSEM); slit-slat collimation.
Adapting physiologically-based pharmacokinetic models for machine learning applications
Authors: Habiballah Sohaib , Reisfeld Brad 
Published: September 2023

AbstractBoth machine learning and physiologically-based pharmacokinetic models are becoming essential components of the drug development process. Integrating the predictive capabilities of physiologically-based pharmacokinetic (PBPK) models within machine learning (ML) pipelines could offer significant benefits in improving the accuracy and scope of drug screening and evaluation procedures. Here, we describe the development and testing of a self-contained machine learning module capable of faithfully recapitulating summary pharmacokinetic (PK) parameters produced by a full PBPK model, given a set of input drug-specific and regimen-specific information. Because of its widespread use in characterizing the disposition of orally administered drugs, the PBPK model chosen to demonstrate the methodology was an open-source implementation of a state-of-the-art compartmental and transit model called . The model was tested for drug formulations spanning a large range of solubility and absorption characteristics, and was evaluated for concordance against predictions of and relevant experimental data. In general, the values predicted by the ML models were within 20% of those of the PBPK model across the range of drug and formulation properties. However, summary PK parameter predictions from both the ML model and full PBPK model were occasionally poor with respect to those derived from experiments, suggesting deficiencies in the underlying PBPK model.
Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress
Authors: Son Yongjun , Min Jihyeon , Shin Yoonjae , Park Woojun 
Published: September 2023

AbstractBoth culture-independent and culture-dependent analyses using Nanopore-based 16S rRNA sequencing showed that short-term exposure of Antarctic soils to low temperature increased biomass with lower bacterial diversity and maintained high numbers of the phylum Proteobacteria, Firmicute, and Actinobacteria including Pseudarthrobacter species. The psychrophilic Pseudarthrobacter psychrotolerans YJ56 had superior growth at 13 °C, but could not grow at 30 °C, compared to other bacteria isolated from the same Antarctic soil. Unlike a single rod-shaped cell at 13 °C, strain YJ56 at 25 °C was morphologically shifted into a filamentous bacterium with several branches. Comparative genomics of strain YJ56 with other genera in the phylum Actinobacteria indicate remarkable copy numbers of rimJ genes that are possibly involved in dual functions, acetylation of ribosomal proteins, and stabilization of ribosomes by direct binding. Our proteomic data suggested that Actinobacteria cells experienced physiological stresses at 25 °C, showing the upregulation of chaperone proteins, GroEL and catalase, KatE. Level of proteins involved in the assembly of 50S ribosomal proteins and L29 in 50S ribosomal proteins increased at 13 °C, which suggested distinct roles of many ribosomal proteins under different conditions. Taken together, our data highlights the cellular filamentation and protein homeostasis of a psychrophilic YJ56 strain in coping with high-temperature stress.
Frictional resistance calculation and jacking force prediction of rectangular pipe jacking
Authors: Kong Chao , Guan Guoqing , Gu Song , Zhou Zaiyan , Wang Haiyan 
Published: September 2023

AbstractIn practical engineering, whilst estimating the jacking force of rectangular pipe jacking using an empirical formula, the results obtained from said formula deviate from reality and manifest inadequate engineering guidance. The equations governing the applied force during the installation of rectangular pipe jacking have been derived for various contact states involving the interaction between the pipe, slurry, and soil. The distinct stress conditions in the pipe jacking process as well as the shear-friction mechanism between the pipe and the surrounding soil have been taken into account. The displacement control method is introduced to simulate the pipe–slurry–soil contact friction during the pipe jacking process in FLAC3D. Additionally, the pipe jacking behavior, pipe–slurry–soil contact frictional force, and variation law of the jacking force are also simulated. Mutual verification was carried out using the results obtained from field monitoring, numerical and theoretical. The findings are as follows: the established equations for calculating pipe jacking force are highly applicable across various conditions of pipe–slurry–soil contact, and the outcomes derived from theoretical formulas align remarkably well with those obtained through field monitoring and numerical simulation. During the jacking process, the sidewalls exhibit initial partial sliding followed by a complete movement as the jacking force intensifies and subsequently diminishes, eventually attaining stability during the behavior adjustment phase. Moreover, the bottom pipe–soil contact is the most common situation in actual construction.
Sugarcane nitrogen nutrition estimation with digital images and machine learning methods
Authors: You Hui , Zhou Muchen , Zhang Junxiang , Peng Wei , Sun Cuimin 
Published: September 2023

AbstractThe color and texture characteristics of crops can reflect their nitrogen (N) nutrient status and help optimize N fertilizer management. This study conducted a one-year field experiment to collect sugarcane leaf images at tillering and elongation stages using a commercial digital camera and extract leaf image color feature (CF) and texture feature (TF) parameters using digital image processing techniques. By analyzing the correlation between leaf N content and feature parameters, feature dimensionality reduction was performed using principal component analysis (PCA), and three regression methods (multiple linear regression; MLR, random forest regression; RF, stacking fusion model; SFM) were used to construct N content estimation models based on different image feature parameters. All models were built using five-fold cross-validation and grid search to verify the model performance and stability. The results showed that the models based on color-texture integrated principal component features (C-T-PCA) outperformed the single-feature models based on CF or TF. Among them, SFM had the highest accuracy for the validation dataset with the model coefficient of determination (R2) of 0.9264 for the tillering stage and 0.9111 for the elongation stage, with the maximum improvement of 9.85% and 8.91%, respectively, compared with the other tested models. In conclusion, the SFM framework based on C-T-PCA combines the advantages of multiple models to enhance the model performance while enhancing the anti-interference and generalization capabilities. Combining digital image processing techniques and machine learning facilitates fast and nondestructive estimation of crop N-substance nutrition.