bluuebunny/crossref_metadata_2025_split huggingface dataset:
First dated phylogenetic reconstruction of the genus Tamarix (Tamaricaceae): biogeographical implications and hybridization processes in the Mediterranean Basin
Authors: Terrones Alejandro , Juan Ana 
Published: July 2023

Abstract
The genus Tamarix comprises trees and shrubs that grow mainly in saline habitats. Previous phylogenetic analyses have shown incongruence between different gene trees, which suggest that hybridization processes might have been present in the past. However, the complex pattern of colonization of the Western Mediterranean region has yet to be understood, and no dated phylogeny that reconciles the different gene trees is currently available. The objectives of the study are: (i) to reconstruct the first dated species tree of the genus Tamarix from previously published data, (ii) to evaluate the occurrence of past hybridization, and (iii) to discuss biogeographical implications, mainly focused on the Mediterranean Basin. Our results show that the separation between Tamarix and Myricaria occurred 28.49 Mya, and the crown age of the genus Tamarix is dated at 16.65 Mya. Past hybridization processes might be present in three species: Tamarix amplexicaulis, Tamarix canariensis, and Tamarix minoa. Various colonization events are probable in the Western Mediterranean: a first colonization in the Early Miocene, Tamarix africana during the Late Miocene, and Tamarix boveana and Tamarix gallica during the Pleistocene. In addition, the genus Tamarix migrated to south-western Africa around 5.8 Mya, probably through an ancient arid African corridor, or a long-distance dispersal event.
Catholic Censorship and the Demise of Knowledge Production in Early Modern Italy
Authors: Blasutto Fabio , de la Croix David 
Published: July 2023

Abstract
Censorship makes new ideas less available to others, but also reduces the number of people choosing to develop non-compliant ideas. We propose a new method to measure the effect of censorship on knowledge growth, accounting for the agents’ choice between compliant and non-compliant occupations. We apply our method to the Catholic Church’s censorship of books written by members of Italian universities and academies over the period 1400–750. We highlight new facts: once censorship was introduced, censored authors were of better quality than the non-censored authors, but this gap shrank over time and the intensity of censorship decreased over time. We use these facts to identify the deep parameters of a novel endogenous growth model that links censorship to knowledge diffusion and occupational choice. We conclude that the average log publication per scholar in Italy would have been 43% higher if censorship had not been present, while the effect of adverse macroeconomic processes is almost four times smaller. The induced reallocation of talents towards compliant activities explains half the effect of censorship.
Introduction to the special issue: the economic history of the arts
Authors: Borowiecki Karol J 
Published: July 2023

AbstractThis is the Introduction to the Special Issue on the Economic History of the Arts. It argues that economic history is well suited to study the arts. It also posits that the value of the discipline lies, among others, in its interdisciplinarity and the possibility to study creativity in history. Finally, attempts are made to coin the name of this field of research and some thoughts are shared on the way forward.
Equilibria and oscillations in cheat–cooperator dynamics
Authors: Liu Ming , Wild Geoff , West Stuart A 
Published: July 2023

Abstract
Cooperative societies can be threatened by cheats, who invest less in cooperation and exploit the contributions of others. The impact of cheats depends on the extent to which they are maintained in the population. However, different empirical studies, across organisms ranging from RNA replicators to bacteria, have shown diverse cheat–cooperator dynamics. These vary from approaching a stable equilibrium to dynamic cyclical oscillations. The reason for this variation remains unclear. Here, we develop a theoretical model to identify the factors that determine whether dynamics should tend toward stable equilibria or cyclical oscillations. Our analyses show that (1) a combination of both periodic population bottlenecks and density-dependent selection on cheating is required to produce cyclical oscillations and (2) the extent of frequency-dependent selection for cheating can influence the amplitude of these oscillations but does not lead to oscillations alone. Furthermore, we show that stochastic group formation (demographic stochasticity) can generate different forms of oscillation, over a longer time scale, across growth cycles. Our results provide experimentally testable hypotheses for the processes underlying cheat–cooperator dynamics.
Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities
Authors: Osburn Ernest D , Moon Cooper , Stephenson Torrey , Kittipalawattanapol Kawinwit , Jones Menna , Strickland Michael S , Lynch Laurel M 
Published: July 2023

Abstract
Forest disturbance has well-characterized effects on soil microbial communities in tropical and northern hemisphere ecosystems, but little is known regarding effects of disturbance in temperate forests of the southern hemisphere. To address this question, we collected soils from intact and degraded Eucalyptus forests along an east–west transect across Tasmania, Australia, and characterized prokaryotic and fungal communities using amplicon sequencing. Forest degradation altered soil microbial community composition and function, with consistent patterns across soil horizons and regions of Tasmania. Responses of prokaryotic communities included decreased relative abundance of Acidobacteriota, nitrifying archaea, and methane-oxidizing prokaryotes in the degraded forest sites, while fungal responses included decreased relative abundance of some saprotrophic taxa (e.g. litter saprotrophs). Forest degradation also reduced network connectivity in prokaryotic communities and increased the importance of dispersal limitation in assembling both prokaryotic and fungal communities, suggesting recolonization dynamics drive microbial composition following disturbance. Further, changes in microbial functional groups reflected changes in soil chemical properties—reductions in nitrifying microorganisms corresponded with reduced NO3-N pools in the degraded soils. Overall, our results show that soil microbiota are highly responsive to forest degradation in eucalypt forests and demonstrate that microbial responses to degradation will drive changes in key forest ecosystem functions.
Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation
Authors: Stroupe Sam , Martone Carly , McCann Blake , Juras Rytis , Kjöllerström Helena Josefina , Raudsepp Terje , Beard Donald , Davis Brian W , Derr James N 
Published: July 2023

Abstract
We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from a F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies. To demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of 3 true albino bison and 44 wild-type pelage color bison. Through the examination of genomic variants fixed in the albino cohort and absent in the controls, we identified a nonsynonymous single nucleotide polymorphism (SNP) mutation on chromosome 29 in exon 3 of the tyrosinase gene (c.1114C&gt;T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provides a highly robust and informative resource for genomics investigations for this iconic North American species.
Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity
Authors: Collington Emma , Lobb Briallen , Mazen Nooran Abu , Doxey Andrew C , Glerum D Moira 
Published: July 2023

Abstract
The terminal electron acceptor of most aerobic respiratory chains, cytochrome c oxidase (COX), has been highly conserved throughout evolution, from aerobic prokaryotes to complex eukaryotes. Oxygen metabolism in parasitic helminths differs significantly from that of most aerobic eukaryotes, as these organisms can switch between aerobic and anaerobic metabolisms throughout their life cycles. Early studies suggested a lack of COX activity in certain parasitic helminths, and the role of COX in helminth mitochondria remains unclear. To determine whether a functional COX is widely present in helminths, we analyzed the phylogenetic distribution of oxygen metabolism systems across 155 helminth genomes, investigating three distinct sets of protein-coding genes involved in different aspects of oxygen metabolism: COX and its assembly factors, peroxisomes, and the most abundant reactive oxygen species (ROS)-metabolizing proteins. While glycolytic and citric acid cycle enzymes are highly conserved in helminthic species, we observed an apparent widespread absence of essential COX genes across 52% of helminth species investigated. While the most common proteins involved in the defense against ROS are highly maintained across virtually all lineages, we also observed an apparent absence of essential peroxisomal protein-coding genes in 42% of species investigated. Our results suggest that a subset of parasitic helminths utilize oxygen differently from related, nonparasitic species such as Caenorhabditis elegans, with significant differences in their mitochondrial electron transport chains and peroxisomes. The identification of substantive differences between parasite and host metabolism offers a new avenue for the development of anthelmintic agents that could target these divergent pathways.
Of Crimes and Crowns
Authors: Bocchese Marco 
Published: July 2023

Abstract
This article explains variation in state cooperation with International Criminal Court (ICC)’s investigations and prosecutions across cases and over time. The idea motivating this study stems from the observation of the mixed record of state cooperation with ICC operations. For legal professionals and scholars this observation is puzzling, since states falling within the ICC’s territorial jurisdiction are legally bound to provide full judicial assistance to the Court. Thus, why do some countries entertain collaborative relations with the ICC while others display hostility towards it? I argue that state leaders’ perceptions of potential ICC indictment best explain variation in state behaviour. This article aims to contribute to a better understanding of how state attitudes form and of the extent to which external actors, spearheaded by the ICC Prosecutor’s Office (OTP), can change them. The research findings suggest that: 1) neither formal state consent (ratification) nor regime type are reliable predictors of state cooperation; 2) state leaders’ perception of potential ICC indictment appears better suited to correctly predict state behaviour in all the situations investigated by the OTP; 3) the OTP’s signalling strategy — including the timing of its intervention — affects state leaders’ perception of future ICC indictment and, in turn, the prospects of state cooperation; 4) when state authorities deny cooperation, regime change provides a one-time opportunity to start ICC–state relations anew.
Suppressing c-FOS expression by G-quadruplex ligands inhibits osimertinib-resistant non-small cell lung cancer
Authors: Lu Kai , Wang Hsin-Chiao , Tu Yi-Chen , Chang Cheng-Chung , Lou Pei-Jen , Chang Ta-Chau , Lin Jing-Jer 
Published: July 2023

Abstract

Background
Osimertinib is the first-line therapy for patients with non-small cell lung cancer harboring epidermal growth factor receptor–activating alterations. Although osimertinib has been shown to elicit profound patient responses, cancer cells frequently develop additional alterations that sustain their proliferation capacity. This acquired resistance represents a substantial hurdle in precision medicine for patients with lung cancer.

Methods
The biological and cellular properties of the G-quadruplex ligand BMVC-8C3O and its anticancer activities were evaluated in non-small cell lung carcinomas. In addition, combined treatment with BMVC-8C3O and osimertinib was evaluated for its effects on the growth of osimertinib-resistant tumors in vivo.

Results
We demonstrate that BMVC-8C3O effectively suppresses c-FOS expression by stabilizing G-rich sequences located at the c-FOS promoter. The suppression c-FOS expression by BMVC-8C3O increases the sensitivity of acquired resistant cancer cells to osimertinib. Combining BMVC-8C3O and osimertinib has a synergistic effect in inhibiting the growth of acquired resistant cancers both in vitro and in mouse models. The combined inhibitory effect is not limited to BMVC-8C3O, either: several G-quadruplex ligands show varying levels of inhibition activity. We also show that simultaneous inhibition of both the c-FOS and PI3K/AKT pathways by BMVC-8C3O and osimertinib synergistically inhibits the growth of acquired resistant cancer cells.

Conclusion
These findings unveil a synthetic lethal strategy to prevent and inhibit epidermal growth factor receptor–altered lung cancers with acquired osimertinib resistance. G-quadruplex ligands have the potential to be integrated into current osimertinib-based treatment regimens.
Annular pancreas as a cause of neonatal duodenal obstruction, a case report
Authors: Gutiérrez-González Jorge Aurelio , González De La Torre Emilia , Armijo-Borjón Edgar Alan , Alarcón-Sandoval Abraham Alexander , Reyna-Sepulveda Francisco Javier , Montes-Tapia Fernando Felix , Muñoz-Maldonado Gerardo Enrique 
Published: July 2023

Abstract
The annular pancreas (AP) is an uncommon congenital anomaly, characterised by a circumferential envelope in the second portion of the duodenum. In recent years, some genetic component has been found in the etiology. A newborn full-term male, weighing at 1910 g at birth, had a history of intrauterine growth restriction and diagnosis of tetralogy of Fallot, Down syndrome and congenital hypothyroidism. Duodenal membrane is suspected after persistent postprandial vomiting and abdominal distension; his abdomen was distended, hyperresonant and soft. The gastroduodenal series showed data compatible with a duodenal membrane so exploratory laparotomy was performed, finding the pancreas completely wrapping the second portion of the duodenum, so a diamond-shaped-duodenoduodenostomy anastomosis was performed. The AP should be considered, especially in male neonates with postprandial vomiting, abdominal distension, who show some other congenital anomaly, and in the abdominal X-ray, the sign of the double bubble is observed.
Unexpected shunt-dependent hydrocephalus after unruptured aneurysm surgery—a case report
Authors: Kim Myungsoo , Kim Byoung-Joon , Yoon Sang-Youl , Kwak Youngseok 
Published: July 2023

Abstract
A chronic hydrocephalus after unruptured aneurysm surgery is an extremely rare condition. Its etiology and pathophysiology are also unclear. We report a case of chronic hydrocephalus in a patient who underwent permanent shunt placement after unruptured aneurysm clipping surgery. A 65-year-old man developed chronic hydrocephalus requiring shunt placement after clipping surgery of left anterior cerebral artery aneurysm and right middle cerebral artery aneurysm. This case shows that chronic hydrocephalus is a possible complication of unruptured aneurysm surgery, which can be resolved with an appropriate shunt operation.
A phospho-dawn of protein modification anticipates light onset in the picoeukaryoteOstreococcus tauri
Authors: Noordally Zeenat B , Hindle Matthew M , Martin Sarah F , Seaton Daniel D , Simpson T Ian , Le Bihan Thierry , Millar Andrew J 
Published: July 2023

AbstractDiel regulation of protein levels and protein modification had been less studied than transcript rhythms. Here, we compare transcriptome data under light–dark cycles with partial proteome and phosphoproteome data, assayed using shotgun MS, from the alga Ostreococcus tauri, the smallest free-living eukaryote. A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic. Mathematical modelling showed that light-stimulated protein synthesis can account for the observed clustering of protein peaks in the daytime. Prompted by night-peaking and apparently dark-stable proteins, we also tested cultures under prolonged darkness, where the proteome changed less than under the diel cycle. Among the dark-stable proteins were prasinophyte-specific sequences that were also reported to accumulate when O. tauri formed lipid droplets. In the phosphoproteome, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation suggests that a clock-regulated phospho-dawn prepares green cells for daytime functions. Acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase, implicating the clock-related casein kinases 1 and 2 in phase-specific regulation, alternating with the CMGC protein kinase family. Understanding the dynamic phosphoprotein network should be facilitated by the minimal kinome and proteome of O. tauri. The data are available from ProteomeXchange, with identifiers PXD001734, PXD001735, and PXD002909.
Insulin receptor substrate 2 gene Gly1057Asp polymorphism is a risk factor for nonalcoholic fatty liver disease
Authors: Nouri Shadi , Mahmoudi Touraj , Hojjati Farzaneh , Najafabadi Zeinab Nourmohammadi , Shafiee Radmehr , Sayedsalehi Shiva , Dehghanitafti Atefeh , Ardalani Abbas , Kohansal Kiarash , Rezamand Gholamreza , Asadi Asadollah , Nobakht Hossein , Dabiri Reza , Farahani Hamid , Tabaeian Seidamir Pasha , Zali Mohammad Reza 
Published: July 2023

Abstract

Objective
Nonalcoholic fatty liver disease (NAFLD), which is an emerging global chronic liver disease, has a close association with insulin resistance. We aimed to determine whether the Gly1057Asp (rs1805097) polymorphism of the insulin receptor substrate 2 (IRS2) gene is associated with NAFLD.

Methods
Using the polymerase chain reaction-restriction fragment length polymorphism method, 135 patients with biopsy-proven NAFLD and 135 controls underwent IRS2 genotype analysis.

Results
Genotype and allele distributions of the IRS2 gene Gly1057Asp variant conformed to the Hardy-Weinberg equilibrium in both the case and control groups (P &gt; .05). The Asp/Asp genotype of IRS2 gene Gly1057Asp polymorphism compared with Gly/Gly genotype was associated with a 2.1-fold increased risk for NAFLD after adjustment for confounding factors (P = .029; odds ratio = 2.10, 95% CI = 1.23-3.97).

Conclusion
Our findings revealed for the first time that the Gly1057Asp Asp/Asp genotype of the IRS2 gene is a marker of increased NAFLD susceptibility; however, studies in other populations are required to confirm the results.
Isolation of new Paraburkholderia strains for polyhydroxybutyrate production
Authors: Ivaldi Corinne , Foy Clothilde , Castex Stéphanie , Vallée Alexis , Rémond Caroline , Besaury Ludovic 
Published: July 2023

Abstract
Polyhydroxyalkanoates (PHAs) are bioplastics that can serve as substitutes for petroleum-based plastics with the advantages of being biodegradable, biocompatible, and biobased. The microbial production of polyhydroxyalkanoates is generally conducted in the presence of sugar mixes rich in monosaccharides. In this study, molecular and cultural approaches based on forest soils enriched with hydrocarbon complexes led to the identification and isolation of microbial strains affiliated with Paraburkholderia sp. that dominated the microbial communities that are recognized among the top polyhydroxyalkanoates producers. The genome sequencing of those isolated affiliated strains showed that compared to the reference type strain of their species, they harbored more gene copies of the enzymes involved in PHB synthesis. The microbial conversion of sugar mixes for the newly isolated strains showed a higher PHB production (g/L) and content (%) than was exhibited by the reference strain type of that genus Paraburkholderia for PHB production (P. sacchari LMG 19450T).
The Oxidation and Functionalization of Multi-walled Carbon Nanotubes with Fluorescein-isothiocyanate Improve Germination and Early Development of Avena sativa
Authors: Marco Antonio Alemán-Méndez , Javier Villegas Moreno , Kumar-Tiwari Dhirendra , Abraham Zamudio Durán Nicolás , Juárez-Cisneros Gladys 
Published: July 2023

Abstract
The use of multiwalled carbon nanotubes (MWCNTs) in plant systems has been extensively studied in the last decade, however, the structural modification of these nanoparticles changes the effects when interacting with biological systems, so this work gives us more information on the effects of the oxidation and functionalization of the MWCNTs, where these nanoparticles increased the speed of germination as well as the total germination and in the same way improved the biomass of the plant.
Zinc Oxide Nanoparticles: An Environmentally Friendly Alternative to Improve Early Germination of Zea mays
Authors: García Neftali Rangel , Borjas-García Salomón , Kumar-Tiwari Dhirendra , Cisneros Gladys Juárez , Villegas-Moreno Javier 
Published: July 2023

Abstract
The application of nanoparticles (NPs) in the field of agriculture represents a novel, efficient and low-cost alternative to replace supplies of conventional agriculture. Zinc oxide nanoparticles (NpsZnO) have been shown to have a positive effect on the development of various vegetable species. For this study, NpsZnO were synthesized by the sol-gel method, and subsequently, its absorption in Zea mays seeds and its effect on germination were evaluated. The results showed mesoporous nanoparticles were obtained. In addition, the seeds exposed to the nanoparticles showed a significantly higher concentration of zinc compared to the seeds control, showing values of up to 275 ppm compared to the control which contained an average of 75 ppm. An increase in germination was also observed, obtaining the best effect in the concentration of 16 µg/mL. The growth-promoting effect of the applied NPs on seed germination could be due to the activity of zinc as a precursor in the synthesis of phytoregulators. However, there is a lack of studies in research such as this one to confirm this inference.