bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbonate chemistry and carbon sequestration driven by inorganic carbon outwelling from mangroves and saltmarshes
Authors: Reithmaier Gloria M. S. , Cabral Alex , Akhand Anirban , Bogard Matthew J. , Borges Alberto V. , Bouillon Steven , Burdige David J. , Call Mitchel , Chen Nengwang , Chen Xiaogang , Cotovicz Luiz C. , Eagle Meagan J. , Kristensen Erik , Kroeger Kevin D. , Lu Zeyang , Maher Damien T. , Pérez-Lloréns J. Lucas , Ray Raghab , Taillardat Pierre , Tamborski Joseph J. , Upstill-Goddard Rob C. , Wang Faming , Wang Zhaohui Aleck , Xiao Kai , Yau Yvonne Y. Y. , Santos Isaac R. 
Published: December 2023

AbstractMangroves and saltmarshes are biogeochemical hotspots storing carbon in sediments and in the ocean following lateral carbon export (outwelling). Coastal seawater pH is modified by both uptake of anthropogenic carbon dioxide and natural biogeochemical processes, e.g., wetland inputs. Here, we investigate how mangroves and saltmarshes influence coastal carbonate chemistry and quantify the contribution of alkalinity and dissolved inorganic carbon (DIC) outwelling to blue carbon budgets. Observations from 45 mangroves and 16 saltmarshes worldwide revealed that >70% of intertidal wetlands export more DIC than alkalinity, potentially decreasing the pH of coastal waters. Porewater-derived DIC outwelling (81 ± 47 mmol m−2 d−1 in mangroves and 57 ± 104 mmol m−2 d−1 in saltmarshes) was the major term in blue carbon budgets. However, substantial amounts of fixed carbon remain unaccounted for. Concurrently, alkalinity outwelling was similar or higher than sediment carbon burial and is therefore a significant but often overlooked carbon sequestration mechanism.
Interleukin 31 receptor α promotes smooth muscle cell contraction and airway hyperresponsiveness in asthma
Authors: Akkenepally Santhoshi V. , Yombo Dan J. K. , Yerubandi Sanjana , Reddy Geereddy Bhanuprakash , Deshpande Deepak A. , McCormack Francis X. , Madala Satish K. 
Published: December 2023

AbstractAsthma is a chronic inflammatory airway disease characterized by airway hyperresponsiveness (AHR), inflammation, and goblet cell hyperplasia. Multiple cytokines, including IFNγ, IL-4, and IL-13 are associated with asthma; however, the mechanisms underlying the effects of these cytokines remain unclear. Here, we report a significant increase in the expression of IL-31RA, but not its cognate ligand IL-31, in mouse models of allergic asthma. In support of this, IFNγ, IL-4, and IL-13 upregulated IL-31RA but not IL-31 in both human and mice primary airway smooth muscle cells (ASMC) isolated from the airways of murine and human lungs. Importantly, the loss of IL-31RA attenuated AHR but had no effect on inflammation and goblet cell hyperplasia in mice challenged with allergens or treated with IL-13 or IFNγ. We show that IL-31RA functions as a positive regulator of muscarinic acetylcholine receptor 3 expression, augmenting calcium levels and myosin light chain phosphorylation in human and murine ASMC. These findings identify a role for IL-31RA in AHR that is distinct from airway inflammation and goblet cell hyperplasia in asthma.
An allele-selective inter-chromosomal protein bridge supports monogenic antigen expression in the African trypanosome
Authors: Faria Joana R. C. , Tinti Michele , Marques Catarina A. , Zoltner Martin , Yoshikawa Harunori , Field Mark C. , Horn David 
Published: December 2023

AbstractUPF1-like helicases play roles in telomeric heterochromatin formation and X-chromosome inactivation, and also in monogenic variant surface glycoprotein (VSG) expression via VSG exclusion-factor-2 (VEX2), a UPF1-related protein in the African trypanosome. We show that VEX2 associates with chromatin specifically at the single active VSG expression site on chromosome 6, forming an allele-selective connection, via VEX1, to the trans-splicing locus on chromosome 9, physically bridging two chromosomes and the VSG transcription and splicing compartments. We further show that the VEX-complex is multimeric and self-regulates turnover to tightly control its abundance. Using single cell transcriptomics following VEX2-depletion, we observed simultaneous derepression of many other telomeric VSGs and multi-allelic VSG expression in individual cells. Thus, an allele-selective, inter-chromosomal, and self-limiting VEX1-2 bridge supports monogenic VSG expression and multi-allelic VSG exclusion.
In operando cryo-STEM of pulse-induced charge density wave switching in TaS2
Authors: Hart James L. , Siddique Saif , Schnitzer Noah , Funni Stephen D. , Kourkoutis Lena F. , Cha Judy J. 
Published: December 2023

AbstractThe charge density wave material 1T-TaS2 exhibits a pulse-induced insulator-to-metal transition, which shows promise for next-generation electronics such as memristive memory and neuromorphic hardware. However, the rational design of TaS2 devices is hindered by a poor understanding of the switching mechanism, the pulse-induced phase, and the influence of material defects. Here, we operate a 2-terminal TaS2 device within a scanning transmission electron microscope at cryogenic temperature, and directly visualize the changing charge density wave structure with nanoscale spatial resolution and down to 300 μs temporal resolution. We show that the pulse-induced transition is driven by Joule heating, and that the pulse-induced state corresponds to the nearly commensurate and incommensurate charge density wave phases, depending on the applied voltage amplitude. With our in operando cryogenic electron microscopy experiments, we directly correlate the charge density wave structure with the device resistance, and show that dislocations significantly impact device performance. This work resolves fundamental questions of resistive switching in TaS2 devices, critical for engineering reliable and scalable TaS2 electronics.
UniKP: a unified framework for the prediction of enzyme kinetic parameters
Authors: Yu Han , Deng Huaxiang , He Jiahui , Keasling Jay D. , Luo Xiaozhou 
Published: December 2023

AbstractPrediction of enzyme kinetic parameters is essential for designing and optimizing enzymes for various biotechnological and industrial applications, but the limited performance of current prediction tools on diverse tasks hinders their practical applications. Here, we introduce UniKP, a unified framework based on pretrained language models for the prediction of enzyme kinetic parameters, including enzyme turnover number (kcat), Michaelis constant (Km), and catalytic efficiency (kcat / Km), from protein sequences and substrate structures. A two-layer framework derived from UniKP (EF-UniKP) has also been proposed to allow robust kcat prediction in considering environmental factors, including pH and temperature. In addition, four representative re-weighting methods are systematically explored to successfully reduce the prediction error in high-value prediction tasks. We have demonstrated the application of UniKP and EF-UniKP in several enzyme discovery and directed evolution tasks, leading to the identification of new enzymes and enzyme mutants with higher activity. UniKP is a valuable tool for deciphering the mechanisms of enzyme kinetics and enables novel insights into enzyme engineering and their industrial applications.
Neuronal substrates of egg-laying behaviour at the abdominal ganglion of Drosophila melanogaster
Authors: Oliveira-Ferreira Cristina , Gaspar Miguel , Vasconcelos Maria Luísa 
Published: December 2023

AbstractEgg-laying in Drosophila is the product of post-mating physiological and behavioural changes that culminate in a stereotyped sequence of actions. Egg-laying harbours a great potential as a paradigm to uncover how the appropriate motor circuits are organized and activated to generate behaviour. To study this programme, we first describe the different phases of the egg-laying programme and the specific actions associated with each phase. Using a combination of neuronal activation and silencing experiments, we identify neurons (OvAbg) in the abdominal ganglion as key players in egg-laying. To generate and functionally characterise subsets of OvAbg, we used an intersectional approach with neurotransmitter specific lines—VGlut, Cha and Gad1. We show that OvAbg/VGlut neurons promote initiation of egg deposition in a mating status dependent way. OvAbg/Cha neurons are required in exploration and egg deposition phases, though activation leads specifically to egg expulsion. Experiments with the OvAbg/Gad1 neurons show they participate in egg deposition. We further show a functional connection of OvAbg neurons with brain neurons. This study provides insight into the organization of neuronal circuits underlying complex motor behaviour.
Pyridine-mediated B–B bond cleavage of tetrahydroxydiboron to synthesize n-doped SWCNTs with long-term air stability
Authors: Tanaka Naoki , Hamasuna Aoi , Yamaguchi Itsuki , Kato Koichiro , Fujigaya Tsuyohiko 
Published: December 2023

AbstractNeutral radicals, including carbon radicals, are highly useful chemical species for the functionalization of semiconducting materials to change their electrical and optical properties owing to their high reactivity. However, boron radicals have been limited to synthetic and reaction chemistry, with rare utilization in materials science. In this study, a mixture of tetrahydroxydiboron (B2(OH)4) and pyridine derivatives was found to act as an electron dopant for single-walled carbon nanotubes (SWCNTs) because of the electron transfer from pyridine-mediated boron radicals generated by B–B bond dissociation to neutral radicals. In particular, the radical formed from a mixture of B2(OH)4 and 4-phenylpyridine ((4-Phpy)B(OH)2·) efficiently doped electrons into the SWCNT films; thus, n-type SWCNTs with long-term air stability for more than 50 days at room temperature were prepared. Furthermore, the experimental and theoretical surface analyses revealed that the formation of stable cations from ((4-Phpy)B(OH)2·) and the efficient interaction with SWCNTs due to their high planarity served as the mechanism for their stable doping.
Characteristics of brain glucose metabolism and metabolic connectivity in noise-induced hearing loss
Authors: Shin Seunghyeon , Nam Hyun-Yeol 
Published: December 2023

AbstractThe purpose of this study was to evaluate the differences in cerebral glucose metabolism and metabolic connectivity between noise-induced hearing loss (NIHL) subjects and normal subjects. Eighty-nine subjects who needed close observation for NIHL or were diagnosed with NIHL and 89 normal subjects were enrolled. After pre-processing of positron emission tomography images including co-registration, spatial normalization, and smoothing, a two-sample t-test was conducted to compare cerebral glucose metabolism between the two groups. To evaluate metabolic connectivity between two groups, BRAPH–BRain Analysis using graPH theory, a software package to perform graph theory analysis of the brain connectome was used. NIHL subjects showed hypometabolism compared to normal subjects in both insulae (x − 38, y − 18, z 4; × 42, y − 12, z 4) and right superior temporal gyrus (× 44, y 16, z − 20). No brain regions showed hypermetabolism in the NIHL subjects. In metabolic connectivity analysis, NIHL subjects showed decreased average strength, global efficiency, local efficiency, and mean clustering coefficient when compared with normal subjects. Decreased glucose metabolism and metabolic connectivity in NIHL subject might reflect decreased auditory function. It might be characteristic of sensorineural hearing loss.
Characterization of a new mouse line triggering transient oligodendrocyte progenitor depletion
Authors: Brousse B. , Mercier O. , Magalon K. , Gubellini P. , Malapert P. , Cayre M. , Durbec P. 
Published: December 2023

AbstractOligodendrocyte progenitor cells (OPC) are the main proliferative cells in the healthy adult brain. They produce new myelinating oligodendrocytes to ensure physiological myelin remodeling and regeneration after various pathological insults. Growing evidence suggests that OPC have other functions. Here, we aimed to develop an experimental model that allows the specific ablation of OPC at the adult stage to unravel possible new functions. We generated a transgenic mouse expressing a floxed human diphtheria toxin receptor under the control of the PDGFRa promoter, crossed with an Olig2Cre mouse to limit the recombination to the oligodendrocyte lineage in the central nervous system. We determined a diphtheria toxin dose to substantially decrease OPC density in the cortex and the corpus callosum without triggering side toxicity after a few daily injections. OPC density was normalized 7 days post-treatment, showing high repopulation capacity from few surviving OPC. We took advantage of this strong but transient depletion to show that OPC loss was associated with behavioral impairment, which was restored by OPC recovery, as well as disruption of the excitation/inhibition balance in the sensorimotor cortex, reinforcing the hypothesis of a neuromodulatory role of OPC in the adult brain.
Smartphone based colorimetric approach for quantitative determination of uric acid using Image J
Authors: Elagamy Samar H. , Adly Latifa , Abdel Hamid Mohamed Ahmed 
Published: December 2023

AbstractRecently, significant attention has been directed towards digital image colorimetry DIC using mobile applications or available software programs, which offer the advantage of analyzing samples without the need for sophisticated instruments. One such image processing program is Image J, widely used for obtaining quantitative information from scientific images. Image J could measure the color intensities by quantifying of the RGB (red–green–blue) gray levels across the images of colored substances. These values are correlated to the color intensities through conversion to CMY (cyan–magenta–yellow) values which are proportional to the color intensities. The objective of this study is to develop an innovative analytical method for the quantitative determination of uric acid using Image J for color quantification. Image J was utilized to analyze images captured by smart phone for successive concentrations of uric acid that were previously treated with phosphotungstate to develop a blue color. The proposed method has been applied for determination of uric acid in real urine using standard addition method and the results were compared with UV/VIS spectrophotometry as a reference method. In this research, we will also assess the effectiveness of quantitative analysis using Image J in comparison to a mobile application, namely RGB Color Detector.
Investigation of genetic diversity and polyandry of Leptinotarsa decemlineata using X-linked microsatellite markers
Authors: Sedlák P. , Sedláková V. , Vašek J. , Melounová M. , Čílová D. , Vejl P. , Habuštová O. Skoková , Doležal P. , Hausvater E. 
Published: December 2023

AbstractA panel of X-linked microsatellite markers was newly designed using the data from a previous sequencing project available in NCBI and used for a study of the Colorado potato beetle (CPB, Leptinotarsa decemlineata) X-haplotype variability. The analysis of scaffolds 49 and 61 (newly identified as fragments of CPB chromosome X) found ten high-quality markers, which were arranged in two PCR multiplexes and evaluated in both 420 CPB adults, collected from 14 localities of Czechia and Slovakia, and 866 larvae from five single-female families from two more Czech localities. Length polymorphisms found in 6 loci have predicted 192 potential X-haplotypes, however, only 36 combinations were detected in the adult males (N = 189), and seven additional ones in the larvae. The X-haplotypes were also generally unevenly distributed; five of the most frequent haplotypes were detected in 55% of males, 19 repeating up to ten-times in 38.7% of males and the remained 12 occurred uniquely in 6.3% of males. Bulk analysis of X-haplotypes dissimilarity indicated seven haplotype groups diversified by mutations and recombinations. Two haplotypes showed a distinctive regional distribution, which indicates an east–west disruption of CPB migration probably caused by different environments of localities in the South Bohemia region and Vysocina region. On the contrary, the results indicate a south–north migration corridor alongside the Vltava River. In the single-female families, from 6 to 13 distinct paternal haplotypes were detected, which proved and quantified a frequented polyandry in CPB.
Molecular data representation based on gene embeddings for cancer drug response prediction
Authors: Park Sejin , Lee Hyunju 
Published: December 2023

AbstractCancer drug response prediction is a crucial task in precision medicine, but existing models have limitations in effectively representing molecular profiles of cancer cells. Specifically, when these models represent molecular omics data such as gene expression, they employ a one-hot encoding-based approach, where a fixed gene set is selected for all samples and omics data values are assigned to specific positions in a vector. However, this approach restricts the utilization of embedding-vector-based methods, such as attention-based models, and limits the flexibility of gene selection. To address these issues, our study proposes gene embedding-based fully connected neural networks (GEN) that utilizes gene embedding vectors as input data for cancer drug response prediction. The GEN allows for the use of embedding-vector-based architectures and different gene sets for each sample, providing enhanced flexibility. To validate the efficacy of GEN, we conducted experiments on three cancer drug response datasets. Our results demonstrate that GEN outperforms other recently developed methods in cancer drug prediction tasks and offers improved gene representation capabilities. All source codes are available at https://github.com/DMCB-GIST/GEN/.
Optimizing daylight in west-facing facades for LEED V4.1 compliance using metaheuristic approach
Authors: Son Pham Vu Hong , Huyen Vo Thi Bich 
Published: December 2023

AbstractThis study introduces an optimized design approach for west-facing room façades to improve daylighting while adhering to LEED v4.1 sustainability criteria. Employing parametric modeling, metaheuristic optimization, and validated daylight simulations, the research highlights the African Vulture Optimization Algorithm's success in achieving 100% LEED compliance and superior performance over random models in daylight sufficiency and glare reduction. Light-colored materials and transparent glazing emerged as beneficial for LEED points. Despite computational limitations and the need for empirical validation, this method offers architects versatile and sustainable design solutions. Comparative analysis reveals the algorithm's strong performance, although opportunities exist for refinement. Future research directions include contrasting this algorithm with other optimization methods, focusing on empirical backing, assessing environmental and human-centric impacts, adapting to varied building types and conditions, and examining diverse geographical and material factors. This work advances daylight-integrated façade design, suggesting a more comprehensive framework for building performance optimization.
In-situ directed energy deposition of Al based low density steel for automotive applications
Authors: Rott Matěj , Li Ying , Koukolíková Martina , Šípová Martina , Salvetr Pavel , Nový Zbyšek , Wolf Gerhard , Džugan Jan 
Published: December 2023

AbstractThis work deals with the fabrication of one low density steel by mixing AISI S2 tool steel and AlSi10Mg powders using powder-based directed energy deposition (P-DED) technique. Two approaches of mixing powders were compared-continuous mixing during the process (in-situ) and mixing the powder prior to the process (premixed). The P-DED sample was characterised by a variety of techniques such as optical microscopy, scanning electron microscopy, electron backscatter diffraction, X-ray diffraction, and hardness measurement. Our findings demonstrate the successful achievement of steel with a 8 wt. % AlSi10Mg addition when two dissimilar powders are premixed, resulting in approximately 12% reduction in the density of S2 steel. Optimizing the powder feed rate and the ratio of AlSi10Mg powder contribute to an improvement of printability, eliminating materials separation, leading to a homogenous deposited part. Compared to the in-situ mixing case, the premixed process within the current process window generates a more homogeneous microstructure consisting of three phases: Ferrite, Fe3Al and Fe3AlC carbide. Whereas, the in-situ sample exhibits only two phases Ferrite and Fe3Al. The hardness of the premixed sample is found to be slightly higher compared to the in-situ sample.
A novel lifting point location optimization method of transmission line tower based on improved grey wolf optimizer
Authors: Wang Guolin , Ding Pengjie , Huang Chaosheng , Yu Zhongliang 
Published: December 2023

AbstractIn the erection process of transmission line tower, the appropriate lifting point position is an important factor in ensuring the stability and balance of the lifting process and preventing deformation and damage to the towers. In this paper, a improved grey wolf optimization algorithm is proposed to solve the issues of low optimization efficiency and easily getting trapped in local minima when optimizing the lifting point position of transmission line towers. The improved algorithm includes the use of a good point-set strategy to enhance the initialization method of grey wolf individuals, ensuring a more uniform distribution of the population and reducing ineffective searches in the early stages of optimization. Furthermore, two random operators are utilized to combine and mutate the optimal grey wolf position, thereby enhancing the algorithm's ability to escape local optima. Finally, the trend information of the optimization process is considered, and the median value of the population is used to improve the stability of the optimization algorithm. Experimental results demonstrate that the proposed algorithm has better optimization performance and faster convergence speed compared to genetic algorithm, particle swarm optimization algorithm, and artificial fish swarm algorithm. It effectively addresses the optimization problem of lifting point position for transmission line towers.
AAV capsid bioengineering in primary human retina models
Authors: Westhaus Adrian , Eamegdool Steven S. , Fernando Milan , Fuller-Carter Paula , Brunet Alicia A. , Miller Annie L. , Rashwan Rabab , Knight Maddison , Daniszewski Maciej , Lidgerwood Grace E. , Pébay Alice , Hewitt Alex , Santilli Giorgia , Thrasher Adrian J. , Carvalho Livia S. , Gonzalez-Cordero Anai , Jamieson Robyn V. , Lisowski Leszek 
Published: December 2023

AbstractAdeno-associated viral (AAV) vector-mediated retinal gene therapy is an active field of both pre-clinical as well as clinical research. As with other gene therapy clinical targets, novel bioengineered AAV variants developed by directed evolution or rational design to possess unique desirable properties, are entering retinal gene therapy translational programs. However, it is becoming increasingly evident that predictive preclinical models are required to develop and functionally validate these novel AAVs prior to clinical studies. To investigate if, and to what extent, primary retinal explant culture could be used for AAV capsid development, this study performed a large high-throughput screen of 51 existing AAV capsids in primary human retina explants and other models of the human retina. Furthermore, we applied transgene expression-based directed evolution to develop novel capsids for more efficient transduction of primary human retina cells and compared the top variants to the strongest existing benchmarks identified in the screening described above. A direct side-by-side comparison of the newly developed capsids in four different in vitro and ex vivo model systems of the human retina allowed us to identify novel AAV variants capable of high transgene expression in primary human retina cells.