bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of the visual system in ray-finned fishes
Authors: Hofmann Michael H. , Gebhardt Isabelle C. 
Published: December 2023

Abstract
The vertebrate eye allows to capture an enormous amount of detail about the surrounding world which can only be exploited with sophisticated central information processing. Furthermore, vision is an active process due to head and eye movements that enables the animal to change the gaze and actively select objects to investigate in detail. The entire system requires a coordinated coevolution of its parts to work properly. Ray-finned fishes offer a unique opportunity to study the evolution of the visual system due to the high diversity in all of its parts. Here, we are bringing together information on retinal specializations (fovea), central visual centers (brain morphology studies), and eye movements in a large number of ray-finned fishes in a cladistic framework. The nucleus glomerulosus-inferior lobe system is well developed only in Acanthopterygii. A fovea, independent eye movements, and an enlargement of the nucleus glomerulosus-inferior lobe system coevolved at least five times independently within Acanthopterygii. This suggests that the nucleus glomerulosus-inferior lobe system is involved in advanced object recognition which is especially well developed in association with a fovea and independent eye movements. None of the non-Acanthopterygii have a fovea (except for some deep sea fish) or independent eye movements and they also lack important parts of the glomerulosus-inferior lobe system. This suggests that structures for advanced visual object recognition evolved within ray-finned fishes independent of the ones in tetrapods and non-ray-finned fishes as a result of a coevolution of retinal, central, and oculomotor structures.
Water Stress Dominates 21st‐Century Tropical Land Carbon Uptake
Authors: Levine Paul A. , Bloom A. Anthony , Bowman Kevin W. , Reager John T. , Worden John R. , Liu Junjie , Parazoo Nicholas C. , Meyer Victoria , Konings Alexandra G. , Longo Marcos 
Published: December 2023

AbstractWater stress regulates land‐atmosphere carbon dioxide (CO2) exchanges in the tropics; however, its role remains poorly characterized due to the confounding roles of radiation, temperature and canopy dynamics. In particular, uncertainty stems from the relative roles of plant‐available water (supply) and atmospheric water vapor deficit (demand) as mechanistic drivers of photosynthetic carbon (C) uptake variability. Using satellite measurements of gravity, CO2 and fluorescence to constrain a mechanistic carbon‐water cycle model from 2001 to 2018, we found that the interannual variability (IAV) of water stress on photosynthetic C uptake was 52% greater than the combined effects of other factors. Surprisingly, the dominance of water stress on C uptake IAV was greater in the wet tropics (94%) than in the dry tropics (26%). Plant‐available water supply and atmospheric demand both contributed to the IAV of water stress on photosynthetic C uptake across the tropics, but the IAV of demand effects was 21% greater than the IAV of supply effects (33% greater in the wet tropics and 6% greater in the dry tropics). We found that the IAV of water stress on C uptake was 24% greater than the IAV of the combination of other factors in the net land‐atmosphere C sink in the whole tropics, 26% greater in the wet tropics, and 7% greater in the dry tropics. Given the recent trends in tropical precipitation and atmospheric humidity, our findings indicate that water stress——from both supply and demand——will likely dominate the climate response of land C sink across tropical ecosystems in the coming decades.
Lower‐Crustal Normal Faulting and Lithosphere Rheology in the Atlas Foreland
Authors: Wimpenny Sam , Craig Tim , Blackwell Alice 
Published: December 2023

AbstractEarthquakes beneath the foreland basins of the Andes and Tibet are rare but follow a simple pattern, with normal faulting from 0 to 20 km depth and reverse‐faulting from 30 to 50 km depth. The switch in faulting style with depth suggests that the stresses generated by foreland flexure are large enough to break faults, with opposite senses of horizontal strain either side of a neutral surface in the mid‐crust. In this study, we document a 31 km‐deep Mw 5.2 normal‐faulting earthquake in the forelands of the Algerian Atlas Mountains near Biskra. The Biskra earthquake is of interest, as it indicates that the lower crust of the Atlas forelands is in extension at the same depth that the Tibetan and Andean forelands are in compression. In order to match the gravity anomalies and the depth of normal faulting near Biskra, we find that models of lithospheric flexure require the neutral surface to be >35 km deep and at least the top 5–10 km of the lithospheric mantle supports elastic bending stresses. The differences in the pattern of earthquakes between the forelands of Tibet, the Andes and the Algerian Atlas can be explained by differences in the buoyancy forces acting between these mountain ranges and their lowlands that place the forelands into varying amounts of net compression. Our results suggest the upper mantle beneath cratonic foreland lithosphere may therefore support bending stresses of the order of 10s of MPa, likely because it is cool and the strain rates associated with bending are low.
RNA-mediated symmetry breaking enables singular olfactory receptor choice
Authors: Pourmorady Ariel D. , Bashkirova Elizaveta V. , Chiariello Andrea M. , Belagzhal Houda , Kodra Albana , Duffié Rachel , Kahiapo Jerome , Monahan Kevin , Pulupa Joan , Schieren Ira , Osterhoudt Alexa , Dekker Job , Nicodemi Mario , Lomvardas Stavros 
Published: December 2023

AbstractOlfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, where every olfactory neuron stably transcribes one of approximately 2,000 or more OR alleles1,2. OR gene choice is mediated by a multichromosomal enhancer hub that activates transcription at a single OR3,4, followed by OR-translation-dependent feedback that stabilizes this choice5,6. Here, using single-cell genomics, we show formation of many competing hubs with variable enhancer composition, only one of which retains euchromatic features and transcriptional competence. Furthermore, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, whereas OR RNA inhibits transcription of competing ORs over distance, promoting transition to transcriptional singularity. Whereas OR transcription is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, indicating that there may be sequential non-coding and coding mechanisms that are implemented by OR alleles for transcriptional prevalence. We propose that coding OR mRNAs possess non-coding functions that influence nuclear architecture, enhance their own transcription and inhibit transcription from their competitors, with generalizable implications for probabilistic cell fate decisions.
Structures of the promoter-bound respiratory syncytial virus polymerase
Authors: Cao Dongdong , Gao Yunrong , Chen Zhenhang , Gooneratne Inesh , Roesler Claire , Mera Cristopher , D’Cunha Paul , Antonova Anna , Katta Deepak , Romanelli Sarah , Wang Qi , Rice Samantha , Lemons Wesley , Ramanathan Anita , Liang Bo 
Published: December 2023

AbstractThe respiratory syncytial virus (RSV) polymerase is a multifunctional RNA-dependent RNA polymerase composed of the large (L) protein and the phosphoprotein (P). It transcribes the RNA genome into ten viral mRNAs and replicates full-length viral genomic and antigenomic RNAs1. The RSV polymerase initiates RNA synthesis by binding to the conserved 3′-terminal RNA promoters of the genome or antigenome2. However, the lack of a structure of the RSV polymerase bound to the RNA promoter has impeded the mechanistic understanding of RSV RNA synthesis. Here we report cryogenic electron microscopy structures of the RSV polymerase bound to its genomic and antigenomic viral RNA promoters, representing two of the first structures of an RNA-dependent RNA polymerase in complex with its RNA promoters in non-segmented negative-sense RNA viruses. The overall structures of the promoter-bound RSV polymerases are similar to that of the unbound (apo) polymerase. Our structures illustrate the interactions between the RSV polymerase and the RNA promoters and provide the structural basis for the initiation of RNA synthesis at positions 1 and 3 of the RSV promoters. These structures offer a deeper understanding of the pre-initiation state of the RSV polymerase and could aid in antiviral research against RSV.
Online searches to evaluate misinformation can increase its perceived veracity
Authors: Aslett Kevin , Sanderson Zeve , Godel William , Persily Nathaniel , Nagler Jonathan , Tucker Joshua A. 
Published: December 2023

AbstractConsiderable scholarly attention has been paid to understanding belief in online misinformation1,2, with a particular focus on social networks. However, the dominant role of search engines in the information environment remains underexplored, even though the use of online search to evaluate the veracity of information is a central component of media literacy interventions3–5. Although conventional wisdom suggests that searching online when evaluating misinformation would reduce belief in it, there is little empirical evidence to evaluate this claim. Here, across five experiments, we present consistent evidence that online search to evaluate the truthfulness of false news articles actually increases the probability of believing them. To shed light on this relationship, we combine survey data with digital trace data collected using a custom browser extension. We find that the search effect is concentrated among individuals for whom search engines return lower-quality information. Our results indicate that those who search online to evaluate misinformation risk falling into data voids, or informational spaces in which there is corroborating evidence from low-quality sources. We also find consistent evidence that searching online to evaluate news increases belief in true news from low-quality sources, but inconsistent evidence that it increases belief in true news from mainstream sources. Our findings highlight the need for media literacy programmes to ground their recommendations in empirically tested strategies and for search engines to invest in solutions to the challenges identified here.
Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts
Authors: Ferretti Luca , Wymant Chris , Petrie James , Tsallis Daphne , Kendall Michelle , Ledda Alice , Di Lauro Francesco , Fowler Adam , Di Francia Andrea , Panovska-Griffiths Jasmina , Abeler-Dörner Lucie , Charalambides Marcos , Briers Mark , Fraser Christophe 
Published: December 2023

AbstractHow likely is it to become infected by SARS-CoV-2 after being exposed? Almost everyone wondered about this question during the COVID-19 pandemic. Contact-tracing apps1,2 recorded measurements of proximity3 and duration between nearby smartphones. Contacts—individuals exposed to confirmed cases—were notified according to public health policies such as the 2 m, 15 min guideline4,5, despite limited evidence supporting this threshold. Here we analysed 7 million contacts notified by the National Health Service COVID-19 app6,7 in England and Wales to infer how app measurements translated to actual transmissions. Empirical metrics and statistical modelling showed a strong relation between app-computed risk scores and actual transmission probability. Longer exposures at greater distances had risk similar to that of shorter exposures at closer distances. The probability of transmission confirmed by a reported positive test increased initially linearly with duration of exposure (1.1% per hour) and continued increasing over several days. Whereas most exposures were short (median 0.7 h, interquartile range 0.4–1.6), transmissions typically resulted from exposures lasting between 1 h and several days (median 6 h, interquartile range 1.4–28). Households accounted for about 6% of contacts but 40% of transmissions. With sufficient preparation, privacy-preserving yet precise analyses of risk that would inform public health measures, based on digital contact tracing, could be performed within weeks of the emergence of a new pathogen.
Accurate detection of identity-by-descent segments in human ancient DNA
Authors: Ringbauer Harald , Huang Yilei , Akbari Ali , Mallick Swapan , Olalde Iñigo , Patterson Nick , Reich David 
Published: December 2023

AbstractLong DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.
BridgePRS leverages shared genetic effects across ancestries to increase polygenic risk score portability
Authors: Hoggart Clive J. , Choi Shing Wan , García-González Judit , Souaiaia Tade , Preuss Michael , O’Reilly Paul F. 
Published: December 2023

AbstractHere we present BridgePRS, a novel Bayesian polygenic risk score (PRS) method that leverages shared genetic effects across ancestries to increase PRS portability. We evaluate BridgePRS via simulations and real UK Biobank data across 19 traits in individuals of African, South Asian and East Asian ancestry, using both UK Biobank and Biobank Japan genome-wide association study summary statistics; out-of-cohort validation is performed in the Mount Sinai (New York) BioMe biobank. BridgePRS is compared with the leading alternative, PRS-CSx, and two other PRS methods. Simulations suggest that the performance of BridgePRS relative to PRS-CSx increases as uncertainty increases: with lower trait heritability, higher polygenicity and greater between-population genetic diversity; and when causal variants are not present in the data. In real data, BridgePRS has a 61% larger average R2 than PRS-CSx in out-of-cohort prediction of African ancestry samples in BioMe (P = 6 × 10−5). BridgePRS is a computationally efficient, user-friendly and powerful approach for PRS analyses in non-European ancestries.
Anodal cerebellar t-DCS impacts skill learning and transfer on a robotic surgery training task
Authors: Caccianiga Guido , Mooney Ronan A. , Celnik Pablo A. , Cantarero Gabriela L. , Brown Jeremy D. 
Published: December 2023

AbstractThe cerebellum has demonstrated a critical role during adaptation in motor learning. However, the extent to which it can contribute to the skill acquisition of complex real-world tasks remains unclear. One particularly challenging application in terms of motor activities is robotic surgery, which requires surgeons to complete complex multidimensional visuomotor tasks through a remotely operated robot. Given the need for high skill proficiency and the lack of haptic feedback, there is a pressing need for understanding and improving skill development. We investigated the effect of cerebellar transcranial direct current stimulation applied during the execution of a robotic surgery training task. Study participants received either real or sham stimulation while performing a needle driving task in a virtual (simulated) and a real-world (actual surgical robot) setting. We found that cerebellar stimulation significantly improved performance compared to sham stimulation at fast (more demanding) execution speeds in both virtual and real-world training settings. Furthermore, participants that received cerebellar stimulation more effectively transferred the skills they acquired during virtual training to the real world. Our findings underline the potential of non-invasive brain stimulation to enhance skill learning and transfer in real-world relevant tasks and, more broadly, its potential for improving complex motor learning.
On chaos control of nonlinear fractional Newton-Leipnik system via fractional Caputo-Fabrizio derivatives
Authors: Almutairi Najat , Saber Sayed 
Published: December 2023

AbstractIn this work, we present a design for a Newton-Leipnik system with a fractional Caputo-Fabrizio derivative to explain its chaotic characteristics. This time-varying fractional Caputo-Fabrizio derivative approach is applied to solve the model numerically, and to check the solution’s existence and uniqueness. The existence and uniqueness of results of a fractional-order model under the Caputo-Fabrizio fractional operator have been proved by fixed point theory. As well, we achieved a stable result by applying the Ulam-Hyers concept. Chaos is controlled by linear controllers. Furthermore, the Lyapunov exponent of the system indicates that the chaos control findings are accurate. Based on weighted covariant Lyapunov vectors we construct a background covariance matrix using the Kaplan-Yorke dimension. Using a numerical example, this suggested method is illustrated for its applicability and efficiency.
Synthesis of COF-SO3H immobilized on manganese ferrite nanoparticles as an efficient nanocomposite in the preparation of spirooxindoles
Authors: Moein Najafabadi Samira , Safaei Ghomi Javad 
Published: December 2023

AbstractThe synthesis of sulfonamide-functionalized magnetic porous nanocomposites is highly significant in chemistry due to their exceptional properties and potential as catalysts. COFs are a new class of organic porous polymers and have significant advantages such as low density, high chemical and thermal stability, and mechanical strength. Therefore, we decided to synthesize COFs based on magnetic nanoparticles, by doing so, we can also prevent the agglomeration of MnFe2O4. MnFe2O4@COF–SO3H possesses a large specific surface area, supermagnetism, and is acidic, making it an optimal catalyst for organic reactions. This particular catalyst was effectively employed in the green and rapid synthesis of various spiro-pyrano chromenes, while several analytical techniques were utilized to analyze its structural integrity and functional groups. The role of a specific site of MnFe2O4@COF–SO3H was confirmed through different control experiments in a one-pot reaction mechanism. It was determined that MnFe2O4@COF–SO3H acts as a bifunctional acid–base catalyst in the one-pot preparation of spirooxindole derivatives. The formation of a spiro skeleton in the multicomponent reaction involved the construction of three new σ bonds (one C–O bond and two C–C bonds) within a single process. The efficiency of the MnFe2O4@COF–SO3H complex is investigated in the synthesis of spirooxindoles of malononitrile, and various isatins with 1,3‐dicarbonyles. The nanocatalyst demonstrated excellent catalytic activity that gave the corresponding coupling products good to excellent yields. Furthermore, the heterogeneous magnetic nanocatalyst used in this study demonstrated recoverability after five cycles with minimal loss of activity.
Simplicial complex entropy for time series analysis
Authors: Guzmán-Vargas Lev , Zabaleta-Ortega Alvaro , Guzmán-Sáenz Aldo 
Published: December 2023

AbstractThe complex behavior of many systems in nature requires the application of robust methodologies capable of identifying changes in their dynamics. In the case of time series (which are sensed values of a system during a time interval), several methods have been proposed to evaluate their irregularity. However, for some types of dynamics such as stochastic and chaotic, new approaches are required that can provide a better characterization of them. In this paper we present the simplicial complex approximate entropy, which is based on the conditional probability of the occurrence of elements of a simplicial complex. Our results show that this entropy measure provides a wide range of values with details not easily identifiable with standard methods. In particular, we show that our method is able to quantify the irregularity in simulated random sequences and those from low-dimensional chaotic dynamics. Furthermore, it is possible to consistently differentiate cardiac interbeat sequences from healthy subjects and from patients with heart failure, as well as to identify changes between dynamical states of coupled chaotic maps. Our results highlight the importance of the structures revealed by the simplicial complexes, which holds promise for applications of this approach in various contexts.
Maternal determinants of dietary patterns in infancy and early childhood in the Growing up in New Zealand cohort
Authors: Gontijo de Castro Teresa , Lovell Amy , Santos Leonardo Pozza , Jones Beatrix , Wall Clare 
Published: December 2023

AbstractGiven the importance of diet in early life, assessing children’s diet is crucial to guide interventions. Using data from a nationally generalizable New Zealand (NZ) birth cohort we examined children’s dietary patterns at 9- (n = 6259), 24- (n = 6292), and 54-months (n = 6131), and their association with maternal sociodemographic and health behaviours. At each time-point, children's dietary patterns were identified using principal components analysis. We then used multivariate linear regression to examine associations between each pattern and maternal variables. At 9-, 24- and 54-months, two dietary patterns were identified, explaining 36.4%, 35.3% and 33.6% of children's intake variability, respectively. Refined high in sugar, salt and fat dietary pattern, at all time-points, was characterized by high positive loadings in white/refined breads and cereals, and items with high sugar, sodium, and fat content. At 24-months, Refined high in sugar, salt and fat also included a high positive loading with protein food groups. Fruit and vegetables dietary pattern, at all time-points, had high positive loadings for fruits and vegetables (with type varying across time-points). Fruit and vegetables also included high loading in whole grain options of breads and cereals at 24-months and the protein food group was part of this dietary pattern at 9- and 54-months. Children’s scores on the Refined high in sugar, salt and fat pattern had strong associations with maternal smoking habits, education level, ethnicity, and maternal scores in the “Junk” and “Traditional/White bread” dietary patterns (constructed from an antenatal interview). Children’s scores on the Fruit and vegetables pattern had strong associations with the maternal scores in the dietary pattern “Health Conscious”. Interventions to improve diet in early life in NZ need to be responsive to ethnicity and suitable for people of all education levels. Interventions that improve maternal health behaviours may also improve children’s diet.