bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustainable reference points for multispecies coral reef fisheries
Authors: Zamborain-Mason Jessica , Cinner Joshua E. , MacNeil M. Aaron , Graham Nicholas A. J. , Hoey Andrew S. , Beger Maria , Brooks Andrew J. , Booth David J. , Edgar Graham J. , Feary David A. , Ferse Sebastian C. A. , Friedlander Alan M. , Gough Charlotte L. A. , Green Alison L. , Mouillot David , Polunin Nicholas V. C. , Stuart-Smith Rick D. , Wantiez Laurent , Williams Ivor D. , Wilson Shaun K. , Connolly Sean R. 
Published: September 2023

AbstractSustainably managing fisheries requires regular and reliable evaluation of stock status. However, most multispecies reef fisheries around the globe tend to lack research and monitoring capacity, preventing the estimation of sustainable reference points against which stocks can be assessed. Here, combining fish biomass data for >2000 coral reefs, we estimate site-specific sustainable reference points for coral reef fisheries and use these and available catch estimates to assess the status of global coral reef fish stocks. We reveal that >50% of sites and jurisdictions with available information have stocks of conservation concern, having failed at least one fisheries sustainability benchmark. We quantify the trade-offs between biodiversity, fish length, and ecosystem functions relative to key benchmarks and highlight the ecological benefits of increasing sustainability. Our approach yields multispecies sustainable reference points for coral reef fisheries using environmental conditions, a promising means for enhancing the sustainability of the world’s coral reef fisheries.
Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines
Authors: Shoer Saar , Shilo Smadar , Godneva Anastasia , Ben-Yacov Orly , Rein Michal , Wolf Bat Chen , Lotan-Pompan Maya , Bar Noam , Weiss Ervin I. , Houri-Haddad Yael , Pilpel Yitzhak , Weinberger Adina , Segal Eran 
Published: September 2023

AbstractDiabetes and associated comorbidities are a global health threat on the rise. We conducted a six-month dietary intervention in pre-diabetic individuals (NCT03222791), to mitigate the hyperglycemia and enhance metabolic health. The current work explores early diabetes markers in the 200 individuals who completed the trial. We find 166 of 2,803 measured features, including oral and gut microbial species and pathways, serum metabolites and cytokines, show significant change in response to a personalized postprandial glucose-targeting diet or the standard of care Mediterranean diet. These changes include established markers of hyperglycemia as well as novel features that can now be investigated as potential therapeutic targets. Our results indicate the microbiome mediates the effect of diet on glycemic, metabolic and immune measurements, with gut microbiome compositional change explaining 12.25% of serum metabolites variance. Although the gut microbiome displays greater compositional changes compared to the oral microbiome, the oral microbiome demonstrates more changes at the genetic level, with trends dependent on environmental richness and species prevalence in the population. In conclusion, our study shows dietary interventions can affect the microbiome, cardiometabolic profile and immune response of the host, and that these factors are well associated with each other, and can be harnessed for new therapeutic modalities.
Nonporous amorphous superadsorbents for highly effective and selective adsorption of iodine in water
Authors: Zhou Wei , Li Aimin , Zhou Min , Xu Yiyao , Zhang Yi , He Qing 
Published: September 2023

AbstractAdsorbents widely utilized for environmental remediation, water purification, and gas storage have been usually reported to be either porous or crystalline materials. In this contribution, we report the synthesis of two covalent organic superphane cages, that are utilized as the nonporous amorphous superadsorbents for aqueous iodine adsorption with the record–breaking iodine adsorption capability and selectivity. In the static adsorption system, the cages exhibit iodine uptake capacity of up to 8.41 g g−1 in I2 aqueous solution and 9.01 g g−1 in I3− (KI/I2) aqueous solution, respectively, even in the presence of a large excess of competing anions. In the dynamic flow-through experiment, the aqueous iodine adsorption capability for I2 and I3− can reach up to 3.59 and 5.79 g g−1, respectively. Moreover, these two superphane cages are able to remove trace iodine in aqueous media from ppm level (5.0 ppm) down to ppb level concentration (as low as 11 ppb). Based on a binding–induced adsorption mechanism, such nonporous amorphous molecular materials prove superior to all existing porous adsorbents. This study can open up a new avenue for development of state–of–the–art adsorption materials for practical uses with conceptionally new nonporous amorphous superadsorbents (NAS).
Layer-dependent exciton polarizability and the brightening of dark excitons in few-layer black phosphorus
Authors: Lei Yuchen , Ma Junwei , Luo Jiaming , Huang Shenyang , Yu Boyang , Song Chaoyu , Xing Qiaoxia , Wang Fanjie , Xie Yuangang , Zhang Jiasheng , Mu Lei , Ma Yixuan , Wang Chong , Yan Hugen 
Published: September 2023

AbstractThe evolution of excitons from 2D to 3D is of great importance in photo-physics, yet the layer-dependent exciton polarizability hasn’t been investigated in 2D semiconductors. Here, we determine the exciton polarizabilities for 3- to 11-layer black phosphorus—a direct bandgap semiconductor regardless of the thickness—through frequency-resolved photocurrent measurements on dual-gate devices and unveil the carrier screening effect in relatively thicker samples. By taking advantage of the broadband photocurrent spectra, we are also able to reveal the exciton response for higher-index subbands under the gate electrical field. Surprisingly, dark excitons are brightened with intensity even stronger than the allowed transitions above certain electrical field. Our study not only sheds light on the exciton evolution with sample thickness, but also paves a way for optoelectronic applications of few-layer BP in modulators, tunable photodetectors, emitters and lasers.
Decorated bacteria-cellulose ultrasonic metasurface
Authors: Li Zong-Lin , Chen Kun , Li Fei , Shi Zhi-Jun , Sun Qi-Li , Li Peng-Qi , Peng Yu-Gui , Huang Lai-Xin , Yang Guang , Zheng Hairong , Zhu Xue-Feng 
Published: September 2023

AbstractCellulose, as a component of green plants, becomes attractive for fabricating biocompatible flexible functional devices but is plagued by hydrophilic properties, which make it easily break down in water by poor mechanical stability. Here we report a class of SiO2-nanoparticle-decorated bacteria-cellulose meta-skin with superior stability in water, excellent machining property, ultrathin thickness, and active bacteria-repairing capacity. We further develop functional ultrasonic metasurfaces based on meta-skin paper-cutting that can generate intricate patterns of ~10 μm precision. Benefited from the perfect ultrasound insulation of surface Cassie-Baxter states, we utilize meta-skin paper-cutting to design and fabricate ultrathin (~20 μm) and super-light (<20 mg) chip-scale devices, such as nonlocal holographic meta-lens and the 3D imaging meta-lens, realizing complicated acoustic holograms and high-resolution 3D ultrasound imaging in far fields. The decorated bacteria-cellulose ultrasonic metasurface opens the way for exploiting flexible and biologically degradable metamaterial devices with functionality customization and key applications in advanced biomedical engineering technologies.
Antigravitropic PIN polarization maintains non-vertical growth in lateral roots
Authors: Roychoudhry Suruchi , Sageman-Furnas Katelyn , Wolverton Chris , Grones Peter , Tan Shutang , Molnár Gergely , De Angelis Martina , Goodman Heather L. , Capstaff Nicola , Lloyd James P. B. , Mullen Jack , Hangarter Roger , Friml Jiří , Kepinski Stefan 
Published: September 2023

AbstractLateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.
Structural basis for abscisic acid efflux mediated by ABCG25 in Arabidopsis thaliana
Authors: Ying Wei , Liao Lianghuan , Wei Hong , Gao Yongxiang , Liu Xin , Sun Linfeng 
Published: September 2023

AbstractAbscisic acid (ABA) is a phytohormone essential to the regulation of numerous aspects of plant growth and development. The cellular level of ABA is critical to its signalling and is determined by its rate of biosynthesis, catabolism and the rates of ABA transport. ABCG25 in Arabidopsis thaliana has been identified to be an ABA exporter and play roles in regulating stomatal closure and seed germination. However, its ABA transport mechanism remains unknown. Here we report the structures of ABCG25 under different states using cryo-electron microscopy single particle analysis: the apo state and ABA-bound state of the wild-type ABCG25 and the ATP-bound state of the ATPase catalytic mutant. ABCG25 forms a homodimer. ABA binds to a cone-shaped, cytosolic-facing cavity formed in the middle of the transmembrane domains. Key residues in ABA binding are identified and verified by a cell-based ABA transport assay. ATP binding leads to closing of the nucleotide-binding domains of opposing monomers and conformational transitions of the transmembrane domains. Together, these results provide insights into the substrate recognition and transport mechanisms of ABCG25 in Arabidopsis, and facilitate our understanding of the ABA transport and signalling pathway in plants.
Colonic phosphocholine is correlated with Candida tropicalis and promotes diarrhea and pathogen clearance
Authors: Zhou Xihong , He Yiwen , Chen Jingqing , Xiong Xia , Yin Jie , Liang Jing , Peng Can , Huang Chunxia , Guan Guiping , Yin Yulong 
Published: September 2023

AbstractDiarrhea is characterized by alterations in the gut microbiota, metabolites, and host response to these changes. Studies have focused on the role of commensal bacteria in diarrhea; however, the effect of fungi on its pathogenesis remains unexplored. Here, using post-weaned piglets with or without diarrhea, we found an unexpected decrease in the abundance of Candida tropicalis in diarrheal piglets. We also observed increased accumulation of reactive oxygen species (ROS) and the formation of neutrophil extracellular traps (NETs) in the colonic tissues of diarrheal piglets. Using dectin-1-knockout mice, we found that the over-accumulation of ROS killed C. tropicalis by promoting NET formation, which was dependent on dectin-1. The decreased abundance of C. tropicalis resulted in reduced phosphocholine consumption. Then, colonic phosphocholine accumulation drives water efflux by increasing cAMP levels by activating adenylyl cyclase, which promotes the clearance of pathogenic bacteria. Collectively, we demonstrated that phosphocholine is correlated with colonic C. tropicalis and promotes diarrhea and pathogen clearance. Our results suggest that mycobiota colonizing the colon might be involved in maintaining intestinal metabolic homeostasis through the consumption of certain metabolites.
Transverse energy injection scales at the base of the solar corona
Authors: Sharma Rahul , Morton Richard J. 
Published: September 2023

AbstractAlfvén wave turbulence models lie at the heart of many investigations into the winds and extreme-ultraviolet and X-ray emission from cool, solar-like stars. The models provide insights into mass loss, magnetic spin down and exoplanet habitability. Yet they currently rely on ad hoc estimates of critical parameters. One critical but unknown parameter is the perpendicular correlation length, which controls the turbulent heating rate and, hence, has a role in determining the properties of coronal plasma. Here, using the Coronal Multi-channel Polarimeter, we measure the correlation length of Alfvénic waves at the base of the corona. The measurements are an order of magnitude closer to the Sun than previous estimates for the perpendicular correlation length. Our analysis shows the values are broadly homogeneous through the corona and have a distribution sharply peaked around 7.6–9.3 Mm. The measured correlation length is comparable to the expected scales associated with supergranulation. The results provide a stringent constraint for Alfvén wave turbulence modelling.
Unveiling global species abundance distributions
Authors: Callaghan Corey T. , Borda-de-Água Luís , van Klink Roel , Rozzi Roberto , Pereira Henrique M. 
Published: September 2023

AbstractWhether most species are rare or have some intermediate abundance is a long-standing question in ecology. Here, we use more than one billion observations from the Global Biodiversity Information Facility to assess global species abundance distributions (gSADs) of 39 taxonomic classes of eukaryotic organisms from 1900 to 2019. We show that, as sampling effort increases through time, the shape of the gSAD is unveiled; that is, the shape of the sampled gSAD changes, revealing the underlying gSAD. The fraction of species unveiled for each class decreases with the total number of species in that class and increases with the number of individuals sampled, with some groups, such as birds, being fully unveiled. The best statistical fit for almost all classes was the Poisson log-normal distribution. This strong evidence for a universal pattern of gSADs across classes suggests that there may be general ecological or evolutionary mechanisms governing the commonness and rarity of life on Earth.
Single-cell RNA sequencing of murine hearts for studying the development of the cardiac conduction system
Authors: Ren Huiying , Zhou Xiaolin , Yang Jun , Kou Kun , Chen Tangting , Pu Zhaoli , Ye Kejun , Fan Xuehui , Zhang Dan , Kang Xinjiang , Fan Zhongcai , Lei Ming , Sun Tianyi , Tan Xiaoqiu , Ou Xianhong 
Published: September 2023

AbstractThe development of the cardiac conduction system (CCS) is essential for correct heart function. However, critical details on the cell types populating the CCS in the mammalian heart during the development remain to be resolved. Using single-cell RNA sequencing, we generated a large dataset of transcriptomes of ~0.5 million individual cells isolated from murine hearts at six successive developmental corresponding to the early, middle and late stages of heart development. The dataset provides a powerful library for studying the development of the heart’s CCS and other cardiac components. Our initial analysis identified distinct cell types between 20 to 26 cell types across different stages, of which ten are involved in forming the CCS. Our dataset allows researchers to reuse the datasets for data mining and a wide range of analyses. Collectively, our data add valuable transcriptomic resources for further study of cardiac development, such as gene expression, transcriptional regulation and functional gene activity in developing hearts, particularly the CCS.
Simulating individual movement in fish
Authors: Pike Thomas W. , Burman Oliver H. P. 
Published: September 2023

AbstractAccurately quantifying an animal’s movement is crucial for developing a greater empirical and theoretical understanding of its behaviour, and for simulating biologically plausible movement patterns. However, we have a relatively poor understanding of how animals move at fine temporal scales and in three-dimensional environments. Here, we collected high temporal resolution data on the three-dimensional spatial positions of individual three-spined sticklebacks (Gasterosteus aculeatus), allowing us to derive statistics describing key geometric characteristics of their movement and to quantify the extent to which this varies between individuals. We then used these statistics to develop a simple model of fish movement and evaluated the biological plausibility of simulated movement paths using a Turing-type test, which quantified the association preferences of live fish towards animated conspecifics following either ‘real’ (i.e., based on empirical measurements) or simulated movements. Live fish showed no difference in their response to ‘real’ movement compared to movement simulated by the model, although significantly preferred modelled movement over putatively unnatural movement patterns. The model therefore has the potential to facilitate a greater understanding of the causes and consequences of individual variation in movement, as well as enabling the construction of agent-based models or real-time computer animations in which individual fish move in biologically feasible ways.
A hybrid in silico/in-cell controller for microbial bioprocesses with process-model mismatch
Authors: Ohkubo Tomoki , Soma Yuki , Sakumura Yuichi , Hanai Taizo , Kunida Katsuyuki 
Published: September 2023

AbstractBioprocess optimization using mathematical models is prevalent, yet the discrepancy between model predictions and actual processes, known as process-model mismatch (PMM), remains a significant challenge. This study proposes a novel hybrid control system called the hybrid in silico/in-cell controller (HISICC) to address PMM by combining model-based optimization (in silico feedforward controller) with feedback controllers utilizing synthetic genetic circuits integrated into cells (in-cell feedback controller). We demonstrated the efficacy of HISICC using two engineered Escherichia coli strains, TA1415 and TA2445, previously developed for isopropanol (IPA) production. TA1415 contains a metabolic toggle switch (MTS) to manage the competition between cell growth and IPA production for intracellular acetyl-CoA by responding to external input of isopropyl β-d-1-thiogalactopyranoside (IPTG). TA2445, in addition to the MTS, has a genetic circuit that detects cell density to autonomously activate MTS. The combination of TA2445 with an in silico controller exemplifies HISICC implementation. We constructed mathematical models to optimize IPTG input values for both strains based on the two-compartment model and validated these models using experimental data of the IPA production process. Using these models, we evaluated the robustness of HISICC against PMM by comparing IPA yields with two strains in simulations assuming various magnitudes of PMM in cell growth rates. The results indicate that the in-cell feedback controller in TA2445 effectively compensates for PMM by modifying MTS activation timing. In conclusion, the HISICC system presents a promising solution to the PMM problem in bioprocess engineering, paving the way for more efficient and reliable optimization of microbial bioprocesses.
110-million-years-old fossil suggests early parasitism in shrimps
Authors: Lima Daniel , Alencar Damares R. , Santana William , Oliveira Naiara C. , Saraiva Antônio Á. F. , Oliveira Gustavo R. , Boyko Christopher B. , Pinheiro Allysson P. 
Published: September 2023

AbstractDirect evidence of paleo-parasitism in crustaceans is very scarce. Epicaridean isopods are obligatory parasites of crustaceans, including decapods such as crabs, shrimps, and lobsters. Their interaction with hosts is known from fossils as far back as the Jurassic through deformations of the branchial cuticle on the hosts. Their small size and low fossilization potential, outside of those larvae that have been found in amber, makes understanding the group’s evolution challenging. Here, we report the oldest evidence of paleo-parasitism in marine shrimps and an imprint of a putative adult parasite that appears to be an epicaridean isopod. Our results suggest that the parasite–host interaction between epicaridean isopods and marine shrimps started at least 110 million years ago, and the Tethys Sea was a possible dispersal pathway for this lineage of parasites during the Jurassic and Cretaceous, as known for other marine organisms through most of the Mesozoic and Cenozoic. The oldest fossil records of bopyrid swellings associated with a large number of decapods from the Jurassic in Europe suggest that the Tethys region was a center of epicaridean distribution as a whole. Recent parasitic isopods found on dendrobranchiate shrimps are restricted to the Indo-Pacific and may represent a relict group of a lineage of parasites more widely distributed in the Mesozoic.
Brainwave activities reflecting depressed mood: a pilot study
Authors: Morita Masahiko , Otsu Ryusei , Kawasaki Masahiro 
Published: September 2023

AbstractEarly diagnosis and treatment of depression are desirable but currently difficult due to a lack of established biomarkers. Although biomarkers for depression based on electroencephalogram (EEG) data have long been explored, most existing methods are thought to capture cognitive decline caused by depression and are unsuccessful in detecting signs of depression. Here we report that some brainwave activities involving phase resetting reflect the depressed mood at the time, which can be easily monitored by measuring the resting EEG with eyes closed for 1 min with a few electrodes. We instructed 10 participants (nine healthy and one diagnosed with depression, aged 18–34) to record their EEG for 14–26 days. We found that indicators of depressed mood were correlated with the occurrence frequency of EEG phase resetting. For most participants, the correlation coefficients swung systematically between large positive and large negative values with respect to EEG frequency; however, the frequencies at which they were maximum or minimum differed among participants. Although this study is in the pilot phase and needs further experimentation, the results are expected to lead to innovative biomarkers for early detection of depression and may contribute to a better understanding and treatment of depression.