bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of tree-on-tree interactions and abiotic conditions on woody communities in Brazilian savannas
Authors: Chagas Davi Borges , Rapini Alessandro , Villa Pedro Manuel , Collevatti Rosane Garcia
Published: July 2023

Fire plays a crucial role in shaping plant communities in South American savannas. However, the impact of biotic interactions on tree communities still needs to be better explored. In this study, we evaluated the influence of tree-on-tree interactions and abiotic conditions on the structure and diversity of woody communities in savannas of Central Brazil. We used plots of 10 × 10 m in three preservation areas of savanna to assess the abundance and composition of juveniles and adults in woody communities associated with two Apocynaceae tree species:Hancornia speciosa, postulated to show negative interactions with the associated tree community, andHimatanthus obovatus, postulated to show positive interactions. Our results revealed that while abiotic factors, represented by the altitude, are more critical in shaping the community of juvenile trees, tree-on-tree interactions have a stronger influence on adult tree populations, driving community dynamics during plant recruitment. Specifically,Hancornia speciosareduces the abundance of adults, whereasHimatanthus obovatusenhances their relative abundance; both shape the composition of tree communities. Consequently, tree-on-tree interactions create distinct mosaics at various stages of regeneration, contributing to savanna dynamics and conservation.
Contrasting Drought Propagation Into the Terrestrial Water Cycle Between Dry and Wet Regions
Authors: Li Wantong , Reichstein Markus , O Sungmin , May Carla , Destouni Georgia , Migliavacca Mirco , Kraft Basil , Weber Ulrich , Orth Rene
Published: July 2023

Drought's intensity and duration have increased in many regions over the last decades. However, the propagation of drought‐induced water deficits through the terrestrial water cycle is not fully understood at a global scale. Here we study responses of monthly evaporation (ET) and runoff to soil moisture droughts occurring between 2001 and 2015 using independent gridded datasets based on machine learning‐assisted upscaling of satellite and in‐situ observations. We find that runoff and ET show generally contrasting drought responses across climate regimes. In wet regions, runoff is strongly reduced while ET is decoupled from soil moisture decreases and enhanced by sunny and warm weather typically accompanying soil moisture droughts. In drier regions, ET is reduced during droughts due to vegetation water stress, while runoff is largely unchanged as precipitation deficits are typically low in these regions and ET decreases are buffering runoff reductions. While these water flux drought responses are controlled by the large‐scale climate regimes, they are additionally modulated by local vegetation characteristics. Land surface models capture the observed water cycle responses to drought in the case of runoff, but not for ET where the ET deficit (surplus) is overestimated (underestimated), related to a misrepresentation of the general soil moisture‐evaporation interplay. In summary, our study illustrates how the joint analysis of machine learning‐enhanced Earth observations can advance the understanding of global eco‐hydrological processes, as well as the validation of land surface models.
Modeling the Morphological Responses of the Yellow River Delta to the Water‐Sediment Regulation Scheme: The Role of Impulsive River Floods and Density‐Driven Flows
Authors: Wu Guoxiang , Wang Kemeng , Liang Bingchen , Wu Xiao , Wang Houjie , Li Huajun , Shi Benwei
Published: July 2023

Morphological evolution of river deltas depends to a large extent on river discharges, which are usually highly unsteady due to natural hydrological cycles and anthropogenic regulations. However, it is unclear that how and to what extent the discharge fluctuations influence the delta morphology. In this study, we focus on the morphological response of the Yellow River Delta to the Water‐Sediment Regulation Schemes, which generate impulsive floods and deliver high sediment load within a short time. Tracking the fate of fluvial sediment released by 10 historical events reveals that 51.3%, 19.7%, and 17.8% of fluvial sediment are deposited in the delta front, the subaerial delta and the prodelta, respectively. Hypopycnal and hyperpycnal flows occur alternately during different phases of the regulation schemes, and the latter contribute to 32% of the deposition volume with 10% of the duration. To explore the effects of river discharge schematizations on delta evolution, numerical experiments are conducted to compare models forced by unsteady and constant discharges, with the latter being a common practice in delta morphology modeling. We show that the constant‐discharge simplification fails to capture the highly‐depositional hyperpycnal flows, leading to dramatic underestimation of river mouth depositions. In addition, we demonstrate that including the 3D flow‐sediment interactions are critical in reproducing the correct plume structures, bed surface sediment compositions and deposition patterns. Our study highlights the importance of proper river discharge schematizations and full consideration of flow‐sediment interactions in modeling deltas affected by episodic river floods and high suspended sediment concentrations.
Optimal Postprocessing Strategies With LSTM for Global Streamflow Prediction in Ungauged Basins
Authors: Tang Senlin , Sun Fubao , Liu Wenbin , Wang Hong , Feng Yao , Li Ziwei
Published: July 2023

Streamflow prediction in ungauged basins (PUB) is challenging, and Long Short‐Term Memory (LSTM) is widely used to for such predictions, owing to its excellent migration performance. Traditional LSTM forced by meteorological data and catchment attribute data barely highlight the optimum data integration strategy for LSTM and its migration from data‐rich basins to ungauged ones. In this study, we experimented with 1,897 global catchments and found that LSTM‐corrected Global Hydrological Models (GHMs) outperformed uncorrected GHMs, improving the median Nash‐Sutcliff efficiency (NSE) from 0.03 to 0.66. Notably, there was a large gap between traditional LSTM modeling in ungauged basins and autoregressive modeling in data‐rich basins, and GHM‐forced LSTM were an effective way to close this gap in ungauged basins. The spatial heterogeneity of the performance of GHM‐forced LSTM was mainly influenced by three metrics (dryness, the leaf area index and latitude), which described the hydrological similarity among catchments. Weaker hydrological similarity among continental catchments results in larger variability in GHM‐forced LSTM, with the best performance in Siberia (NSE, 0.54) and the worst in North America (NSE, 0.10). However, the migration performance of GHM‐forced LSTM was significantly improved (NSE, 0.63) in ungauged basins when hydrological similarity was considered. This study stressed the advantages of GHM‐forced LSTM and due significance should be attached to hydrological similarities among catchments to improve hydrological prediction in ungauged catchments.
Coevolution of Extreme Sea Levels and Sea‐Level Rise Under Global Warming
Authors: Boumis Georgios , Moftakhari Hamed R. , Moradkhani Hamid
Published: July 2023

Design of coastal defense structures like seawalls and breakwaters can no longer be based on stationarity assumption. In many parts of the world, an anticipated sea‐level rise (SLR) due to climate change will constitute present‐day extreme sea levels inappropriate for future coastal flood risk assessments since it will significantly increase their probability of occurrence. Here, we first show that global annual maxima sea levels (AMSLs) have been increasing in magnitude over the last decades, primarily due to a positive shift in mean sea level (MSL). Then, we apply non‐stationary extreme value theory to model the extremal behavior of sea levels with MSL as a covariate and quantify the evolution of AMSLs in the following decades using revised probabilistic sea‐level rise projections. Our analysis reveals that non‐stationary distributions exhibit distinct differences compared to simply considering stationary conditions with a change in location parameter equal to the amount of MSL rise. With the use of non‐stationary distributions, we show that by the year 2050 many locations will experience their present‐day 100‐yr return level as an event with return period less than 15 and 9 years under the moderate (RCP4.5) and high (RCP8.5) representative concentration pathways. Also, we find that by the end of this century almost all locations examined will encounter their current 100‐yr return level on an annual basis, even if CO2 concentration is kept at moderate levels (RCP4.5). Our assessment accounts for large uncertainty by incorporating ambiguities in both SLR projections and non‐stationary extreme value distribution parameters via a Monte Carlo simulation.
Xrcc5/Ku80 is required for the repair of DNA damage in fully grown meiotically arrested mammalian oocytes
Authors: Cai Xuebi , Stringer Jessica M. , Zerafa Nadeen , Carroll John , Hutt Karla J.
Published: July 2023

Mammalian oocytes spend most of their life in a unique state of cell cycle arrest at meiotic prophase I, during which time they are exposed to countless DNA-damaging events. Recent studies have shown that DNA double-strand break repair occurs predominantly via the homologous recombination (HR) pathway in small non-growing meiotically arrested oocytes (primordial follicle stage). However, the DNA repair mechanisms employed by fully grown meiotically arrested oocytes (GV-stage) have not been studied in detail. Here we established a conditional knockout mouse model to explore the role of Ku80, a critical component of the nonhomologous end joining (NHEJ) pathway, in the repair of DNA damage in GV oocytes. GV oocytes lacking Ku80 failed to repair etoposide-induced DNA damage, even when only low levels of damage were sustained. This indicates Ku80 is needed to resolve DSBs and that HR cannot compensate for a compromised NHEJ pathway in fully-grown oocytes. When higher levels of DNA damage were induced, a severe delay in M-phase entry was observed in oocytes lacking XRCC5 compared to wild-type oocytes, suggesting that Ku80-dependent repair of DNA damage is important for the timely release of oocytes from prophase I and resumption of meiosis. Ku80 was also found to be critical for chromosome integrity during meiotic maturation following etoposide exposure. These data demonstrate that Ku80, and NHEJ, are vital for quality control in mammalian GV stage oocytes and reveal that DNA repair pathway choice differs in meiotically arrested oocytes according to growth status.
Beta cell dysfunction induced by bone morphogenetic protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding
Authors: Urizar Adriana Ibarra , Prause Michala , Ingerslev Lars Roed , Wortham Matthew , Sui Yinghui , Sander Maike , Williams Kristine , Barrès Romain , Larsen Martin R. , Christensen Gitte Lund , Billestrup Nils
Published: July 2023

Insufficient insulin secretion is a hallmark of type 2 diabetes and has been attributed to beta cell identity loss characterized by decreased expression of several key beta cell genes. The pro-inflammatory factor BMP-2 is upregulated in islets of Langerhans from individuals with diabetes and acts as an inhibitor of beta cell function and proliferation. Exposure to BMP-2 induces expression of Id1-4, Hes-1, and Hey-1 which are transcriptional regulators associated with loss of differentiation. The aim of this study was to investigate the mechanism by which BMP-2 induces beta cell dysfunction and loss of cell maturity. Mouse islets exposed to BMP-2 for 10 days showed impaired glucose-stimulated insulin secretion and beta cell proliferation. BMP-2-induced beta cell dysfunction was associated with decreased expression of cell maturity and proliferation markers specific to the beta cell such as Ins1, Ucn3, and Ki67 and increased expression of Id1-4, Hes-1, and Hey-1. The top 30 most regulated proteins significantly correlated with corresponding mRNA expression. BMP-2-induced gene expression changes were associated with a predominant reduction in acetylation of H3K27 and a decrease in NeuroD1 chromatin binding activity. These results show that BMP-2 induces loss of beta cell maturity and suggest that remodeling of H3K27ac and decreased NeuroD1 DNA binding activity participate in the effect of BMP-2 on beta cell dysfunction.
Profiling of basal and ligand-dependent GPCR activities by means of a polyvalent cell-based high-throughput platform
Authors: Zeghal Manel , Laroche Geneviève , Freitas Julia Douglas , Wang Rebecca , Giguère Patrick M.
Published: July 2023

Representing the most attractive and successful druggable receptors of the proteome, GPCRs regulate a myriad of physiological and pathophysiological functions. Although over half of present pharmaceuticals target GPCRs, the advancement of drug discovery is hampered by a lack of adequate screening tools, the majority of which are limited to probing agonist-induced G-protein and β-arrestin-2-mediated events as a measure of receptor activation. Here, we develop Tango-Trio, a comprehensive cell-based high-throughput platform comprising cumate-inducible expression of transducers, capable of the parallelized profiling of both basal and agonist-dependent GPCR activities. We capture the functional diversity of GPCRs, reporting β-arrestin-1/2 couplings, selectivities, and receptor internalization signatures across the GPCRome. Moreover, we present the construction of cumate-induced basal activation curves at approximately 200 receptors, including over 50 orphans. Overall, Tango-Trio’s robustness is well-suited for the functional characterization and screening of GPCRs, especially for parallel interrogation, and is a valuable addition to the pharmacological toolbox.
Closed-loop brain stimulation augments fear extinction in male rats
Authors: Sierra Rodrigo Ordoñez , Pedraza Lizeth Katherine , Barcsai Lívia , Pejin Andrea , Li Qun , Kozák Gábor , Takeuchi Yuichi , Nagy Anett J. , Lőrincz Magor L. , Devinsky Orrin , Buzsáki György , Berényi Antal
Published: July 2023

Dysregulated fear reactions can result from maladaptive processing of trauma-related memories. In post-traumatic stress disorder (PTSD) and other psychiatric disorders, dysfunctional extinction learning prevents discretization of trauma-related memory engrams and generalizes fear responses. Although PTSD may be viewed as a memory-based disorder, no approved treatments target pathological fear memory processing. Hippocampal sharp wave-ripples (SWRs) and concurrent neocortical oscillations are scaffolds to consolidate contextual memory, but their role during fear processing remains poorly understood. Here, we show that closed-loop, SWR triggered neuromodulation of the medial forebrain bundle (MFB) can enhance fear extinction consolidation in male rats. The modified fear memories became resistant to induced recall (i.e., ‘renewal’ and ‘reinstatement’) and did not reemerge spontaneously. These effects were mediated by D2 receptor signaling-induced synaptic remodeling in the basolateral amygdala. Our results demonstrate that SWR-triggered closed-loop stimulation of the MFB reward system enhances extinction of fearful memories and reducing fear expression across different contexts and preventing excessive and persistent fear responses. These findings highlight the potential of neuromodulation to augment extinction learning and provide a new avenue to develop treatments for anxiety disorders.
Fano resonant optical coatings platform for full gamut and high purity structural colors
Authors: ElKabbash Mohamed , Hoffman Nathaniel , Lininger Andrew R. , Jalil Sohail A. , Letsou Theodore , Hinczewski Michael , Strangi Giuseppe , Guo Chunlei
Published: July 2023

Structural coloring is a photostable and environmentally friendly coloring approach that harnesses optical interference and nanophotonic resonances to obtain colors with a range of applications including display technologies, colorful solar panels, steganography, décor, data storage, and anticounterfeiting measures. We show that optical coatings exhibiting the photonic Fano Resonance present an ideal platform for structural coloring; they provide full color access, high color purity, high brightness, controlled iridescence, and scalable manufacturing. We show that an additional oxide film deposited on Fano resonant optical coatings (FROCs) increases the color purity (up to 99%) and color gamut coverage range of FROCs to 61% of the CIE color space. For wide-area structural coloring applications, FROCs have a significant advantage over existing structural coloring schemes.
RAS-independent ERK activation by constitutively active KSR3 in non-chordate metazoa
Authors: Chessel Aline , De Crozé Noémie , Molina Maria Dolores , Taberner Laura , Dru Philippe , Martin Luc , Lepage Thierry
Published: July 2023

During early development of the sea urchin embryo, activation of ERK signalling in mesodermal precursors is not triggered by extracellular RTK ligands but by a cell-autonomous, RAS-independent mechanism that was not understood. We discovered that in these cells, ERK signalling is activated through the transcriptional activation of a gene encoding a protein related to Kinase Suppressor of Ras, that we named KSR3. KSR3 belongs to a family of catalytically inactive allosteric activators of RAF. Phylogenetic analysis revealed that genes encoding kinase defective KSR3 proteins are present in most non-chordate metazoa but have been lost in flies and nematodes. We show that the structure of KSR3 factors resembles that of several oncogenic human RAF mutants and that KSR3 from echinoderms, cnidarians and hemichordates activate ERK signalling independently of RAS when overexpressed in cultured cells. Finally, we used the sequence of KSR3 factors to identify activating mutations of human B-RAF. These findings reveal key functions for this family of factors as activators of RAF in RAS-independent ERK signalling in invertebrates. They have implications on the evolution of the ERK signalling pathway and suggest a mechanism for its co-option in the course of evolution.
Structure of engineered hepatitis C virus E1E2 ectodomain in complex with neutralizing antibodies
Authors: Metcalf Matthew C. , Janus Benjamin M. , Yin Rui , Wang Ruixue , Guest Johnathan D. , Pozharski Edwin , Law Mansun , Mariuzza Roy A. , Toth Eric A. , Pierce Brian G. , Fuerst Thomas R. , Ofek Gilad
Published: July 2023

Hepatitis C virus (HCV) is a major global health burden as the leading causative agent of chronic liver disease and hepatocellular carcinoma. While the main antigenic target for HCV-neutralizing antibodies is the membrane-associated E1E2 surface glycoprotein, the development of effective vaccines has been hindered by complications in the biochemical preparation of soluble E1E2 ectodomains. Here, we present a cryo-EM structure of an engineered, secreted E1E2 ectodomain of genotype 1b in complex with neutralizing antibodies AR4A, HEPC74, and IGH520. Structural characterization of the E1 subunit and C-terminal regions of E2 reveal an overall architecture of E1E2 that concurs with that observed for non-engineered full-length E1E2. Analysis of the AR4A epitope within a region of E2 that bridges between the E2 core and E1 defines the structural basis for its broad neutralization. Our study presents the structure of an E1E2 complex liberated from membrane via a designed scaffold, one that maintains all essential structural features of native E1E2. The study advances the understanding of the E1E2 heterodimer structure, crucial for the rational design of secreted E1E2 antigens in vaccine development.
Cryo-EM and femtosecond spectroscopic studies provide mechanistic insight into the energy transfer in CpcL-phycobilisomes
Authors: Zheng Lvqin , Zhang Zhengdong , Wang Hongrui , Zheng Zhenggao , Wang Jiayu , Liu Heyuan , Chen Hailong , Dong Chunxia , Wang Guopeng , Weng Yuxiang , Gao Ning , Zhao Jindong
Published: July 2023

Phycobilisomes (PBS) are the major light harvesting complexes of photosynthesis in the cyanobacteria and red algae. CpcL-PBS is a type of small PBS in cyanobacteria that transfers energy directly to photosystem I without the core structure. Here we report the cryo-EM structure of the CpcL-PBS from the cyanobacterium Synechocystis sp. PCC 6803 at 2.6-Å resolution. The structure shows the CpcD domain of ferredoxin: NADP+ oxidoreductase is located at the distal end of CpcL-PBS, responsible for its attachment to PBS. With the evidence of ultrafast transient absorption and fluorescence spectroscopy, the roles of individual bilins in energy transfer are revealed. The bilin 1Iβ822 located near photosystem I has an enhanced planarity and is the red-bilin responsible for the direct energy transfer to photosystem I.
Direct mapping of kidney function by DCE-MRI urography using a tetrazinanone organic radical contrast agent
Authors: Calvert Nicholas D. , Kirby Alexia , Suchý Mojmír , Pallister Peter , Torrens Aidan A. , Burger Dylan , Melkus Gerd , Schieda Nicola , Shuhendler Adam J.
Published: July 2023

Chronic kidney disease (CKD) and acute kidney injury (AKI) are ongoing global health burdens. Glomerular filtration rate (GFR) is the gold standard measure of kidney function, with clinical estimates providing a global assessment of kidney health without spatial information of kidney- or region-specific dysfunction. The addition of dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) to the anatomical imaging already performed would yield a ‘one-stop-shop’ for renal assessment in cases of suspected AKI and CKD. Towards urography by DCE-MRI, we evaluated a class of nitrogen-centered organic radicals known as verdazyls, which are extremely stable even in highly reducing environments. A glucose-modified verdazyl, glucoverdazyl, provided contrast limited to kidney and bladder, affording functional kidney evaluation in mouse models of unilateral ureteral obstruction (UUO) and folic acid-induced nephropathy (FAN). Imaging outcomes correlated with histology and hematology assessing kidney dysfunction, and glucoverdazyl clearance rates were found to be a reliable surrogate measure of GFR.
The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells
Authors: Kunkel Thaddeus J. , Townsend Alice , Sullivan Kyle A. , Merlet Jean , Schuchman Edward H. , Jacobson Daniel A. , Lieberman Andrew P.
Published: July 2023

The intracellular cholesterol transporter NPC1 functions in late endosomes and lysosomes to efflux unesterified cholesterol, and its deficiency causes Niemann–Pick disease Type C, an autosomal recessive lysosomal disorder characterized by progressive neurodegeneration and early death. Here, we use single-nucleus RNA-seq on the forebrain of Npc1−/− mice at P16 to identify cell types and pathways affected early in pathogenesis. Our analysis uncovers significant transcriptional changes in the oligodendrocyte lineage during developmental myelination, accompanied by diminished maturation of myelinating oligodendrocytes. We identify upregulation of genes associated with neurogenesis and synapse formation in Npc1−/− oligodendrocyte lineage cells, reflecting diminished gene silencing by H3K27me3. Npc1−/− oligodendrocyte progenitor cells reproduce impaired maturation in vitro, and this phenotype is rescued by treatment with GSK-J4, a small molecule inhibitor of H3K27 demethylases. Moreover, mobilizing stored cholesterol in Npc1−/− mice by a single administration of 2-hydroxypropyl-β-cyclodextrin at P7 rescues myelination, epigenetic marks, and oligodendrocyte gene expression. Our findings highlight an important role for NPC1 in oligodendrocyte lineage maturation and epigenetic regulation, and identify potential targets for therapeutic intervention.
Toll-like receptor mediated inflammation directs B cells towards protective antiviral extrafollicular responses
Authors: Lam Jonathan H. , Baumgarth Nicole
Published: July 2023

Extrafollicular plasmablast responses (EFRs) are considered to generate antibodies of low affinity that offer little protection from infections. Paradoxically, high avidity antigen-B cell receptor engagement is thought to be the main driver of B cell differentiation, whether in EFRs or slower-developing germinal centers (GCs). Here we show that influenza infection rapidly induces EFRs, generating protective antibodies via Toll-like receptor (TLR)-mediated mechanisms that are both B cell intrinsic and extrinsic. B cell-intrinsic TLR signals support antigen-stimulated B cell survival, clonal expansion, and the differentiation of B cells via induction of IRF4, the master regulator of B cell differentiation, through activation of NF-kB c-Rel. Provision of sustained TLR4 stimulation after immunization shifts the fate of virus-specific B cells towards EFRs instead of GCs, prompting rapid antibody production and improving their protective capacity over antigen/alum administration alone. Thus, inflammatory signals act as B cell fate-determinants for the rapid generation of protective antiviral extrafollicular responses.
Laser maskless fast patterning for multitype microsupercapacitors
Authors: Yuan Yongjiu , Li Xin , Jiang Lan , Liang Misheng , Zhang Xueqiang , Wu Shouyu , Wu Junrui , Tian Mengyao , Zhao Yang , Qu Liangti
Published: July 2023

Downsizing electrode architectures have significant potential for microscale energy storage devices. Asymmetric micro-supercapacitors play an essential role in various applications due to their high voltage window and energy density. However, efficient production and sophisticated miniaturization of asymmetric micro-supercapacitors remains challenging. Here, we develop a maskless ultrafast fabrication of multitype micron-sized (10 × 10 μm2) micro-supercapacitors via temporally and spatially shaped femtosecond laser. MXene/1T-MoS2 can be integrated with laser-induced MXene-derived TiO2 and 1T-MoS2-derived MoO3 to generate over 6,000 symmetric micro-supercapacitors or 3,000 asymmetric micro-supercapacitors with high-resolution (200 nm) per minute. The asymmetric micro-supercapacitors can be integrated with other micro devices, thanks to the ultrahigh specific capacitance (220 mF cm−2 and 1101 F cm−3), voltage windows in series (52 V), energy density (0.495 Wh cm−3) and power density (28 kW cm−3). Our approach enables the industrial manufacturing of multitype micro-supercapacitors and improves the feasibility and flexibility of micro-supercapacitors in practical applications.
Variation in bridgmanite grain size accounts for the mid-mantle viscosity jump
Authors: Fei Hongzhan , Ballmer Maxim D. , Faul Ulrich , Walte Nicolas , Cao Weiwei , Katsura Tomoo
Published: July 2023

A viscosity jump of one to two orders of magnitude in the lower mantle of Earth at 800–1,200-km depth is inferred from geoid inversions and slab-subducting speeds. This jump is known as the mid-mantle viscosity jump1,2. The mid-mantle viscosity jump is a key component of lower-mantle dynamics and evolution because it decelerates slab subduction3, accelerates plume ascent4and inhibits chemical mixing5. However, because phase transitions of the main lower-mantle minerals do not occur at this depth, the origin of the viscosity jump remains unknown. Here we show that bridgmanite-enriched rocks in the deep lower mantle have a grain size that is more than one order of magnitude larger and a viscosity that is at least one order of magnitude higher than those of the overlying pyrolitic rocks. This contrast is sufficient to explain the mid-mantle viscosity jump1,2. The rapid growth in bridgmanite-enriched rocks at the early stage of the history of Earth and the resulting high viscosity account for their preservation against mantle convection5–7. The high Mg:Si ratio of the upper mantle relative to chondrites8, the anomalous142Nd:144Nd,182W:184W and3He:4He isotopic ratios in hot-spot magmas9,10, the plume deflection4and slab stagnation in the mid-mantle3as well as the sparse observations of seismic anisotropy11,12can be explained by the long-term preservation of bridgmanite-enriched rocks in the deep lower mantle as promoted by their fast grain growth.
A rise-to-threshold process for a relative-value decision
Authors: Vijayan Vikram , Wang Fei , Wang Kaiyu , Chakravorty Arun , Adachi Atsuko , Akhlaghpour Hessameddin , Dickson Barry J. , Maimon Gaby
Published: July 2023

Whereas progress has been made in the identification of neural signals related to rapid, cued decisions1–3, less is known about how brains guide and terminate more ethologically relevant decisions in which an animal’s own behaviour governs the options experienced over minutes4–6. Drosophila search for many seconds to minutes for egg-laying sites with high relative value7,8 and have neurons, called oviDNs, whose activity fulfills necessity and sufficiency criteria for initiating the egg-deposition motor programme9. Here we show that oviDNs express a calcium signal that (1) dips when an egg is internally prepared (ovulated), (2) drifts up and down over seconds to minutes—in a manner influenced by the relative value of substrates—as a fly determines whether to lay an egg and (3) reaches a consistent peak level just before the abdomen bend for egg deposition. This signal is apparent in the cell bodies of oviDNs in the brain and it probably reflects a behaviourally relevant rise-to-threshold process in the ventral nerve cord, where the synaptic terminals of oviDNs are located and where their output can influence behaviour. We provide perturbational evidence that the egg-deposition motor programme is initiated once this process hits a threshold and that subthreshold variation in this process regulates the time spent considering options and, ultimately, the choice taken. Finally, we identify a small recurrent circuit that feeds into oviDNs and show that activity in each of its constituent cell types is required for laying an egg. These results argue that a rise-to-threshold process regulates a relative-value, self-paced decision and provide initial insight into the underlying circuit mechanism for building this process.
Evolution of a minimal cell
Authors: Moger-Reischer R. Z. , Glass J. I. , Wise K. S. , Sun L. , Bittencourt D. M. C. , Lehmkuhl B. K. , Schoolmaster D. R. , Lynch M. , Lennon J. T.
Published: July 2023

Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life1,2. Here we report on how an engineered minimal cell3,4contends with the forces of evolution compared with theMycoplasma mycoidesnon-minimal cell from which it was synthetically derived. Mutation rates were the highest among all reported bacteria, but were not affected by genome minimization. Genome streamlining was costly, leading to a decrease in fitness of greater than 50%, but this deficit was regained during 2,000 generations of evolution. Despite selection acting on distinct genetic targets, increases in the maximum growth rate of the synthetic cells were comparable. Moreover, when performance was assessed by relative fitness, the minimal cell evolved 39% faster than the non-minimal cell. The only apparent constraint involved the evolution of cell size. The size of the non-minimal cell increased by 80%, whereas the minimal cell remained the same. This pattern reflected epistatic effects of mutations inftsZ, which encodes a tubulin-homologue protein that regulates cell division and morphology5,6. Our findings demonstrate that natural selection can rapidly increase the fitness of one of the simplest autonomously growing organisms. Understanding how species with small genomes overcome evolutionary challenges provides critical insights into the persistence of host-associated endosymbionts, the stability of streamlined chassis for biotechnology and the targeted refinement of synthetically engineered cells2,7–9.
Forecasting virus outbreaks with social media data via neural ordinary differential equations
Authors: Núñez Matías , Barreiro Nadia L. , Barrio Rafael A. , Rackauckas Christopher
Published: July 2023

During the Covid-19 pandemic, real-time social media data could in principle be used as an early predictor of a new epidemic wave. This possibility is examined here by employing a neural ordinary differential equation (neural ODE) trained to forecast viral outbreaks in a specific geographic region. It learns from multivariate time series of signals derived from a novel set of large online polls regarding COVID-19 symptoms. Once trained, the neural ODE can capture the dynamics of interconnected local signals and effectively estimate the number of new infections up to two months in advance. In addition, it may predict the future consequences of changes in the number of infected at a certain period, which might be related with the flow of individuals entering or exiting a region. This study provides persuasive evidence for the predictive ability of widely disseminated social media surveys for public health applications.
Learning and memory in hybrid migratory songbirds: cognition as a reproductive isolating barrier across seasons
Authors: Alario Ashley , Trevino Marlene , Justen Hannah , Woodman Constance J. , Roth Timothy C. , Delmore Kira E.
Published: July 2023

Hybrid zones can be used to identify traits that maintain reproductive isolation and contribute to speciation. Cognitive traits may serve as post-mating reproductive isolating barriers, reducing the fitness of hybrids if, for example, misexpression occurs in hybrids and disrupts important neurological mechanisms. We tested this hypothesis in a hybrid zone between two subspecies of Swainson’s thrushes (Catharus ustulatus) using two cognitive tests—an associative learning spatial test and neophobia test. We included comparisons across the sexes and seasons (spring migration and winter), testing if hybrid females performed worse than males (as per Haldane’s rule) and if birds (regardless of ancestry or sex) performed better during migration, when they are building navigational maps and encountering new environments. We documented reduced cognitive abilities in hybrids, but this result was limited to males and winter. Hybrid females did not perform worse than males in either season. Although season was a significant predictor of performance, contrary to our prediction, all birds learned faster during the winter. The hypothesis that cognitive traits could serve as post-mating isolating barriers is relatively new; this is one of the first tests in a natural hybrid zone and non-food-caching species. We also provide one of the first comparisons of cognitive abilities between seasons. Future neurostructural and neurophysiological work should be used to examine mechanisms underlying our behavioral observations.
Multimodal deep learning for COVID-19 prognosis prediction in the emergency department: a bi-centric study
Authors: Dipaola Franca , Gatti Mauro , Giaj Levra Alessandro , Menè Roberto , Shiffer Dana , Faccincani Roberto , Raouf Zainab , Secchi Antonio , Rovere Querini Patrizia , Voza Antonio , Badalamenti Salvatore , Solbiati Monica , Costantino Giorgio , Savevski Victor , Furlan Raffaello
Published: July 2023

Predicting clinical deterioration in COVID-19 patients remains a challenging task in the Emergency Department (ED). To address this aim, we developed an artificial neural network using textual (e.g. patient history) and tabular (e.g. laboratory values) data from ED electronic medical reports. The predicted outcomes were 30-day mortality and ICU admission. We included consecutive patients from Humanitas Research Hospital and San Raffaele Hospital in the Milan area between February 20 and May 5, 2020. We included 1296 COVID-19 patients. Textual predictors consisted of patient history, physical exam, and radiological reports. Tabular predictors included age, creatinine, C-reactive protein, hemoglobin, and platelet count. TensorFlow tabular-textual model performance indices were compared to those of models implementing only tabular data. For 30-day mortality, the combined model yielded slightly better performances than the tabular fastai and XGBoost models, with AUC 0.87 ± 0.02, F1 score 0.62 ± 0.10 and an MCC 0.52 ± 0.04 (p < 0.32). As for ICU admission, the combined model MCC was superior (p < 0.024) to the tabular models. Our results suggest that a combined textual and tabular model can effectively predict COVID-19 prognosis which may assist ED physicians in their decision-making process.
Heat stress tolerance indices for identification of the heat tolerant wheat genotypes
Authors: Lamba Kavita , Kumar Mukesh , Singh Vikram , Chaudhary Lakshmi , Sharma Rajat , Yashveer Shikha , Dalal M. S.
Published: July 2023

Heat stress is one of the major challenges in wheat cultivation because it coincides with the flowering period and limits the crop productivity. This study was conducted for evaluation of 50 wheat genotypes to identify the heat stress tolerant genotypes for improvement of stress tolerance. All genotypes were cultivated for two consecutive years (2018–2020) under normal and late sown conditions. The results of the study revealed that the combined analysis of variance indicated significant variations among genotypes for all the studied stress indices. The reduction in mean grain yield of all genotypes under stress condition as compared to non-stress condition, indicating that the heat stress significantly affect the grain yield. The correlation analysis showed that the negative correlation of tolerance index and stress susceptibility percentage index with the grain yield of genotypes under heat stress condition (Ys) and a highly positive correlation of stress tolerance index, mean productivity, geometric mean, harmonic mean and mean relative performance with grain yield (Yp and Ys) under both conditions, helped accurately to identify the desirable genotypes. From the results obtained from principal component, biplot and cluster analysis, it was reported that HD 2967, WH 1249, HI 1617, WH 1202, WH 1021 and WH 1142 are suitable and good yielding genotypes under both conditions. Thus, above genotypes can be used for cultivation at high temperature or as genetic resources for introducing genetic variations in wheat genotypes to improve stress tolerance.
Alprazolam exposure during adolescence induces long-lasting dysregulation in reward sensitivity to morphine and second messenger signaling in the VTA-NAc pathway
Authors: Cardona-Acosta Astrid M. , Sial Omar K. , Parise Lyonna F. , Gnecco Tamara , Enriquez Marti Giselle , Bolaños-Guzmán Carlos A.
Published: July 2023

Increased use of benzodiazepines in adolescents have been reported, with alprazolam (ALP) being the most abused. Drug abuse during adolescence can induce changes with lasting consequences. This study investigated the neurobiological consequences of ALP exposure during adolescence in C57BL/6J male mice. Mice received ALP (0, 0.5, 1.0 mg/kg) once/daily (postnatal day 35–49). Changes in responsiveness to morphine (2.5, 5.0 mg/kg), using the conditioned place preference paradigm, were assessed 24-h and 1-month after ALP exposure. In a separate experiment, mice received ALP (0, 0.5 mg/kg) and then sacrificed 24-h or 1-month after treatment to assess levels of extracellular signal regulated kinase 1/2 (ERK1/2) gene expression, protein phosphorylation, and downstream targets (CREB, AKT) within the ventral tegmental area (VTA) and nucleus accumbens (NAc). ALP-pretreated mice developed a strong preference to the compartment(s) paired with a subthreshold dose (2.5 mg/kg) of MOR short-term, and this effect was also present in the 1-month group. Adolescent ALP exposure resulted in dysregulation of ERK-signaling within the VTA-NAc pathway 24-h and 1-month after ALP exposure. Results indicate ALP exposure during adolescence potentiates the rewarding properties of MOR and induces persistent changes in ERK-signaling within the VTA-NAc pathway, a brain circuit highly implicated in the regulation of both drug reward and mood- related behaviors.
Entropy structural characterization of zeolites BCT and DFT with bond-wise scaled comparison
Authors: Arockiaraj Micheal , Paul Daniel , Ghani Muhammad Usman , Tigga Sushil , Chu Yu-Ming
Published: July 2023

Entropy of a connected network is a quantitative measure from information theory that has triggered a plethora of research domains in molecular chemistry, biological sciences and computer programming due to its inherent capacity to explore the structural characteristics of complex molecular frameworks that have low structural symmetry as well as high diversity. The analysis of the structural order is greatly simplified through the topological indices based graph entropy metrics, which are then utilized to predict the structural features of molecular frameworks. This predictability has not only revolutionized the study of zeolitic frameworks but has also given rise to new generations of frameworks. We make a comparative study of two versatile framework topologies namely zeolites BCT and DFT, which have been widely utilized to create a new generation of frameworks known as metal organic frameworks. We discuss bond-additive topological indices and compute entropy measure descriptors for zeolites BCT and DFT using degree and degree-sum parameters. In addition, we perform bond-wise scaled comparative analysis between BCT and DFT which shows that zeolite BCT has greater entropy values compared to zeolite DFT.
Experimental demonstration of a new near-infrared spectroscopy technique based on optical dual-comb: DC-NIRS
Authors: Barreiro Roberto , Sanabria-Macías Frank , Posada Julio , Martín-Mateos Pedro , de Dios Cristina
Published: July 2023

We present a novel near-infrared spectroscopy technique based on Dual-Comb optical interrogation (DC-NIRS) applied to dispersive media. The technique recovers the frequency response of the medium under investigation by sampling its spectral response in amplitude and phase. The DC-NIRS reference and sample signals are generated using electro-optic modulation which offers a cost-effective, integrable solution while providing high adaptability to the interrogated medium. A careful choice of both line spacing and optical span of the frequency comb ensures that the retrieved information enables the reconstruction of the temporal impulse response of the medium, known as the diffuse-time-of-flight (DTOF), to obtain its optical properties with a 70 µs temporal resolution and 32 ps photon propagation delay resolution. Furthermore, the DC-NIRS technique also offers enhanced penetration due to noiseless optical amplification (interferometric detection). The presented technique was demonstrated on a static bio-mimetic phantom of known optical properties reproducing a typical brain’s optical response. The DTOF and optical properties of the phantom were measured, showing the capabilities of this new technique on the estimation of absolute optical properties with a deviation under 3%. Compared to current technologies, our DC-NIRS technique provides enhanced temporal resolution, spatial location capabilities, and penetration depth, with an integrable and configurable cost-effective architecture, paving the way to next-generation, non-invasive and portable systems for functional brain imaging, and brain-computer interfaces, among other. The system is patent pending PCT/ES2022/070176.
Parameter prediction of coiled tubing drilling based on GAN–LSTM
Authors: Zhang Wanxing , Bai Kai , Zhan Ce , Tu Binrui
Published: July 2023

With the increasing development of coiled tubing drilling technology, the advantages of coiled tubing drilling technology are becoming more and more obvious. In the operation process of coiled tubing, Due to various different drilling parameters, manufacturing defects, and improper human handling, the coiled tubing can curl up and cause stuck drilling or shortened service life problems. Circulation pressure, wellhead pressure, and total weight have an important influence on the working period of coiled tubing. For production safety, this paper predicts circulation pressure, ROP, wellhead pressure, and finger weight using GAN–LSTM after studying drilling engineering theory and analyzing a large amount of downhole data. Experimental results show that GAN–LSTM can predict the parameters of circulation pressure, wellhead pressure ROP and total weight to a certain extent. After much training, the accuracy is about 90%, which is about 17% higher than that of the GAN and LSTM. It has a certain guiding significance for coiled tubing operation, increasing operational safety and drilling efficiency, thus reducing production costs.
Minimally invasive intrathoracic negative-pressure therapy and flexible thoracoscopy (FlexVATS) for patients with pleural empyema
Authors: Stüben Björn-Ole , Plitzko Gabriel A. , Sauerbeck Julia , Busch Philipp , Melling Nathaniel , Reeh Matthias , Izbicki Jakob R. , Rösch Thomas , Bachmann Kai , Tachezy Michael
Published: July 2023

To determine whether a new surgical method using a flexible endoscope (FlexVATS) to perform sparing debridement and apply negative-pressure therapy without extensive decortication may be an alternative treatment option for empyema. Surgical treatment of pleural empyema is associated with considerable postoperative complications and mortality rates, and alternative treatment options are being explored to improve patient outcomes. This was a prospective case series. Seventeen consecutive patients treated with FlexVATS between February 2021 and August 2022 were included in the study. Only patients for whom FlexVATS was the first therapeutic intervention for pleural empyema were included. Treatment success, defined as infection resolution, was the primary endpoint of the study. The secondary endpoints were length of hospital stay, 90-day mortality, and empyema cavity volume reduction. Patients who had previously been treated for pleural empyema by either drainage or surgery were excluded. The trial was performed as a single-centre study at a tertiary medical centre in Germany. In total, 17 patients with pleural empyema were included in the study. The median (IQR) duration of vacuum treatment was 15 days (8–35 days). Twelve of the 17 (71%) patients were successfully treated, and a significant reduction in the empyema cavity volume was observed. 41% of the dressing changes were performed outside the operating room. Compared with a historic cohort of conventionally treated patients (decortication via VATS or thoracotomy), the 90-day mortality rates tended to be lower without reaching statistical significance. Three patients (18%) died in hospital during treatment. No negative pressure-therapy-related complications were observed. FlexVATS therapy is a promising alternative therapy for both healthy and debilitated patients with pleural empyema. Larger randomised trials are required to validate this treatment option.
“Functional upcycling” of polymer waste towards the design of new materials
Authors: Guselnikova Olga , Semyonov Oleg , Sviridova Elizaveta , Gulyaev Roman , Gorbunova Alina , Kogolev Dmitry , Trelin Andrii , Yamauchi Yusuke , Boukherroub Rabah , Postnikov Pavel
Published: July 2023

Functional upcycling is post-polymerisation modification or surface functionalisation of plastic waste without considerable polymer chain destruction to produce a new upcycled material with added value.
Regulating the crystallization dynamics through hydrogen bonding for high efficiency tin halide perovskite solar cells
Authors: Tang Zhiyue , Wu Cheng , Wang Shurong , Xiao Yu , Ding Liming , Hao Feng
Published: July 2023

The hydrogen bonding between aniline and formamidinium iodide regulated the crystallization process and optimized the crystal orientation of the tin halide perovskite.
Bis(naphthobipyrrolyl)methene-derived hexapyrrolic BODIPY as a single-molecule helicate with near-infrared emission
Authors: Sahoo Sipra Sucharita , Panda Pradeepta K.
Published: July 2023

A NIR emissive helical bis(naphthobipyrrolyl)methene-derived open chain hexapyrrolic BODIPY has been synthesized with a fluorescence quantum yield up to 0.27.