bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracing References: Re-dating and Interpreting Abel-Rémusat’s Chinese-French Dictionary Manuscript Dictionnaire chinois
Authors: Li Rui , Hansen Annette Skovsted 
Published: January 2022

Abstract
This study presents answers to the question of how one dictionary can help us understand the implications for lexicography of limited access to other dictionaries. We carefully analyzed the microstructure and macrostructure of Abel-Rémusat’s Chinese-French dictionary manuscript Dictionnaire chinois dated 1808 by systematically tracing the references noted at each entry in the dictionary. Based on his meticulous references to a large variety of Chinese language sources, this article confirms that Abel-Rémusat finished his first draft in 1808. However, tracing the references to a wide variety of sources including many references to Dictionnaire chinois, français et latin [Chinese, French, and Latin Dictionary, 1813], published in 1813 by Chrétien-Louis-Joseph de Guignes (1759–1845), we re-date the manuscript. This discovery allowed us to understand how Abel-Rémusat 1) used different types of resources when dictionaries of Chinese and various European languages were unavailable and 2) compensated initially by inventing his own macrostructure, microstructure and systems for retrieving Chinese characters until he could consult other dictionaries that offered him guidance and inspired him to make corrections in his manuscript. Our findings show how the resources available determined his approach to lexicography and lead us to conclude that he gradually developed his approach based on a combination of inspiration from and confusion caused by the limited, but very diverse resources, he located and referenced.
Islam and Suicide Terrorism: An Empirical Analysis
Authors: Choi Seung-Whan , Brown Davis 
Published: January 2022

AbstractWhether Islam is responsible for increased suicide terrorist attacks is a salient but highly controversial issue. Using independently produced demographics data, we investigate whether there is a correlation between Islam and suicide attacks. We find that (1) countries with greater Muslim populations are likely to experience more suicide attacks, (2) countries with greater Sunni Muslim populations are likely to encounter more suicide attacks, and (3) countries with greater Hanafi Muslim populations, in contrast to other Sunni legal schools, face the greatest risk of experiencing suicide attacks. The overall analysis suggests that Islam is positively associated with suicide attacks, although the degree of its association is not uniform among all branches.
Weaponizing Language: Linguistic Vectors of Ethnic Oppression
Authors: Dubinsky Stanley , Starr Harvey 
Published: January 2022

AbstractAs part of a larger project studying language conflict, this paper documents ways in which the oppression of language use on the part of a dominant language/ethnic group is instrumentalized as a tool to inflict gratuitous societal pain and punishment upon nondominant ethnolinguistic groups and their individual members. Our arguments will be illustrated primarily by three contemporary cases: (1) the Uyghur minority in the PRC, (2) the Kurdish minority in Turkey, and (3) the Hungarian minority in Slovakia. This article also seeks to provide an example of ways in which important empirical questions in the political science/international relations literature might be more fully addressed with the help of linguistics, which is a focus of our ongoing language conflict project.
Curating the Profane: Johann Joachim Winckelmann, Neoclassical Art Historian and First Curator of a Public Profane Museum
Authors: Ruprecht Louis Arthur 
Published: January 2022

Abstract
Few contemporary visitors to public art museums consider the religious oddity of most such collections at their inception. From the so-called Elgin Marbles in the British Museum, to the Winged Victory of Samothrace in the Louvre, and the Apollo Belvedere and Laocoön Group in the Vatican Museums, classical statuary constituted the heart (if not the soul) of most public art museums in the first several generations of the “museum era.” In this article, I present archival evidence from the Vatican Library and the Vatican Library’s Secret Archives confirming that Johann Joachim Winckelmann (1717–1768), better known as a neoclassical evangelist and art historian, was also the semi-secret curator of the Vatican’s first “Profane Museum.” Founded in 1767, expanded and completed in 1792, looted by French Revolutionaries in 1797, and repatriated in 1818, this museum first “curated the profane,” enabling the domestication of pagan idols, first in the name of fine art and later in the name of national treasure. It thereby offered a casual flirtation with pagan form that would have a very long subsequent cultural reach and influence.
Integrating landmark modeling framework and machine learning algorithms for dynamic prediction of tuberculosis treatment outcomes
Authors: Kheirandish Maryam , Catanzaro Donald , Crudu Valeriu , Zhang Shengfan 
Published: January 2022

AbstractObjectiveThis study aims to establish an informative dynamic prediction model of treatment outcomes using follow-up records of tuberculosis (TB) patients, which can timely detect cases when the current treatment plan may not be effective.Materials and MethodsWe used 122 267 follow-up records from 17 958 new cases of pulmonary TB in the Republic of Moldova. A dynamic prediction framework integrating landmark modeling and machine learning algorithms was designed to predict patient outcomes during the course of treatment. Sensitivity and positive predictive value (PPV) were calculated to evaluate performance of the model at critical time points. New measures were defined to determine when follow-up laboratory tests should be conducted to obtain most informative results.ResultsThe random-forest algorithm performed better than support vector machine and penalized multinomial logistic regression models for predicting TB treatment outcomes. For all 3 outcome classes (ie, cured, not cured, and died after 24 months following treatment initiation), sensitivity and PPV of prediction models improved as more follow-up information was collected. Specifically, sensitivity and PPV increased from 0.55 to 0.84 and from 0.32 to 0.88, respectively, for the not cured class.ConclusionThe dynamic prediction framework utilizes longitudinal laboratory test results to predict patient outcomes at various landmarks. Sputum culture and smear results are among the important variables for prediction; however, the most recent sputum result is not always the most informative one. This framework can potentially facilitate a more effective treatment monitoring program and provide insights for policymakers toward improved guidelines on follow-up tests.
‘C-type’ closed state and gating mechanisms of K2P channels revealed by conformational changes of the TREK-1 channel
Authors: Zhang Qiansen , Fu Jie , Zhang Shaoying , Guo Peipei , Liu Shijie , Shen Juwen , Guo Jiangtao , Yang Huaiyu , Yao Xuebiao 
Published: January 2022

ABSTRACTTwo-pore domain potassium (K2P) channels gate primarily within the selectivity filter, termed ‘C-type’ gating. Due to the lack of structural insights into the nonconductive (closed) state, ‘C-type’ gating mechanisms remain elusive. Here, molecular dynamics (MD) simulations on TREK-1, a K2P channel, revealed that M4 helix movements induce filter closing in a novel ‘deeper-down’ structure that represents a ‘C-type’ closed state. The ‘down’ structure does not represent the closed state as previously proposed and instead acts as an intermediate state in gating. The study identified the allosteric ‘seesaw’ mechanism of M4 helix movements in modulating filter closing. Finally, guided by this recognition of K2P gating mechanisms, MD simulations revealed that gain-of-function mutations and small-molecule activators activate TREK-1 by perturbing state transitions from open to closed states. Together, we reveal a ‘C-type’ closed state and provide mechanical insights into gating procedures and allosteric regulations for K2P channels.
Inhibiting DHN- and DOPA-melanin biosynthesis pathway increased the therapeutic value of itraconazole in Madurella mycetomatis infected Galleria mellonella
Authors: Lim Wilson , Konings Mickey , Parel Florianne , Eadie Kimberly , Strepis Nikolaos , Fahal Ahmed , Verbon Annelies , van de Sande Wendy W J 
Published: January 2022

Abstract

Eumycetoma is a neglected tropical disease, and Madurella mycetomatis, the most common causative agent of this disease forms black grains in hosts. Melanin was discovered to be one of the constituents in grains. Melanins are hydrophobic, macromolecular pigments formed by oxidative polymerisation of phenolic or indolic compounds. M. mycetomatis was previously known to produce DHN-melanin and pyomelanin in vitro. These melanin was also discovered to decrease M. mycetomatis’s susceptibility to antifungals itraconazole and ketoconazole in vitro. These findings, however, have not been confirmed in vivo. To discover the melanin biosynthesis pathways used by M. mycetomatis in vivo and to determine if inhibiting melanin production would increase M. mycetomatis's susceptibility to itraconazole, inhibitors targeting DHN-, DOPA- and pyomelanin were used. Treatment with DHN-melanin inhibitors tricyclazole, carpropamid, fenoxanil and DOPA-melanin inhibitor glyphosate in M. mycetomatis infected Galleria mellonella larvae resulted in presence of non-melanized grains. Our finding suggested that M. mycetomatis is able to produce DOPA-melanin in vivo. Inhibiting DHN-melanin with carpropamid in combination with the antifungal itraconazole also significantly increased larvae survival. Our results suggested that combination treatment of antifungals and melanin inhibitors can be an alternative treatment strategy that can be further explored. Since the common black-grain eumycetoma causing agents uses similar melanin biosynthesis pathways, this strategy may be applied to them and other eumycetoma causative agents.

Lay Summary
Melanin protects fungi from environmental stress and antifungals. We have discovered that Madurella mycetomatis produces DHN-, pyomelanin and DOPA-melanin in vivo. Inhibiting M. mycetomatis DHN-melanin biosynthesis increases therapeutic value of the antifungal itraconazole in vivo.
Ultraluminous high-redshift quasars from SkyMapper – II. New quasars and the bright end of the luminosity function
Authors: Onken Christopher A , Wolf Christian , Bian Fuyan , Fan Xiaohui , Hon Wei Jeat , Raithel David , Tisserand Patrick , Lai Samuel 
Published: January 2022

ABSTRACT
We search for ultraluminous Quasi-Stellar Objects (QSOs) at high redshift using photometry from the SkyMapper Southern Survey Data Release 3 (DR3), in combination with 2MASS, VHS DR6, VIKING DR5, AllWISE, and CatWISE2020, as well as parallaxes and proper motions from Gaia DR2 and eDR3. We report 142 newly discovered Southern QSOs at 3.8 &lt; z &lt; 5.5, of which 126 have M145 &lt; −27 AB mag and are found in a search area of 14 486 deg2. This Southern sample, utilizing the Gaia astrometry to offset wider photometric colour criteria, achieves unprecedented completeness for an ultraluminous QSO search at high redshift. In combination with already known QSOs, we construct a sample that is &gt;80 per cent complete for M145 &lt; −27.33 AB mag at z = 4.7 and for M145 &lt; −27.73 AB mag at z = 5.4. We derive the bright end of the QSO luminosity function at rest frame 145 nm for z = 4.7–5.4 and measure its slope to be β = −3.60 ± 0.37 and β = −3.38 ± 0.32 for two different estimates of the faint-end QSO density adopted from the literature. We also present the first z ∼ 5 QSO luminosity function at rest frame 300 nm.
A new photometric study of M14 (NGC 6402): an interpretation of the horizontal branch and beyond
Authors: Yepez M A , Arellano Ferro A , Deras D , Bustos Fierro I , Muneer S , Schröder K-P 
Published: January 2022

ABSTRACT
We present a CCD VI photometric study of the globular cluster M14. Particular attention is given to the variable stars. This allowed new classifications and cluster membership considerations. New variables are reported: 3 RRc, 18 SR, and 1 SX Phe. The Fourier decomposition of RR Lyrae light curves lead to the mean cluster metallicity of [Fe/H]ZW = −1.3 ± 0.2. Several independent methods yield a mean distance of 9.36 ± 0.16 kpc. A colour–magnitude diagram outlined by the cluster members enabled a matching with theoretical predictions of isochrones and zero-age horizontal branches (HBs), whose fitting to the observations is in good agreement with the above distance and metallicity. The Oosterhoff type of M14 is confirmed as Oo-int, and the pulsating mode distribution of RR Lyrae stars on the HB shows that the bimodal region of the instability strip is shared by RRab and RRc stars. By modelling the mass-loss at the red giant branch after the He flash events, we were able to represent the blue tail of the HB, using a core mass of 0.48 M⊙ and total masses of 0.52–0.55 M⊙. A progenitor star on the main sequence (MS) of 0.84 M⊙ reaches the HB in about 12.5 Gyr, consonant with previous age determinations of the cluster. Type II Cepheids of M14 may be interpreted as products of post-HB evolution, driven by the complex processes involving the burning of the very thin low mass hydrogen and helium shells of these stars and their minuscule envelopes. No pieces of evidence were found in favour of M14 being of extragalactic origin.
An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias
Authors: Latrille Thibault , Lartillot Nicolas 
Published: January 2022

Abstract
Phylogenetic codon models are routinely used to characterize selective regimes in coding sequences. Their parametric design, however, is still a matter of debate, in particular concerning the question of how to account for differing nucleotide frequencies and substitution rates. This problem relates to the fact that nucleotide composition in protein-coding sequences is the result of the interactions between mutation and selection. In particular, because of the structure of the genetic code, the nucleotide composition differs between the three coding positions, with the third position showing a more extreme composition. Yet, phylogenetic codon models do not correctly capture this phenomenon and instead predict that the nucleotide composition should be the same for all three positions. Alternatively, some models allow for different nucleotide rates at the three positions, an approach conflating the effects of mutation and selection on nucleotide composition. In practice, it results in inaccurate estimation of the strength of selection. Conceptually, the problem comes from the fact that phylogenetic codon models do not correctly capture the fixation bias acting against the mutational pressure at the mutation–selection equilibrium. To address this problem and to more accurately identify mutation rates and selection strength, we present an improved codon modeling approach where the fixation rate is not seen as a scalar, but as a tensor. This approach gives an accurate representation of how mutation and selection oppose each other at equilibrium and yields a reliable estimate of the mutational process, while disentangling the mean fixation probabilities prevailing in different mutational directions.
A Collaborative Classroom Investigation of the Evolution of SABATH Methyltransferase Substrate Preference Shifts over 120 My of Flowering Plant History
Authors: Dubs Nicole M , Davis Breck R , de Brito Victor , Colebrook Kate C , Tiefel Ian J , Nakayama Madison B , Huang Ruiqi , Ledvina Audrey E , Hack Samantha J , Inkelaar Brent , Martins Talline R , Aartila Sarah M , Albritton Kelli S , Almuhanna Sarah , Arnoldi Ryan J , Austin Clara K , Battle Amber C , Begeman Gregory R , Bickings Caitlin M , Bradfield Jonathon T , Branch Eric C , Conti Eric P , Cooley Breana , Dotson Nicole M , Evans Cheyone J , Fries Amber S , Gilbert Ivan G , Hillier Weston D , Huang Pornkamol , Hyde Kaitlin W , Jevtovic Filip , Johnson Mark C , Keeler Julie L , Lam Albert , Leach Kyle M , Livsey Jeremy D , Lo Jonathan T , Loney Kevin R , Martin Nich W , Mazahem Amber S , Mokris Aurora N , Nichols Destiny M , Ojha Ruchi , Okorafor Nnanna N , Paris Joshua R , Reboucas Thais Fuscaldi , Sant’Anna Pedro Beretta , Seitz Mathew R , Seymour Nathan R , Slaski Lila K , Stemaly Stephen O , Ulrich Benjamin R , Van Meter Emile N , Young Meghan L , Barkman Todd J 
Published: January 2022

Abstract
Next-generation sequencing has resulted in an explosion of available data, much of which remains unstudied in terms of biochemical function; yet, experimental characterization of these sequences has the potential to provide unprecedented insight into the evolution of enzyme activity. One way to make inroads into the experimental study of the voluminous data available is to engage students by integrating teaching and research in a college classroom such that eventually hundreds or thousands of enzymes may be characterized. In this study, we capitalize on this potential to focus on SABATH methyltransferase enzymes that have been shown to methylate the important plant hormone, salicylic acid (SA), to form methyl salicylate. We analyze data from 76 enzymes of flowering plant species in 23 orders and 41 families to investigate how widely conserved substrate preference is for SA methyltransferase orthologs. We find a high degree of conservation of substrate preference for SA over the structurally similar metabolite, benzoic acid, with recent switches that appear to be associated with gene duplication and at least three cases of functional compensation by paralogous enzymes. The presence of Met in active site position 150 is a useful predictor of SA methylation preference in SABATH methyltransferases but enzymes with other residues in the homologous position show the same substrate preference. Although our dense and systematic sampling of SABATH enzymes across angiosperms has revealed novel insights, this is merely the “tip of the iceberg” since thousands of sequences remain uncharacterized in this enzyme family alone.
53BP1-ACLY-SLBP-coordinated activation of replication-dependent histone biogenesis maintains genomic integrity
Authors: Wu TingTing , Jun Semo , Choi Eun-Ji , Sun Jiao , Yang Eun-Bi , Lee Hyun-Seo , Kim Sang-Yong , Fahmi Naima Ahmed , Jiang Qibing , Zhang Wei , Yong Jeongsik , Lee Jung-Hee , You Ho Jin 
Published: January 2022

Abstract
p53-binding protein 1 (53BP1) regulates the DNA double-strand break (DSB) repair pathway and maintains genomic integrity. Here we found that 53BP1 functions as a molecular scaffold for the nucleoside diphosphate kinase-mediated phosphorylation of ATP-citrate lyase (ACLY) which enhances the ACLY activity. This functional association is critical for promoting global histone acetylation and subsequent transcriptome-wide alterations in gene expression. Specifically, expression of a replication-dependent histone biogenesis factor, stem-loop binding protein (SLBP), is dependent upon 53BP1-ACLY-controlled acetylation at the SLBP promoter. This chain of regulation events carried out by 53BP1, ACLY, and SLBP is crucial for both quantitative and qualitative histone biogenesis as well as for the preservation of genomic integrity. Collectively, our findings reveal a previously unknown role for 53BP1 in coordinating replication-dependent histone biogenesis and highlight a DNA repair-independent function in the maintenance of genomic stability through a regulatory network that includes ACLY and SLBP.
Radiation-induced neuroinflammation: a potential protective role for poly(ADP-ribose) polymerase inhibitors?
Authors: Gutierrez-Quintana Rodrigo , Walker David J , Williams Kaye J , Forster Duncan M , Chalmers Anthony J 
Published: January 2022

AbstractRadiotherapy (RT) plays a fundamental role in the treatment of glioblastoma (GBM). GBM are notoriously invasive and harbor a subpopulation of cells with stem-like features which exhibit upregulation of the DNA damage response (DDR) and are radioresistant. High radiation doses are therefore delivered to large brain volumes and are known to extend survival but also cause delayed toxicity with 50%–90% of patients developing neurocognitive dysfunction. Emerging evidence identifies neuroinflammation as a critical mediator of the adverse effects of RT on cognitive function. In addition to its well-established role in promoting repair of radiation-induced DNA damage, activation of poly(ADP-ribose) polymerase (PARP) can exacerbate neuroinflammation by promoting secretion of inflammatory mediators. Therefore, PARP represents an intriguing mechanistic link between radiation-induced activation of the DDR and subsequent neuroinflammation. PARP inhibitors (PARPi) have emerged as promising new agents for GBM when given in combination with RT, with multiple preclinical studies demonstrating radiosensitizing effects and at least 3 compounds being evaluated in clinical trials. We propose that concomitant use of PARPi could reduce radiation-induced neuroinflammation and reduce the severity of radiation-induced cognitive dysfunction while at the same time improving tumor control by enhancing radiosensitivity.
Surrogacy Beyond Prognosis: The Importance of “Trial-Level” Surrogacy
Authors: Buyse Marc , Saad Everardo D , Burzykowski Tomasz , Regan Meredith M , Sweeney Christopher S 
Published: January 2022

Abstract
Many candidate surrogate endpoints are currently assessed using a 2-level statistical approach, which consists in checking whether (1) the potential surrogate is associated with the final endpoint in individual patients and (2) the effect of treatment on the surrogate can be used to reliably predict the effect of treatment on the final endpoint. In some situations, condition (1) is fulfilled but condition (2) is not. We use concepts of causal inference to explain this apparently paradoxical situation, illustrating this review with 2 contrasting examples in operable breast cancer: the example of pathological complete response (pCR) and that of disease-free survival (DFS). In a previous meta-analysis, pCR has been shown to be a strong and independent prognostic factor for event-free survival (EFS) and overall survival (OS) after neoadjuvant treatment of operable breast cancer. Yet, in randomized trials, the effects of experimental treatments on pCR have not translated into predictable effects on EFS or OS, making pCR an “individual-level” surrogate, but not a “trial-level” surrogate. In contrast, DFS has been shown to be an acceptable surrogate for OS at both the individual and trial levels in early, HER2-positive breast cancer. The distinction between the prognostic and predictive roles of a tentative surrogate, not always made in the literature, avoids unnecessary confusion and allows better understanding of what it takes to validate a surrogate endpoint that is truly able to replace a final endpoint.