bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sinai Arabic MS 68: A Multidisciplinary Approach to the Study of a Unique Arabic Gospel Manuscript
Authors: Stokes Phillip W , Abou-Khatwa Noha , Leube Georg 
Published: August 2024

Abstract
The study of the Bible in Arabic has become a topic of increasing interest among scholars of the intellectual history of the Islamic world, as well as Christianity in areas under Islamic rule. Nevertheless, most Arabic Bible manuscripts remain largely, or even totally, unstudied. While the textual and theological dimensions of these translations are attracting increasing scholarly attention, their linguistic analysis remains dominated by a traditionalist approach now completely outdated. This paper has two goals, one descriptive and one methodological. First, we aim to fully describe the Arabic Gospel manuscript Sinai Arabic MS 68, traditionally dated to the 14th century CE but which we date to the 16th century CE, perhaps in the aftermath of the fall of the Mamluk empire. Our description focuses on the linguistic nature of the manuscript, but includes discussions of its history and materiality as well. Second, we propose a methodological approach to studying the language of the text that takes seriously non-Classical components and contextualizes these features within what is known from other such non-Classical compositions, including especially Christian manuscripts. We conclude that the manuscript was produced by artisans and a scribe with significant courtly experience, and shows evidence of multiple normative linguistic registers, which argues strongly for the importance of broadening the framework within which scholars interpret such ‘Middle Arabic’ texts.
Children's Rhymes and Nature in Mehri, A Modern South Arabian Language
Authors: Al-Qumairi Saeed , Boom Andrea , Watson Janet C E 
Published: August 2024

Abstract
In many parts of the developed and developing world, traditional children's rhymes are under threat. The disappearance of these traditional rhymes could impact children's phonological development (Di Liberto et al., 2023, Harper, 2011), awareness of their natural environment, and their appreciation (and later composition) of poetry by older speakers. While rhymes in literate societies are often documented and can thus can be retrieved, this is not the case for the Mahrah and other exclusively oral societies. In this paper, we examine traditional children's rhymes in Mehri, an endangered Modern South Arabian language (MSAL), focusing on rhymes and riddles and the significance of their impending loss within al-Mahrah governorate in Yemen. We conclude by suggesting ways in which the Mehri community, in collaboration with native-speaker and non-native-speaker researchers, can revitalize this genre of poetry.
Chrysanthemum lavandulifolium homolog CYCLIN A2;1 modulates cell division in ray florets
Authors: Zhang Peng , Wang Yahui , Wang Zhimin , Di Shengqiang , Zhang Xinyi , Ma Di , Bao Zhilong , Ma Fangfang 
Published: August 2024

Abstract
The morphology of ray florets in chrysanthemums is tightly associated with cell division and expansion, both of which require proper progression of the cell cycle. Here, we identified a Chrysanthemum lavandulifolium homolog, CYCLIN A2;1 (CYCA2;1), the expression of which in ray florets is negatively correlated with petal width. We found that CYC2a, a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor in the CYCLOIDEA2 (CYC2) family, interacts with and stabilizes CYC2b, and the latter can bind to the promoter of CYCA2;1 to activate its transcription. Overexpression of CYCA2;1 in C. lavandulifolium reduced the size of capitula and ray florets. Cytological analysis revealed that CYCA2;1 overexpression inhibited both cell division and expansion via repression of the mitotic cell cycle in ray florets, the latitudinal development of which was more relatively negatively influenced, thereby leading to increased ratios of petal length to width at later developmental stages. Yeast two-hybrid library screening revealed multiple proteins that interacted with CYCA2;1 including ACTIN-RELATED PROTEIN7 (ARP7), and silencing ARP7 inhibited the development of ray florets. Co-immunoprecipitation assays confirmed that CYCA2;1 could induce the degradation of ARP7 to inhibit the development of ray florets. Taken together, our results indicate the presence of a regulatory network in ray floret development in chrysanthemum consisting of CYC2b–CYCA2;1–ARP7 that acts via governing mitosis. The identification of this network has the potential to facilitate breeding efforts targeted at producing novel ornamental traits in the flowers.
Analytical evaluation of the automated interleukin-6 assay on the Roche cobas e602 analyzer
Authors: Gant Kanegusuku Anastasia , Carll Timothy , Yeo Kiang-Teck J 
Published: August 2024

Abstract

Background
Interleukin-6 (IL-6) is a proinflammatory cytokine that is associated with many inflammatory diseases. This validation study evaluates the automated Roche Elecsys IL-6 electrochemiluminescent immunoassay that has been granted emergency use authorization by the US Food and Drug Administration.

Methods
The Elecsys IL-6 assay was evaluated for precision, linearity, interference (by hemoglobin, bilirubin, triglycerides, and biotin) and clinical performance was compared to the V-PLEX Human IL-6 immunoassay (Meso Scale Discovery), performed by a reference laboratory.

Results
The Elecsys IL-6 assay is precise (intra-assay &lt;3% coefficient of variation [CV], interassay &lt;5% CV), exhibits an analytical measurable range of 1.5-4790 pg/mL, and is tolerant of significant interferences (H &lt; 2522, I &lt;62, L&lt;2101, biotin &lt;50 ng/mL). Comparison with the V-PLEX assay revealed a 2.95 slope bias in patient samples evaluated for IL-6 concentration (n = 43, range = 1.5-1891 pg/mL, y = 2.95x – 32.7, r2 = 0.84). Bland-Altman analysis revealed an absolute mean bias of 152 pg/mL (SD = 254 pg/mL), or a mean percentage difference of 73%.

Conclusion
The Roche IL-6 assay showed good analytical performance. The large systematic bias compared with another reference method precludes using multiple methods to monitor IL-6 response. The random-access nature of an automated IL-6 assay on the Roche platform makes the test available on demand.
Perpetrator knowledge: a Bayesian account
Authors: Jellema Hylke 
Published: August 2024

Abstract
Perpetrator knowledge (also known as “guilty knowledge,” “insider knowledge,” “crime knowledge,” or “first-hand knowledge”) is an important, but undertheorized type of criminal evidence. This article clarifies this concept in several ways. First, it offers a precise, probabilistic definition of what perpetrator knowledge is. Second, the article provides a taxonomy of arguments relating to perpetrator knowledge. This classification is based on an analysis of 438 Dutch criminal cases in which this concept was mentioned. Third, it models these arguments using Bayesian networks. Fourth, the article explains a potential reasoning error relating to perpetrator knowledge, namely the fallacy of appeal to probability.
Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method
Authors: Zhou Ziyou , Zhu Fei , Ma Shiyang , Tan Caixia , Yang Hang , Zhang Peipei , Xu Yizhong , Qin Rongliu , Luo Yuying , Chen Jie , Pan Pinhua 
Published: August 2024

Abstract
Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 ( and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines.
Mycology laboratory diagnostic capacity for invasive fungal diseases in public hospitals in Vietnam
Authors: Hieu Vu Ngoc , Hiep Nguyen Le , Hang Le Minh , Lau-Goodchild Bianca A , Van Duong Nguyen , Linh Nguyen Thuy , Beardsley Justin , Dat Vu Quoc 
Published: August 2024

Abstract
This was a cross-sectional study on the availability of laboratory infrastructure and capacity for the diagnosis of invasive fungal diseases in 24 public hospitals in Vietnam in 2023. Among the hospitals surveyed, 66.7% (14/21) had specialized personnel assigned for mycology testing, and 95.8% (23/24) had a separate microbiology laboratory space. Microscopy and culture methods are available in nearly all laboratories for isolate identification. Antifungal susceptibility testing is only performed for yeasts in 16/24 (66.7%) laboratories. Non-culture methods are hardly used in laboratories. Strengthening local laboratory capacities is essential to meeting health needs in these endemic regions.
Gas permeability and mechanical properties of dust grain aggregates at hyper- and zero-gravity
Authors: Capelo Holly L , Bodénan Jean-David , Jutzi Martin , Kühn Jonas , Cerubini Romain , Jost Bernhard , Stöckli Linus , Spadaccia Stefano , Herny Clemence , Gundlach Bastian , Kargl Günter , Surville Clément , Mayer Lucio , Schönbächler Maria , Thomas Nicolas , Pommerol Antoine 
Published: August 2024

ABSTRACT
Particle–particle and particle–gas processes significantly impact planetary precursors such as dust aggregates and planetesimals. We investigate gas permeability ($\kappa$) in 12 granular samples, mimicking planetesimal dust regoliths. Using parabolic flights, this study assesses how gravitational compression – and lack thereof – influences gas permeation, impacting the equilibrium state of low-gravity objects. Transitioning between micro- and hyper-gravity induces granular sedimentation dynamics, revealing collective dust–grain aerodynamics. Our experiments measure $\kappa$ across Knudsen number (Kn) ranges, reflecting transitional flow. Using mass and momentum conservation, we derive $\kappa$ and calculate pressure gradients within the granular matrix. Key findings: (i) As confinement pressure increases with gravitational load and mass flow, $\kappa$ and average pore space decrease. This implies that a planetesimal’s unique dust-compaction history limits subsurface volatile outflows. (ii) The derived pressure gradient enables tensile strength determination for asteroid regolith simulants with cohesion. This offers a unique approach to studying dust-layer properties when suspended in confinement pressures comparable to the equilibrium state on planetesimals surfaces, which will be valuable for modelling their collisional evolution. (iii) We observe a dynamical flow symmetry breaking when granular material moves against the pressure gradient. This occurs even at low Reynolds numbers, suggesting that Stokes numbers for drifting dust aggregates near the Stokes–Epstein transition require a drag force modification based on permeability.
V407 Lup, an intermediate polar nova
Authors: Orio M , Melicherčík M , Ciroi S , Canton V , Aydi E , Buckley D A H , Dobrotka A , Luna G J M , Ness J 
Published: August 2024

ABSTRACT
We present X-ray and optical observations of nova V407 Lup (Nova Lup 2016), previously well monitored in outburst, as it returned to quiescent accretion. The X-ray light curve in 2020 February revealed a clear flux modulation with a stable period of 564.64 $\pm$ 0.64 s, corresponding to the period measured in outburst and attributed to the spin of a magnetized white dwarf in an intermediate polar (IP) system. This detection in quiescence is consistent with the IP classification proposed after the nova eruption. The XMM–Newton EPIC X-ray flux is ${\simeq} 1.3 \times 10^{-12}$ erg cm$^{-2}$ s$^{-1}$ at a distance, most likely, larger than 5 kpc, emitted in the whole 0.2–12 keV range without a significant cut-off energy. The X-ray spectra are complex; they can be fitted including a power-law component with a relatively flat slope (a power-law index $\simeq$ 1), although, alternatively, a hard thermal component at kT$\ge$ 19 keV also yields a good fit. The SALT optical spectra obtained in 2019 March and 2022 May are quite typical of IPs, with strong emission lines, including some due to a high ionization potential, like He ii at 4685.7 Å. Nebular lines of O [iii] were prominent in 2019 March, but their intensity and equivalent width appeared to be decreasing during that month, and they were no longer detectable in 2022, indicating that the nova ejecta dispersed. Complex profiles of the He ii lines of V407 Lup are also characteristic of IPs, giving further evidence for this classification.
Radiative association for the formation of phosphorus monochloryl cation (PCl+) and aluminium monochloride (AlCl)
Authors: Chen Yang , Lin Xiaohe , Xiao Lidan , Li Zijian , Zhang Songbin , Cheng Yongjun , Wu Yong , de Almeida Amaury A , Andreazza Carmen M , Yan Bing 
Published: August 2024

ABSTRACT
Cross-sections and rate coefficients for the radiative association processes of Al(2P) with Cl(2P) for the formation of aluminium monochloride (AlCl) and P+(3P) with Cl(2P) to form phosphorus monochloryl cation (PCl+) have been estimated as a function of temperature. Rate coefficients have been estimated from cross-sections, which are calculated using a quantum mechanical method. They are found to vary from 4.95 × 10–21 to 4.24 × 10–16 and from 7.10 × 10–18 to 3.50 × 10–17 cm3 s–1 for AlCl and PCl+, respectively, for temperatures ranging from 10 to 15 000 K. The obtained rate constants are fitted with the Arrhenius–Kooij functions for incorporation into astrochemical reaction data bases.
Probing solar wind velocity from simultaneous superior solar conjunction radio science experiments of BepiColombo and Akatsuki missions
Authors: Cappuccio P , Imamura T , Doria I , Chiba S , Stefano I di , Shiota D , Asmar S , Iess L 
Published: August 2024

ABSTRACT
A radio link directly probing the inner solar corona offers the possibility to characterize solar wind properties, including velocity, density, turbulence, and even the axial ratio. In this study, we leveraged radiometric data obtained during a joint superior solar conjunction of the ESA/JAXA BepiColombo mission and the JAXA Akatsuki mission. Our objective is to ascertain the solar wind velocity by analysing Doppler-shift timeseries of radio signals exchanged between the two spacecraft and two distinct ground stations. We conducted a cross-correlation analysis to determine the travel time of large-scale plasma density fluctuations as they intersect with the downlink signals of both spacecraft. This method is applied to the data collected on 2021 March 13 and 2021 March 14. The analysis of the March 13 data has shown that the two Doppler residuals timeseries present a clear correlation at a time-lag of 2910 s. Using the knowledge of the relative distance between the two probe-ground station lines of sight at the closest approach to the Sun, we estimated the solar wind velocity to be $421\pm 21$ km s−1. Following the same procedure for the second experiment, we estimated the solar wind speed velocity to be $336\pm 7$ km s−1. These results are compatible with the sampling of the slow solar wind at heliographic latitudes of $-22^\circ$ and $-26^\circ$, respectively.
Methods for evaluating unsupervised vector representations of genomic regions
Authors: Zheng Guangtao , Rymuza Julia , Gharavi Erfaneh , LeRoy Nathan J , Zhang Aidong , Sheffield Nathan C 
Published: August 2024

Abstract
Representation learning models have become a mainstay of modern genomics. These models are trained to yield vector representations, or embeddings, of various biological entities, such as cells, genes, individuals, or genomic regions. Recent applications of unsupervised embedding approaches have been shown to learn relationships among genomic regions that define functional elements in a genome. Unsupervised representation learning of genomic regions is free of the supervision from curated metadata and can condense rich biological knowledge from publicly available data to region embeddings. However, there exists no method for evaluating the quality of these embeddings in the absence of metadata, making it difficult to assess the reliability of analyses based on the embeddings, and to tune model training to yield optimal results. To bridge this gap, we propose four evaluation metrics: the cluster tendency score (CTS), the reconstruction score (RCS), the genome distance scaling score (GDSS), and the neighborhood preserving score (NPS). The CTS and RCS statistically quantify how well region embeddings can be clustered and how well the embeddings preserve information in training data. The GDSS and NPS exploit the biological tendency of regions close in genomic space to have similar biological functions; they measure how much such information is captured by individual region embeddings in a set. We demonstrate the utility of these statistical and biological scores for evaluating unsupervised genomic region embeddings and provide guidelines for learning reliable embeddings.
Trends in drug development for rare and intractable diseases based on the KEGG NETWORK
Authors: Tanabe Mao , Hirata Makoto , Sakate Ryuichi 
Published: August 2024

Abstract
The pathophysiological mechanisms underlying many rare and intractable diseases remain unclear, and there are few drugs for the treatment of these diseases. An understanding of approved drugs is important to improve drug development. In DDrare (Database of Drug Development for Rare Diseases), the targets of drugs in clinical trials are mapped to the KEGG PATHWAY to be grasped on molecular networks. In this study, to understand the relationship between drug targets and disease genes, we mapped them to the KEGG NETWORK (networks) defined as functionally meaningful segments of pathways. We found that disease genes tended to be included in networks characteristic for each disease group, whereas drug targets were mapped to networks common to many disease groups. The number of drugs targeting the networks containing disease genes was small in every disease group. However, because several studies have recently addressed that the drugs targeting proteins with genetic evidence of disease association are more likely to be approved, we confirmed the results using the KEGG NETWORK and integrating the risk genes obtained from the latest GWAS data. The results were clearer and more detailed than those of previous studies, which suggests a direction for future drug development.
Immune landscape of isocitrate dehydrogenase-stratified primary and recurrent human gliomas
Authors: Gupta Pravesh , Dang Minghao , Oberai Shivangi , Migliozzi Simona , Trivedi Rakesh , Kumar Gayatri , Peshoff Mekenzie , Milam Nancy , Ahmed Aml , Bojja Krishna , Tran Tuan M , Gumin Joy , Kamiya-Matsuoka Carlos , Huse Jason , Cox Kathryn , Li Jianzhuo , Shehwana Huma , Sheth Sameer A , Saxon Rodriguez , Baohua Sun , Parker Kerrigan Brittany , Maheshwari Atul , Parra Cuentas Edwin Roger , Navin Nicholas E , Heimberger Amy B , Lang Frederick F , Iavarone Antonio , Clise-Dwyer Karen , Wang Linghua , Bhat Krishna P 
Published: August 2024

Abstract

Background
Human gliomas are classified using isocitrate dehydrogenase (IDH) status as a prognosticator; however, the influence of genetic differences and treatment effects on ensuing immunity remains unclear.

Methods
In this study, we used sequential single-cell transcriptomics on 144 678 and spectral cytometry on over 2 million immune cells encompassing 48 human gliomas to decipher their immune landscape.

Results
We identified 22 distinct immune cell types that contribute to glioma immunity. Specifically, brain-resident microglia (MG) were reduced with a concomitant increase in CD8+ T lymphocytes during glioma recurrence independent of IDH status. In contrast, IDH-wild type-associated patterns, such as an abundance of antigen-presenting cell-like MG and cytotoxic CD8+ T cells, were observed. Beyond elucidating the differences in IDH, relapse, and treatment-associated immunity, we discovered novel inflammatory MG subpopulations expressing granulysin, a cytotoxic peptide that is otherwise expressed in lymphocytes only. Furthermore, we provide a robust genomic framework for defining macrophage polarization beyond M1/M2 paradigm and reference signatures of glioma-specific tumor immune microenvironment (termed GlioTIME-36) for deconvoluting transcriptomic datasets.

Conclusions
This study provides advanced optics of the human pan-glioma immune contexture as a valuable guide for translational and clinical applications.
Macrophage migration inhibitory factor as a therapeutic target in neuro-oncology: A review
Authors: Jarmula Jakub , Lee Juyeun , Lauko Adam , Rajappa Prajwal , Grabowski Matthew M , Dhawan Andrew , Chen Peiwen , Bucala Richard , Vogelbaum Michael A , Lathia Justin D 
Published: August 2024

AbstractPrimary central nervous system (CNS) tumors affect tens of thousands of patients each year, and there is a significant need for new treatments. Macrophage migration inhibitory factor (MIF) is a cytokine implicated in multiple tumorigenic processes such as cell proliferation, vascularization, and immune evasion and is therefore a promising therapeutic target in primary CNS tumors. There are several MIF-directed treatments available, including small-molecule inhibitors, peptide drugs, and monoclonal antibodies. However, only a small number of these drugs have been tested in preclinical models of primary CNS tumors, and even fewer have been studied in patients. Moreover, the brain has unique therapeutic requirements that further make effective targeting challenging. In this review, we summarize the latest functions of MIF in primary CNS tumor initiation and progression. We also discuss advances in MIF therapeutic development and ongoing preclinical studies and clinical trials. Finally, we discuss potential future MIF therapies and the strategies required for successful clinical translation.