bluuebunny/crossref_metadata_2025_split huggingface dataset:
A critical examination of robustness and generalizability of machine learning prediction of materials properties
Authors: Li Kangming , DeCost Brian , Choudhary Kamal , Greenwood Michael , Hattrick-Simpers Jason 
Published: April 2023

AbstractRecent advances in machine learning (ML) have led to substantial performance improvement in material database benchmarks, but an excellent benchmark score may not imply good generalization performance. Here we show that ML models trained on Materials Project 2018 can have severely degraded performance on new compounds in Materials Project 2021 due to the distribution shift. We discuss how to foresee the issue with a few simple tools. Firstly, the uniform manifold approximation and projection (UMAP) can be used to investigate the relation between the training and test data within the feature space. Secondly, the disagreement between multiple ML models on the test data can illuminate out-of-distribution samples. We demonstrate that the UMAP-guided and query by committee acquisition strategies can greatly improve prediction accuracy by adding only 1% of the test data. We believe this work provides valuable insights for building databases and models that enable better robustness and generalizability.
Oxidative dissolution of Cr-doped UO2 nuclear fuel
Authors: Smith Hannah , Cordara Théo , Gausse Clémence , Pepper Sarah E. , Corkhill Claire L. 
Published: April 2023

AbstractAlternative UO2 nuclear fuels, incorporating Cr as a dopant, are currently in use in light–water reactors. Dissolution experiments using Cr-doped UO2, performed as a function of Cr content in a simplified groundwater solution and under oxic conditions, established that the addition of Cr to the UO2 matrix systematically reduced the normalised dissolution rate of U at 25 and 40 °C. This effect was most notable under dilute solution conditions, and is the result of galvanic coupling between Cr and U, resulting from the presence of Cr2+ in the UO2 matrix, as corroborated by activation energy determination. Under conditions of solution saturation, where schoepite ((UO2)8O2(OH)12·(H2O)12) and Na2U2O7·6H2O were identified as secondary phases, the rate of U dissolution was invariant with Cr content. Moreover, at 60 °C, the trend was reversed and the rate of U dissolution increased with increasing Cr content. Under these conditions, other factors, including U solubility or bicarbonate-surface interactions, exert a stronger influence on the U dissolution kinetics than Cr. Increased grain size, a feature of Cr-doped UO2 fuel, was also found to reduce the normalised dissolution rate of U. In establishing the mechanisms by which Cr dopants influence UO2 fuel dissolution, it can be concluded that, overall, Cr-doped UO2 nuclear fuel possesses similar dissolution kinetics to undoped UO2 fuel, giving confidence for its eventual disposal in a geological facility.
Neuroprotective actions of a fatty acid nitroalkene in Parkinson’s disease
Authors: Di Maio Roberto , Keeney Matthew T. , Cechova Veronika , Mortimer Amanda , Sekandari Ahssan , Rowart Pascal , Greenamyre J. Timothy , Freeman Bruce A. , Fazzari Marco 
Published: April 2023

AbstractTo date there are no therapeutic strategies that limit the progression of Parkinson’s disease (PD). The mechanisms underlying PD-related nigrostriatal neurodegeneration remain incompletely understood, with multiple factors modulating the course of PD pathogenesis. This includes Nrf2-dependent gene expression, oxidative stress, α-synuclein pathology, mitochondrial dysfunction, and neuroinflammation. In vitro and sub-acute in vivo rotenone rat models of PD were used to evaluate the neuroprotective potential of a clinically-safe, multi-target metabolic and inflammatory modulator, the electrophilic fatty acid nitroalkene 10-nitro-oleic acid (10-NO2-OA). In N27-A dopaminergic cells and in the substantia nigra pars compacta of rats, 10-NO2-OA activated Nrf2-regulated gene expression and inhibited NOX2 and LRRK2 hyperactivation, oxidative stress, microglial activation, α-synuclein modification, and downstream mitochondrial import impairment. These data reveal broad neuroprotective actions of 10-NO2-OA in a sub-acute model of PD and motivate more chronic studies in rodents and primates.
Towards practical and massively parallel quantum computing emulation for quantum chemistry
Authors: Shang Honghui , Fan Yi , Shen Li , Guo Chu , Liu Jie , Duan Xiaohui , Li Fang , Li Zhenyu 
Published: April 2023

AbstractQuantum computing is moving beyond its early stage and seeking for commercial applications in chemical and biomedical sciences. In the current noisy intermediate-scale quantum computing era, the quantum resource is too scarce to support these explorations. Therefore, it is valuable to emulate quantum computing on classical computers for developing quantum algorithms and validating quantum hardware. However, existing simulators mostly suffer from the memory bottleneck so developing the approaches for large-scale quantum chemistry calculations remains challenging. Here we demonstrate a high-performance and massively parallel variational quantum eigensolver (VQE) simulator based on matrix product states, combined with embedding theory for solving large-scale quantum computing emulation for quantum chemistry on HPC platforms. We apply this method to study the torsional barrier of ethane and the quantification of the protein–ligand interactions. Our largest simulation reaches 1000 qubits, and a performance of 216.9 PFLOP/s is achieved on a new Sunway supercomputer, which sets the state-of-the-art for quantum computing emulation for quantum chemistry.
Endothelial Brg1 fine-tunes Notch signaling during zebrafish heart regeneration
Authors: Xiao Chenglu , Hou Junjie , Wang Fang , Song Yabing , Zheng Jiyuan , Luo Lingfei , Wang Jianbin , Ding Wanqiu , Zhu Xiaojun , Xiong Jing-Wei 
Published: April 2023

AbstractMyocardial Brg1 is essential for heart regeneration in zebrafish, but it remains unknown whether and how endothelial Brg1 plays a role in heart regeneration. Here, we found that bothbrg1mRNA and protein were induced in cardiac endothelial cells after ventricular resection and endothelium-specific overexpression of dominant-negativeXenopusBrg1 (dn-xbrg1) inhibited myocardial proliferation and heart regeneration and increased cardiac fibrosis. RNA-seq and ChIP-seq analysis revealed that endothelium-specific overexpression ofdn-xbrg1changed the levels of H3K4me3 modifications in the promoter regions of the zebrafish genome and induced abnormal activation of Notch family genes upon injury. Mechanistically, Brg1 interacted with lysine demethylase 7aa (Kdm7aa) to fine-tune the level of H3K4me3 within the promoter regions of Notch family genes and thus regulatednotchgene transcription. Together, this work demonstrates that the Brg1-Kdm7aa-Notch axis in cardiac endothelial cells, including the endocardium, regulates myocardial proliferation and regeneration via modulating the H3K4me3 of thenotchpromoters in zebrafish.
Topographical mapping of catecholaminergic axon innervation in the flat-mounts of the mouse atria: a quantitative analysis
Authors: Zhang Yuanyuan , Bizanti Ariege , Harden Scott W. , Chen Jin , Bendowski Kohlton , Hoover Donald B. , Gozal David , Shivkumar Kalyanam , Heal Maci , Tappan Susan , Cheng Zixi Jack 
Published: April 2023

AbstractThe sympathetic nervous system is crucial for controlling multiple cardiac functions. However, a comprehensive, detailed neuroanatomical map of the sympathetic innervation of the heart is unavailable. Here, we used a combination of state-of-the-art techniques, including flat-mount tissue processing, immunohistochemistry for tyrosine hydroxylase (TH, a sympathetic marker), confocal microscopy and Neurolucida 360 software to trace, digitize, and quantitatively map the topographical distribution of the sympathetic postganglionic innervation in whole atria of C57Bl/6 J mice. We found that (1) 4–5 major extrinsic TH-IR nerve bundles entered the atria at the superior vena cava, right atrium (RA), left precaval vein and the root of the pulmonary veins (PVs) in the left atrium (LA). Although these bundles projected to different areas of the atria, their projection fields partially overlapped. (2) TH-IR axon and terminal density varied considerably between different sites of the atria with the greatest density of innervation near the sinoatrial node region (P < 0.05, n = 6). (3) TH-IR axons also innervated blood vessels and adipocytes. (4) Many principal neurons in intrinsic cardiac ganglia and small intensely fluorescent cells were also strongly TH-IR. Our work provides a comprehensive topographical map of the catecholaminergic efferent axon morphology, innervation, and distribution in the whole atria at single cell/axon/varicosity scale that may be used in future studies to create a cardiac sympathetic-brain atlas.
Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis
Authors: Nishimura Motoi , Tanaka Tomoaki , Murata Syota , Miyabe Akiko , Ishige Takayuki , Kawasaki Kenji , Yokoyama Masataka , Hashimoto Naoko , Yamagata Kazuyuki , Nagano Hidekazu , Tojo-Nishimura Satomi , Matsushita Kazuyuki 
Published: April 2023

AbstractAlthough polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA methylation information. Herein, we propose a simple extension for bisulfite sequencing to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical isolates or flora. Multiple displacement amplification without DNA denaturation was used to preferentially pre-amplify single-stranded bacterial DNA after bisulfite conversion. Following the pre-amplification, the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing, enabling the simultaneous identification of DNA methylation status and sequence data. We used this approach (termed sm16S rDNA PCR/sequencing) to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii and different methylation motifs among Enterococcus faecalis strains from small volumes of clinical specimens. Further, our analysis suggested that M. MmnI may be correlated to erythromycin resistance. Thus, sm16S rDNA PCR/sequencing is a useful extension method for analyzing the DNA methylation of 16S rDNA regions in a microflora, providing additional information not provided by conventional PCR. Given the relationship between DNA methylation status and drug resistance in bacteria, we believe this technique can be effectively applied in clinical sample testing.
Asperuloside attenuates cadmium-induced toxicity by inhibiting oxidative stress, inflammation, fibrosis and apoptosis in rats
Authors: Kong Zhiyang , Liu Chunhong , Olatunji Opeyemi Joshua 
Published: April 2023

AbstractThis present study investigated the protective effects of asperuloside (ASP) against cadmium-induced nephrocardiac toxicity. Rats were treated with 50 mg/kg of ASP for five weeks and CdCl2 (5 mg/kg, p.o., once daily) during the last 4 weeks of ASP treatment. The serum levels of blood urea nitrogen (BUN), creatinine (Scr), aspartate transaminase (AST), creatine kinase-MB (CK-MB), troponin T (TnT) and lactate dehydrogenase (LDH) were evealuted. Oxido-inflammatory parameters were detected via malondialdehyde (MDA), reduced glutathione (GSH), catalase (CAT), superoxide dismutase (SOD), tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), interleukin-1beta (IL-1β) and nuclear factor kappa B (NF-κB). Additionally, the cardiorenal levels of caspase 3, transforming growth factor-β (TGF-β), α-smooth muscle actin (α-SMA), collagen IV and Bcl2 were measured by ELISA or immunohistochemical assays. The results indicated that ASP significantly decreased Cd-instigated oxidative stress, serum BUN, Scr, AST, CK-MB, TnT and LDH as well as histopathological alterations. Furthermore, ASP notably attenuated Cd-induced cardiorenal and apoptosis and fibrosis by reducing caspase 3 and TGF-β levels, as well as reducing the stain intensity of a-SMA and collagen IV, while increasing Bcl2 intensity. These results revealed that ASP attenuated Cd induced cardiac and renal toxicity which may be attributed to reducing oxidative stress, inflammation, fibrosis and apoptosis.
Influence of the hierarchical architecture of multi-core iron oxide nanoflowers on their magnetic properties
Authors: Neumann Stefan , Kuger Laura , Arlt Carsten-Rene , Franzreb Matthias , Rafaja David 
Published: April 2023

AbstractMagnetic properties of superparamagnetic iron oxide nanoparticles are controlled mainly by their particle size and by their particle size distribution. Magnetic properties of multi-core iron oxide nanoparticles, often called iron oxide nanoflowers (IONFs), are additionally affected by the interaction of magnetic moments between neighboring cores. The knowledge about the hierarchical structure of IONFs is therefore essential for understanding the magnetic properties of IONFs. In this contribution, the architecture of multi-core IONFs was investigated using correlative multiscale transmission electron microscopy (TEM), X-ray diffraction and dynamic light scattering. The multiscale TEM measurements comprised low-resolution and high-resolution imaging as well as geometric phase analysis. The IONFs contained maghemite with the average chemical composition $$\gamma$$
γ
-Fe$$_{2.72\pm 0.02}$$

2.72
±
0.02

O$$_4$$

4

. The metallic vacancies located on the octahedral lattice sites of the spinel ferrite structure were partially ordered. Individual IONFs consisted of several cores showing frequently a specific crystallographic orientation relationship between direct neighbors. This oriented attachment may facilitate the magnetic alignment within the cores. Individual cores were composed of partially coherent nanocrystals having almost the same crystallographic orientation. The sizes of individual constituents revealed by the microstructure analysis were correlated with the magnetic particle sizes that were obtained from fitting the measured magnetization curve by the Langevin function.
Real-time respiratory motion prediction using photonic reservoir computing
Authors: Liang Zhizhuo , Zhang Meng , Shi Chengyu , Huang Z. Rena 
Published: April 2023

AbstractRespiration induced motion is a well-recognized challenge in many clinical practices including upper body imaging, lung tumor motion tracking and radiation therapy. In this work, we present a recurrent neural network algorithm that was implemented in a photonic delay-line reservoir computer (RC) for real-time respiratory motion prediction. The respiratory motion signals are quasi-periodic waveforms subject to a variety of non-linear distortions. In this work, we demonstrated for the first time that RC can be effective in predicting short to medium range of respiratory motions within practical timescales. A double-sliding window technology is explored to enable the real-time establishment of an individually trained model for each patient and the real-time processing of live-streamed respiratory motion data. A breathing dataset from a total of 76 patients with breathing speeds ranging from 3 to 20 breaths per minute (BPM) is studied. Motion prediction of look-ahead times of 66.6, 166.6, and 333 ms are investigated. With a 333 ms look-ahead time, the real-time RC model achieves an average normalized mean square error (NMSE) of 0.025, an average mean absolute error (MAE) of 0.34 mm, an average root mean square error (RMSE) of 0.45 mm, an average therapeutic beam efficiency (TBE) of 94.14% for an absolute error (AE) < 1 mm, and 99.89% for AE < 3 mm. This study demonstrates that real-time RC is an efficient computing framework for high precision respiratory motion prediction.
The impact of pericytes on the stability of microvascular networks in response to nanoparticles
Authors: Dibble Matthew , Di Cio’ Stefania , Luo Piaopiao , Balkwill Frances , Gautrot Julien E. 
Published: April 2023

AbstractRecapitulating the normal physiology of the microvasculature is pivotal in the development of more complex in-vitro models and organ-on-chip designs. Pericytes are an important component of the vasculature, promoting vessel stability, inhibiting vascular permeability and maintaining the vascular hierarchical architecture. The use of such co-culture for the testing of therapeutics and nanoparticle safety is increasingly considered for the validation of therapeutic strategies. This report presents the use of a microfluidic model for such applications. Interactions between endothelial cells and pericytes are first explored. We identify basal conditions required to form stable and reproducible endothelial networks. We then investigate interactions between endothelial cells and pericytes via direct co-culture. In our system, pericytes prevented vessel hyperplasia and maintained vessel length in prolonged culture (> 10 days). In addition, these vessels displayed barrier function and expression of junction markers associated with vessel maturation, including VE-cadherin, β-catenin and ZO-1. Furthermore, pericytes maintained vessel integrity following stress (nutrient starvation) and prevented vessel regression, in contrast to the striking dissociation of networks in endothelial monocultures. This response was also observed when endothelial/pericyte co-cultures were exposed to high concentrations of moderately toxic cationic nanoparticles used for gene delivery. This study highlights the importance of pericytes in protecting vascular networks from stress and external agents and their importance to the design of advanced in-vitro models, including for the testing of nanotoxicity, to better recapitulate physiological response and avoid false positives.
Marginal leaf galls on Pliocene leaves from India indicate mutualistic behavior between Ipomoea plants and Eriophyidae mites
Authors: Hazra Taposhi , Adroit Benjamin , Denk Thomas , Wappler Torsten , Sarkar Subhankar Kumar , Bera Subir , Khan Mahasin Ali 
Published: April 2023

AbstractWe report a new type of fossil margin galls arranged in a linear series on dicot leaf impressions from the latest Neogene (Pliocene) sediments of the Chotanagpur Plateau, Jharkhand, eastern India. We collected ca. 1500 impression and compression leaf fossils, of which 1080 samples bear arthropod damage referable to 37 different damage types (DT) in the ‘GuidetoInsect(andOther)DamageTypesinCompressedPlantFossils’. A few leaf samples identified as Ipomoea L. (Convolvulaceae) have specific margin galls that do not match any galling DT previously described. This type of galling is characterized by small, linearly arranged, irregular, sessile, sub-globose, solitary, indehiscent, solid pouch-galls with irregular ostioles. The probable damage inducers of the present galling of the foliar margin might be members of Eriophyidae (Acari). The new type of gall suggests that marginal gall-inducing mites on leaves of Ipomoea did not change their host preference at the genus level since the Pliocene. The development of marginal leaf galling in Ipomoea is linked to extrafloral nectaries that do not offer protection against arthropod galling but indirectly protect the plant against herbivory from large mammals.
Two-generation exposure to a high-fat diet induces the change of salty taste preference in rats
Authors: Serirukchutarungsee Saranya , Watari Ippei , Narukawa Masataka , Podyma-Inoue Katarzyna Anna , Sangsuriyothai Pornchanok , Ono Takashi 
Published: April 2023

AbstractHigh-fat diet (HFD) leads to multiple complications, including taste alteration. This study observed the effect of a two-generation exposure to an HFD on the peripheral taste system in offspring. Ten pregnant Wistar rats were assigned a standard diet (SD) (n = 5) or HFD (n = 5) from day 7 of pregnancy through the lactation. Thirty-six male and female 3-week-old offspring were measured for body weight and blood glucose level, and the circumvallate papillae were collected. The other twenty-four 3-week-old offspring were weaned on the same diet as their mothers and raised individually. The taste preference behaviors were studied using the two-bottle taste preference test and analyzed five basic tastes (sweet, bitter, umami, sour, and salty). The expressions of epithelial sodium channel alpha subunit (ENaCα) and angiotensin II receptor type 1 (AT1) in the circumvallate papilla were analyzed by immunohistochemical staining and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We found increased body weight and salty taste preference of offspring from the HFD group in both sexes. Correspondingly, the AT1 level of the taste bud cells significantly increased in 3-week-old female offspring from the HFD group. An increase in AT1 levels may be a risk factor for changes in salty taste preference.
Application of machine learning algorithm in predicting distant metastasis of T1 gastric cancer
Authors: Tian HuaKai , Liu Zitao , Liu Jiang , Zong Zhen , Chen YanMei , Zhang Zuo , Li Hui 
Published: April 2023

AbstractDistant metastasis (DM) is relatively uncommon in T1 stage gastric cancer (GC). The aim of this study was to develop and validate a predictive model for DM in stage T1 GC using machine learning (ML) algorithms. Patients with stage T1 GC from 2010 to 2017 were screened from the public Surveillance, Epidemiology and End Results (SEER) database. Meanwhile, we collected patients with stage T1 GC admitted to the Department of Gastrointestinal Surgery of the Second Affiliated Hospital of Nanchang University from 2015 to 2017. We applied seven ML algorithms: logistic regression, random forest (RF), LASSO, support vector machine, k-Nearest Neighbor, Naive Bayesian Model, Artificial Neural Network. Finally, a RF model for DM of T1 GC was developed. The AUC, sensitivity, specificity, F1-score and accuracy were used to evaluate and compare the predictive performance of the RF model with other models. Finally, we performed a prognostic analysis of patients who developed distant metastases. Independent risk factors for prognosis were analysed by univariate and multifactorial regression. K-M curves were used to express differences in survival prognosis for each variable and subvariable. A total of 2698 cases were included in the SEER dataset, 314 with DM, and 107 hospital patients were included, 14 with DM. Age, T-stage, N-stage, tumour size, grade and tumour location were independent risk factors for the development of DM in stage T1 GC. A combined analysis of seven ML algorithms in the training and test sets found that the RF prediction model had the best prediction performance (AUC: 0.941, Accuracy: 0.917, Recall: 0.841, Specificity: 0.927, F1-score: 0.877). The external validation set ROCAUC was 0.750. Meanwhile, survival prognostic analysis showed that surgery (HR = 3.620, 95% CI 2.164–6.065) and adjuvant chemotherapy (HR = 2.637, 95% CI 2.067–3.365) were independent risk factors for survival prognosis in patients with DM from stage T1 GC. Age, T-stage, N-stage, tumour size, grade and tumour location were independent risk factors for the development of DM in stage T1 GC. ML algorithms had shown that RF prediction models had the best predictive efficacy to accurately screen at-risk populations for further clinical screening for metastases. At the same time, aggressive surgery and adjuvant chemotherapy can improve the survival rate of patients with DM.