bluuebunny/crossref_metadata_2025_split huggingface dataset:
An improved SNAP-ADAR tool enables efficient RNA base editing to interfere with post-translational protein modification
Authors: Kiran Kumar Karthika Devi , Singh Shubhangi , Schmelzle Stella Maria , Vogel Paul , Fruhner Carolin , Hanswillemenke Alfred , Brun Adrian , Wettengel Jacqueline , Füll Yvonne , Funk Lukas , Mast Valentin , Botsch J. Josephine , Reautschnig Philipp , Li Jin Billy , Stafforst Thorsten 
Published: August 2024

AbstractRNA base editing relies on the introduction of adenosine-to-inosine changes into target RNAs in a highly programmable manner in order to repair disease-causing mutations. Here, we propose that RNA base editing could be broadly applied to perturb protein function by removal of regulatory phosphorylation and acetylation sites. We demonstrate the feasibility on more than 70 sites in various signaling proteins and identify key determinants for high editing efficiency and potent down-stream effects. For the JAK/STAT pathway, we demonstrate both, negative and positive regulation. To achieve high editing efficiency over a broad codon scope, we applied an improved version of the SNAP-ADAR tool. The transient nature of RNA base editing enables the comparably fast (hours to days), dose-dependent (thus partial) and reversible manipulation of regulatory sites, which is a key advantage over DNA (base) editing approaches. In summary, PTM interference might become a valuable field of application of RNA base editing.
Multiplexed volumetric CLEM enabled by scFvs provides insights into the cytology of cerebellar cortex
Authors: Han Xiaomeng , Lu Xiaotang , Li Peter H. , Wang Shuohong , Schalek Richard , Meirovitch Yaron , Lin Zudi , Adhinarta Jason , Murray Karl D. , MacNiven Leah M. , Berger Daniel R. , Wu Yuelong , Fang Tao , Meral Elif Sevde , Asraf Shadnan , Ploegh Hidde , Pfister Hanspeter , Wei Donglai , Jain Viren , Trimmer James S. , Lichtman Jeff W. 
Published: August 2024

AbstractMapping neuronal networks is a central focus in neuroscience. While volume electron microscopy (vEM) can reveal the fine structure of neuronal networks (connectomics), it does not provide molecular information to identify cell types or functions. We developed an approach that uses fluorescent single-chain variable fragments (scFvs) to perform multiplexed detergent-free immunolabeling and volumetric-correlated-light-and-electron-microscopy on the same sample. We generated eight fluorescent scFvs targeting brain markers. Six fluorescent probes were imaged in the cerebellum of a female mouse, using confocal microscopy with spectral unmixing, followed by vEM of the same sample. The results provide excellent ultrastructure superimposed with multiple fluorescence channels. Using this approach, we documented a poorly described cell type, two types of mossy fiber terminals, and the subcellular localization of one type of ion channel. Because scFvs can be derived from existing monoclonal antibodies, hundreds of such probes can be generated to enable molecular overlays for connectomic studies.
Rare and highly destructive wildfires drive human migration in the U.S.
Authors: McConnell Kathryn , Fussell Elizabeth , DeWaard Jack , Whitaker Stephan , Curtis Katherine J. , St. Denis Lise , Balch Jennifer , Price Kobie 
Published: August 2024

AbstractThe scale of wildfire impacts to the built environment is growing and will likely continue under rising average global temperatures. We investigate whether and at what destruction threshold wildfires have influenced human mobility patterns by examining the migration effects of the most destructive wildfires in the contiguous U.S. between 1999 and 2020. We find that only the most extreme wildfires (258+ structures destroyed) influenced migration patterns. In contrast, the majority of wildfires examined were less destructive and did not cause significant changes to out- or in-migration. These findings suggest that, for the past two decades, the influence of wildfire on population mobility was rare and operated primarily through destruction of the built environment.
Contributions of network structure, chemoarchitecture and diagnostic categories to transitions between cognitive topographies
Authors: Luppi Andrea I. , Singleton S. Parker , Hansen Justine Y. , Jamison Keith W. , Bzdok Danilo , Kuceyeski Amy , Betzel Richard F. , Misic Bratislav 
Published: August 2024

AbstractThe mechanisms linking the brain’s network structure to cognitively relevant activation patterns remain largely unknown. Here, by leveraging principles of network control, we show how the architecture of the human connectome shapes transitions between 123 experimentally defined cognitive activation maps (cognitive topographies) from the NeuroSynth meta-analytic database. Specifically, we systematically integrated large-scale multimodal neuroimaging data from functional magnetic resonance imaging, diffusion tractography, cortical morphometry and positron emission tomography to simulate how anatomically guided transitions between cognitive states can be reshaped by neurotransmitter engagement or by changes in cortical thickness. Our model incorporates neurotransmitter-receptor density maps (18 receptors and transporters) and maps of cortical thickness pertaining to a wide range of mental health, neurodegenerative, psychiatric and neurodevelopmental diagnostic categories (17,000 patients and 22,000 controls). The results provide a comprehensive look-up table charting how brain network organization and chemoarchitecture interact to manifest different cognitive topographies, and establish a principled foundation for the systematic identification of ways to promote selective transitions between cognitive topographies.
Rapid, biochemical tagging of cellular activity history in vivo
Authors: Zhang Run , Anguiano Maribel , Aarrestad Isak K. , Lin Sophia , Chandra Joshua , Vadde Sruti S. , Olson David E. , Kim Christina K. 
Published: August 2024

AbstractIntracellular calcium (Ca2+) is ubiquitous to cell signaling across biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated split-TurboID (CaST) labels activated cells within 10 min with an exogenously delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST readout can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice.
Personalizing driver safety interfaces via driver cognitive factors inference
Authors: Sumner Emily S. , DeCastro Jonathan , Costa Jean , Gopinath Deepak E. , Kimani Everlyne , Hakimi Shabnam , Morgan Allison , Best Andrew , Nguyen Hieu , Brooks Daniel J. , ul Haq Bassam , Patrikalakis Andrew , Yasuda Hiroshi , Sieck Kate , Balachandran Avinash , Chen Tiffany L. , Rosman Guy 
Published: August 2024

AbstractRecent advances in AI and intelligent vehicle technology hold the promise of revolutionizing mobility and transportation through advanced driver assistance systems (ADAS). Certain cognitive factors, such as impulsivity and inhibitory control have been shown to relate to risky driving behavior and on-road risk-taking. However, existing systems fail to leverage such factors in assistive driving technologies adequately. Varying the levels of these cognitive factors could influence the effectiveness and acceptance of ADAS interfaces. We demonstrate an approach for personalizing driver interaction via driver safety interfaces that are are triggered based on the inference of the driver’s latent cognitive states from their driving behavior. To accomplish this, we adopt a data-driven approach and train a recurrent neural network to infer impulsivity and inhibitory control from recent driving behavior. The network is trained on a population of human drivers to infer impulsivity and inhibitory control from recent driving behavior. Using data collected from a high-fidelity vehicle motion simulator experiment, we demonstrate the ability to deduce these factors from driver behavior. We then use these inferred factors to determine instantly whether or not to engage a driver safety interface. This approach was evaluated using leave-one-out cross validation using actual human data. Our evaluations reveal that our personalized driver safety interface that captures the cognitive profile of the driver is more effective in influencing driver behavior in yellow light zones by reducing their inclination to run through them.
Spacing effects on flows around two square cylinders in staggered arrangement via LBM
Authors: Refaie Ali Ahmed , Abbasi Waqas Sarwar , Bibi Bakhtawar , Rahman Hamid , Ul Islam Shams , Hussain Majeed Afraz , Ahmad Irshad 
Published: August 2024

AbstractThis study presents a computational analysis of fluid flow characteristics around two staggered arranged square cylinders using the Lattice Boltzmann Method (LBM). With Reynolds number (Re) fixed at 200, numerical simulations explore the influence of varying gap ratios (G) ranging from 0 to 10 times the cylinder size. Emphasis is placed on understanding the impact of cylinders spacing on flow structure mechanisms and induced forces. Investigation of fluid flow parameters includes vorticity behavior, pressure streamlines, and variations in drag and lift coefficients alongside the Strouhal number under different values of G. From the results, four distinct flow patterns emerge: single bluff body flow, flip flopping flow, modulated synchronized flow, and synchronized flow, each exhibiting unique characteristics. This study reveals the strong dependence of fluid forces on G, with low spacing values leading to complex vortex structures and fluctuating forces influenced by jet flow effects. At higher spacing values, proximity effects between cylinders diminish, resulting in a smoother periodic flow. The Strouhal number, average drag force and the rms values of drag and lift force coefficients vary abruptly at narrow gaps and become smooth at higher gap ratios. Unlike the tandem and side-by-side arrangements the staggered cylinders arrangement is found to have significant impact on the pressure variations around both cylinders. Overall, this research could contribute to a comprehensive understanding of staggered cylinder arrangements and their implications for engineering applications.
A latent class analysis of biosecurity attitudes and decision-making strategies of swine producers in the United States
Authors: Baye Richmond Silvanus , Zia Asim , Merrill Scott C. , Clark Eric M. , Smith Julia M. , Koliba Christopher 
Published: August 2024

AbstractThe 2018 African swine fever (ASF) outbreak highlighted the importance of biosecurity in food production systems. Despite the significant economic impacts, the sociopsychological consequences on decision-making have been overlooked. Previous studies have focused on algebraic models and simulation-based models without considering the complex psychological and social factors that influence farmers' biosecurity behaviors and decision-making processes. This study aims to classify livestock producers into distinct subgroups based on their attitudes towards biosecurity. We conducted a survey presenting producers with three scenarios to assess their willingness to report suspected ASF cases, trust in government agencies, risk perception, biosecurity knowledge, willingness to purchase livestock insurance, motivation to invest in biosecurity, readiness to report suspected infections, and intention to contact a veterinarian. Using latent class analysis, we identified three distinct classes: Biosecurity Sceptics, Biosecurity Compliant, and Biosecurity Ultra-Compliant. Our results show that producer characteristics significantly influence biosecurity attitudes and class membership, with small-scale producers less likely to adopt ultra-compliant biosecurity practices. Attending at least one eradication program encouraged biosecurity compliance. This research informs the design of targeted food policy and risk communication strategies that account for attitudes of livestock producers to encourage biosecurity adoption and reduce the likelihood of Tier 1 disease incursion.
A hybrid FeOx/CoOx/Pt ternary nanocatalyst for augmented catalysis of formic acid electro-oxidation
Authors: Mohammad Ahmad M. , Al-Qodami Bilquis Ali , Al-Akraa Islam M. , Allam Nageh K. , Alalawy Hafsa H. 
Published: August 2024

AbstractPlatinum-based catalysts that have long been used as the anodes for the formic acid electro-oxidation (FAO) in the direct formic acid fuel cells (DFAFCs) were susceptible to retrogradation in performance due to CO poisoning that impaired the technology transfer in industry. This work is designed to overcome this challenge by amending the Pt surface sequentially with nanosized cobalt (nano-CoOx, fibril texture of ca. 200 nm in particle size) and iron (nano-FeOx, nanorods of particle size and length of 80 and 253 nm, respectively) oxides. This enriched the Pt surface with oxygenated groups that boosted FAO and mitigated the CO poisoning. The unfilled d-orbitals of the transition metals and their tendency to vary their oxidations states presumed their participation in a faster mechanism of FAO. Engineering the Pt surface in this FeOx/CoOx/Pt hierarchy resulted in a remarkable activity toward FAO, that exceeded four times that of the Pt catalyst with up to ca. 2.5 times improvement in the catalytic tolerance against CO poisoning. This associated a ca. − 32 mV shift in the onset potential of FAO which increased to − 40 mV with a post-activation of the same catalyst at − 0.5 in 0.2 mol L–1 NaOH, displaying the catalyst's competitiveness in reducing overpotentials in DFAFCs. It also exhibited a favorable amelioration in the catalytic durability in long-termed chronoamperometric electrolysis. The electrochemical impedance spectroscopy and the CO stripping voltammetry were employed to elucidate the origin of enhancement.
Synergistic effect of TiO2 nanoparticles and poly (ethylene-co-vinyl acetate) on the morphology and crystallization behavior of polylactic acid
Authors: El-Taweel Safaa H. 
Published: August 2024

AbstractThe impact of adding ethylene vinyl acetate copolymer (EVA 80) and 1 wt% TiO2 nanoparticles on the morphology and crystallization behavior of poly(lactic acid) blends was investigated using DSC, SEM, and POM. Thermal analysis revealed the enhancement of crystallinity of PLA in the presence of TiO2 and higher EVA 80 content in the blend. The PLA and EVA 80 components showed compatibility, as evidenced by the shift of the glass transition temperatures of the PLA phase in the blend to lower values compared to neat PLA. The lower temperature shift of the cold crystallization of the PLA and the formation of the small spherulites of the PLA in the blends indicated that the EVA 80 and TiO2 act as a nucleating agent for crystallization. The non-isothermal crystallization parameters of the composites were evaluated using Avrami's modified model, the MO approach, and Friedman’s isoconversional method. The Avrami’s modified rate constant (K) and the effective activation energy values significantly increased with the incorporation of EVA 80 and TiO2 nanoparticles. Furthermore, the thermogravimetric analysis (TGA) showed improved thermal stability of PLA by adding EVA 80 and TiO2.
Exploring green environmental composites as hosts for shielding materials using experimental, theoretical and Geant4 simulation methods
Authors: Alabsy Mahmoud T. , Abbas Mahmoud I. , Sharaby Mahmoud A. , Elzaher Mohamed Abd , Doma A. S. , El-Khatib Ahmed M. 
Published: August 2024

AbstractRice straw is considered an agricultural waste harmful to the environment, which is abundant in most parts of the world. From this point, the present study is devoted to preparing new composites of two types of glue based on rice straw as a plentiful, low-cost matrix. Straw glue samples were prepared by mixing 20% wt. of rice straw with 80% wt. of animal glue (RS-An) and polyvinyl acetate (RS-PVAC) at different thicknesses of 1, 2, and 3 cm. The chemical composition of the prepared samples was identified by energy dispersive X-ray analysis and their morphology was examined using a scanning electron microscope. The mechanical test explored that RS-An and RS-PVAC respectively required a stress of 25.2 and 25.5 MPa before reaching the breaking point. γ-ray shielding performance was analyzed and determined at numerous photon energies from 0.059 to 1.408 MeV emitted from five-point γ-rays sources using NaI (Tl). Linear attenuation coefficient was calculated by obtaining the area under the peak of the energy spectrum observed from Genie 2000 software in the presence and absence of the sample. The experimental results of mass attenuation coefficient were compared with theoretical data of XCOM software with relative deviation ranging from 0.10 to 2.99%. Geant4 Monte Carlo simulation code was also employed to validate the experimental results. The relative deviation of XCOM and Geant4 outcomes was 0.09–1.77%, which indicates a good agreement between them. Other radiation shielding parameters such as half value layer (HVL), tenth value layer, and mean free path were calculated in three ways: experimentally, theoretically from the XCOM database, and by simulation using Geant4 code. Additionally, effective atomic number (Zeff), effective atomic number (Neff), equivalent atomic number (Zeq), and buildup factors were evaluated. It was confirmed that the γ-ray shielding properties were further boosted by mixing rice straw with the animal glue compared to the synthetic one.
Topographical anatomy of the septum verum and its white matter connections
Authors: Barany Laszlo , Meszaros Cintia , Alpar Alan , Ganslandt Oliver , Hore Nirjhar , Delev Daniel , Schnell Oliver , Kurucz Peter 
Published: August 2024

AbstractThe human septum verum represents a small but clinically important region of the brain. Based on the results of animal experiments, the stimulation of its medial part was recently proposed with various indications like epilepsy or cognitive impairment after traumatic brain injury. The aim of our study was to present the anatomical relationships of the human septum verum using fiber dissection and histological analysis to support its research and provide essential information for future deep brain stimulation therapies. 16 human cadaveric brains were dissected according to Klingler’s method. To validate our macroscopical findings, 12 samples obtained from the dissected brains and 2 additional specimens from unfrozen brains were prepared for histological examinations. We identified the following white matter connections of the septum verum: (1) the precommissural fibers of the fornix; (2) the inferior fascicle of the septum pellucidum; (3) the cingulum; (4) the medial olfactory stria; (5) the ventral amygdalofugal pathway; (6) the stria medullaris of the thalamus and (7) the stria terminalis. Moreover, we could distinguish a less-known fiber bundle connecting the postcommissural column of the fornix to the stria medullaris of the thalamus and the anterior thalamic nuclei. In this study we present valuable anatomical information about this region to promote safe and effective deep brain stimulation therapies in the future.
Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method
Authors: Włodarski Tomasz , Streit Julian O. , Mitropoulou Alkistis , Cabrita Lisa D. , Vendruscolo Michele , Christodoulou John 
Published: August 2024

AbstractCryogenic electron microscopy (cryo-EM) has emerged as a powerful method for the determination of structures of complex biological molecules. The accurate characterisation of the dynamics of such systems, however, remains a challenge. To address this problem, we introduce cryoENsemble, a method that applies Bayesian reweighting to conformational ensembles derived from molecular dynamics simulations to improve their agreement with cryo-EM data, thus enabling the extraction of dynamics information. We illustrate the use of cryoENsemble to determine the dynamics of the ribosome-bound state of the co-translational chaperone trigger factor (TF). We also show that cryoENsemble can assist with the interpretation of low-resolution, noisy or unaccounted regions of cryo-EM maps. Notably, we are able to link an unaccounted part of the cryo-EM map to the presence of another protein (methionine aminopeptidase, or MetAP), rather than to the dynamics of TF, and model its TF-bound state. Based on these results, we anticipate that cryoENsemble will find use for challenging heterogeneous cryo-EM maps for biomolecular systems encompassing dynamic components.
Novel multifibrillar carbon and oxidation-stable carbon/ceramic hybrid fibers consisting of thousands of individual nanofibers with high tensile strength
Authors: Denk Jakob , Liao Xiaojian , Knolle Wolfgang , Kahnt Axel , Greiner Andreas , Schafföner Stefan , Agarwal Seema , Motz Günter 
Published: August 2024

AbstractIn this study, multifibrillar carbon and carbon/ceramic (C/SiCON) fibers consisting of thousands of single nanofibers are continuously manufactured. The process starts with electrospinning of polyacrylonitrile (PAN) and PAN/oligosilazane precursors resulting in poorly aligned polymer fibers. Subsequent stretching leads to parallel aligned multifibrillar fibers, which are continuously stabilized and pyrolyzed to C or C/SiCON hybrid fibers. The multifibrillar carbon fibers show a high tensile strength of 911 MPa and Young’s modulus of 154 GPa, whereas the multifibrillar C/SiCON fibers initially have only tensile strengths of 407 MPa and Young’s modulus of 77 GPa, due to sticking of the nanofibers during the stabilization in air. Additional curing with electron beam radiation, results in a remarkable increase in tensile strength of 707 MPa and Young's modulus of 98 GPa. The good mechanical properties are highlighted by the low linear density of the multifibrillar C/SiCON fibers (~ 1 tex) compared to conventional C and SiC fiber bundles (~ 200 tex). In combination with the large surface area of the fibers better mechanical properties of respective composites with a reduced fiber content can be achieved. In addition, the developed approach offers high potential to produce advanced endless multifibrillar carbon and C/SiCON nanofibers in an industrial scale.