bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wet and Dry Cold Surges Over the Maritime Continent
Authors: Tan I. , Reeder M. J. , Singh M. S. , Birch C. E. , Peatman S. C. 
Published: June 2023

AbstractCold surges are synoptic weather systems that occur over the Maritime Continent during the boreal winter. They are characterized by the strengthening of prevailing low‐level northerly to north‐easterly winds, temperature falls of a few degrees over several days, and in some cases, heavy prolonged rainfall and flooding. We investigate the synoptic structure and development of cold surges through composites of dry, moderate and wet surges. Each surge category is defined by the distribution of precipitation averaged within a specified domain over the equatorial South China Sea. Dry surges are characterized by cross‐equatorial flow and positive mean sea‐level pressure anomalies that reach the Southern Hemisphere, and enhanced descent or weaker ascent. Wet surges are characterized by limited cross‐equatorial flow, low‐pressure anomalies over the equator, and enhanced moisture and ascent. The local diurnal precipitation patterns are consistent with the convection being controlled by the mid‐tropospheric buoyancy of an idealized entraining plume. This buoyancy diagnostic suggests that wet surges are characterized by a moister free troposphere because this reduces the effect of entrainment and allows deep convection to develop. On the large scale, the environment in which wet or dry cold surges form is closely related to the Madden‐Julian Oscillation (MJO) phase. Dry and moderate surges occur predominantly in the suppressed phases of the MJO, while wet surges often herald the eastward propagation of the MJO convective envelope. Finally, convectively active phases in the Australian monsoon are more likely following dry cold surges, and are sometimes associated with the MJO.
Climate Evolution Through the Onset and Intensification of Northern Hemisphere Glaciation
Authors: McClymont E. L. , Ho S. L. , Ford H. L. , Bailey I. , Berke M. A. , Bolton C. T. , De Schepper S. , Grant G. R. , Groeneveld J. , Inglis G. N. , Karas C. , Patterson M. O. , Swann G. E. A. , Thirumalai K. , White S. M. , Alonso‐Garcia M. , Anand P. , Hoogakker B. A. A. , Littler K. , Petrick B. F. , Risebrobakken B. , Abell J. T. , Crocker A. J. , de Graaf F. , Feakins S. J. , Hargreaves J. C. , Jones C. L. , Markowska M. , Ratnayake A. S. , Stepanek C. , Tangunan D. 
Published: June 2023

AbstractThe Pliocene Epoch (∼5.3–2.6 million years ago, Ma) was characterized by a warmer than present climate with smaller Northern Hemisphere ice sheets, and offers an example of a climate system in long‐term equilibrium with current or predicted near‐future atmospheric CO2concentrations (pCO2). A long‐term trend of ice‐sheet expansion led to more pronounced glacial (cold) stages by the end of the Pliocene (∼2.6 Ma), known as the “intensification of Northern Hemisphere Glaciation” (iNHG). We assessed the spatial and temporal variability of ocean temperatures and ice‐volume indicators through the late Pliocene and early Pleistocene (from 3.3 to 2.4 Ma) to determine the character of this climate transition. We identified asynchronous shifts in long‐term means and the pacing and amplitude of shorter‐term climate variability, between regions and between climate proxies. Early changes in Antarctic glaciation and Southern Hemisphere ocean properties occurred even during the mid‐Piacenzian warm period (∼3.264–3.025 Ma) which has been used as an analog for future warming. Increased climate variability subsequently developed alongside signatures of larger Northern Hemisphere ice sheets (iNHG). Yet, some regions of the ocean felt no impact of iNHG, particularly in lower latitudes. Our analysis has demonstrated the complex, non‐uniform and globally asynchronous nature of climate changes associated with the iNHG. Shifting ocean gateways and ocean circulation changes may have pre‐conditioned the later evolution of ice sheets with falling atmosphericpCO2. Further development of high‐resolution, multi‐proxy reconstructions of climate is required so that the full potential of the rich and detailed geological records can be realized.
ChatGPT: A Threat or an Opportunity for Scientists?
Authors: Florindo F. 
Published: June 2023

AbstractThe emergence of artificial intelligence (AI) has brought about numerous opportunities and challenges for scientists in various fields. One notable advancement in AI is OpenAI’s ChatGPT (Generative Pretrained Transformer), a powerful language model based on the GPT‐3.5 architecture that can generate text resembling human‐like responses. Like any technological advancement, the risk‐benefit opinions of ChatGPT diverge among scientists. This paper explores the implications of AI and, in particular, ChatGPT, delving into its potential as both a threat and an opportunity for scientists. It examines the risks associated with misinformation, ethical considerations, and the impact on traditional research processes. Ultimately, the argument put forth is that while ChatGPT and chatbots like it do present challenges, they also have the potential to significantly transform scientific inquiry and foster innovation.
A New Model for Charge Separation by Proton Transfer During Collision Between Ice Particles in Thunderstorms
Authors: Kang Heon , Jayaratne Rohan , Williams Earle 
Published: June 2023

AbstractField and laboratory observations strongly support the view that the development of electric fields in thunderstorms is caused by charge separation during rebounding collisions between ice crystals and graupels, followed by their gravitational separation. Although several plausible microphysical mechanisms have been proposed to explain the physics of charge separation, none have been found to be fully consistent with the experimental evidence, and a fresh approach is necessary. We propose a new mechanism for charge separation in ice‐ice collisions based on the fundamental molecular mechanism of charge transport in ice, involving the diffusion of H+ ions (excess protons or positive ionic defects) via a proton hopping relay along the hydrogen‐bond network of ice and the trapping and release of H+ ions from L‐orientational defects. The collision of two ice particles leads to the formation of a transient crystalline ice bridge at the contact point, which is spontaneously driven by the tendency for ice sintering, permitting rapid H+ diffusion between the two particles. Charge separation is achieved by the asymmetry in the concentrations of H+ ions or L‐orientational defects between the two ice surfaces. The proposed H+ transport mechanism successfully explains the direction and magnitude of charge transfer as well as its dependence on the relative growth rates of the two ice surfaces observed in laboratory studies. In addition, it offers a molecular‐level interpretation of the empirical rule that, during a collision, the faster‐growing ice surface is positively charged at the expense of negative charging of the slower‐growing or sublimating ice surface.
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
Authors: Tóth Endre Gy. , Cseke Klára , Benke Attila , Lados Botond B. , Tomov Vladimir T. , Zhelev Petar , Kámpel József D. , Borovics Attila , Köbölkuti Zoltán A. 
Published: June 2023

AbstractKnowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species’ significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.
Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus
Authors: Pénzes Judit J. , Pham Hanh T. , Chipman Paul , Smith Emmanuel W. , McKenna Robert , Tijssen Peter 
Published: June 2023

AbstractParvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, “pinning” the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.
Relationships of temperature and biodiversity with stability of natural aquatic food webs
Authors: Zhao Qinghua , Van den Brink Paul J. , Xu Chi , Wang Shaopeng , Clark Adam T. , Karakoç Canan , Sugihara George , Widdicombe Claire E. , Atkinson Angus , Matsuzaki Shin-ichiro S. , Shinohara Ryuichiro , He Shuiqing , Wang Yingying. X. G. , De Laender Frederik 
Published: June 2023

AbstractTemperature and biodiversity changes occur in concert, but their joint effects on ecological stability of natural food webs are unknown. Here, we assess these relationships in 19 planktonic food webs. We estimate stability as structural stability (using the volume contraction rate) and temporal stability (using the temporal variation of species abundances). Warmer temperatures were associated with lower structural and temporal stability, while biodiversity had no consistent effects on either stability property. While species richness was associated with lower structural stability and higher temporal stability, Simpson diversity was associated with higher temporal stability. The responses of structural stability were linked to disproportionate contributions from two trophic groups (predators and consumers), while the responses of temporal stability were linked both to synchrony of all species within the food web and distinctive contributions from three trophic groups (predators, consumers, and producers). Our results suggest that, in natural ecosystems, warmer temperatures can erode ecosystem stability, while biodiversity changes may not have consistent effects.
Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization
Authors: Jin Xiaofan , Yu Feiqiao B. , Yan Jia , Weakley Allison M. , Dubinkina Veronika , Meng Xiandong , Pollard Katherine S. 
Published: June 2023

AbstractMicrobial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.
Isolation of full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of Escherichia coli
Authors: Robinson Michael-Paul , Jung Jinjoo , Lopez-Barbosa Natalia , Chang Matthew , Li Mingji , Jaroentomeechai Thapakorn , Cox Emily C. , Zheng Xiaolu , Berkmen Mehmet , DeLisa Matthew P. 
Published: June 2023

AbstractHere we describe a facile and robust genetic selection for isolating full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of redox-engineered Escherichia coli cells. The method is based on the transport of a bifunctional substrate comprised of an antigen fused to chloramphenicol acetyltransferase, which allows positive selection of bacterial cells co-expressing cytoplasmic IgGs called cyclonals that specifically capture the chimeric antigen and sequester the antibiotic resistance marker in the cytoplasm. The utility of this approach is first demonstrated by isolating affinity-matured cyclonal variants that specifically bind their cognate antigen, the leucine zipper domain of a yeast transcriptional activator, with subnanomolar affinities, which represent a ~20-fold improvement over the parental IgG. We then use the genetic assay to discover antigen-specific cyclonals from a naïve human antibody repertoire, leading to the identification of lead IgG candidates with affinity and specificity for an influenza hemagglutinin-derived peptide antigen.
Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries
Authors: Gert Krista R. B. , Panser Karin , Surm Joachim , Steinmetz Benjamin S. , Schleiffer Alexander , Jovine Luca , Moran Yehu , Kondrashov Fyodor , Pauli Andrea 
Published: June 2023

AbstractMolecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization.
Liquid metal droplets bouncing higher on thicker water layer
Authors: Dai Yuhang , Li Minfei , Ji Bingqiang , Wang Xiong , Yang Siyan , Yu Peng , Wang Steven , Hao Chonglei , Wang Zuankai 
Published: June 2023

AbstractLiquid metal (LM) has gained increasing attention for a wide range of applications, such as flexible electronics, soft robots, and chip cooling devices, owing to its low melting temperature, good flexibility, and high electrical and thermal conductivity. In ambient conditions, LM is susceptible to the coverage of a thin oxide layer, resulting in unwanted adhesion with underlying substrates that undercuts its originally high mobility. Here, we discover an unusual phenomenon characterized by the complete rebound of LM droplets from the water layer with negligible adhesion. More counterintuitively, the restitution coefficient, defined as the ratio between the droplet velocities after and before impact, increases with water layer thickness. We reveal that the complete rebound of LM droplets originates from the trapping of a thinly low-viscosity water lubrication film that prevents droplet-solid contact with low viscous dissipation, and the restitution coefficient is modulated by the negative capillary pressure in the lubrication film as a result of the spontaneous spreading of water on the LM droplet. Our findings advance the fundamental understanding of complex fluids’ droplet dynamics and provide insights for fluid control.
Senescent cardiomyocytes contribute to cardiac dysfunction following myocardial infarction
Authors: Redgrave Rachael E. , Dookun Emily , Booth Laura K. , Camacho Encina Maria , Folaranmi Omowumi , Tual-Chalot Simon , Gill Jason H. , Owens W. Andrew , Spyridopoulos Ioakim , Passos João F. , Richardson Gavin D. 
Published: June 2023

AbstractMyocardial infarction is a leading cause of morbidity and mortality. While reperfusion is now standard therapy, pathological remodelling leading to heart failure remains a clinical problem. Cellular senescence has been shown to contribute to disease pathophysiology and treatment with the senolytic navitoclax attenuates inflammation, reduces adverse myocardial remodelling and results in improved functional recovery. However, it remains unclear which senescent cell populations contribute to these processes. To identify whether senescent cardiomyocytes contribute to disease pathophysiology post-myocardial infarction, we established a transgenic model in which p16 (CDKN2A) expression was specifically knocked-out in the cardiomyocyte population. Following myocardial infarction, mice lacking cardiomyocyte p16 expression demonstrated no difference in cardiomyocyte hypertrophy but exhibited improved cardiac function and significantly reduced scar size in comparison to control animals. This data demonstrates that senescent cardiomyocytes participate in pathological myocardial remodelling. Importantly, inhibition of cardiomyocyte senescence led to reduced senescence-associated inflammation and decreased senescence-associated markers within other myocardial lineages, consistent with the hypothesis that cardiomyocytes promote pathological remodelling by spreading senescence to other cell-types. Collectively this study presents the demonstration that senescent cardiomyocytes are major contributors to myocardial remodelling and dysfunction following a myocardial infarction. Therefore, to maximise the potential for clinical translation, it is important to further understand the mechanisms underlying cardiomyocyte senescence and how to optimise senolytic strategies to target this cell lineage.
Pre-flight body weight effects on urinary calcium excretion in space
Authors: Thamer Semran , Stevanovic Mirjana , Buckey Jay C. 
Published: June 2023

AbstractMicrogravity-induced bone loss increases urinary calcium excretion which increases kidney stone formation risk. Not all individuals show the same degree of increase in urinary calcium and some pre-flight characteristics may help identify individuals who may benefit from in-flight monitoring. In weightlessness the bone is unloaded, and the effect of this unloading may be greater for those who weigh more. We studied whether pre-flight body weight was associated with increased in-flight urinary calcium excretion using data from Skylab and the International Space Station (ISS). The study was reviewed and approved by the National Aeronautics and Space Administration (NASA) electronic Institutional Review Board (eIRB) and data were sourced from the Longitudinal Study of Astronaut Health (LSAH) database. The combined Skylab and ISS data included 45 participants (9 Skylab, 36 ISS). Both weight and day in flight were positively related to urinary calcium excretion. There was also an interaction between weight and day in flight with higher weight associated with higher calcium excretion earlier in the mission. This study shows that pre-flight weight is also a factor and could be included in the risk assessments for bone loss and kidney stone formation in space.
Efficient, cell-based simulations of cardiac electrophysiology; The Kirchhoff Network Model (KNM)
Authors: Jæger Karoline Horgmo , Tveito Aslak 
Published: June 2023

AbstractMathematical models based on homogenized representation of cardiac tissue have greatly improved our understanding of cardiac electrophysiology. However, these models are too coarse to investigate the dynamics at the level of the myocytes since the cells are not present in homogenized models. Recently, fine scale models have been proposed to allow for cell-level resolution of the dynamics, but these models are too computationally expensive to be used in applications like whole heart simulations of large animals. To address this issue, we propose a model that balances computational demands and physiological accuracy. The model is founded on Kirchhoff’s current law, and represents every myocyte in the tissue. This allows specific properties to be assigned to individual cardiomyocytes, and other cell types like fibroblasts can be added to the model in an accurate manner while keeping the computing efforts reasonable.