bluuebunny/crossref_metadata_2025 huggingface dataset:
Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
Authors: Chen Baohua , Bai Yulin , Wang Jiaying , Ke Qiaozhen , Zhou Zhixiong , Zhou Tao , Pan Ying , Wu Renxie , Wu Xiongfei , Zheng Weiqiang , Xu Peng
Published: April 2023

The large yellow croaker (Larimichthyscrocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies.
Phosphoinositides in plant-pathogen interaction: trends and perspectives
Authors: Zarreen Fauzia , Kumar Kamal , Chakraborty Supriya
Published: April 2023

Phosphoinositides are important regulatory membrane lipids, with a role in plant development and cellular function. Emerging evidence indicates that phosphoinositides play crucial roles in plant defence and are also utilized by pathogens for infection. In this review, we highlight the role of phosphoinositides in plant-pathogen interaction and the implication of this remarkable convergence in the battle against plant diseases.
g-C3N4-based photocatalysts for organic pollutant removal: a critical review
Authors: Luo Yidan , Zhu Yaowei , Han Yu , Ye Huiyin , Liu Ruochen , Lan Yuanwang , Xue Mingshan , Xie Xianchuan , Yu Shuohan , Zhang Longshuai , Yin Zuozhu , Gao Bin
Published: April 2023

With rapid global industrialization, environmental pollution has become one of the major problems of human society. Photocatalysis can be applied to solve environmental problem by using inexhaustible solar energy. As a novel two-dimensional material, graphite carbon nitride (g-C3N4) has been widely applied in many photocatalytic reactions. However, in terms of its practical applications, g-C3N4still has limitations, including poor photoexcited charge separation, limited range of visible light absorption, and low surface areas. Hence, current research on g-C3N4mainly focuses on improving its photocatalytic performance. In this review, we summarize various methods to improve g-C3N4’s light absorption and photo-induced charge transfer, including vacancy engineering, morphology control, heteroatom doping, and forming heterostructure. The applications of g-C3N4and its derivatives in photodegradation of organic pollutants are also discussed in detail. Finally, the challenges and future research directions of g-C3N4photocatalysts are summarized to promote their environmental applications.

Graphical Abstract
A systematic literature review of cyber-security data repositories and performance assessment metrics for semi-supervised learning
Authors: Mvula Paul K. , Branco Paula , Jourdan Guy-Vincent , Viktor Herna L.
Published: April 2023

In Machine Learning, the datasets used to build models are one of the main factors limiting what these models can achieve and how good their predictive performance is. Machine Learning applications for cyber-security or computer security are numerous including cyber threat mitigation and security infrastructure enhancement through pattern recognition, real-time attack detection, and in-depth penetration testing. Therefore, for these applications in particular, the datasets used to build the models must be carefully thought to be representative of real-world data. However, because of the scarcity of labelled data and the cost of manually labelling positive examples, there is a growing corpus of literature utilizing Semi-Supervised Learning with cyber-security data repositories. In this work, we provide a comprehensive overview of publicly available data repositories and datasets used for building computer security or cyber-security systems based on Semi-Supervised Learning, where only a few labels are necessary or available for building strong models. We highlight the strengths and limitations of the data repositories and sets and provide an analysis of the performance assessment metrics used to evaluate the built models. Finally, we discuss open challenges and provide future research directions for using cyber-security datasets and evaluating models built upon them.
Network Science in Archaeology
Authors: Brughmans Tom , Peeples Matthew A.
Published: April 2023

The Cambridge Manual to Archaeological Network Science provides the first comprehensive guide to a field of research that has firmly established itself within archaeological practice in recent years. Network science methods are commonly used to explore big archaeological datasets and are essential for the formal study of past relational phenomena: social networks, transport systems, communication, and exchange. The volume offers a step-by-step description of network science methods and explores its theoretical foundations and applications in archaeological research, which are elaborately illustrated with archaeological examples. It also covers a vast range of network science techniques that can enhance archaeological research, including network data collection and management, exploratory network analysis, sampling issues and sensitivity analysis, spatial networks, and network visualisation. An essential reference handbook for both beginning and experienced archaeological network researchers, the volume includes boxes with definitions, boxed examples, exercises, and online supplementary learning and teaching materials.
Dynamic Approaches to Phonological Processing
Authors: Hatfield Hunter
Published: April 2023

Natural language occurs in time. Events happen earlier, later, or simultaneously with other events; however, this temporal dimension is often downplayed or overlooked. This Element introduces readers with a background in structural linguistics to dynamic approaches to phonological processing. It covers models of serial order, speech production and speech perception, with special attention to how they can enhance one another. The work then asks whether dynamic approaches have the potential to change how we think of phonological structure. Key ideas discussed include phonemes and auditory targets, control mechanisms creating structure, and the shape of phonological representations in a dynamic context. The work should function as a bridge for those with linguistic questions who want to learn answers derived from the study of speech as a dynamic system.
Purrieties of Language
Authors: Podhovnik Edith
Published: April 2023

After conquering the Internet, cats are now taking on linguistics! Since the advent of social media, cats have become a topic central to online communication, and the multitude of cat-related accounts now online has made this a world-wide phenomenon. Through cat-inspired varieties of language, we have developed a genre of cat-inspired vocabulary. And on our special social media accounts for our cats, we take on their identities, as we post, write, talk, and chat - as our feline friends. This innovative book provides linguistic analyses of the cyber 'Cativerse', exploring online language variation, and explaining key linguistic concepts – all through the lens of cat-related communication. Each chapter explores a different sociolinguistic phenomena, drawing on fun and engaging examples including memes, hashtags, captions and 'LOLcats', from platforms such as Instagram, Facebook, YouTube and Twitter. Innovative yet accessible, it is catnip for all 'hoomans' interested in how language is used online.
Understanding Species
Authors: Wilkins John S.
Published: April 2023

Are species worth saving? Can they be resurrected by technology? What is the use of species in biomedicine? These questions all depend on a clear definition of the concept of 'species', yet biologists have long struggled to define this term. In this accessible book, John S. Wilkins provides an introduction to the concept of 'species' in biology, philosophy, ethics, policymaking and conservation. Using clear language and easy-to-understand examples throughout, the book provides a history of species and why we use them. It encourages readers to appreciate the philosophical depth of the concept as well as its connections to logic and science. For any interested reader, this short text highlights the complexities of a single idea in biology, the problems with the concept of 'species' and the benefits of it in helping us to answer the bigger questions and understand our living world.
Empirical Parameterization of Broadband VLF Attenuation in the Earth‐Ionosphere Waveguide
Authors: Said Ryan , Gołkowski Marek , Harid Vijay
Published: April 2023

The Earth‐ionosphere waveguide (EIW) determines the propagation of Very Low Frequency (VLF; ∼3−30 kHz) waves. Characterizing the waveguide is a longstanding challenge due to its large spatial scale and the complex variability of the lower ionosphere. Here we apply a novel linear basis function regression technique to characterize attenuation in the EIW using broadband measurements of lightning‐generated radio waves. The process begins with defining a basis function set, which ideally encompasses a feature set that can predict the variability seen in VLF attenuation properties. With this basis set defined, a system of linear equations is then constructed using sensor pair observations to eliminate the dependency on source amplitude in each observation. Using this formalism, an empirical attenuation model for broadband signals from lightning is constructed and the dependence on attenuation properties with the boundary conditions is explored. The empirically derived results show attenuation rates over ice that are 12 dB/Mm higher compared to paths over saltwater. Well‐known east/west attenuation rate asymmetry stemming from anisotropic reflection coefficients of the ionosphere is also demonstrated and investigated. For example, under a daytime ionosphere, westward‐propagating waves suffer up to 2.8 dB/Mm greater attenuation compared to eastward‐propagating waves. The trained model is used for propagation corrections in a global lightning locating system (LLS), but this technique can be expanded to further study VLF attenuation rates by employing different sets of basis functions.
Foreshock Ion Motion Across Discontinuities: Formation of Foreshock Transients
Authors: Liu Terry Z. , Angelopoulos Vassilis , Vu Andrew , Zhang Hui
Published: April 2023

In the ion foreshock, hot flow anomalies (HFAs) and foreshock bubbles (FBs) are two types of foreshock transients that have the strongest fluctuations, which can disturb the magnetosphere‐ionosphere system and increase shock acceleration efficiency. They form due to interaction between the foreshock ions and solar wind discontinuities: the direction of the foreshock ion‐driven current and whether it decreases or increases the magnetic field strength behind the discontinuity determine whether the transient's formation can be promoted or suppressed. Thus, to predict the HFA and FB formation and forecast their space weather effects, it is necessary to predict the foreshock ion‐driven current direction. In this study, we derive analytical equations of foreshock ion velocities within discontinuities to estimate foreshock ion‐driven current direction, which provides a quantitative criterion of HFA and FB formation. To validate the criterion, we use Acceleration Reconnection Turbulence & Electrodynamics of Moon's Interaction with the Sun to observe pristine solar wind discontinuities and calculate discontinuity parameters. We use Magnetospheric Multiscale to observe the foreshock ion motion around the discontinuities and show that the data support our model. This study is another step toward a predictive model of HFA and FB formation so that we can forecast their space weather effects at Earth using solar wind observations at lunar orbit or L1.
Wave Climate Variability and Trends in Tuvalu Based on a 44‐Year High‐Resolution Wave Hindcast
Authors: Wandres Moritz , Espejo Antonio , Damlamian Hervé
Published: April 2023

Waves are one of the main causes of coastal flooding and shoreline change in low‐lying atoll nations like Tuvalu. A detailed understanding of Tuvalu’s wave climate is therefore critical for decision‐makers, coastal engineers, and disaster‐risk managers. Here, we investigate Tuvalu’s wind‐wave climate, changes due to large‐scale climate variability, and long‐term trends. A 44‐year (1979–2022) high‐resolution wave hindcast was developed using the unstructured version of the wave model Simulating Waves Nearshore (SWAN). The model resolution varied between 20 km offshore in deep water and 300 m close to shore. The model was forced with the European Centre for Medium‐Range Weather Forecasts Reanalysis v5 (ERA5) wind and boundary wave conditions. Northern and Southern Hemisphere winter months produced the largest and most powerful waves. Through the analysis of the directional wave energy spectra, we identified three main wave energy sources: (a) extratropical storms in the Southern Ocean; (b) extratropical storms in the North Pacific; and (c) easterly trade winds. Slightly positive trends in high‐frequency (∼10 s) wave energy from the east and low‐frequency (∼15 s) wave energy from the southwest were linked to an intensification of trade winds and an intensification and poleward displacement of the Southern Ocean storm belt over recent decades. The interannual variability of Tuvalu’s wave climate was strongly linked to large‐scale climate modes such as El Niño Southern Oscillation, Pacific Decadal Oscillation, and Arctic and Antarctic Oscillation. The study builds on previous research and significantly enhances the understanding of Tuvalu’s wave climate variability.
Thermospheric Temperature and Density Variability During 3–4 February 2022 Minor Geomagnetic Storm
Authors: Laskar F. I. , Sutton E. K. , Lin D. , Greer K. R. , Aryal S. , Cai X. , Pedatella N. M. , Eastes R. W. , Wang W. , Codrescu M. V. , McClintock W. E.
Published: April 2023

Themospheric conditions during a minor geomagnetic event of 3 and 4 February 2022 has been investigated using disk temperature (Tdisk) observations from Global‐scale Observations of the Limb and Disk (GOLD) mission and model simulations. GOLD observed that the Tdisk increases by more than 60 K during the storm event when compared with pre‐storm quiet days. A comparison of the Tdisk with effective temperatures (Teff, i.e., a weighted average based on airglow emission layer) from Mass Spectrometer Incoherent Scatter radar version 2 (MSIS2) and Multiscale Atmosphere‐Geospace Environment (MAGE) models shows that MAGE outperforms MSIS2 during this particular event. MAGE underestimates the Teff by about 2%, whereas MSIS2 underestimates it by 7%. As temperature enhancements lead to an expansion of the thermosphere and resulting density changes, the value of the temperature enhancement observed by GOLD can be utilized to find a GOLD equivalent MSIS2 (GOLD‐MSIS) simulation—from a set of MSIS2 runs obtained by varying geomagnetic ap index values. From the MSIS‐GOLD run we found that the thermospheric density enhancement varies with altitude from 15% (at 150) to 80% (at 500 km). Independent simulations from the MAGE model also show a comparable enhancement in neutral density. These results suggest that even a modest storm could impact the thermospheric densities significantly and GOLD data can be used to improve the empirical and assimilative models of the thermosphere.
Non-Hermitian chiral degeneracy of gated graphene metasurfaces
Authors: Baek Soojeong , Park Sang Hyun , Oh Donghak , Lee Kanghee , Lee Sangha , Lim Hosub , Ha Taewoo , Park Hyun Sung , Zhang Shuang , Yang Lan , Min Bumki , Kim Teun-Teun
Published: April 2023

Non-Hermitian degeneracies, also known as exceptional points (EPs), have been the focus of much attention due to their singular eigenvalue surface structure. Nevertheless, as pertaining to a non-Hermitian metasurface platform, the reduction of an eigenspace dimensionality at the EP has been investigated mostly in a passive repetitive manner. Here, we propose an electrical and spectral way of resolving chiral EPs and clarifying the consequences of chiral mode collapsing of a non-Hermitian gated graphene metasurface. More specifically, the measured non-Hermitian Jones matrix in parameter space enables the quantification of nonorthogonality of polarisation eigenstates and half-integer topological charges associated with a chiral EP. Interestingly, the output polarisation state can be made orthogonal to the coalesced polarisation eigenstate of the metasurface, revealing the missing dimension at the chiral EP. In addition, the maximal nonorthogonality at the chiral EP leads to a blocking of one of the cross-polarised transmission pathways and, consequently, the observation of enhanced asymmetric polarisation conversion. We anticipate that electrically controllable non-Hermitian metasurface platforms can serve as an interesting framework for the investigation of rich non-Hermitian polarisation dynamics around chiral EPs.
Tardigrade-inspired extremotolerant glycerogels
Authors: Mredha Md. Tariful Islam , Lee Yoonseong , Rama Varma Adith Varma , Gupta Tanish , Manimel Wadu Rumesh Rangana , Jeon Insu
Published: April 2023

We developed extremotolerant glycerogels (GGs) with well-modulated polymer structures, functions, and properties, inspired by the tun formation of tardigrades. GGs comprising extreme protected intra- and intermolecular networks are obtained through a very slow structure building process, which includes the smooth replacement of water in predesigned hydrogels with glycerol and thermal annealing while retaining the structures and functions of the original hydrogels. Four different GGs are fabricated as proofs-of-concept using different crosslinkers and polymers. Although various polyol-based wide-temperature-tolerant gels fabricated by conventional methods fail to demonstrate stabilities at low and high temperature extremes simultaneously, the GGs fabricated by our bioinspired method exhibit long-term stability (approaching one month) over an extremely wide temperature range (−50–80 °C) and thermal-shock-absorption capabilities at 150 °C. Furthermore, our versatile method enables us to program GGs with wide ranges of stiffness, strength, stretchability, and toughness values and elasticity, plasticity, hysteresis, and self-recoverability capabilities. The self-weldability, electrical patternability, and applicability characteristics of the GGs as electrolytes and supercapacitors demonstrate their complex 3D designability and facile functionalization capability aspects. The various functional GGs developed through the proposed method are applicable for the design of diverse extremotolerant, flexible, and stretchable devices for biological, electrical/electronic, and soft robotics applications.
Distributed processing for value-based choice by prelimbic circuits targeting anterior-posterior dorsal striatal subregions in male mice
Authors: Choi Kyuhyun , Piasini Eugenio , Díaz-Hernández Edgar , Cifuentes Luigim Vargas , Henderson Nathan T. , Holly Elizabeth N. , Subramaniyan Manivannan , Gerfen Charles R. , Fuccillo Marc V.
Published: April 2023

Fronto-striatal circuits have been implicated in cognitive control of behavioral output for social and appetitive rewards. The functional diversity of prefrontal cortical populations is strongly dependent on their synaptic targets, with control of motor output mediated by connectivity to dorsal striatum. Despite evidence for functional diversity along the anterior-posterior striatal axis, it is unclear how distinct fronto-striatal sub-circuits support value-based choice. Here we found segregated prefrontal populations defined by anterior/posterior dorsomedial striatal target. During a feedback-based 2-alternative choice task, single-photon imaging revealed circuit-specific representations of task-relevant information with prelimbic neurons targeting anterior DMS (PL::A-DMS) robustly modulated during choices and negative outcomes, while prelimbic neurons targeting posterior DMS (PL::P-DMS) encoded internal representations of value and positive outcomes contingent on prior choice. Consistent with this distributed coding, optogenetic inhibition of PL::A-DMS circuits strongly impacted choice monitoring and responses to negative outcomes while inhibition of PL::P-DMS impaired task engagement and strategies following positive outcomes. Together our data uncover PL populations engaged in distributed processing for value-based choice.
Atomic-scale origin of the low grain-boundary resistance in perovskite solid electrolyte Li0.375Sr0.4375Ta0.75Zr0.25O3
Authors: Lee Tom , Qi Ji , Gadre Chaitanya A. , Huyan Huaixun , Ko Shu-Ting , Zuo Yunxing , Du Chaojie , Li Jie , Aoki Toshihiro , Wu Ruqian , Luo Jian , Ong Shyue Ping , Pan Xiaoqing
Published: April 2023

Oxide solid electrolytes (OSEs) have the potential to achieve improved safety and energy density for lithium-ion batteries, but their high grain-boundary (GB) resistance generally is a bottleneck. In the well-studied perovskite oxide solid electrolyte, Li3xLa2/3-xTiO3(LLTO), the ionic conductivity of grain boundaries is about three orders of magnitude lower than that of the bulk. In contrast, the related Li0.375Sr0.4375Ta0.75Zr0.25O3(LSTZ0.75) perovskite exhibits low grain boundary resistance for reasons yet unknown. Here, we use aberration-corrected scanning transmission electron microscopy and spectroscopy, along with an active learning moment tensor potential, to reveal the atomic scale structure and composition of LSTZ0.75 grain boundaries. Vibrational electron energy loss spectroscopy is applied for the first time to reveal atomically resolved vibrations at grain boundaries of LSTZ0.75 and to characterize the otherwise unmeasurable Li distribution therein. We find that Li depletion, which is a major reason for the low grain boundary ionic conductivity of LLTO, is absent for the grain boundaries of LSTZ0.75. Instead, the low grain boundary resistivity of LSTZ0.75 is attributed to the formation of a nanoscale defective cubic perovskite interfacial structure that contained abundant vacancies. Our study provides new insights into the atomic scale mechanisms of low grain boundary resistivity.
Carbon reduction technology pathways for existing buildings in eight cities
Authors: Ang Yu Qian , Berzolla Zachary Michael , Letellier-Duchesne Samuel , Reinhart Christoph F.
Published: April 2023

We work with policymakers in eight cities worldwide to identify technology pathways toward their near- and long-term carbon emissions reduction targets for existing buildings. Based on policymakers’ interests, we define city-specific shallow and deep retrofitting packages along with onsite photovoltaic generation potential. Without further grid decarbonization measures, stock-wide implementation of these retrofits in the investigated neighborhoods reduces energy use and carbon emissions by up to 66% and 84%, respectively, helping Braga, Dublin, Florianopolis, Middlebury, and Singapore to meet their 2030 goals. With projected grid decarbonization, Florianopolis and Singapore will reach their 2050 goals. The remaining emissions stem from municipalities not planning to electrify heating and/or domestic hot water use. Different climates and construction practices lead to varying retrofit packages, suggesting that comparable technology pathway analyses should be conducted for municipalities worldwide. Twenty months after the project ended, seven cities have implemented policy measures or expanded the analysis across their building stock.
Anomalous deep-red luminescence of perylene black analogues with strong π-π interactions
Authors: Tang Ningning , Zhou Jiadong , Wang Liangxuan , Stolte Matthias , Xie Guojing , Wen Xinbo , Liu Linlin , Würthner Frank , Gierschner Johannes , Xie Zengqi
Published: April 2023

Perylene bisimide (PBI) dyes are known as red, maroon and black pigments, whose colors depend on the close π−π stacking arrangement. However, contrary to the luminescent monomers, deep-red and black PBI pigments are commonly non- or only weakly fluorescent due to (multiple) quenching pathways. Here, we introduce N-alkoxybenzyl substituted PBIs that contain close π stacking arrangement (exhibiting dπ−π ≈ 3.5 Å, and longitudinal and transversal displacements of 3.1 Å and 1.3 Å); however, they afford deep-red emitters with solid-state fluorescence quantum yields (ΦF) of up to 60%. Systematic photophysical and computational studies in solution and in the solid state reveal a sensitive interconversion of the PBI-centred locally excited state and a charge transfer state, which depends on the dihedral angle (θ) between the benzyl and alkoxy groups. This effectively controls the emission process, and enables high ΦF by circumventing the common quenching pathways commonly observed for perylene black analogues.
Mid-latitudinal habitable environment for marine eukaryotes during the waning stage of the Marinoan snowball glaciation
Authors: Song Huyue , An Zhihui , Ye Qin , Stüeken Eva E. , Li Jing , Hu Jun , Algeo Thomas J. , Tian Li , Chu Daoliang , Song Haijun , Xiao Shuhai , Tong Jinnan
Published: April 2023

During the Marinoan Ice Age (ca. 654–635 Ma), one of the ‘Snowball Earth’ events in the Cryogenian Period, continental icesheets reached the tropical oceans. Oceanic refugia must have existed for aerobic marine eukaryotes to survive this event, as evidenced by benthic phototrophic macroalgae of the Songluo Biota preserved in black shales interbedded with glacial diamictites of the late Cryogenian Nantuo Formation in South China. However, the environmental conditions that allowed these organisms to thrive are poorly known. Here, we report carbon-nitrogen-iron geochemical data from the fossiliferous black shales and adjacent diamictites of the Nantuo Formation. Iron-speciation data document dysoxic-anoxic conditions in bottom waters, whereas nitrogen isotopes record aerobic nitrogen cycling perhaps in surface waters. These findings indicate that habitable open-ocean conditions were more extensive than previously thought, extending into mid-latitude coastal oceans and providing refugia for eukaryotic organisms during the waning stage of the Marinoan Ice Age.
Intercellular exchange of Wnt ligands reduces cell population heterogeneity during embryogenesis
Authors: Hatakeyama Yudai , Saito Nen , Mii Yusuke , Takada Ritsuko , Shinozuka Takuma , Takemoto Tatsuya , Naoki Honda , Takada Shinji
Published: April 2023

Wnt signaling is required to maintain bipotent progenitors for neural and paraxial mesoderm cells, the neuromesodermal progenitor (NMP) cells that reside in the epiblast and tailbud. Since epiblast/tailbud cells receive Wnt ligands produced by one another, this exchange may average out the heterogeneity of Wnt signaling levels among these cells. Here, we examined this possibility by replacing endogenous Wnt3a with a receptor-fused form that activates signaling in producing cells, but not in neighboring cells. Mutant mouse embryos show a unique phenotype in which maintenance of many NMP cells is impaired, although some cells persist for long periods. The epiblast cell population of these embryos increases heterogeneity in Wnt signaling levels as embryogenesis progresses and are sensitive to retinoic acid, an endogenous antagonist of NMP maintenance. Thus, mutual intercellular exchange of Wnt ligands in the epiblast cell population reduces heterogeneity and achieves robustness to environmental stress.
Electrified hydrocarbon-to-oxygenates coupled to hydrogen evolution for efficient greenhouse gas mitigation
Authors: Leow Wan Ru , Völker Simon , Meys Raoul , Huang Jianan Erick , Jaffer Shaffiq A. , Bardow André , Sargent Edward H.
Published: April 2023

Chemicals manufacture is among the top greenhouse gas contributors. More than half of the associated emissions are attributable to the sum of ammonia plus oxygenates such as methanol, ethylene glycol and terephthalic acid. Here we explore the impact of electrolyzer systems that couple electrically-powered anodic hydrocarbon-to-oxygenate conversion with cathodic H2 evolution reaction from water. We find that, once anodic hydrocarbon-to-oxygenate conversion is developed with high selectivities, greenhouse gas emissions associated with fossil-based NH3 and oxygenates manufacture can be reduced by up to 88%. We report that low-carbon electricity is not mandatory to enable a net reduction in greenhouse gas emissions: global chemical industry emissions can be reduced by up to 39% even with electricity having the carbon footprint per MWh available in the United States or China today. We conclude with considerations and recommendations for researchers who wish to embark on this research direction.
Carbon-sink potential of continuous alfalfa agriculture lowered by short-term nitrous oxide emission events
Authors: Anthony Tyler L. , Szutu Daphne J. , Verfaillie Joseph G. , Baldocchi Dennis D. , Silver Whendee L.
Published: April 2023

Alfalfa is the most widely grown forage crop worldwide and is thought to be a significant carbon sink due to high productivity, extensive root systems, and nitrogen-fixation. However, these conditions may increase nitrous oxide (N2O) emissions thus lowering the climate change mitigation potential. We used a suite of long-term automated instrumentation and satellite imagery to quantify patterns and drivers of greenhouse gas fluxes in a continuous alfalfa agroecosystem in California. We show that this continuous alfalfa system was a large N2O source (624 ± 28 mg N2O m2 y−1), offsetting the ecosystem carbon (carbon dioxide (CO2) and methane (CH4)) sink by up to 14% annually. Short-term N2O emissions events (i.e., hot moments) accounted for ≤1% of measurements but up to 57% of annual emissions. Seasonal and daily trends in rainfall and irrigation were the primary drivers of hot moments of N2O emissions. Significant coherence between satellite-derived photosynthetic activity and N2O fluxes suggested plant activity was an important driver of background emissions. Combined data show annual N2O emissions can significantly lower the carbon-sink potential of continuous alfalfa agriculture.
TREM2+ and interstitial-like macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques
Authors: Upadhyay Amit A. , Viox Elise G. , Hoang Timothy N. , Boddapati Arun K. , Pino Maria , Lee Michelle Y.-H. , Corry Jacqueline , Strongin Zachary , Cowan David A. , Beagle Elizabeth N. , Horton Tristan R. , Hamilton Sydney , Aoued Hadj , Harper Justin L. , Edwards Christopher T. , Nguyen Kevin , Pellegrini Kathryn L. , Tharp Gregory K. , Piantadosi Anne , Levit Rebecca D. , Amara Rama R. , Barratt-Boyes Simon M. , Ribeiro Susan P. , Sekaly Rafick P. , Vanderford Thomas H. , Schinazi Raymond F. , Paiardini Mirko , Bosinger Steven E.
Published: April 2023

The immunopathological mechanisms driving the development of severe COVID-19 remain poorly defined. Here, we utilize a rhesus macaque model of acute SARS-CoV-2 infection to delineate perturbations in the innate immune system. SARS-CoV-2 initiates a rapid infiltration of plasmacytoid dendritic cells into the lower airway, commensurate with IFNA production, natural killer cell activation, and a significant increase of blood CD14-CD16+ monocytes. To dissect the contribution of lung myeloid subsets to airway inflammation, we generate a longitudinal scRNA-Seq dataset of airway cells, and map these subsets to corresponding populations in the human lung. SARS-CoV-2 infection elicits a rapid recruitment of two macrophage subsets: CD163+MRC1-, and TREM2+ populations that are the predominant source of inflammatory cytokines. Treatment with baricitinib (Olumiant®), a JAK1/2 inhibitor is effective in eliminating the influx of non-alveolar macrophages, with a reduction of inflammatory cytokines. This study delineates the major lung macrophage subsets driving airway inflammation during SARS-CoV-2 infection.
Early indicators of tidal ecosystem shifts in estuaries
Authors: Fivash Gregory S. , Temmerman Stijn , Kleinhans Maarten G. , Heuner Maike , van der Heide Tjisse , Bouma Tjeerd J.
Published: April 2023

Forecasting transitions between tidal ecosystem states, such as between bare tidal flats and vegetated marshes, is crucial because it may imply the irreversible loss of valuable ecosystem services. In this study, we combine geospatial analyses of three European estuaries with a simple numerical model to demonstrate that the development of micro-topographic patterning on tidal flats is an early indicator of marsh establishment. We first show that the development of micro-topographic patterns precedes vegetation establishment, and that patterns tend to form only on tidal flats with a slope of <0.3 degrees. Numerical modelling then provides an explanation for the formation of micro-topography due to the natural concentration of draining surface water over very gentle slopes. We find this early indicator to be robust across three estuaries where anthropogenic deepening and narrowing has occurred in recent decades, which may suggest its broader applicability to other estuaries with similar morphological management.
Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism
Authors: Baden Pascale , Perez Maria Jose , Raji Hariam , Bertoli Federico , Kalb Stefanie , Illescas María , Spanos Fokion , Giuliano Claudio , Calogero Alessandra Maria , Oldrati Marvin , Hebestreit Hannah , Cappelletti Graziella , Brockmann Kathrin , Gasser Thomas , Schapira Anthony H. V. , Ugalde Cristina , Deleidi Michela
Published: April 2023

Mutations in GBA1, the gene encoding the lysosomal enzyme β-glucocerebrosidase (GCase), which cause Gaucher’s disease, are the most frequent genetic risk factor for Parkinson’s disease (PD). Here, we employ global proteomic and single-cell genomic approaches in stable cell lines as well as induced pluripotent stem cell (iPSC)-derived neurons and midbrain organoids to dissect the mechanisms underlying GCase-related neurodegeneration. We demonstrate that GCase can be imported from the cytosol into the mitochondria via recognition of internal mitochondrial targeting sequence-like signals. In mitochondria, GCase promotes the maintenance of mitochondrial complex I (CI) integrity and function. Furthermore, GCase interacts with the mitochondrial quality control proteins HSP60 and LONP1. Disease-associated mutations impair CI stability and function and enhance the interaction with the mitochondrial quality control machinery. These findings reveal a mitochondrial role of GCase and suggest that defective CI activity and energy metabolism may drive the pathogenesis of GCase-linked neurodegeneration.
Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes
Authors: Saha Liton Kumar , Saha Sourav , Yang Xi , Huang Shar-yin Naomi , Sun Yilun , Jo Ukhyun , Pommier Yves
Published: April 2023

Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a “self-trapping” TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
Construction of a synthetic metabolic pathway for biosynthesis of 2,4-dihydroxybutyric acid from ethylene glycol
Authors: Frazão Cláudio J. R. , Wagner Nils , Rabe Kenny , Walther Thomas
Published: April 2023

Ethylene glycol is an attractive two-carbon alcohol substrate for biochemical product synthesis as it can be derived from CO2 or syngas at no sacrifice to human food stocks. Here, we disclose a five-step synthetic metabolic pathway enabling the carbon-conserving biosynthesis of the versatile platform molecule 2,4-dihydroxybutyric acid (DHB) from this compound. The linear pathway chains ethylene glycol dehydrogenase, D-threose aldolase, D-threose dehydrogenase, D-threono-1,4-lactonase, D-threonate dehydratase and 2-oxo-4-hydroxybutyrate reductase enzyme activities in succession. We screen candidate enzymes with D-threose dehydrogenase and D-threonate dehydratase activities on cognate substrates with conserved carbon-centre stereochemistry. Lastly, we show the functionality of the pathway by its expression in an Escherichia coli strain and production of 1 g L−1 and 0.8 g L−1 DHB from, respectively, glycolaldehyde or ethylene glycol.
Genipin prevents alpha-synuclein aggregation and toxicity by affecting endocytosis, metabolism and lipid storage
Authors: Rosado-Ramos Rita , Poças Gonçalo M. , Marques Daniela , Foito Alexandre , M. Sevillano David , Lopes-da-Silva Mafalda , Gonçalves Luís G. , Menezes Regina , Ottens Marcel , Stewart Derek , Ibáñez de Opakua Alain , Zweckstetter Markus , Seabra Miguel C. , Mendes César S. , Outeiro Tiago Fleming , Domingos Pedro M. , Santos Cláudia N.
Published: April 2023

Parkinson’s Disease (PD) is a common neurodegenerative disorder affecting millions of people worldwide for which there are only symptomatic therapies. Small molecules able to target key pathological processes in PD have emerged as interesting options for modifying disease progression. We have previously shown that a (poly)phenol-enriched fraction (PEF) of Corema album L. leaf extract modulates central events in PD pathogenesis, namely α-synuclein (αSyn) toxicity, aggregation and clearance. PEF was now subjected to a bio-guided fractionation with the aim of identifying the critical bioactive compound. We identified genipin, an iridoid, which relieves αSyn toxicity and aggregation. Furthermore, genipin promotes metabolic alterations and modulates lipid storage and endocytosis. Importantly, genipin was able to prevent the motor deficits caused by the overexpression of αSyn in a Drosophila melanogaster model of PD. These findings widens the possibility for the exploitation of genipin for PD therapeutics.
Associations between mental health, blood pressure and the development of hypertension
Authors: Schaare H. Lina , Blöchl Maria , Kumral Deniz , Uhlig Marie , Lemcke Lorenz , Valk Sofie L. , Villringer Arno
Published: April 2023

Multiple studies have reported a link between mental health and high blood pressure with mixed or even contradictory findings. Here, we resolve those contradictions and further dissect the cross-sectional and longitudinal relationship between mental health, systolic blood pressure, and hypertension using extensive psychological, medical and neuroimaging data from the UK Biobank. We show that higher systolic blood pressure is associated with fewer depressive symptoms, greater well-being, and lower emotion-related brain activity. Interestingly, impending hypertension is associated with poorer mental health years before HTN is diagnosed. In addition, a stronger baseline association between systolic blood pressure and better mental health was observed in individuals who develop hypertension until follow-up. Overall, our findings offer insights on the complex relationship between mental health, blood pressure, and hypertension, suggesting that—via baroreceptor mechanisms and reinforcement learning—the association of higher blood pressure with better mental health may ultimately contribute to the development of hypertension.
Evaluating the evidence for exponential quantum advantage in ground-state quantum chemistry
Authors: Lee Seunghoon , Lee Joonho , Zhai Huanchen , Tong Yu , Dalzell Alexander M. , Kumar Ashutosh , Helms Phillip , Gray Johnnie , Cui Zhi-Hao , Liu Wenyuan , Kastoryano Michael , Babbush Ryan , Preskill John , Reichman David R. , Campbell Earl T. , Valeev Edward F. , Lin Lin , Chan Garnet Kin-Lic
Published: April 2023

Due to intense interest in the potential applications of quantum computing, it is critical to understand the basis for potential exponential quantum advantage in quantum chemistry. Here we gather the evidence for this case in the most common task in quantum chemistry, namely, ground-state energy estimation, for generic chemical problems where heuristic quantum state preparation might be assumed to be efficient. The availability of exponential quantum advantage then centers on whether features of the physical problem that enable efficient heuristic quantum state preparation also enable efficient solution by classical heuristics. Through numerical studies of quantum state preparation and empirical complexity analysis (including the error scaling) of classical heuristics, in both ab initio and model Hamiltonian settings, we conclude that evidence for such an exponential advantage across chemical space has yet to be found. While quantum computers may still prove useful for ground-state quantum chemistry through polynomial speedups, it may be prudent to assume exponential speedups are not generically available for this problem.
Mapping the landscape of genetic dependencies in chordoma
Authors: Sharifnia Tanaz , Wawer Mathias J. , Goodale Amy , Lee Yenarae , Kazachkova Mariya , Dempster Joshua M. , Muller Sandrine , Levy Joan , Freed Daniel M. , Sommer Josh , Kalfon Jérémie , Vazquez Francisca , Hahn William C. , Root David E. , Clemons Paul A. , Schreiber Stuart L.
Published: April 2023

Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We apply genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirms a known chordoma dependency,TBXT(T; brachyury), and identifies a range of additional dependencies, includingPTPN11, ADAR, PRKRA, LUC7L2, SRRM2,SLC2A1, SLC7A5, FANCM, andTHAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, are also recovered. We find genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates withADARdependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded byPTPN11, have potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.
New constraints on Cenozoic subduction between India and Tibet
Authors: Liu Liang , Liu Lijun , Morgan Jason. P. , Xu Yi-Gang , Chen Ling
Published: April 2023

The type of lithosphere subducted between India and Tibet since the Paleocene remains controversial; it has been suggested to be either entirely continental, oceanic, or a mixture of the two. As the subduction history of this lost lithosphere strongly shaped Tibetan intraplate tectonism, we attempt to further constrain its nature and density structure with numerical models that aim to reproduce the observed history of magmatism and crustal thickening in addition to present-day plateau properties between 83°E and 88°E. By matching time-evolving geological patterns, here we show that Tibetan tectonism away from the Himalayan syntaxis is consistent with the initial indentation of a craton-like terrane at 55 ± 5 Ma, followed by a buoyant tectonic plate with a thin crust, e.g., a broad continental margin (Himalandia). This new geodynamic scenario can explain the seemingly contradictory observations that had led to competing hypotheses like the subduction of Greater India versus largely oceanic subduction prior to Indian indentation.
Correction of Clcn1 alternative splicing reverses muscle fiber type transition in mice with myotonic dystrophy
Authors: Hu Ningyan , Kim Eunjoo , Antoury Layal , Wheeler Thurman M.
Published: April 2023

In myotonic dystrophy type 1 (DM1), deregulated alternative splicing of the muscle chloride channel Clcn1 causes myotonia, a delayed relaxation of muscles due to repetitive action potentials. The degree of weakness in adult DM1 is associated with increased frequency of oxidative muscle fibers. However, the mechanism for glycolytic-to-oxidative fiber type transition in DM1 and its relationship to myotonia are uncertain. Here we cross two mouse models of DM1 to create a double homozygous model that features progressive functional impairment, severe myotonia, and near absence of type 2B glycolytic fibers. Intramuscular injection of an antisense oligonucleotide for targeted skipping of Clcn1 exon 7a corrects Clcn1 alternative splicing, increases glycolytic 2B levels to ≥ 40% frequency, reduces muscle injury, and improves fiber hypertrophy relative to treatment with a control oligo. Our results demonstrate that fiber type transitions in DM1 result from myotonia and are reversible, and support the development of Clcn1-targeting therapies for DM1.
All-optical closed-loop voltage clamp for precise control of muscles and neurons in live animals
Authors: Bergs Amelie C. F. , Liewald Jana F. , Rodriguez-Rozada Silvia , Liu Qiang , Wirt Christin , Bessel Artur , Zeitzschel Nadja , Durmaz Hilal , Nozownik Adrianna , Dill Holger , Jospin Maëlle , Vierock Johannes , Bargmann Cornelia I. , Hegemann Peter , Wiegert J. Simon , Gottschalk Alexander
Published: April 2023

Excitable cells can be stimulated or inhibited by optogenetics. Since optogenetic actuation regimes are often static, neurons and circuits can quickly adapt, allowing perturbation, but not true control. Hence, we established an optogenetic voltage-clamp (OVC). The voltage-indicator QuasAr2 provides information for fast, closed-loop optical feedback to the bidirectional optogenetic actuator BiPOLES. Voltage-dependent fluorescence is held within tight margins, thus clamping the cell to distinct potentials. We established the OVC in muscles and neurons of Caenorhabditis elegans, and transferred it to rat hippocampal neurons in slice culture. Fluorescence signals were calibrated to electrically measured potentials, and wavelengths to currents, enabling to determine optical I/V-relationships. The OVC reports on homeostatically altered cellular physiology in mutants and on Ca2+-channel properties, and can dynamically clamp spiking in C. elegans. Combining non-invasive imaging with control capabilities of electrophysiology, the OVC facilitates high-throughput, contact-less electrophysiology in individual cells and paves the way for true optogenetic control in behaving animals.