bluuebunny/crossref_metadata_2025_split huggingface dataset:
A theory for colors of strongly correlated electronic systems
Authors: Acharya Swagata , Pashov Dimitar , Weber Cedric , van Schilfgaarde Mark , Lichtenstein Alexander I. , Katsnelson Mikhail I. 
Published: September 2023

AbstractMany strongly correlated transition metal insulators are colored, even though they have band gaps much larger than the highest energy photons from the visible light. An adequate explanation for the color requires a theoretical approach able to compute subgap excitons in periodic crystals, reliably and without free parameters—a formidable challenge. The literature often fails to disentangle two important factors: what makes excitons form and what makes them optically bright. We pick two archetypal cases as examples: NiO with green color and MnF2 with pink color, and employ two kinds of ab initio many body Green’s function theories; the first, a perturbative theory based on low-order extensions of the GW approximation, is able to explain the color in NiO, while the same theory is unable to explain why MnF2 is pink. We show its color originates from higher order spin-flip transitions that modify the optical response, which is contained in dynamical mean-field theory (DMFT). We show that symmetry lowering mechanisms may determine how ‘bright’ these excitons are, but they are not fundamental to their existence.
Human blood vessel organoids reveal a critical role for CTGF in maintaining microvascular integrity
Authors: Romeo Sara G. , Secco Ilaria , Schneider Edoardo , Reumiller Christina M. , Santos Celio X. C. , Zoccarato Anna , Musale Vishal , Pooni Aman , Yin Xiaoke , Theofilatos Konstantinos , Trevelin Silvia Cellone , Zeng Lingfang , Mann Giovanni E. , Pathak Varun , Harkin Kevin , Stitt Alan W. , Medina Reinhold J. , Margariti Andriana , Mayr Manuel , Shah Ajay M. , Giacca Mauro , Zampetaki Anna 
Published: September 2023

AbstractThe microvasculature plays a key role in tissue perfusion and exchange of gases and metabolites. In this study we use human blood vessel organoids (BVOs) as a model of the microvasculature. BVOs fully recapitulate key features of the human microvasculature, including the reliance of mature endothelial cells on glycolytic metabolism, as concluded from metabolic flux assays and mass spectrometry-based metabolomics using stable tracing of 13C-glucose. Pharmacological targeting of PFKFB3, an activator of glycolysis, using two chemical inhibitors results in rapid BVO restructuring, vessel regression with reduced pericyte coverage. PFKFB3 mutant BVOs also display similar structural remodelling. Proteomic analysis of the BVO secretome reveal remodelling of the extracellular matrix and differential expression of paracrine mediators such as CTGF. Treatment with recombinant CTGF recovers microvessel structure. In this work we demonstrate that BVOs rapidly undergo restructuring in response to metabolic changes and identify CTGF as a critical paracrine regulator of microvascular integrity.
Evidence of bifunctionality of carbons and metal atoms in catalyzed acetylene hydrochlorination
Authors: Giulimondi Vera , Ruiz-Ferrando Andrea , Giannakakis Georgios , Surin Ivan , Agrachev Mikhail , Jeschke Gunnar , Krumeich Frank , López Núria , Clark Adam H. , Pérez-Ramírez Javier 
Published: September 2023

AbstractCarbon supports are ubiquitous components of heterogeneous catalysts for acetylene hydrochlorination to vinyl chloride, from commercial mercury-based systems to more sustainable metal single-atom alternatives. Their potential co-catalytic role has long been postulated but never unequivocally demonstrated. Herein, we evidence the bifunctionality of carbons and metal sites in the acetylene hydrochlorination catalytic cycle. Combining operando X-ray absorption spectroscopy with other spectroscopic and kinetic analyses, we monitor the structure of single metal atoms (Pt, Au, Ru) and carbon supports (activated, non-activated, and nitrogen-doped) from catalyst synthesis, using various procedures, to operation at different conditions. Metal atoms exclusively activate hydrogen chloride, while metal-neighboring sites in the support bind acetylene. Resolving the coordination environment of working metal atoms guides theoretical simulations in proposing potential binding sites for acetylene in the support and a viable reaction profile. Expanding from single-atom to ensemble catalysis, these results reinforce the importance of optimizing both metal and support components to leverage the distinct functions of each for advancing catalyst design.
Bayesian analyses indicate bivalves did not drive the downfall of brachiopods following the Permian-Triassic mass extinction
Authors: Guo Zhen , Flannery-Sutherland Joseph T. , Benton Michael J. , Chen Zhong-Qiang 
Published: September 2023

AbstractCertain times of major biotic replacement have often been interpreted as broadly competitive, mediated by innovation in the succeeding clades. A classic example was the switch from brachiopods to bivalves as major seabed organisms following the Permian-Triassic mass extinction (PTME), ~252 million years ago. This was attributed to competitive exclusion of brachiopods by the better adapted bivalves or simply to the fact that brachiopods had been hit especially hard by the PTME. The brachiopod-bivalve switch is emblematic of the global turnover of marine faunas from Palaeozoic-type to Modern-type triggered by the PTME. Here, using Bayesian analyses, we find that unexpectedly the two clades displayed similar large-scale trends of diversification before the Jurassic. Insight from a multivariate birth-death model shows that the extinction of major brachiopod clades during the PTME set the stage for the brachiopod-bivalve switch, with differential responses to high ocean temperatures post-extinction further facilitating their displacement by bivalves. Our study strengthens evidence that brachiopods and bivalves were not competitors over macroevolutionary time scales, with extinction events and environmental stresses shaping their divergent fates.
Complex multi-fault rupture and triggering during the 2023 earthquake doublet in southeastern Türkiye
Authors: Liu Chengli , Lay Thorne , Wang Rongjiang , Taymaz Tuncay , Xie Zujun , Xiong Xiong , Irmak Tahir Serkan , Kahraman Metin , Erman Ceyhun 
Published: September 2023

AbstractTwo major earthquakes (MW 7.8 and MW 7.7) ruptured left-lateral strike-slip faults of the East Anatolian Fault Zone (EAFZ) on February 6, 2023, causing >59,000 fatalities and ~$119B in damage in southeastern Türkiye and northwestern Syria. Here we derived kinematic rupture models for the two events by inverting extensive seismic and geodetic observations using complex 5-6 segment fault models constrained by satellite observations and relocated aftershocks. The larger event nucleated on a splay fault, and then propagated bilaterally ~350 km along the main EAFZ strand. The rupture speed varied from 2.5-4.5 km/s, and peak slip was ~8.1 m. 9-h later, the second event ruptured ~160 km along the curved northern EAFZ strand, with early bilateral supershear rupture velocity (>4 km/s) followed by a slower rupture speed (~3 km/s). Coulomb Failure stress increase imparted by the first event indicates plausible triggering of the doublet aftershock, along with loading of neighboring faults.
Quantum key distribution in a packet-switched network
Authors: Mandil Reem , DiAdamo Stephen , Qi Bing , Shabani Alireza 
Published: September 2023

AbstractPacket switching revolutionized the Internet by allowing the efficient use of network resources for data transmission. In a previous work, we introduced packet switching in quantum networks as a path to the Quantum Internet and presented a proof-of-concept for its application to quantum key distribution (QKD). In this paper, we outline a three-step approach for key rate optimization in a packet-switched network. Our simulated results show that practical key rates may be achieved in a sixteen-user network with no optical storage capacity. Under certain network conditions, we may improve the key rate by using an ultra-low-loss fiber delay line to store packets during network delays. We also find that implementing cut-off storage times in a strategy analogous to real-time selection in free-space QKD can significantly enhance performance. Our work demonstrates that packet switching is imminently suitable as a platform for QKD, an important step towards developing large-scale and integrated quantum networks.
Ontology for the Avida digital evolution platform
Authors: Ortega Raúl , Wulff Enrique , Fortuna Miguel A. 
Published: September 2023

AbstractThe Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for the description of Avida, the most widely used computational approach for performing experimental evolution using digital organisms–self-replicating computer programs that evolve within a user-defined computational environment. The lack of a clearly defined vocabulary makes some biologists feel reluctant to embrace the field of digital evolution. This integrated framework empowers biologists by equipping them with the necessary tools to explore and analyze the field of digital evolution more effectively. By leveraging the vocabulary of Avida, researchers can gain deeper insights into the evolutionary processes and dynamics of digital organisms. In addition, OntoAvida allows researchers to make inference based on certain rules and constraints, facilitate the reproducibility of in silico evolution experiments and trace the provenance of the data stored in avidaDB–an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms. OntoAvida is part of the Open Biological and Biomedical Ontologies (OBO Foundry) and is available at http://www.obofoundry.org/ontology/ontoavida.html.
The first high-quality chromosome-level genome of Eretmochelys imbricata using HiFi and Hi-C data
Authors: Guo Yusong , Tang Jiao , Zhuo Zixuan , Huang Jingru , Fu Zhenli , Song Jiahao , Liu Min , Dong Zhongdian , Wang Zhongduo 
Published: September 2023

AbstractEretmochelys imbricata, a critically endangered sea turtle inhabiting tropical oceans and protected across the world, had an unknown genome sequence until now. In this study, we used HiFi reads and Hi-C technology to assemble a high-quality, chromosome-level genome of E. imbricata. The genome size was 2,138.26 Mb, with contig N50 length of 123.49 Mb and scaffold N50 of 137.21 Mb. Approximately 97.52% of the genome sequence was anchored to 28 chromosomes. A total of 20,206 protein-coding genes were predicted. We also analyzed the evolutionary relationships, gene family expansions, and positive selection of E. imbricata. Our results revealed that E. imbricata diverged from Chelonia mydas 38 million years ago and had enriched olfactory receptors and aging-related genes. Our genome will be useful for studying E. imbricata and its conservation.
High throughput compound screening in neuronal cells identifies statins as activators of ataxin 3 expression
Authors: Stahl Fabian , Schmitt Ina , Denner Philip , de Boni Laura , Wüllner Ullrich , Breuer Peter 
Published: September 2023

AbstractThe spinocerebellar ataxias (SCA) comprise a group of inherited neurodegenerative diseases. SCA3 is the most common form, caused by the expansion of CAG repeats within the ataxin 3 (ATXN3) gene. The mutation results in the expression of an abnormal protein, containing long polyglutamine (polyQ) stretches. The polyQ stretch confers a toxic gain of function and leads to misfolding and aggregation of ATXN3 in neurons. Thus, modulators of ATXN3 expression could potentially ameliorate the pathology in SCA3 patients. Therefore, we generated a CRISPR/Cas9 modified ATXN3-Exon4-Luciferase (ATXN3-LUC) genomic fusion- and control cell lines to perform a reporter cell line-based high-throughput screen comprising 2640 bioactive compounds, including the FDA approved drugs. We found no unequivocal inhibitors of, but identified statins as activators of the LUC signal in the ATXN3-LUC screening cell line. We further confirmed that Simvastatin treatment of wild type SK-N-SH cells increases ATXN3 mRNA and protein levels which likely results from direct binding of the activated sterol regulatory element binding protein 1 (SREBP1) to the ATXN3 promotor. Finally, we observed an increase of normal and expanded ATXN3 protein levels in a patient-derived cell line upon Simvastatin treatment, underscoring the potential medical relevance of our findings.
Experimental study of erodible bed scoured by the debris flow in the narrow-steep gully
Authors: Wu Yu , Ji Jiejie , Qi Shunchao , Wang Xiekang , Li Dong , Li Hongtao , Yang Xingguo , Yao Qiang 
Published: September 2023

AbstractIn recent years, debris flows have frequently erupted in the narrow-steep gully of the earthquake-hit Wenchuan region, displaying high flow velocities and powerful scouring abilities. However, few scouring studies in the narrow-steep gully have been conducted. A model experiment simulated the debris flow scouring process in a narrow-steep flume, in which several important physical parameters, including the debris flow density (ρ), flume slope (θ), and grain size of the sediment (D), were varied to investigate their influences on the erodible strength. The experimental flows were composed of 50 L of water and grains, which scoured 2.3 m of erodible bed down a steeply inclined flume. A high-speed camera photographed the scouring processes, while a 3D laser device captured the final bed shapes. The experiments show that the debris flow first collides with the sediment at the head of the gully to form a pit, which is enlarged by continuous impact; the velocity of the debris flow out of the pit is significantly reduced due to the change in flow direction, resulting in a much lesser scouring effect after the pit; and finally, the gully bed presents the shape of a pit at the entrance and a groove in the middle and rear. The critical scour slope, where the gully bed shows scouring, increases with increasing debris flow density but decreases with increasing grain size of sediment. Following scouring, the maximum scouring depth is further positively correlated with the flume slope. In narrow-steep gullies, the gully bed is extremely susceptible to scouring by debris flow with a low density, and even headward erosion appears, at which the maximum scouring depth only increased from 148.04 to 149.97 mm, but the erosion amount had a significant increase of 36.9%. The research results have an important significance for revealing the disaster-causing phenomena and mechanisms of debris flows in the narrow-steep gully.
Cellular shortening and calcium dynamics are improved by noisy stimulus in a model of cardiomyopathy
Authors: Morales-Rubio Russell , Bernal-Ramírez Judith , Rubio-Infante Nestor , Luévano-Martínez Luis A. , Ríos Amelia , Escalante Bruno A. , García-Rivas Gerardo , Rodríguez González Jesús 
Published: September 2023

AbstractNoise is present in cell biology. The capability of cells to respond to noisy environment have become essential. This study aimed to investigate whether noise can enhance the contractile response and Ca2+ handling in cardiomyocytes from a cardiomyopathy model. Experiments were conducted in an experimental setup with Gaussian white noise, frequency, and amplitude control to stimulate myocytes. Cell shortening, maximal shortening velocity, time to peak shortening, and time to half relaxation variables were recorded to cell shortening. Ca2+ transient amplitude and raise rate variables were registered to measure Ca2+ transients. Our results for cell shortening, Ca2+ transient amplitude, and raise rate suggest that cell response improve when myocytes are noise stimulated. Also, cell shortening, maximal shortening velocity, Ca2+ transient amplitude, and raise improves in control cells. Altogether, these findings suggest novel characteristics in how cells improve their response in a noisy environment.
A novel retinoic acid receptor-γ agonist antagonizes immune checkpoint resistance in lung cancers by altering the tumor immune microenvironment
Authors: Wei Cheng-Hsin , Huang Lu , Kreh Blair , Liu Xiuxia , Tyutyunyk-Massey Liliya , Kawakami Masanori , Chen Zibo , Shi Mi , Kozlov Serguei , Chan King C. , Andresson Thorkell , Carrington Mary , Vuligonda Vidyasagar , Sanders Martin E. , Horowitz Amir , Hwu Patrick , Peng Weiyi , Dmitrovsky Ethan , Liu Xi 
Published: September 2023

AbstractAll-trans-retinoic acid (ATRA), the retinoic acid receptors (RARs) agonist, regulates cell growth, differentiation, immunity, and survival. We report that ATRA-treatment repressed cancer growth in syngeneic immunocompetent, but not immunodeficient mice. The tumor microenvironment was implicated: CD8+ T cell depletion antagonized ATRA’s anti-tumorigenic effects in syngeneic mice. ATRA-treatment with checkpoint blockade did not cooperatively inhibit murine lung cancer growth. To augment ATRA’s anti-tumorigenicity without promoting its pro-tumorigenic potential, an RARγ agonist (IRX4647) was used since it regulates T cell biology. Treating with IRX4647 in combination with an immune checkpoint (anti-PD-L1) inhibitor resulted in a statistically significant suppression of syngeneic 344SQ lung cancers in mice—a model known for its resistance to checkpoints and characterized by low basal T cell and PD-L1 expression. This combined treatment notably elevated CD4+ T-cell presence within the tumor microenvironment and increased IL-5 and IL-13 tumor levels, while simultaneously decreasing CD38 in the tumor stroma. IL-5 and/or IL-13 treatments increased CD4+ more than CD8+ T-cells in mice. IRX4647-treatment did not appreciably affect in vitro lung cancer growth, despite RARγ expression. Pharmacokinetic analysis found IRX4647 plasma half-life was 6 h in mice. Yet, RARα antagonist (IRX6696)-treatment with anti-PD-L1 did not repress syngeneic lung cancer growth. Together, these findings provide a rationale for a clinical trial investigating an RARγ agonist to augment check point blockade response in cancers.
Inferring the diurnal variability of OH radical concentrations over the Amazon from BVOC measurements
Authors: Ringsdorf A. , Edtbauer A. , Vilà-Guerau de Arellano J. , Pfannerstill E. Y. , Gromov S. , Kumar V. , Pozzer A. , Wolff S. , Tsokankunku A. , Soergel M. , Sá M. O. , Araújo A. , Ditas F. , Poehlker C. , Lelieveld J. , Williams J. 
Published: September 2023

AbstractThe atmospheric oxidation of biogenic volatile organic compounds (BVOC) by OH radicals over tropical rainforests impacts local particle production and the lifetime of globally distributed chemically and radiatively active gases. For the pristine Amazon rainforest during the dry season, we empirically determined the diurnal OH radical variability at the forest-atmosphere interface region between 80 and 325 m from 07:00 to 15:00 LT using BVOC measurements. A dynamic time warping approach was applied showing that median averaged mixing times between 80 to 325 m decrease from 105 to 15 min over this time period. The inferred OH concentrations show evidence for an early morning OH peak (07:00–08:00 LT) and an OH maximum (14:00 LT) reaching 2.2 (0.2, 3.8) × 106 molecules cm−3 controlled by the coupling between BVOC emission fluxes, nocturnal NOx accumulation, convective turbulence, air chemistry and photolysis rates. The results were evaluated with a turbulence resolving transport (DALES), a regional scale (WRF-Chem) and a global (EMAC) atmospheric chemistry model.
Two new species of Trichocomaceae (Eurotiales), accommodated in Rasamsonia and Talaromyces section Bacillispori, from the Czech Republic
Authors: Špetík Milan , Eichmeier Aleš , Burgová Jana , Houbraken Jos 
Published: September 2023

AbstractDuring a previous study on microfungi associated with clematis roots, Penicillium-like fungi were isolated and identified based on morphology. In this study, we subjected those strains to a detailed examination which led to the proposal of two taxonomic novelties, named Rasamsonia chlamydospora and Talaromyces clematidis. The first taxon is characterized by rough-walled mycelium, acerose to flask shaped phialides, cylindrical conidia and by production of chlamydospore-like structures. The four-loci-based phylogeny analysis delineated the taxon as a taxonomic novelty in Rasamsonia. Talaromyces clematidis is characterized by restricted growth on Czapek yeast extract agar, dichloran 18% glycerol agar and yeast extract sucrose agar, and production of yellow ascomata on oatmeal agar. Phylogenetic analyses placed this taxon as a taxonomic novelty in Talaromyces sect. Bacillispori. Both taxa are introduced here with detailed descriptions, photoplates and information on their phylogenetic relationship with related species.
Differential regulatory control of curli (csg) gene expression in Salmonella enterica serovar Typhi requires more than a functional CsgD regulator
Authors: Ou Camille , Dozois Charles M. , Daigle France 
Published: September 2023

AbstractThe human-specific Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a systemic disease with no known reservoir. Curli fimbriae are major components of biofilm produced by Salmonella and are encoded by the csg gene cluster (csgBAC and csgDEFG). The role of curli in S. Typhi is unknown, although detection of anti-curli antibodies suggests they are produced during host infection. In this study, we investigated curli gene expression in S. Typhi. We demonstrated that the CsgD regulatory protein binds weakly to the csgB promoter. Yet, replacing S. Typhi csgD with the csgD allele from S. Typhimurium did not modify the curli negative phenotype on Congo Red medium suggesting that differential regulation of curli gene expression in S. Typhi is not dependent on modification of the CsgD regulator. The entire csg gene cluster from S. Typhimurium was also cloned into S. Typhi, but again, despite introduction of a fully functional csg gene cluster from S. Typhimurium, curli were still not detected in S. Typhi. Thus, in addition to intrinsic genomic differences in the csg gene cluster that have resulted in production of a modified CsgD protein, S. Typhi has likely undergone other changes independent of the csg gene cluster that have led to distinctive regulation of csg genes compared to other Salmonella serovars.
Soil moisture controls the partitioning of carbon stocks across a managed boreal forest landscape
Authors: Larson Johannes , Wallerman Jörgen , Peichl Matthias , Laudon Hjalmar 
Published: September 2023

AbstractBoreal forests sequester and store vast carbon (C) pools that may be subject to significant feedback effects induced by climatic warming. The boreal landscape consists of a mosaic of forests and peatlands with wide variation in total C stocks, making it important to understand the factors controlling C pool sizes in different ecosystems. We therefore quantified the total C stocks in the organic layer, mineral soil, and tree biomass in 430 plots across a 68 km2 boreal catchment. The organic layer held the largest C pool, accounting for 39% of the total C storage; tree and mineral C pools accounted for 38% and 23%, respectively. The size of the soil C pool was positively related to modelled soil moisture conditions, especially in the organic soil layer (R2 = 0.50). Conversely, the tree C pool exhibited a unimodal relationship: storage was highest under intermediate wetness conditions. The magnitude and variation in the total soil C stocks observed in this work were comparable to those found at the national level in Sweden, suggesting that C accumulation in boreal landscapes is more sensitive to local variation resulting primarily from differences in soil moisture conditions than to regional differences in climate, nitrogen deposition, and parent material.