bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the prediction accuracy of machine learning algorithms in crosslinguistic vowel classification
Authors: Georgiou Georgios P. 
Published: September 2023

AbstractMachine learning algorithms can be used for the prediction of nonnative sound classification based on crosslinguistic acoustic similarity. To date, very few linguistic studies have compared the classification accuracy of different algorithms. This study aims to assess how well machines align with human speech perception by assessing the ability of three machine learning algorithms, namely, linear discriminant analysis (LDA), decision tree (C5.0), and neural network (NNET), to predict the classification of second language (L2) sounds in terms of first language (L1) categories. The models were trained using the first three formants and duration of L1 vowels and fed with the same acoustic features of L2 vowels. To validate their accuracy, adult L2 speakers completed a perceptual classification task. The results indicated that NNET predicted with success the classification of all L2 vowels with the highest proportion in terms of L1 categories, while LDA and C5.0 missed only one vowel each. Furthermore, NNET exhibited superior accuracy in predicting the full range of above chance responses, followed closely by LDA. C5.0 did not meet the anticipated performance levels. The findings can hold significant implications for advancing both the theoretical and practical frameworks of speech acquisition.
Negative chemotaxis of Ligilactobacillus agilis BKN88 against gut-derived substances
Authors: Suzuki Shunya , Yokota Kenji , Igimi Shizunobu , Kajikawa Akinobu 
Published: September 2023

AbstractLigilactobacillus agilis is a motile lactic acid bacterium found in the gastrointestinal tracts of animals. The findings of our previous study suggest that the motility of L. agilis BKN88 enables gut colonization in murine models. However, the chemotactic abilities of motile lactobacilli remain unknown. This study aimed to identify the gut-derived chemoeffectors and their corresponding chemoreceptors in L. agilis BKN88. Chemotaxis assays with chemotactic and non-chemotactic (ΔcheA) L. agilis strains revealed that low pH, organic acids, and bile salts served as repellents. L. agilis BKN88 was more sensitive to bile and acid than the gut-derived non-motile lactobacilli, implying that L. agilis might utilize motility and chemotaxis instead of exhibiting stress tolerance/resistance. L. agilis BKN88 contains five putative chemoreceptor genes (mcp1–mcp5). Chemotaxis assays using a series of chemoreceptor mutants revealed that each of the five chemoreceptors could sense multiple chemoeffectors and that these chemoreceptors were functionally redundant. Mcp2 and Mcp3 sensed all tested chemoeffectors. This study provides further insights into the interactions between chemoreceptors and ligands of motile lactobacilli and the unique ecological and evolutionary features of motile lactobacilli, which may be distinct from those of non-motile lactobacilli.
Integrating single-cell and bulk RNA sequencing to predict prognosis and immunotherapy response in prostate cancer
Authors: Wen Xiao Yan , Wang Ru Yi , Yu Bei , Yang Yue , Yang Jin , Zhang Han Chao 
Published: September 2023

AbstractProstate cancer (PCa) stands as a prominent contributor to morbidity and mortality among males on a global scale. Cancer-associated fibroblasts (CAFs) are considered to be closely connected to tumour growth, invasion, and metastasis. We explored the role and characteristics of CAFs in PCa through bioinformatics analysis and built a CAFs-based risk model to predict prognostic treatment and treatment response in PCa patients. First, we downloaded the scRNA-seq data for PCa from the GEO. We extracted bulk RNA-seq data for PCa from the TCGA and GEO and adopted “ComBat” to remove batch effects. Then, we created a Seurat object for the scRNA-seq data using the package “Seurat” in R and identified CAF clusters based on the CAF-related genes (CAFRGs). Based on CAFRGs, a prognostic model was constructed by univariate Cox, LASSO, and multivariate Cox analyses. And the model was validated internally and externally by Kaplan–Meier analysis, respectively. We further performed GO and KEGG analyses of DEGs between risk groups. Besides, we investigated differences in somatic mutations between different risk groups. We explored differences in the immune microenvironment landscape and ICG expression levels in the different groups. Finally, we predicted the response to immunotherapy and the sensitivity of antitumour drugs between the different groups. We screened 4 CAF clusters and identified 463 CAFRGs in PCa scRNA-seq. We constructed a model containing 10 prognostic CAFRGs by univariate Cox, LASSO, and multivariate Cox analysis. Somatic mutation analysis revealed that TTN and TP53 were significantly more mutated in the high-risk group. Finally, we screened 31 chemotherapeutic drugs and targeted therapeutic drugs for PCa. In conclusion, we identified four clusters based on CAFs and constructed a new CAFs-based prognostic signature that could predict PCa patient prognosis and response to immunotherapy and might suggest meaningful clinical options for the treatment of PCa.
Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots
Authors: Tian Yulu , Liu Xue , Xu Yuanjiang , Yu Benxia , Wang Le , Qu Xianyou 
Published: September 2023

AbstractTiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people’s republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.
Assessing the global ocean science community: understanding international collaboration, concerns and the current state of ocean basin research
Authors: Potter Ross W. K. , Pearson Brodie C. 
Published: September 2023

AbstractWeb of Science data covering 2000–2020 was used to analyse trends in ocean research, specific to the five ocean basins (Arctic, Atlantic, Indian, Pacific, Southern), to investigate its state and any underlying concerns for addressing UN Decade of Ocean Science goals and UN Sustainable Development Goal 14 “Life Below Water”. Though Atlantic research has dominated, Pacific research is nearing parity with its neighbour due to significant output growth by China and is soon likely to become the most researched basin. International collaboration, built around G7 countries and China, has increased by 10 percentage points since 2000 but research remains mainly domestic. Outside these countries, there has been growth in collaborations involving Small Island Developing States and a doubling of South America’s global share of ocean basin papers. However, sub-Saharan African research output has not mirrored this expansion. Further growth could be catalysed by increased support for educational efforts and infrastructure development, particularly given the highly specialised and institutionally driven nature of ocean basin research.
Implications of ubiquitination and the maintenance of replication fork stability in cancer therapy
Authors: Xia Donghui , Zhu Xuefei , Wang Ying , Gong Peng , Su Hong-Shu , Xu Xingzhi 
Published: September 2023

AbstractDNA replication forks are subject to intricate surveillance and strict regulation by sophisticated cellular machinery. Such close regulation is necessary to ensure the accurate duplication of genetic information and to tackle the diverse endogenous and exogenous stresses that impede this process. Stalled replication forks are vulnerable to collapse, which is a major cause of genomic instability and carcinogenesis. Replication stress responses, which are organized via a series of coordinated molecular events, stabilize stalled replication forks and carry out fork reversal and restoration. DNA damage tolerance and repair pathways such as homologous recombination and Fanconi anemia also contribute to replication fork stabilization. The signaling network that mediates the transduction and interplay of these pathways is regulated by a series of post-translational modifications, including ubiquitination, which affects the activity, stability, and interactome of substrates. In particular, the ubiquitination of replication protein A and proliferating cell nuclear antigen at stalled replication forks promotes the recruitment of downstream regulators. In this review, we describe the ubiquitination-mediated signaling cascades that regulate replication fork progression and stabilization. In addition, we discuss the targeting of replication fork stability and ubiquitination system components as a potential therapeutic approach for the treatment of cancer.
A comparison of conductive ink usage optimization techniques used in fabrication of epidermal UHF radio frequency identification tags for medical and sensing applications
Authors: Oyeka Dumtoochukwu Obiora , Batchelor John , Saunders Rachel 
Published: September 2023

AbstractThe aim of this work is to assess the performance of various inkjet printing techniques. These techniques are aimed at optimizing the volume of conductive ink used in the fabrication of inkjet printed Radio Frequency Identification tags. It is also possible that they can be used in fabricating other electronic and electromagnetic devices and structures. Three ink optimization approaches were examined viz. gridded (meshed) designs, conductive area trimming and selective ink deposition. The volume of conductive ink utilized in tag fabrication and the measured on‐body (forearm) read range of the tag were used to develop a figure of merit which determined the best printing approach. Although the longest read range was obtained from the tag with 48% conductive area trimming (Trim 1), the best figure of merit, that is, the tag with the best balance between measured read range and utilized conductive ink, was obtained from the tag that had its surface area trimmed by 65% (Trim 2). It is however suggested that optimum use of conductive ink would be achieved with a combination of 65% surface area trimming and selective ink deposition technique.
Percutaneous drainage and combined praziquantel-albendazole therapy: a novel approach for the treatment of simple echinococcal liver cysts
Authors: Richter Joachim , Lindner Andreas K. , Geisel Dominik , Fleckenstein Florian Nima , Torsello Giovanni Federico , Millet Pascual-Leone Belén , Ivanov Olga , Zöllner Caroline , Wilde Anne-Christine Beatrix , Equihua Martinez Gabriela 
Published: September 2023

AbstractCystic echinococcosis (CE) is a worldwide helminthic zoonosis causing serious disease in humans. The WHO Informal Working Group on Echinococcosis recommends a stage-specific treatment approach of hepatic CE that facilitates the decision on what therapy option is most appropriate. Percutaneous aspiration, instillation of a scolicide, e.g., ethanol or hypertonic saline, and subsequent re-aspiration (PAIR) have been advocated for treating medium-size unilocular WHO-stage CE1 cysts. PAIR can pose a risk of toxic cholangitis because of spillage of ethanol in the case of a cysto-biliary fistula or of life-threatening hypernatriaemia when hypertonic saline is used. The purpose of our study is to develop an alternative, safe, minimally invasive method to treat CE1 cysts, avoiding the use of toxic topic scolicides.We opt for percutaneous drainage (PD) in four patients: the intrahepatic drainage catheter is placed under CT-fluoroscopy, intracystic fluid is aspirated, and the viability of intracystic echinococcal protoscolices is assessed microscopically. Oral praziquantel (PZQ) is added to albendazole (ABZ) instead of using topical scolicidals.Protoscolices degenerate within 5 to 10 days after PZQ co-medication at a cumulative dosage of 250 to 335 mg/kg, and the cysts collapse. The cysts degenerate, and no sign of spillage nor relapse is observed in the follow-up time of up to 24 months post-intervention.In conclusion, PD combined with oral PZQ under ABZ coverage is preferable to PAIR in patients with unilocular echinococcal cysts.
Circulating Vitamin D Levels in Patients With Systemic Sclerosis: a
Meta-Analysis
Authors: Lee Young Ho , Song Gwan Gyu 
Published: September 2023

Abstract
Objective This study aimed to evaluate the relationship between
circulating vitamin D levels and systemic sclerosis and to establish an
association between vitamin D deficiency and systemic sclerosis.
Methods We performed a meta-analysis comparing the plasma/serum
vitamin D levels and vitamin D deficiency between patients with systemic
sclerosis and healthy controls and examined correlation coefficients between
circulating vitamin D levels and the Rodnan score.
Results Twenty-one studies involving 1,399 patients with systemic
sclerosis and 1,311 controls were included. The systemic sclerosis group had
significantly lower vitamin D levels than the control group. Stratification by
ethnicity demonstrated significantly decreased vitamin D levels in patients with
systemic sclerosis among European, Asian, Arab, Latin American, and mixed
populations. Stratification by age, sex, and/or body mass index revealed
significantly lower vitamin D levels in the systemic sclerosis group regardless
of the adjustment. Subgroup analysis by sample size revealed significantly lower
vitamin D levels in the systemic sclerosis group by small (n<100) and
large sample numbers (n>100). Stratification by publication year
revealed significantly lower vitamin D levels in the systemic sclerosis group in
both recent and old publication years. However, no significant difference in
vitamin D levels was observed between diffuse and limited types of systemic
sclerosis. Vitamin D deficiency was significantly associated with systemic
sclerosis. The meta-analysis of correlation coefficients revealed a tendency of
inverse correlation between circulating vitamin D levels and the Rodnan
score.
Conclusions Patients with systemic sclerosis had lower circulating vitamin
D levels and higher vitamin D deficiency and there was a tendency of inverse
correlation between circulating vitamin D levels and the Rodnan score.
Straightforward Approach to 5-Substituted 7H-Imidazo[2,1-b] [1,3]thiazines via Cyclization of 2-Alkynylthioimidazoles
Authors: Žutautė Ieva , Misiūnaitė Indrė , Bajarūnaitė Raminta , Bukšnaitienė Rita , Brukštus Algirdas 
Published: September 2023

AbstractElectrophile-initiated nucleophilic cyclization of 2-alkynylthiobenzimidazoles is a useful tool for synthesizing new heterocyclic systems. However, halogen-initiated cyclization demonstrates poor selectivity between electrophilic addition and substitution reactions using other imidazole analogues. In this research, several different coinage metal catalysts were employed to broaden the scope of 7H-imidazo[2,1-b][1,3]thiazines in atom-economic manner. Selective 6-endo-dig pathway reactions were achieved in good to excellent yields using various 2-alkynylthioimidazoles with AuCl as the catalyst in DCE/DCM.
International comparison of activity measurements of a solution of 51Cr
Authors: Broda R , Ziemek T , Bobin Ch , Thiam Ch , Listkowska A , Lech E , Chambon L , Lourenço V , Czudek M , Saganowski P , Tymiński Z , Kołakowska E 
Published: September 2023

Main text
A bilateral comparison between LNE-LNHB, France and the RC POLATOM, Poland on activity measurements of the 51Cr solution was organized in 2022 as the EURAMET project No 1554 and registered as EURAMET.RI(II)-K2.Cr-51 key comparison. In both laboratories, primary activity measurements techniques based on 4π(LS)-γ coincidence and anti-coincidence counting methods were used. LNE-LNHB also performed indicative measurements in a large-well NaI(Tl) detector using the 4πγ method. The final result of the comparison in RC POLATOM was the weighted mean of the results of the 4π(LS)-γ coincidence method and the 4π(LS)-γ anti-coincidence method, and in the LNE-LNHB - the value obtained by the 4π(LS)-γ anti-coincidence method. The power-moderated mean of the final results values was calculated. An additional ampoule containing the same 51Cr solution was sent to the BIPM in order to link the results achieved in the bilateral comparison to the BIPM SIR reference system.
To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database https://www.bipm.org/kcdb/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Percolation of ‘civilisation’ in a homogeneous isotropic universe
Authors: Alinea A L , Jadrin C J C 
Published: September 2023

Abstract
In this work, we consider the spread of a ‘civilisation’ in an idealised homogeneous isotropic universe where all the planets of interest are habitable. Following a framework that goes beyond the usual idea of percolation in common undergraduate computational physics textbooks, we investigate the behaviour of the number of colonised planets with time, and the total colonisation time for three types of universes. These include static, dark energy-dominated, and matter-dominated universes. For all these types of universes, we find a remarkable fit with the Logistic Growth Function for the number of colonised planets with time. This is in spite of the fact that for the matter- and dark-energy dominated universes, the space itself is expanding. For the total colonisation time, T, the case for a dark energy-dominated universe is marked with divergence beyond the linear regime characterised by small values of the Hubble parameter, H. Not all planets in a spherical section of this universe can be ‘colonised’ due to the presence of a shrinking Hubble sphere. In other words, the recession speeds of other planets go beyond the speed of light making them impossible to reach. On the other hand, for a matter-dominated universe, while there is an apparent horizon, the Hubble sphere is growing instead of shrinking. This leads to a finite total colonisation time that depends on the Hubble parameter characterising the Universe; in particular, we find T ∼ H for small H and T ∼ H
2 for large H.
Effects of CO and NO atmospheres on the morphology of Ag, Ni, and Ir nanoparticles
Authors: Li Yanshuang , Zhang Meng , Xu Wen Wu 
Published: September 2023

Abstract
Metal nanoparticles are widely used in multiphase catalytic reactions due to their excellent physicochemical properties, which are mainly determined by their size and shape. Therefore, predicting and controlling the shape and structure of metal nanoparticles under reaction conditions has been a popular topic of interest among researchers. In this study, we conducted a systematical investigation to the equilibrium structure of Ag, Ni, and Ir nanoparticles within a mixed gas environment of CO and NO, employing a multiscale structural reconstruction model. This model demonstrates the ability to accurately predict the equilibrium configuration of metal nanoparticles under reactive conditions. Our investigation reveals a notable presence of negative surface energy in the phase diagrams representing Ag, Ir, and Ni nanoparticle configurations. This distinctive feature signifies that the nanoparticles undergo a process of splitting. While undergoing temperature and total pressure variations, the transformation in the structure of Ni nanoparticles is comparatively less evident in contrast to that of Ag and Ir nanoparticles. This discrepancy primarily stems from the pronounced energy barrier posed by the substantial rejection of CO and NO molecules at the surface of Ni nanoparticles. Notably, the structural modifications within Ag nanoparticles manifest solely within the confines of low-temperature ranges. Furthermore, our observations underscore the significant impact exerted by the ratios of CO and NO partial pressures on both the structure and the count of active sites within the metal nanoparticles.
Fubini–Study metric and topological properties of flat band electronic states: the case of an atomic chain with s − p orbitals
Authors: Espinosa-Champo Abdiel de Jesús , Naumis Gerardo G 
Published: September 2023

Abstract
The topological properties of the flat band states of a one-electron Hamiltonian that describes a chain of atoms with s − p orbitals are explored. This model is mapped onto a Kitaev–Creutz type model, providing a useful framework to understand the topology through a nontrivial winding number and the geometry introduced by the Fubini–Study (FS) metric. This metric allows us to distinguish between pure states of systems with the same topology and thus provides a suitable tool for obtaining the fingerprint of flat bands. Moreover, it provides an appealing geometrical picture for describing flat bands as it can be associated with a local conformal transformation over circles in a complex plane. In addition, the presented model allows us to relate the topology with the formation of compact localized states and pseudo-Bogoliubov modes. Also, the properties of the squared Hamiltonian are investigated in order to provide a better understanding of the localization properties and the spectrum. The presented model is equivalent to two coupled SSH chains under a change of basis.