bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facile synthesis and effect of thermal treatment on MoO3−x@MoS2 (x = 0, 1) bilayer nanostructure: toward photoelectrochemical applications
Authors: Nguyen Tien–Thanh , Nguyen Tien Dai , Vu Thi Bich , Dien Luong Xuan , Le Hoang V , Do Hung Manh , Nguyen Thanh Tung 
Published: November 2023

Abstract
This study reports on the successful synthesis of MoO3-x@MoS2 (x = 0, 1) nanostructure via a one-step hydrothermal combined with the annealing method, which resulted in a well-defined nanoparticle diameter of 280–320 nm and a nanoflake thickness of 12–20 nm. X-ray diffraction analysis confirmed the presence of a hexagonal crystal phase of MoS2, monoclinic MoO2, and orthorhombic α–MoO3 phases belonging to the P63/mmc, P21/c space group, and Pnma space groups, respectively. Thermal annealing resulted in a phase change from MoS2 to MoO3, MoO2, and Mo2S3, resulting in a bilayer structure of MoO3–x@MoS2 and MoS2@Mo2S3 with more catalytic activity sites. We also propose the synthesis of a shelf–hybrid MoO3–x@MoOxSy nanosheet@nanoflake for potential use in photoelectrochemical (PEC) devices. The resulting MoO3–x@MoS2-based photoanode exhibited a well-separated nanostructure that could be compatible with the MoO3–x@MoS2 nanosheet@nanoflake-based PEC device. The PEC measurements revealed a maximum photocurrent density (J) of 1.75 mA cm–2 at 0.52 V (versus RHE), highlighting the excellent performance of our new nanostructure in the PEC application.
Inside MOND: testing gravity with stellar accelerations
Authors: Finan-Jenkin Maxwell , Easther Richard 
Published: November 2023

Abstract
We quantify the differences between stellar accelerations in disk galaxies formed in a
MONDian universe relative to galaxies with the identical baryonic matter distributions and a
fitted cold dark matter halo. In a Milky Way-like galaxy the maximal transverse acceleration is
𝒪(10-9) arcseconds per year per decade, well beyond even the most optimistic
extrapolations of current capabilities. Conversely, the maximum difference in the line-of-sight
acceleration is 𝒪(1) centimetre per second per decade at solar distances from the
galactic centre. This level of precision is within reach of plausible future instruments.
Design and characterization of multichannel front-end electronics for detectors at HIRFL and HIAF
Authors: Wan S. , Yang H. , Zhu J. , Liu C. , Song Y. , Jia Y. , Liu T. , Zhao C. 
Published: November 2023

Abstract
A multichannel front-end readout electronics (MFEE) has been designed for readout in
detectors in the heavy ion facility in Lanzhou (HIRFL) and the high-intensity heavy-ion
accelerator facility (HIAF). With 40 different adjustable gains, this MFEE can meet the need for
most of the experiment. One MFEE can read and process the output signals of 128 channels of a
detector at the same time. MFEE is based on the AD8488 chip and uses Xilinx Kintex 7 series FPGA,
combined with the periphery circuits design, to complete the detector's output charge signal
readout. This paper will discuss the design and performance of the MFEE.
Integral representations for products of Airy functions and their application for analysis of the Green’s function for a particle in a uniform static field
Authors: Flegel A V 
Published: November 2023

Abstract
Representations for products of two Airy functions with different complex arguments in the form of one-dimensional contour integrals are obtained. These representations are used for analysis of the Green’s function for a charged particle in a uniform static electric field. The integral relation between the stationary and time-dependent Green’s functions is discussed in the sense of its analytical properties for complex energy and field strength. It is shown that the Green’s function can be divided into analytic and non-analytic parts with respect to the field strength near its zero.
Effectiveness of the Krotov method in finding controls for open quantum systems
Authors: Fernandes Marllos E F , Fanchini Felipe F , de Lima Emanuel F , Castelano Leonardo K 
Published: November 2023

Abstract
We apply the Krotov method (KM) for open and closed quantum systems to find optimized controls to manipulate qubit/qutrit systems in the presence of the external environment. In the case of unitary optimization, the KM is first applied to a quantum system neglecting its interaction with the environment. The resulting controls from the unitary optimization are then used to drive the system along with the environmental noise. In the case of non-unitary optimization, the KM already takes into account the noise during the optimization process. We consider two distinct computational tasks: target-state preparation and quantum gate implementation. These tasks are carried out in simple qubit/qutrit systems and also in systems presenting leakage states. For the state preparation cases, the controls from the non-unitary optimization outperform the controls from the unitary optimization. However, as we show here, this is not always true for the implementation of quantum gates. There are some situations where the unitary optimization performs equally well compared to the non-unitary optimization. We verify that these situations correspond to either the absence of leakage states or to the effects of dissipation being spread uniformly over the system, including non-computational levels. For such cases, the quantum gate implementation must cover the entire Hilbert space and there is no way to dodge dissipation. On the other hand, if the subspace containing the computational levels and its complement are differently affected by dissipation, the non-unitary optimization becomes effective.
On Hamiltonian structures of quasi-Painlevé equations
Authors: Filipuk Galina , Stokes Alexander 
Published: November 2023

Abstract
We describe the quasi-Painlevé property of a system of ordinary differential equations in terms of a global Hamiltonian structure on an analogue of Okamoto’s space of initial conditions for the Painlevé equations. In the quasi-Painlevé case, the Hamiltonian structure is with respect to a two-form which is allowed to have certain zeroes on the surfaces forming the space of initial conditions, as opposed to holomorphic symplectic forms in the case of the Painlevé equations. We provide the spaces and Hamiltonian structures for several known quasi-Painlevé equations and also for a new example, which we prove to have the quasi-Painlevé property via the Hamiltonian structure and construction of an appropriate auxiliary function which remains bounded on solutions.
Effect of light ellipticity and polarization angle on the transient dynamics of the ground-state Hanle effect
Authors: Grewal Raghwinder Singh 
Published: November 2023

Abstract
We report theoretical investigations on the transient dynamics of the ground-state Hanle effect in the Voigt geometry, where a time-varying scanning magnetic field
B
(t) is applied perpendicular to the light propagation direction. Transient Hanle signals are calculated for different light polarizations using a theoretical model based on the density matrix approach. First, we study the ellipticity dependence of transient Hanle signals in two configurations in which the major axis of the light polarization ellipse (

ε

a

) is aligned either perpendicular or parallel to the field
B
. For

ε

a

⊥

B
, elliptical polarization of the light produces oscillations of frequencies 2ΩL(t) and ΩL(t) simultaneously, where ΩL(t) is the Larmor frequency of the corresponding field
B
(t). On the other hand, in the case of

ε

a

||
B
, only ΩL(t) oscillation is observed using elliptically polarized light. Second, we vary the tilt angle between the polarization vector of a linearly polarized light and the orientation of the field
B
and study its effect on the transient response of Hanle signals. Both the amplitude and the decay rate of the oscillations show a strong dependence on the light ellipticity and tilt angle of the polarization vector. In addition, the influence of the magnetic field sweep rate on the transient signals is demonstrated for given values of light ellipticity and polarization angle.
Q fever infection is a preventable risk associated with pet food manufacturing
Authors: Uren Alexandra M , Harris James , Slinko Vicki , Vosti Fiona , Young Megan 
Published: November 2023

Abstract

Objective
This paper highlights the occupational risk of Q fever from exposure to raw animal products in the context of multiple notified Q fever cases from 2020 to 2023 linked to four pet food manufacturing facilities in South-East Queensland, Australia.

Methods
The Queensland Government Notifiable Conditions System was used to identify Q fever cases linked to pet food manufacturing in the Metro North and Gold Coast Hospital and Health Service areas of Brisbane, Australia. Data on each case from routine public health follow-up were collected and descriptively analysed.

Results
Between 2020 and 2023, 12 confirmed Q fever infections (17% of total cases) were linked to four pet food manufacturing facilities. Eleven cases reported direct or environmental exposure to raw meat and animal products. None were previously vaccinated for Q fever.

Conclusion
These cases demonstrate the increased risk of Q fever infection as part of the pet food manufacturing process, highlighting an underappreciated preventable occupational risk, which can be mitigated with the use of pre-screening and vaccination of workers. All occupations should conduct workplace-based risk assessments to identify risks such as Q fever to prevent adverse negative health outcomes.
Decolonizing US Latinx Students’ Language: El Sur in the Schools of El Norte
Authors: García Ofelia 
Published: November 2023

Abstract
This article considers how the racialized bilingual Latinx students in El Norte live in an epistemological Sur where their knowledge systems, which include their language and cultural practices are discounted. Centring the schooling experience of two US Latinas today, the article theorizes the differences between perceiving their language and bilingualism from the external perspective of dominant schooling institutions of the Global North, and from the inside perspective of racialized speakers. Bringing to bear thinking from an epistemological Sur (Santos 2009), revealed through a decolonizing sociolinguistic approach and Latinx decolonizing research sensibility, the article discusses how tools external to the Latinx experience—academic language and additive bilingualism—have contributed to the subjugation and failure of Latinx students. It ends by proposing translanguaging as a tool that has emerged from Latinx own experience and how its use in their education may open a decolonial option.
Failing Fortunes of Applied Linguistics: Towards Surviving Mastery
Authors: Oostendorp Marcelyn 
Published: November 2023

Abstract
The discourse of mastery is prominent in applied linguistics. The idea of mastery, however, does not remain only on the discourse level: curricula and policies are meant to be implemented, and therefore mastery and all that is associated with it (near perfection, dominance over something, etc.) is also practiced. In this paper, I argue that we might survive mastery by recuperating other ways of being, thinking, and learning. By drawing on examples from the South African higher educational context, I show glimpses of other ways of doing and thinking about language. Drawing inspiration from decolonial theory, I extend the notion of linguistic citizenship by showing that, for applied linguists, vulnerability, relationality, and failure could be points of focus as productive as mastery.
Colonizability and Hermeneutical Injustice in Applied Linguistics Research: (Im)possibilities for Epistemological Delinking
Authors: Barnawi Osman Z , R’boul Hamza 
Published: November 2023

AbstractThe field of applied linguistics is a remarkable case of deep intersection of the skewed geopolitics of knowledge (epistemic inequalities) and language (the ascendency of English as both a topic of research and academic lingua franca). The dominance of the Anglo-sphere through epistemology and language in applied linguistics renders the process of decolonization even more problematic than in other fields, for the only available tools to decolonize are those of coloniality. We argue that despite the end of formal decolonization and the incessant decolonial impulses, the Global South(s) may be still colonizable. Through ages of epistemic dominance, the Global South(s) may have encountered some tensions and challenges to exercise and legitimize ways of theorizing and doing applied linguistics research otherwise. That is, these alternative visions and praxis may again be underpinned by western traditions of thought that have shaped their foundational understandings of what language, linguistics, and practicality are. Epistemological delinking may be impossible as long as decoloniality itself is enunciated through the dominant voices and channels and according to the rationalities against which decoloniality in applied linguistics has been made to be understood. We go beyond the usual question of whether decolonization is possible, to ask: What decolonialities are possible to account for the Global South(s) and their varying degrees of colonizability? We employ what we term ‘collective introspection-retrospection’ as an epistemological journey of re-knowing, re-feeling, re-sensing, and re-imagining alternative epistemologies in applied linguistics.
Sketches Toward a Decolonial Applied Linguistics
Authors: De Fina Anna , Oostendorp Marcelyn , Ortega Lourdes 
Published: November 2023

Abstract
This special issue responds to an increasing interest in decolonial and Southern thinking in applied linguistics. In this Introduction, we first discuss some basic historical facts about colonization, and we highlight some key concepts. We then present the six contributions in the special issue. Three contributions compellingly expose the pervasiveness of coloniality and give reason to doubt that it can ever be overcome; the other three contributions open spaces for the decolonial possibilities of healing, hope, and futurity. We then discuss some key issues in decolonial and Southern scholarship, including the role of non-conventional writing in decolonial research, the differences between decolonial and social justice projects, the difficulties of decolonizing Eurocentric knowledge through Euro-Anglo-Northern tools, and deep inequities in the geopolitics of knowledge. We hope that the special issue will enable readers to re-see long-standing applied linguistics questions through decolonial and Southern lenses. We also hope to make the case why decolonial projects are worth the trouble.
Whoever their partner, female blue tits breed the same
Authors: Delaitre Ségolène , Doutrelant Claire , Caro Samuel P 
Published: November 2023

Abstract
Do females modify their reproductive investment if they do not succeed in pairing with a male that matches their preference? In a two-year experiment, we asked female blue tits (Cyanistes caeruleus) to select among six males, and then successively paired them with their preferred and their most avoided male. We monitored female reproductive investment through nest building activity, timing of breeding, size and number of eggs, number of fertilized eggs, and brood sex ratio. We found that females preferred males with a chromatic coloration (blue UV chroma of the head crown) that matched their own, but also that they preferred males with a lower achromatic coloration (less bright color of the cheeks and head crown). Although females paired with their preferred males tended to build heavier nests during the breeding season, we found no evidence of an effect of the pairing treatment on timing of breeding, or any other aspects of female reproductive investment. We however found that laying dates, clutch sizes, egg sizes, and brood sex ratio were significantly repeatable within females between the two years, despite the opposite pairing treatments. These findings show that in female blue tits, the males with which they are paired do not substantially alter their reproductive decisions.
FEED: a feature selection method based on gene expression decomposition for single cell clustering
Authors: Zhang Chao , Duan Zhi-Wei , Xu Yun-Pei , Liu Jin , Li Hong-Dong 
Published: November 2023

Abstract
Single-cell clustering is a critical step in biological downstream analysis. The clustering performance could be effectively improved by extracting cell-type-specific genes. The state-of-the-art feature selection methods usually calculate the importance of a single gene without considering the information contained in the gene expression distribution. Moreover, these methods ignore the intrinsic expression patterns of genes and heterogeneity within groups of different mean expression levels. In this work, we present a Feature sElection method based on gene Expression Decomposition (FEED) of scRNA-seq data, which selects informative genes to enhance clustering performance. First, the expression levels of genes are decomposed into multiple Gaussian components. Then, a novel gene correlation calculation method is proposed to measure the relationship between genes from the perspective of distribution. Finally, a permutation-based approach is proposed to determine the threshold of gene importance to obtain marker gene subsets. Compared with state-of-the-art feature selection methods, applying FEED on various scRNA-seq datasets including large datasets followed by different common clustering algorithms results in significant improvements in the accuracy of cell-type identification. The source codes for FEED are freely available at https://github.com/genemine/FEED.
RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome
Authors: Jiang Yue , Hu Xuejiao , Fan Shu , Liu Weijiang , Chen Jingjing , Wang Liang , Deng Qianyun , Yang Jing , Yang Aimei , Lou Zheng , Guan Yuanlin , Xia Han , Gu Bing 
Published: November 2023

Abstract
Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from the metagenomic data of clinical samples. Here, we developed a Reads-based Virulence Factors Scanner (RVFScan), an innovative user-friendly online tool that integrates a comprehensive VFG database with similarity matrix-based criteria for VFG prediction and annotation using metagenomic data without the need for assembly. RVFScan demonstrated superior performance compared to previous assembly-based and read-based VFG predictors, achieving a sensitivity of 97%, specificity of 98% and accuracy of 98%. We also conducted a large-scale analysis of 2425 clinical metagenomic datasets to investigate the utility of RVFScan, the species-specific VFG profiles and associations between VFGs and virulence phenotypes for 24 important pathogens were analyzed. By combining genomic comparisons and network analysis, we identified 53 VFGs with significantly higher abundances in hypervirulent Klebsiella pneumoniae (hvKp) than in classical K. pneumoniae. Furthermore, a cohort of 1256 samples suspected of K. pneumoniae infection demonstrated that RVFScan could identify hvKp with a sensitivity of 90%, specificity of 100% and accuracy of 98.73%, with 90% of hvKp samples consistent with clinical diagnosis (Cohen’s kappa, 0.94). RVFScan has the potential to detect VFGs in low-biomass and high-complexity clinical samples using metagenomic reads without assembly. This capability facilitates the rapid identification and targeted treatment of hvKp infections and holds promise for application to other hypervirulent pathogens.
Enhanced annotation of CD45RA to distinguish T cell subsets in single-cell RNA-seq via machine learning
Authors: Ran Ran , Brubaker Douglas K 
Published: November 2023

AbstractMotivationT cell heterogeneity presents a challenge for accurate cell identification, understanding their inherent plasticity, and characterizing their critical role in adaptive immunity. Immunologists have traditionally employed techniques such as flow cytometry to identify T cell subtypes based on a well-established set of surface protein markers. With the advent of single-cell RNA sequencing (scRNA-seq), researchers can now investigate the gene expression profiles of these surface proteins at the single-cell level. The insights gleaned from these profiles offer valuable clues and a deeper understanding of cell identity. However, CD45RA, the isoform of CD45 which distinguishes between naive/central memory T cells and effector memory/effector memory cells re-expressing CD45RA T cells, cannot be well profiled by scRNA-seq due to the difficulty in mapping short reads to genes.ResultsIn order to facilitate cell-type annotation in T cell scRNA-seq analysis, we employed machine learning and trained a CD45RA+/− classifier on single-cell mRNA count data annotated with known CD45RA antibody levels provided by cellular indexing of transcriptomes and epitopes sequencing data. Among all the algorithms we tested, the trained support vector machine with a radial basis function kernel with optimized hyperparameters achieved a 99.96% accuracy on an unseen dataset. The multilayer perceptron classifier, the second most predictive method overall, also achieved a decent accuracy of 99.74%. Our simple yet robust machine learning approach provides a valid inference on the CD45RA level, assisting the cell identity annotation and further exploring the heterogeneity within human T cells. Based on the overall performance, we chose the support vector machine with a radial basis function kernel as the model implemented in our Python package scCD45RA.Availability and implementationThe resultant package scCD45RA can be found at https://github.com/BrubakerLab/ScCD45RA and can be installed from the Python Package Index (PyPI) using the command “pip install sccd45ra.”
aaHash: recursive amino acid sequence hashing
Authors: Wong Johnathan , Kazemi Parham , Coombe Lauren , Warren René L , Birol Inanç 
Published: November 2023

Abstract

Motivation
K-mer hashing is a common operation in many foundational bioinformatics problems. However, generic string hashing algorithms are not optimized for this application. Strings in bioinformatics use specific alphabets, a trait leveraged for nucleic acid sequences in earlier work. We note that amino acid sequences, with complexities and context that cannot be captured by generic hashing algorithms, can also benefit from a domain-specific hashing algorithm. Such a hashing algorithm can accelerate and improve the sensitivity of bioinformatics applications developed for protein sequences.

Results
Here, we present aaHash, a recursive hashing algorithm tailored for amino acid sequences. This algorithm utilizes multiple hash levels to represent biochemical similarities between amino acids. aaHash performs ∼10× faster than generic string hashing algorithms in hashing adjacent k-mers.

Availability and implementation
aaHash is available online at https://github.com/bcgsc/btllib and is free for academic use.