bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coda
Authors: Wills Vanessa Christina 
Published: June 2024

Abstract
This very brief chapter discusses the radical legacy of philosopher Angela Davis. It details her experiences as a professor in the University of California system during the late 1960s, where she was targeted by the Board of Regents due to her Communist Party membership. This chapter highlights the importance of continuing to defend academic freedom in the face of state repression today. The challenges that scholars face, which prevent a serious and productive engagement with Marx’s ideas, come not only from conflicting theoretical commitments and internecine disputes over method, but also from the exercise of legal, economic, and political power aimed squarely at preventing it. Free scholarly inquiry therefore requires engagement with the world both inside and outside of the academy to secure the conditions of its possibility.
The ‘full-flowing stomach’: unwholesome food, climate, and colonialism in King Lear and Kristian Levring’s The King is Alive
Authors: Swanner Seth 
Published: June 2024

Abstract
This article considers Kristian Levring’s 2000 film The King is Alive from a radically open historicist methodology, analysing the film as a product of multiple interleaved archives. An adaptation of King Lear, the film’s relevant archive includes documents from the English Renaissance like the early modern recipe books and seventeenth-century medical treatises that this article uncovers. Yet because The King is Alive was filmed in an abandoned German mining colony in the Namib desert, the archive must also include accounts of the colonialist ‘Scramble for Africa’ more than two centuries after King Lear was written. The methodological deftness of history-as-adaptation allows us to see the film’s anxieties about food that rest at the nexus of these two archives. Shakespeare’s play worries about liminal foods—species-specific foods, foods that fail to nourish, and foods that become poison—but the film updates these concerns to implicate Western imperialism and global capitalism. Surrounded (and, in one instance, killed) by potentially botulistic cans of carrots that remain after the German occupation, the characters in the film must grapple with the toxic leftovers of colonialism, including Shakespeare’s playtext. The film thus asks its audience to consider further archives related to the imperialist roots of the invention of canning, the discovery of vitamins, and the export of Shakespeare as a ‘civilizing’ figure. Finally, the film gestures to the foodway challenges exacerbated by both capitalism and climate change, becoming a palimpsest of archives from across multiple temporalities: a Shakespearean past, a colonialist present, and a warming future.
The Power of Caricature, Caricatures of Power
Authors: Haywood Ian 
Published: June 2024

Abstract
This review article assesses three new books on the “Golden Age” of caricature in Britain and the United States: Tim Clayton’s James Gillray: A Revolution in Satire (2022), Amanda Lahikainen’s Money and Materiality in the Golden Age of Graphic Satire (2022), and Alison M. Stagg’s Prints of a New Kind: Political Caricature in the United States, 1789-1828 (2023). The article considers how satirical cartoons simultaneously educated and entertained the public about important issues, such as political corruption, nation building, and the perils of a credit economy based on paper money.
Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq
Authors: Tong Gregory , Hah Nasun , Martinez Thomas F 
Published: June 2024

Abstract
Accurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease. Empirical identification of translated smORFs is carried out primarily using ribosome profiling (Ribo-seq). While effective, published Ribo-seq datasets can vary drastically in quality and different analysis tools are frequently employed. Here, we examine the impact of these factors on identifying translated smORFs. We compared five commonly used software tools that assess open reading frame translation from Ribo-seq (RibORFv0.1, RibORFv1.0, RiboCode, ORFquant, and Ribo-TISH) and found surprisingly low agreement across all tools. Only ~2% of smORFs were called translated by all five tools, and ~15% by three or more tools when assessing the same high-resolution Ribo-seq dataset. For larger annotated genes, the same analysis showed ~74% agreement across all five tools. We also found that some tools are strongly biased against low-resolution Ribo-seq data, while others are more tolerant. Analyzing Ribo-seq coverage revealed that smORFs detected by more than one tool tend to have higher translation levels and higher fractions of in-frame reads, consistent with what was observed for annotated genes. Together these results support employing multiple tools to identify the most confident microprotein-coding smORFs and choosing the tools based on the quality of the dataset and the planned downstream characterization experiments of the predicted smORFs.
VISH-Pred: an ensemble of fine-tuned ESM models for protein toxicity prediction
Authors: Mall Raghvendra , Singh Ankita , Patel Chirag N , Guirimand Gregory , Castiglione Filippo 
Published: June 2024

Abstract
Peptide- and protein-based therapeutics are becoming a promising treatment regimen for myriad diseases. Toxicity of proteins is the primary hurdle for protein-based therapies. Thus, there is an urgent need for accurate in silico methods for determining toxic proteins to filter the pool of potential candidates. At the same time, it is imperative to precisely identify non-toxic proteins to expand the possibilities for protein-based biologics. To address this challenge, we proposed an ensemble framework, called VISH-Pred, comprising models built by fine-tuning ESM2 transformer models on a large, experimentally validated, curated dataset of protein and peptide toxicities. The primary steps in the VISH-Pred framework are to efficiently estimate protein toxicities taking just the protein sequence as input, employing an under sampling technique to handle the humongous class-imbalance in the data and learning representations from fine-tuned ESM2 protein language models which are then fed to machine learning techniques such as Lightgbm and XGBoost. The VISH-Pred framework is able to correctly identify both peptides/proteins with potential toxicity and non-toxic proteins, achieving a Matthews correlation coefficient of 0.737, 0.716 and 0.322 and F1-score of 0.759, 0.696 and 0.713 on three non-redundant blind tests, respectively, outperforming other methods by over $10\%$ on these quality metrics. Moreover, VISH-Pred achieved the best accuracy and area under receiver operating curve scores on these independent test sets, highlighting the robustness and generalization capability of the framework. By making VISH-Pred available as an easy-to-use web server, we expect it to serve as a valuable asset for future endeavors aimed at discerning the toxicity of peptides and enabling efficient protein-based therapeutics.
Fast and Easy Simultaneous Determination of Riboflavin, Folic Acid, All-Trans-Retinol and α-Tocopherol in Human Serum by LC/MS/MS for Bariatric Patients
Authors: Urinovska Romana , Sistik Pavel , Buzga Marek , Stejskal David 
Published: June 2024

Abstract
The aim of this study was to develop and validate methods for the determination of vitamins B2, B9, E and A in serum using liquid chromatography with mass spectrometry (MS) detection. Vitamin analysis was performed using an ultra performance liquid chromatography combined with tandem MS. The compounds were separated on a BEH C18 RP column (2.1 × 100 mm, 1.7 μm) using a gradient elution with an analysis time of 10 min. Sample preparation included protein precipitation with ethanol. The concentration range in human serum was as follows: riboflavin 5–1000 nmol/L, folic acid 2.5–250 nmol/L, α-tocopherol 0.5–100 μmol/L and all-trans-retinol 25–2500 nmol/L. Accuracy and precision were validated according to Food and Drug Administration guidelines, with coefficients of variation ranging from 3.1–11.7% and recoveries from 94.4–107.5%. Routine monitoring of the complex range of vitamins in bariatric medicine is still not common. This is despite the fact that patients are at risk for glitch deficits, especially of a neurological nature. An analytical method that allows for the complex measurement of both water-soluble and fat-soluble vitamins is important and necessary for the clinical monitoring of bariatric patients. The method we have described could benefit both clinical practice and nutritional research.
Is There a Chinese School of IR Theory?
Authors: Katzenstein Peter J 
Published: June 2024

Abstract
Is there a Chinese School of International Relations (IR) Theory? My answer to this question is ambivalent. Although a Chinese school of IR theory does not exist in the singular, it does exist in the plural. If “birds of a feather flock together,” then the difference in approaches taken by Chinese scholars is as relevant as is the fact that the scholars are all Chinese. The Tsinghua School and moral realism share much with classical realism. Cultural relationalism also offers a distinctive Chinese approach as do Gongsheng/symbiotic and tianxia approaches. That said, Chinese IR scholarship shares with IR scholarship in America, Europe, and the rest of the world its firm anchor in the Newtonian mechanical worldview of the late 19th century. Natural sciences, such as quantum mechanics and scientific cosmology, meanwhile concluded long ago that Newtonianism offers an often practicable yet constricted view of the world. In contrast, the humanities operate with a worldview fully consonant with 20th century physics. It is the social sciences and the analysis of IR which continues to adhere to the mechanical worldview common in the late 19th century—in China and the rest of the world. In both “China” and “the West” IR, scholars are tapping their canes against the pavement, seeking to fathom what will happen next. If historians and semantic modelers are right, like the future, the past is never distant. Always open to reinterpretation, it is like the future—unpredictable.
Macrophage-derived FGFR1 drives atherosclerosis through PLCγ-mediated activation of NF-κB inflammatory signalling pathway
Authors: Wang Lintao , Luo Wu , Zhang Suya , Zhang Junsheng , He Lu , Shi Yifan , Gao Li , Wu Baochuan , Nie Xiaoyan , Hu Chenghong , Han Xue , He Chaoyong , Xu Biao , Liang Guang 
Published: June 2024

Abstract

Aims
Atherosclerosis (AS) is a leading cause of cardiovascular morbidity and mortality. Atherosclerotic lesions show increased levels of proteins associated with the fibroblast growth factor receptor (FGFR) pathway. However, the functional significance and mechanisms governed by FGFR signalling in AS are not known. In the present study, we investigated fibroblast growth factor receptor 1 (FGFR1) signalling in AS development and progression.

Methods and results
Examination of human atherosclerotic lesions and aortas of Apoe−/− mice fed a high-fat diet (HFD) showed increased levels of FGFR1 in macrophages. We deleted myeloid-expressed Fgfr1 in Apoe−/− mice and showed that Fgfr1 deficiency reduces atherosclerotic lesions and lipid accumulations in both male and female mice upon HFD feeding. These protective effects of myeloid Fgfr1 deficiency were also observed when mice with intact FGFR1 were treated with FGFR inhibitor AZD4547. To understand the mechanistic basis of this protection, we harvested macrophages from mice and show that FGFR1 is required for macrophage inflammatory responses and uptake of oxidized LDL. RNA sequencing showed that FGFR1 activity is mediated through phospholipase-C-gamma (PLCγ) and the activation of nuclear factor-κB (NF-κB) but is independent of FGFR substrate 2.

Conclusion
Our study provides evidence of a new FGFR1–PLCγ–NF-κB axis in macrophages in inflammatory AS, supporting FGFR1 as a potentially therapeutic target for AS-related diseases.
Accelerated aging and altered subclinical response to ozone exposure in young, healthy adults
Authors: Weston William C , Bind Marie Abèle , Cascio Wayne E , Devlin Robert B , Diaz-Sanchez David , Ward-Caviness Cavin K 
Published: June 2024

Abstract
Ozone exposure induces a myriad of adverse cardiopulmonary outcomes in humans. Although advanced age and chronic disease are factors that may exacerbate a person’s negative response to ozone exposure, there are no molecular biomarkers of susceptibility. Here, we examine whether epigenetic age acceleration (EAA) is associated with responsiveness to short-term ozone exposure. Using data from a crossover-controlled exposure study (n = 17), we examined whether EAA, as measured in lung epithelial cells collected 24 h after clean air exposure, modifies the observed effect of ozone on autonomic function, cardiac electrophysiology, hemostasis, pulmonary function, and inflammation. EAA was assessed in lung epithelial cells extracted from bronchoalveolar lavage fluids, using the pan-tissue aging clock. We used two analytic approaches: (i) median regression to estimate the association between EAA and the estimated risk difference for subclinical responses to ozone and (ii) a block randomization approach to estimate EAA’s effect modification of subclinical responses. For both approaches, we calculated Fisher-exact P-values, allowing us to bypass large sample size assumptions. In median regression analyses, accelerated epigenetic age modified associations between ozone and heart rate–corrected QT interval (QTc) (${{\hat \beta }}$= 0.12, P-value = 0.007) and between ozone and C-reactive protein (${{\hat \beta }}$ = −0.18, P = 0.069). During block randomization, the directions of association remained consistent for QTc and C-reactive protein; however, the P-values weakened. Block randomization also revealed that responsiveness of plasminogen activator inhibitor-1 (PAI-1) to ozone exposure was modified by accelerated epigenetic aging (PAI-1 difference between accelerated aging-defined block groups = −0.54, P-value = 0.039). In conclusion, EAA is a potential biomarker for individuals with increased susceptibility to ozone exposure even among young, healthy adults.
Vago-splenic signal transduction of cardioprotection in humans
Authors: Lieder Helmut Raphael , Paket Umut , Skyschally Andreas , Rink Andreas D , Baars Theodor , Neuhäuser Markus , Kleinbongard Petra , Heusch Gerd 
Published: June 2024

Abstract

Background and Aims
The spleen serves as an important relay organ that releases cardioprotective factor(s) upon vagal activation during remote ischaemic conditioning (RIC) in rats and pigs. The translation of these findings to humans was attempted.

Methods
Remote ischaemic conditioning or electrical auricular tragus stimulation (ATS) were performed in 10 healthy young volunteers, 10 volunteers with splenectomy, and 20 matched controls. Venous blood samples were taken before and after RIC/ATS or placebo, and a plasma dialysate was infused into isolated perfused rat hearts subjected to global ischaemia/reperfusion.

Results
Neither left nor right RIC or ATS altered heart rate and heart rate variability in the study cohorts. With the plasma dialysate prepared before RIC or ATS, respectively, infarct size (% ventricular mass) in the recipient rat heart was 36 ± 6% (left RIC), 34 ± 3% (right RIC) or 31 ± 5% (left ATS), 35 ± 5% (right ATS), and decreased with the plasma dialysate from healthy volunteers after RIC or ATS to 20 ± 4% (left RIC), 23 ± 6% (right RIC) or to 19 ± 4% (left ATS), 26 ± 9% (right ATS); infarct size was still reduced with plasma dialysate 4 days after ATS and 9 days after RIC. In a subgroup of six healthy volunteers, such infarct size reduction was abrogated by intravenous atropine. Infarct size reduction by RIC or ATS was also abrogated in 10 volunteers with splenectomy, but not in their 20 matched controls.

Conclusions
In humans, vagal innervation and the spleen as a relay organ are decisive for the cardioprotective signal transduction of RIC and ATS.
TURN-ON OF INACTIVE GENES BY PROMOTER RECRUITMENT IN ESCHERICHIA COLI: INVERTED REPEATS RESULTING IN ARTIFICIAL DIVERGENT OPERONS
Authors: Charlier Daniel , Severne Yvonne , Zafarullah Muhamad , Glansdorff Nicolas 
Published: June 2024

ABSTRACT
We have characterized two rearrangements consisting of inverted repeats of the argE gene. The promoters (p) of argE and of argCBH face each other over an internal operator. The rearrangements were obained as reactivations of argE in a strain harboring an argEp deletion on a ?darg prophage. In both cases the repeat included argE and argCBHp on either side of a unique sequence; the result is a divergent operon in which each copy of argCBHp reads into the adjacent argE repeat. In one case, the pair of repeats adjoins the silent parental gene, forming a triplication (← → ←). The other rearrangement consists of a single argE palindrome, but the whole prophage is rearranged into an inverted repeat, analogous to certain λdv's. Both structures could be explained by breakage of a replication fork passing argE and by inaccurate rejoining of strands. The λdv-like rearrangement would result from breakage at both replication forks of a phage or prophage replicating during transient release of immunity. The triplication would imply breaking of a chromosomal replication fork, formation of a cyclic intermediate by recombination between the daughter duplex molecules and reinsertion into the parental argE gene. Formation of a triplication by replication errors involving appropriate strand switchings and branch migrations can not be excluded however.
The coalescent process in models with selection
Authors: Kaplan N L , Darden T , Hudson R R 
Published: June 2024

Abstract
Statistical properties of the process describing the genealogical history of a random sample of genes are obtained for a class of population genetics models with selection. For models with selection, in contrast to models without selection, the distribution of this process, the coalescent process, depends on the distribution of the frequencies of alleles in the ancestral generations. If the ancestral frequency process can be approximated by a diffusion, then the mean and the variance of the number of segregating sites due to selectively neutral mutations in random samples can be numerically calculated. The calculations are greatly simplified if the frequencies of the alleles are tightly regulated. If the mutation rates between alleles maintained by balancing selection are low, then the number of selectively neutral segregating sites in a random sample of genes is expected to substantially exceed the number predicted under a neutral model.
SELECTION AND IDENTIFICATION OF A SPONTANEOUS ALIEN CHROMOSOME TRANSLOCATION IN WHEAT
Authors: Jan Chao-Chien , Dvořák Jan , Qualset Calvin O , Soliman Khairy M 
Published: June 2024

ABSTRACT
A wheat (Triticum aestivum L. emend Thell) disomic addition line (2n = 6x = 44), SH1-152-2, with a pair of Elytrigia pontica (Podp.) Holub 2n = 10x = 70 [syn. Agropyron elongatum (Host) P.B.] chromosomes controlling blue aleurone color was crossed with a short-statured spring wheat ‘Sonora 64’ (T. aestivum). Isoline pairs of blue-disomic addition lines and nonblue euploid lines were produced by selecting plants segregating for blue aleurone for 12 generations. Nineteen of 20 blue aleurone lines were 2n = 44 addition lines, and one had 2n = 42 chromosomes. Several lines of evidence showed that this line had a spontaneous translocation in which the β arm of wheat chromosome 4A was replaced by an Elytrigia chromosome arm carrying the blue aleurone gene. The Elytrigia chromosome in SHI-152-2 appeared to be homologous with E. pontica chromosome 4el1, which also carries the blue aleurone gene. It was concluded that the spontaneous translocation originated from simultaneous misdivision of univalents and subsequent reunion at the centromere of chromosome arm 4Aα with the Elytrigia chromosome arm.
Nipah Virus-Associated Neuropathology in African Green Monkeys During Acute Disease and Convalescence
Authors: Goldin Kerry , Liu Yanling , Rosenke Rebecca , Prado-Smith Jessica , Flagg Meaghan , de Wit Emmie 
Published: June 2024

Abstract

Background
Nipah virus is an emerging zoonotic virus that causes severe respiratory disease and meningoencephalitis. The pathophysiology of Nipah virus meningoencephalitis is poorly understood.

Methods
We have collected the brains of African green monkeys during multiple Nipah virus, Bangladesh studies, resulting in 14 brains with Nipah virus-associated lesions.

Results
The lesions seen in the brain of African green monkeys infected with Nipah virus, Bangladesh were very similar to those observed in humans with Nipah virus, Malaysia infection. We observed viral RNA and antigen within neurons and endothelial cells, within encephalitis foci and in uninflamed portions of the central nervous system (CNS). CD8+ T cells had a consistently high prevalence in CNS lesions. We developed a UNet model for quantifying and visualizing inflammation in the brain in a high-throughput and unbiased manner. While CD8+ T cells had a consistently high prevalence in CNS lesions, the model revealed that CD68+ cells were numerically the immune cell with the highest prevalence in the CNS of Nipah virus-infected animals.

Conclusions
Our study provides an in-depth analysis on Nipah virus infection in the brains of primates, and similarities between lesions in patients and the animals in our study validate this model.
Hair, Roots, and Crystal Balls: Archival Viscerality, Black Conjuring Traditions, and the Study of American Religions
Authors: Greene-Hayes Ahmad 
Published: June 2024

Abstract
Black studies scholars have long argued that archives are violent and dismembering, especially as the universities which house them preserve the physical and immaterial remnants of slavery. Religious studies scholars, especially historians of religion, have begun attending to this quandary while sifting through archives of slavery and religion. This article enters this discourse by focusing on the afterlives of slavery and their relationship to the religious innovations of Black religious actors in the late nineteenth and early twentieth centuries. This article, then, centers the author’s visceral experience in an archival reading room of a university while consulting the material objects of religious practitioners Reverend John L. Reed and Sister Mamie Wade Avant. In the process, the article reconstructs a historical narrative about their lives and argues that religious studies must reckon with the archive of antiblackness and its capture of Black religions.