bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling haze and cloud microphysics in WASP-39b’s atmosphere based on JWST observations
Authors: Arfaux Anthony , Lavvas Panayotis 
Published: March 2024

ABSTRACT
We present a study on the coupling of haze and clouds in the atmosphere of WASP-39b. We developed a cloud microphysics model simulating the formation of Na2S and MgSiO3 condensates over photochemical hazes in gas giant atmospheres. We apply this model to WASP-39b, recently observed with the JWST to study how these heterogeneous components may affect the transit spectrum. We simulate both morning and evening terminators independently and average their transit spectra. While MgSiO3 formation has negligible impact on the spectrum, Na2S condensates produce grey opacities in the water band, in agreement with Hubble Space Telescope (HST) and JWST observations. Moreover, the formation of Na2S on the morning side depletes the atmosphere of its sodium content, decreasing the strength of the Na line. Combining morning and evening profiles results in a good fit of the Na observations. These nominal results assume a small Na2S/haze contact angle (5.7°). Using a larger value (61°) reduces the cloud density and opacity, but the effect on the Na profile and spectral line remains identical. In addition, the presence of haze in the upper atmosphere reproduces the ultraviolet (UV)-visible slope observed in the HST and Very Large Telescope data and contributes to the opacity between the water bands at wavelengths below 2 μm. The averaged spectra are rather insensitive to the variation of eddy diffusion and haze mass flux tested in this study, though the UV-visible slope, probing the haze layer above the clouds, is affected. Finally, our disequilibrium chemistry model, including photochemistry, reproduces the SO2 and CO2 absorption features observed.
Dux activates metabolism-lactylation-MET network during early iPSC reprogramming with Brg1 as the histone lactylation reader
Authors: Hu Xinglin , Huang Xingwei , Yang Yue , Sun Yuchen , Zhao Yanhua , Zhang Zhijing , Qiu Dan , Wu Yanshuang , Wu Guangming , Lei Lei 
Published: March 2024

Abstract
The process of induced pluripotent stem cells (iPSCs) reprogramming involves several crucial events, including the mesenchymal-epithelial transition (MET), activation of pluripotent genes, metabolic reprogramming, and epigenetic rewiring. Although these events intricately interact and influence each other, the specific element that regulates the reprogramming network remains unclear. Dux, a factor known to promote totipotency during the transition from embryonic stem cells (ESC) to 2C-like ESC (2CLC), has not been extensively studied in the context of iPSC reprogramming. In this study, we demonstrate that the modification of H3K18la induced by Dux overexpression controls the metabolism-H3K18la-MET network, enhancing the efficiency of iPSC reprogramming through a metabolic switch and the recruitment of p300 via its C-terminal domain. Furthermore, our proteomic analysis of H3K18la immunoprecipitation experiment uncovers the specific recruitment of Brg1 during reprogramming, with both H3K18la and Brg1 being enriched on the promoters of genes associated with pluripotency and epithelial junction. In summary, our study has demonstrated the significant role of Dux-induced H3K18la in the early reprogramming process, highlighting its function as a potent trigger. Additionally, our research has revealed, for the first time, the binding of Brg1 to H3K18la, indicating its role as a reader of histone lactylation.
txtools: an R package facilitating analysis of RNA modifications, structures, and interactions
Authors: Garcia-Campos Miguel Angel , Schwartz Schraga 
Published: March 2024

Abstract
We present txtools, an R package that enables the processing, analysis, and visualization of RNA-seq data at the nucleotide-level resolution, seamlessly integrating alignments to the genome with transcriptomic representation. txtools’ main inputs are BAM files and a transcriptome annotation, and the main output is a table, capturing mismatches, deletions, and the number of reads beginning and ending at each nucleotide in the transcriptomic space. txtools further facilitates downstream visualization and analyses. We showcase, using examples from the epitranscriptomic field, how a few calls to txtools functions can yield insightful and ready-to-publish results. txtools is of broad utility also in the context of structural mapping and RNA:protein interaction mapping. By providing a simple and intuitive framework, we believe that txtools will be a useful and convenient tool and pave the path for future discovery. txtools is available for installation from its GitHub repository at https://github.com/AngelCampos/txtools.
Methoxsalen Inhibits the Acquisition of Nicotine Self-Administration: Attenuation by Cotinine Replacement in Male Rats
Authors: Ding Zheng-Ming , Neslund Elizabeth M , Sun Dongxiao , Tan Xiaoying 
Published: March 2024

Abstract

Introduction
Cigarette smoking remains the leading preventable cause of disease and death. Nicotine is the primary reinforcing ingredient in cigarettes sustaining addiction. Cotinine is the major metabolite of nicotine that produces a myriad of neurobehavioral effects. Previous studies showed that cotinine-supported self-administration in rats and rats with a history of cotinine self-administration exhibited relapse-like drug-seeking behavior, suggesting that cotinine may also be reinforcing. To date, whether cotinine may contribute to nicotine reinforcement remains unknown. Nicotine metabolism is mainly catalyzed by hepatic CYP2B1/2 enzymes in rats and methoxsalen is a potent CYP2B1/2 inhibitor.

Aims and Methods
The study examined nicotine metabolism, self-administration, and locomotor activity. The hypothesis is that methoxsalen inhibits nicotine self-administration and cotinine replacement attenuates the inhibitory effects of methoxsalen in male rats.

Results
Methoxsalen decreased plasma cotinine levels following a subcutaneous nicotine injection. Repeated daily methoxsalen treatments reduced the acquisition of nicotine self-administration, leading to fewer nicotine infusions, lower nicotine intake, and lower plasma cotinine levels. However, methoxsalen did not alter the maintenance of nicotine self-administration despite a significant reduction of plasma cotinine levels. Cotinine replacement by mixing cotinine with nicotine for self-administration dose-dependently increased plasma cotinine levels and enhanced the acquisition of self-administration. Neither basal nor nicotine-induced locomotor activity was altered by methoxsalen.

Conclusions
These results indicate that methoxsalen inhibition of cotinine formation impaired the acquisition of nicotine self-administration, and cotinine replacement attenuated the inhibitory effects of methoxsalen on the acquisition of self-administration, suggesting that cotinine may contribute to the initial development of nicotine reinforcement.

Implications
Smoking cessation medications targeting nicotine’s effects are only moderately effective, making it imperative to better understand the mechanisms of nicotine misuse. Methoxsalen inhibited nicotine metabolism to cotinine and impaired the acquisition of nicotine self-administration. Cotinine replacement restored plasma cotinine and attenuated the methoxsalen inhibition of nicotine self-administration in rats. These results suggest that (1) the inhibition of nicotine metabolism may be a viable strategy in reducing the development of nicotine reinforcement, (2) methoxsalen may be translationally valuable, and (3) cotinine may be a potential pharmacological target for therapeutic development given its important role in the initial development of nicotine reinforcement.
Virological Suppression and its Predictors Among HIV/AIDS Patients on Antiretroviral Therapy in Ethiopia: Systematic Review and Meta-analysis
Authors: Melak Dagnachew , Bayou Fekade Demeke , Yasin Husniya , Zerga Aregash Abebayehu , Wagaye Birhanu , Ayele Fanos Yeshanew , Kebede Natnael , Mekonen Asnakew Molla , Asfaw Ahmed Hussien , Tsegaw Shambel Ayichew , Mihiretu Mengistu Mera , Tsega Yawkal , Addisu Elsabeth , Cherie Niguss , Birhane Tesfaye , Abegaz Zinet , Endawkie Abel , Mohammed Anissa 
Published: March 2024

Abstract

Background
Achieving viral load suppression is crucial for the prevention of complications and deaths related to HIV infection. Ethiopia has embraced the worldwide 95-95-95 target, but there is no national representative information regarding virological suppression. Therefore, this review aims to determine the pooled virological suppression rate and identify the pooled effect of contributing factors of viral suppression for HIV-positive patients on antiretroviral therapy in Ethiopia.

Methods
We systematically searched websites and databases, including online repositories, to obtain primary studies. Two reviewers assessed the quality of the included articles using the Newcastle-Ottawa Scale appraisal checklist. Publication bias was checked using Egger's regression test, the heterogeneity of the studies was assessed using I2 statistics and Q statistics, and a sensitivity analysis was performed to identify any outlier results in the included studies. The Der Simonian Laird random-effects model was used to estimate the overall proportion of viral suppression, and STATA 17 statistical software was used for all types of analysis.

Results
A total of 21 eligible articles primarily conducted in Ethiopia using HIV program data were used for this quantitative synthesis. The overall pooled virological suppression rate was 71% (95% CI, 64%–77%). The pooled effects of poor adherence to ART (adjusted odds ratio [AOR], 0.33; 95% CI, 0.28–0.40), body mass index (18.5–24.9 kg/m2; AOR, 1.8; 95% CI, 1.37–2.36), disclosure (AOR, 1.41; 95% CI, 1.05–1.89), absence of opportunistic infection (AOR, 1.68; 95% CI, 1.43–1.97), and high baseline viral load count (AOR, 0.65; 95% CI, 0.52–0.81) were identified as significant predictors of viral suppression.

Conclusions
The overall pooled percentage of virological suppression was low compared with the global target of viral suppression and the Ethiopian Public Health Institute report. Poor adherence, normal body mass index, disclosure, absence of opportunistic infection, and high baseline viral load count were factors contributing to viral suppression in Ethiopia. Responsible stakeholders should maximize their efforts to achieve the global target of virological suppression by addressing significant predictors.
Evolutionary Cell Biology
Authors: Lynch Michael R. 
Published: March 2024

Abstract
The fields of molecular evolution, genome evolution, and evolutionary genetics are now well established. Remarkably, however, although all evolutionary modifications begin at the cellular level, and despite the advances made in cell biology and microbiology over the past few decades, there is as yet no recognized discipline of evolutionary cell biology. The goal of this book is to help establish the foundations for this newly-emerging field. Its principal aims are twofold: first, to promote an understanding among evolutionary biologists as to why the cellular details matter if we are to understand the mechanisms of evolution; second, to make clear to non-evolutionary biologists – cell biologists in particular – that evolution is not just a matter of natural selection and optimization, but a process whose reach depends on other population-genetic features such as mutation, recombination, and random genetic drift. Although there are many excellent books on cell biology, microbiology, and biophysics, almost no attention is given to evolution. Likewise, although there are numerous evolutionary biology books on the market, none of them gives more than passing attention to details at the cellular level. Thus, Evolutionary Cell Biology offers a broader understanding of evolutionary processes and an appreciation for the many interesting problems that remain to be solved at the cellular and subcellular levels. Narrative is aimed at both cell biologists and evolutionary biologists. It will be accessible to upper-level undergraduates in biology, and certainly to graduate students in all areas of the life sciences. Professionals from a wide range of fields – cell biology, microbiology, evolution, biophysics, biochemistry, and mathematics – will be exposed to entirely new ideas not traditionally covered in their primary fields of expertise.
Enzymes and Metabolic Pathways
Authors: Lynch Michael R. 
Published: March 2024

Abstract
Metabolic reactions are carried out by enzymes capable of enhancing specific reaction rates by many orders of magnitude above spontaneous background levels. Although specialized for particular functions, most enzymes are also highly promiscuous and have catalytic capacities that are commonly far below the biophysical limits, suggesting that the degree of molecular refinement is generally stalled at a drift barrier. Enzyme promiscuity facilitates the emergence of novel enzyme functions by descent with modification, usually via just a few key amino-acid substitutions. Individual enzymes typically carry out just simple chemical modifications, necessitating the use of multi-step metabolic pathways in the transformation of organic material. Despite their conserved functions, many enzymatic steps and their molecular participants have diverged substantially among phylogenetic lineages, with gene duplication and divergence often playing a role in such remodelling. Overall flux rates are generally influenced most by the enzymes furthest upstream in a pathway. Most catabolic pathways are energetically inefficient, with a substantial amount of energy contained within substrate molecules being lost as heat rather than being converted to ATP. Flux-rate theory suggests that such inefficiency is an inevitable outcome of maximizing the net rate of product formation.
Comparative Analysis of Five Entrepreneurial Ecosystems in Life Sciences
Authors: Alvedalen Janna , Carlsson Bo 
Published: March 2024

AbstractThe entrepreneurial ecosystem (EE) is a popular concept in entrepreneurship studies that describes all actors and the interaction between actors in a specific geographical area or industrial domain. This chapter compares five EEs in life sciences in Sweden and the US, based on own data collection in all five areas. The EEs studied here are in different phases of evolution as a result of different and shifting strategies pursued by major companies in each region. The chapter outlines commonalities and differences between how EEs operate and function in different territorial, institutional, and historical contexts. It also explores how national and local factors influence the rate and nature of entrepreneurship at the regional level.
Alexandria and Apocalypse
Authors: Cioffi Robert 
Published: March 2024

AbstractChapter 4 examines the city of Alexandria, which by the Roman imperial period had long been acknowledged as the first city of Egypt. It argues that for Xenophon’s An Ephesian Tale, Achilles Tatius’ Leucippe and Clitophon, and Heliodorus’ An Ethiopian Story Alexandria was not only a symbol of the power of outsiders to control Egypt, but that it also provided a politically, intellectually, and symbolically charged image to represent resistance to that power. These texts draw on and respond to both Greek and Egyptian traditions—some ethnographic, some apocalyptic—in order to present three very different pictures of the city’s relationship to the rest of Egypt. The chapter shows how authors can work against the view of the city familiar from other Roman imperial literature to represent Alexandria as a labile landscape, one that, in Heliodorus at least, is always in danger of being unwritten and pulled down to its very foundations.
Country, Corporates, and the Construct of BRI
Authors: Jie Yu 
Published: March 2024

AbstractThis chapter seeks to discuss to what extent Chinese companies, mostly state-owned enterprises (SOEs), have become a formidable player in challenging the so-called Liberal International Order (LIO). In particular, it aims to explore the evolving relationships between the Chinese companies and the Chinese central government as Beijing pursues its flagship Belt and Road Initiative (BRI). It intends to analyse whether Chinese SOEs have become a source of destabilizing the existing Liberal International Order and acted as a vehicle of delivering Beijing’s geopolitical ambition through the participation of the BRI. It challenges the conventional wisdom that China is a monolithic player for its deciding foreign policies. Instead, it adopts an ‘inside-out’ approach by examining the actual policy process with a primary focus on individual actors such as the Party, the government department, and the Chinese state-owned companies. It also aims to offer a nascent assessment of the implementation of the ‘dual circulation strategy’ in determining future BRI investments by the Chinese SOEs.
The “Uncongenial Air of Freedom”: Union Occupation and the Slave Trade
Authors: Colby Robert K.D. 
Published: March 2024

Abstract
Chapter 2 explores the effects of Union military successes in 1861 and 1862 on the Confederate slave trade. Slave trading slowly rebounded in the Confederacy following secession and, by the winter of 1861, appeared to be on a path toward relative normality. In the spring of 1862, however, Union forces won several major victories and captured or threatened many of the Confederate States of America’s biggest slave trading centers, including Alexandria, Norfolk, Nashville, Memphis, Natchez, and, most importantly, New Orleans. When US soldiers occupied these cities, they all but ended slave trading in them by refusing to uphold what enslavers understood to be their property rights in man. In doing so, they aided and abetted enslaved people’s ongoing resistance to slavery. With enslavers’ right to hold people as property uncertain, the slave trade virtually ceased in Union-occupied areas.
Sold “Far Out of the Way of Lincoln”: Emancipation and Counterrevolutionary Slave Commerce
Authors: Colby Robert K.D. 
Published: March 2024

Abstract
Chapter 6 explores the intersections between the Confederacy’s surviving slave trade and emancipation. The Civil War provided enslaved people with unprecedented opportunities to seize their freedom—a reality they exploited by the tens, even hundreds, of thousands. As enslaved people embraced this moment, however, enslavers fought against their efforts through the slave trade. Slaveholders used the surviving commerce in slaves to punish people who escaped but failed to make it to freedom, whom they recaptured, or who threatened the existing racial order in any way. Against the slaves’ revolution, then, enslavers deployed the domestic slave trade as a counterrevolutionary weapon. This profoundly shaped the choices available to the people enslaved in the Confederacy and influenced the ways in which they did (or did not) become free during the Civil War.
Animal Sacrifice in the Roman Empire (31 BCE-395 CE)
Authors: Rives J. B. 
Published: March 2024

AbstractThis book explores the changing socioeconomic, political, and cultural significance of animal sacrifice in the Roman imperial period. Although animal sacrifice was only one of a wide range of offerings to the gods, it was distinctive in being more costly than many others and in generating a valuable consumer good: high-quality meat. As a result, it functioned to reinforce social structures that enabled the smooth operation of the Roman Empire: the socioeconomic hierarchies of Graeco-Roman cities, the normative Graeco-Roman culture that bound together urban elites, and the ideological role of the Roman emperor (Part I of the book). At the same time as the practice of animal sacrifice performed these ideological functions, there were also, from an early date, various discourses about animal sacrifice that relocated its meaning from the social to the conceptual sphere, discourses that a range of freelance experts, from Graeco-Roman philosophers to early Christian leaders, deployed as a means of establishing their own social power (Part II). These two aspects of animal sacrifice, as practice and as discourse, intersected both with each other and with larger economic and political developments in ways that, starting in the mid-third century CE, led to its becoming the object of both imperial and ecclesiastical policy. Over the course of the fourth century CE, animal sacrifice was displaced from its central role in the structuring of the empire, redefined as a marker of “paganism,” and eventually prohibited altogether (Part III).
Introduction
Authors: Rives J. B. 
Published: March 2024

AbstractThis introductory chapter defines key terms and presents the book’s analytical framework. It defines animal sacrifice as a ritualized practice involving the slaughter of an animal, parts of which were offered to superhuman powers to win their favor. It also elaborates on two key concepts. The first is social power, analyzed in terms developed by Michael Mann. Social power takes two broad forms: authoritative (commands that are enforced) and diffused (social practices that embody power relations but are not enforced). It derives from a range of sources; the two most important for this book are control of economic resources and physical force on the one hand and ideology on the other. The second key concept is communication, the propagation of diffused power, which takes two distinct but interrelated forms: practice, primarily nonverbal, and discourse, primarily verbal. These two modes of communication align respectively with the immanent and transcendent forms of ideological power. The chapter also addresses cultural transformation, especially the shift from a cultural configuration in which there is little that is analogous to modern conceptions of “religion” to one in which there existed something much closer to “religion” as the term is employed today.
Animal Sacrifice and Euergetism in the Roman Empire
Authors: Rives J. B. 
Published: March 2024

AbstractThis chapter examines how the role of animal sacrifice as an efficient instrument for structuring sociopolitical hierarchies acquired new force in the Hellenistic and Roman periods, becoming integrated into the socioeconomic system of euergetism. In this system, wealthy community members bestowed benefits on fellow citizens in exchange for public honors and superior civic status. In the cities of the Greek east, inscriptions reveal how local benefactors, as magistrates and priests, used their own resources to fund the civic festivals over which they presided, including the animal sacrifices central to them. Their economic and social prominence as sponsors of these events took on concrete form in their ritual prominence as those who presided over the sacrifice and distribution of meat. In the cities of the Latin west, the relationship between animal sacrifice and euergetism was more indirect but still apparent: people who presided over public animal sacrifices as magistrates and priests held their positions by virtue of their wealth. Animal sacrifice was tightly integrated into the euergetic system, which was integral to the sociopolitical organization of the Graeco-Roman city. Given the central role of the city in imperial administration, public animal sacrifice contributed to the smooth functioning of the Roman Empire.