bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Impact of Climate Change on Atmospheric Rivers: A Modeling Perspective
Authors: Ordaz Osorio C. , Booth J. F. , LeGrande A. N. , Naud C. M. 
Published: June 2024

AbstractAtmospheric rivers (ARs) play a crucial role in the poleward transport of water vapor, and the AR‐associated precipitation is a critical component of global water supplies, making it critical that we understand how ARs may change in the future. To approach this issue, integrations of the NASA Goddard Institute for Space Studies global climate model ModelE version 2.1 (GISSE2.1) are employed. Multiple configurations of the model simulating different climates are analyzed: (a) the last‐glacial maximum; (b) present day; (c) the end of the 21st century. The thermodynamic and dynamic components of changes to AR frequency are analyzed using a decomposition method. This method utilizes differences in distinct AR seasonal climatology frequencies derived from various vertically integrated water vapor transport (IVT) thresholds to resolve AR frequency into its components. Global mean state changes in poleward AR frequency for different climates are dominated by precipitable water vapor (PWV) changes. A set of idealized cold and warm climates in which present day sea surface temperatures are uniformly changed are considered for a targeted analysis of the south Pacific Ocean basin. For this analysis, frequency and distribution of AR events in the model runs are analyzed by comparing them to changes in the jet stream as well as the Eulerian storm tracks and low‐level baroclinicity. Latitudinal shifts in the ARs in the south Pacific Ocean basin using our integrations are not as tightly coupled to these two storm‐related climatological metrics in the midlatitudes but fare better on the poleward side of the storm tracks.
Aerosol and Dimethyl Sulfide Sensitivity to Sulfate Chemistry Schemes
Authors: Bhatti Yusuf A. , Revell Laura E. , McDonald Adrian J. , Archibald Alex T. , Schuddeboom Alex J. , Williams Jonny , Hardacre Catherine , Mulcahy Jane , Lin Dongqi 
Published: June 2024

AbstractDimethyl sulfide (DMS) is the largest source of natural sulfur in the atmosphere and undergoes oxidation reactions resulting in gas‐to‐particle conversion to form sulfate aerosol. Climate models typically use independent chemical schemes to simulate these processes, however, the sensitivity of sulfate aerosol to the schemes used by CMIP6 models has not been evaluated. Current climate models offer oversimplified DMS oxidation pathways, adding to the ambiguity surrounding the global sulfur burden. Here, we implemented seven DMS and sulfate chemistry schemes, six of which are from CMIP6 models, in an atmosphere‐only Earth system model. A large spread in aerosol optical depth (AOD) is simulated (0.077), almost twice the magnitude of the pre‐industrial to present‐day increase in AOD. Differences are largely driven by the inclusion of the nighttime DMS oxidation reaction with NO3, and in the number of aqueous phase sulfate reactions. Our analysis identifies the importance of DMS‐sulfate chemistry for simulating aerosols. We suggest that optimizing DMS/sulfur chemistry schemes is crucial for the accurate simulation of sulfate aerosols.
Deep‐Learning‐Based Phase Picking for Volcano‐Tectonic and Long‐Period Earthquakes
Authors: Zhong Yiyuan , Tan Yen Joe 
Published: June 2024

AbstractThe application of deep‐learning‐based seismic phase pickers has surged in recent years. However, the efficacy of these models when applied to monitoring volcano seismicity has yet to be fully evaluated. Here, we first compile a data set of seismic waveforms from various volcanoes globally. We then show that the performances of two widely used deep‐learning pickers deteriorate systematically as the earthquakes' frequency content decreases. Therefore, the performances are especially poor for long‐period earthquakes often associated with fluid/magma movement. Subsequently, we train new models which perform significantly better, including when tested on two data sets where no training data were used: volcanic earthquakes along the Cascadia subduction zone and tectonic low‐frequency earthquakes along the Nankai Trough. Our model/workflow can be applied to improve monitoring of volcano seismicity globally while our compiled data set can be used to benchmark future methods for characterizing volcano seismicity, especially long‐period earthquakes which are difficult to monitor.
Asymmetry in Uranus' High Energy Proton Radiation Belt
Authors: Acevski M. , Masters A. , Zomerdijk‐Russell S. 
Published: June 2024

AbstractUranus is one of the least explored planets in our solar system, it exhibits a unique magnetic field structure which was observed by NASA's Voyager 2 mission nearly 50 years ago. Notably, Uranus displays extreme magnetic field asymmetry, a feature exclusive to the icy giants. We use the Boris algorithm to investigate how high energy protons behave within this unusual magnetic field, which is motivated by Voyager 2's observation of lower‐than‐expected high energy proton radiation belt intensities at Uranus. When considering full drift motions of high energy protons around Uranus, the azimuthal drift velocity can vary by as much as 15% around the planet. This results in areas around Uranus where particles will be more depleted (faster drift) and other regions where there is a surplus of particles (slower drift). This could provide a partial explanation for the “weak” proton radiation belts observed by Voyager 2.
Permafrost Cloud Feedback May Amplify Climate Change
Authors: de Vrese Philipp , Stacke Tobias , Gayler Veronika , Brovkin Victor 
Published: June 2024

AbstractRising temperatures entail important changes in the soil hydrologic processes of the northern permafrost zone. Using the ICON‐Earth System Model, we show that a large‐scale thaw of essentially impervious frozen soil layers may cause a positive feedback by which permafrost degradation amplifies the causative warming. The thawing of the ground increases its hydraulic connectivity and raises drainage rates which facilitates a drying of the landscapes. This limits evapotranspiration and the formation of low‐altitude clouds during the snow‐free season. A decrease in summertime cloudiness, in turn, increases the shortwave radiation reaching the surface, hence, temperatures and advances the permafrost degradation. Our simulations further suggest that the consequences of a permafrost cloud feedback may not be limited to the regional scale. For a near‐complete loss of the high‐latitude permafrost, they show significant temperature impacts on all continents and northern‐hemisphere ocean basins that raise the global mean temperature by 0.25 K.
Relationship Between Circulation Types and Extreme Precipitation Over Scandinavia Is Stable Under Climate Change
Authors: Hansen F. , Belušić D. , Wyser K. 
Published: June 2024

AbstractThe atmospheric large‐scale environment determines the occurrence of local extreme precipitation, and it is unclear how climate change affects this relationship. Here we investigate the present‐day relationship between large‐scale circulation types (CTs) and daily precipitation extremes over Scandinavia and its future change. A 50‐member EC‐Earth3 large ensemble is used to assess future changes against internal variability. We show that CTs are related to extreme precipitation over the entire domain. The intensity of extreme daily precipitation increases in all seasons in the future climate, generally following the strength of warming in the six different future scenarios considered. However, no significant future change is found in the relationship between extreme precipitation and the CTs in any season or scenario. The results have important implications for applications that rely on the stability of this relationship, such as statistical and event‐based dynamical downscaling of future weather and climate predictions and long‐term climate projections.
Big data and deep learning for RNA biology
Authors: Hwang Hyeonseo , Jeon Hyeonseong , Yeo Nagyeong , Baek Daehyun 
Published: June 2024

AbstractThe exponential growth of big data in RNA biology (RB) has led to the development of deep learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL studies in other fields, the successful implementation of DL in RB depends heavily on the effective utilization of large-scale datasets from public databases. In achieving this goal, data encoding methods, learning algorithms, and techniques that align well with biological domain knowledge have played pivotal roles. In this review, we provide guiding principles for applying these DL concepts to various problems in RB by demonstrating successful examples and associated methodologies. We also discuss the remaining challenges in developing DL models for RB and suggest strategies to overcome these challenges. Overall, this review aims to illuminate the compelling potential of DL for RB and ways to apply this powerful technology to investigate the intriguing biology of RNA more effectively.
Optimal design of synthetic circular RNAs
Authors: Choi Seo-Won , Nam Jin-Wu 
Published: June 2024

AbstractCircular RNAs are an unusual class of single-stranded RNAs whose ends are covalently linked via back-splicing. Due to their versatility, the need to express circular RNAs in vivo and in vitro has increased. Efforts have been made to efficiently and precisely synthesize circular RNAs. However, a review on the optimization of the processes of circular RNA design, synthesis, and delivery is lacking. Our review highlights the multifaceted aspects considered when producing optimal circular RNAs and summarizes the available options for each step of exogenous circular RNA design and synthesis, including circularization strategies. Additionally, this review describes several potential applications of circular RNAs.
Linking haploinsufficiency of the autism- and schizophrenia-associated gene Cyfip1 with striatal-limbic-cortical network dysfunction and cognitive inflexibility
Authors: Haddon Josephine E. , Titherage Daniel , Heckenast Julia R. , Carter Jennifer , Owen Michael J. , Hall Jeremy , Wilkinson Lawrence S. , Jones Matthew W. 
Published: June 2024

AbstractImpaired behavioural flexibility is a core feature of neuropsychiatric disorders and is associated with underlying dysfunction of fronto-striatal circuitry. Reduced dosage of Cyfip1 is a risk factor for neuropsychiatric disorder, as evidenced by its involvement in the 15q11.2 (BP1–BP2) copy number variant: deletion carriers are haploinsufficient for CYFIP1 and exhibit a two- to four-fold increased risk of schizophrenia, autism and/or intellectual disability. Here, we model the contributions of Cyfip1 to behavioural flexibility and related fronto-striatal neural network function using a recently developed haploinsufficient, heterozygous knockout rat line. Using multi-site local field potential (LFP) recordings during resting state, we show that Cyfip1 heterozygous rats (Cyfip1+/−) harbor disrupted network activity spanning medial prefrontal cortex, hippocampal CA1 and ventral striatum. In particular, Cyfip1+/− rats showed reduced influence of nucleus accumbens and increased dominance of prefrontal and hippocampal inputs, compared to wildtype controls. Adult Cyfip1+/− rats were able to learn a single cue-response association, yet unable to learn a conditional discrimination task that engages fronto-striatal interactions during flexible pairing of different levers and cue combinations. Together, these results implicate Cyfip1 in development or maintenance of cortico-limbic-striatal network integrity, further supporting the hypothesis that alterations in this circuitry contribute to behavioural inflexibility observed in neuropsychiatric diseases including schizophrenia and autism.
Anti-T-lymphocyte globulin (ATLG) compared to post-transplant cyclophosphamide as GvHD prophylaxis in ALL patients undergoing allogeneic stem cell transplantation
Authors: Steiner Normann , Massoud Radwan , Klyuchnikov Evgeny , Gagelmann Nico , Richter Johanna , Niederwieser Christian , Rathje Kristin , Urbanowicz Tatjana , Kunte Ameya , Engelmann Janik , Ihne Christina , Lastovytska Iryna , Lindhauer Cecilia , Marquard Franziska , Reichard Mirjam , Ryzhkova Alla , Sabauri Rusudan , Schäfersküpper Mathias , Seyedi Niloufar , Kalogeropoulos Georgios , Heidenreich Silke , Rudolph Ina , Zeck Gaby , Janson Dietlinde , Wolschke Christine , Ayuk Francis , Kröger Nicolaus 
Published: June 2024

AbstractWe retrospectively analyzed high-risk ALL patients in CR1 receiving total body irradiation based conditioning regimen with ATLG (n = 74) or PTCy (n = 73) for GVHD prophylaxis. The 3-year OS and LFS were similar in both groups: 65 and 60% in the ATLG group and 64 and 67% in the PTCy group (p = 0.9 and 0.5, respectively). CIR and NRM rate at three years was 12 and 21% after PTCy and 19 and 20% after ATLG (p = 0.4 and p = 0.9, respectively). Acute GvHD grades II-IV and grades III/IV at 100 days was 46 and 19% after PTCy and 33 and 10% after ATLG (p = 0.08 and p = 0.9, respectively). Chronic GvHD of all grade at two years was higher after PTCy: 55% versus 26% (p < 0.001). Based on the propensity score matching (PSM) analysis, aGvHD grades II-IV was trending higher in the PTCy group compared to the ATLG group (p = 0.07). In contrast to the PSM analysis, on multivariate analysis the receipt of PTCy compared with ATLG was associated with a reduced CIR (p = 0.026). Our retrospective single-center analysis shows a lower incidence of acute and chronic GvHD while displaying similar LFS and OS after ATLG compared to PTCy in TBI based allogeneic stem cell transplantation for high-risk ALL.
Carbon nanotubes functionalized with α-aminoisobutyric acid-containing peptide increase gene delivery efficiency in plant mitochondria
Authors: Law Simon Sau Yin , Kuzumoto Mako , Fujita Seiya , Fujigaya Tsuyohiko , Numata Keiji 
Published: June 2024

Abstract
Functionalized carbon nanotubes have shown tremendous promise in the field of plant biotechnology for genetic engineering and cargo delivery; recent findings have shown that they can be delivered within specific organelles, such as mitochondria and chloroplasts, in intact plants. 2-Aminoisobutyric acid is an unnatural amino acid that promotes helical conformation and has been demonstrated to increase membrane permeability. Rational substitution of this amino acid into a mitochondrial targeting peptide induced a helical conformation that, when functionalized onto polymer-coated carbon nanotubes, conferred increased membrane permeability compared with that of the native peptide. The secondary structure was maintained on the surface and, when used to deliver pDNA, led to an increase in gene expression, suggesting that this method may be used to enhance the delivery efficiency of existing functional peptides.
Two distinct archaeal type IV pili structures formed by proteins with identical sequence
Authors: Liu Junfeng , Eastep Gunnar N. , Cvirkaite-Krupovic Virginija , Rich-New Shane T. , Kreutzberger Mark A. B. , Egelman Edward H. , Krupovic Mart , Wang Fengbin 
Published: June 2024

AbstractType IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from small pilin proteins, can be many microns long and serve diverse functions, including adhesion, biofilm formation, motility, and intercellular communication. Here, we determine atomic structures of two distinct adhesive T4P from Saccharolobus islandicus via cryo-electron microscopy (cryo-EM). Unexpectedly, both pili were assembled from the same pilin polypeptide but under different growth conditions. One filament, denoted mono-pilus, conforms to canonical archaeal T4P structures where all subunits are equivalent, whereas in the other filament, the tri-pilus, the same polypeptide exists in three different conformations. The three conformations in the tri-pilus are very different from the single conformation found in the mono-pilus, and involve different orientations of the outer immunoglobulin-like domains, mediated by a very flexible linker. Remarkably, the outer domains rotate nearly 180° between the mono- and tri-pilus conformations. Both forms of pili require the same ATPase and TadC-like membrane pore for assembly, indicating that the same secretion system can produce structurally very different filaments. Our results show that the structures of archaeal T4P appear to be less constrained and rigid than those of the homologous archaeal flagellar filaments that serve as helical propellers.
Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis
Authors: Easter Quinn T. , Fernandes Matuck Bruno , Beldorati Stark Germán , Worth Catherine L. , Predeus Alexander V. , Fremin Brayon , Huynh Khoa , Ranganathan Vaishnavi , Ren Zhi , Pereira Diana , Rupp Brittany T. , Weaver Theresa , Miller Kathryn , Perez Paola , Hasuike Akira , Chen Zhaoxu , Bush Mandy , Qu Xufeng , Lee Janice , Randell Scott H. , Wallet Shannon M. , Sequeira Inês , Koo Hyun , Tyc Katarzyna M. , Liu Jinze , Ko Kang I. , Teichmann Sarah A. , Byrd Kevin M. 
Published: June 2024

AbstractPeriodontitis affects billions of people worldwide. To address relationships of periodontal niche cell types and microbes in periodontitis, we generated an integrated single-cell RNA sequencing (scRNAseq) atlas of human periodontium (34-sample, 105918-cell), including sulcular and junctional keratinocytes (SK/JKs). SK/JKs displayed altered differentiation states and were enriched for effector cytokines in periodontitis. Single-cell metagenomics revealed 37 bacterial species with cell-specific tropism. Fluorescence in situ hybridization detected intracellular 16 S and mRNA signals of multiple species and correlated with SK/JK proinflammatory phenotypes in situ. Cell-cell communication analysis predicted keratinocyte-specific innate and adaptive immune interactions. Highly multiplexed immunofluorescence (33-antibody) revealed peri-epithelial immune foci, with innate cells often spatially constrained around JKs. Spatial phenotyping revealed immunosuppressed JK-microniches and SK-localized tertiary lymphoid structures in periodontitis. Here, we demonstrate impacts on and predicted interactomics of SK and JK cells in health and periodontitis, which requires further investigation to support precision periodontal interventions in states of chronic inflammation.
A blueprint for precise and fault-tolerant analog neural networks
Authors: Demirkiran Cansu , Nair Lakshmi , Bunandar Darius , Joshi Ajay 
Published: June 2024

AbstractAnalog computing has reemerged as a promising avenue for accelerating deep neural networks (DNNs) to overcome the scalability challenges posed by traditional digital architectures. However, achieving high precision using analog technologies is challenging, as high-precision data converters are costly and impractical. In this work, we address this challenge by using the residue number system (RNS) and composing high-precision operations from multiple low-precision operations, thereby eliminating the need for high-precision data converters and information loss. Our study demonstrates that the RNS-based approach can achieve ≥99% FP32 accuracy with 6-bit integer arithmetic for DNN inference and 7-bit for DNN training. The reduced precision requirements imply that using RNS can achieve several orders of magnitude higher energy efficiency while maintaining the same throughput compared to conventional analog hardware with the same precision. We also present a fault-tolerant dataflow using redundant RNS to protect the computation against noise and errors inherent within analog hardware.
Sulfonamide-directed site-selective functionalization of unactivated C(sp3)−H enabled by photocatalytic sequential electron/proton transfer
Authors: Wang Chaodong , Chen Zhi , Sun Jie , Tong Luwei , Wang Wenjian , Song Shengjie , Li Jianjun 
Published: June 2024

AbstractThe generation of alkyl radical from C(sp3)−H substrates via hydrogen atom abstraction represents a desirable yet underexplored strategy in alkylation reaction since involving common concerns remain adequately unaddressed, such as the harsh reaction conditions, limited substrate scope, and the employment of noble metal- or photo-catalysts and stoichiometric oxidants. Here, we utilize the synergistic strategy of photoredox and hydrogen atom transfer (HAT) catalysis to accomplish a general and practical functionalization of unactived C(sp3)−H centers with broad reaction scope, high functional group compatibility, and operational simplicity. A combination of validation experiments and density functional theory reveals that the N-centered radicals, generated from free N − H bond in a stepwise electron/proton transfer event, are the key intermediates that enable an intramolecular 1,5-HAT or intermolecular HAT process for nucleophilic carbon-centered radicals formation to achieve heteroarylation, alkylation, amination, cyanation, azidation, trifluoromethylthiolation, halogenation and deuteration. The practical value of this protocol is further demonstrated by the gram-scale synthesis and the late-stage functionalization of natural products and drug derivatives.
Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target
Authors: Yamamoto Kazuki , Sato Toyotaka , Hao Aili , Asao Kenta , Kaguchi Rintaro , Kusaka Shintaro , Ruddarraju Radhakrishnam Raju , Kazamori Daichi , Seo Kiki , Takahashi Satoshi , Horiuchi Motohiro , Yokota Shin-ichi , Lee Seok-Yong , Ichikawa Satoshi 
Published: June 2024

AbstractMraY (phospho-N-acetylmuramoyl-pentapeptide-transferase) inhibitory natural products are attractive molecules as candidates for a new class of antibacterial agents to combat antimicrobial-resistant bacteria. Structural optimization of these natural products is required to improve their drug-like properties for therapeutic use. However, chemical modifications of these natural products are painstaking tasks due to complex synthetic processes, which is a bottleneck in advancing natural products to the clinic. Here, we develop a strategy for a comprehensive in situ evaluation of the build-up library, which enables us to streamline the preparation of the analogue library and directly assess its biological activities. We apply this approach to a series of MraY inhibitory natural products. Through construction and evaluation of the 686-compound library, we identify promising analogues that exhibit potent and broad-spectrum antibacterial activity against highly drug-resistant strains in vitro as well as in vivo in an acute thigh infection model. Structures of the MraY-analogue complexes reveal distinct interaction patterns, suggesting that these analogues represent MraY inhibitors with unique binding modes. We further demonstrate the generality of our strategy by applying it to tubulin-binding natural products to modulate their tubulin polymerization activities.