bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits
Authors: Lu Yihao , Oliva Meritxell , Pierce Brandon L. , Liu Jin , Chen Lin S. 
Published: March 2024

AbstractGenetic effects on functionally related ‘omic’ traits often co-occur in relevant cellular contexts, such as tissues. Motivated by the multi-tissue methylation quantitative trait loci (mQTLs) and expression QTLs (eQTLs) analysis, we propose X-ING (Cross-INtegrative Genomics) for cross-omics and cross-context integrative analysis. X-ING takes as input multiple matrices of association statistics, each obtained from different omics data types across multiple cellular contexts. It models the latent binary association status of each statistic, captures the major association patterns among omics data types and contexts, and outputs the posterior mean and probability for each input statistic. X-ING enables the integration of effects from different omics data with varying effect distributions. In the multi-tissue cis-association analysis, X-ING shows improved detection and replication of mQTLs by integrating eQTL maps. In the trans-association analysis, X-ING reveals an enrichment of trans-associations in many disease/trait-relevant tissues.
The spliceosome-associated protein CWC15 promotes miRNA biogenesis in Arabidopsis
Authors: Zhou Bangjun , Yu Huihui , Xue Yong , Li Mu , Zhang Chi , Yu Bin 
Published: March 2024

AbstractMicroRNAs (miRNAs) play a key role in regulating gene expression and their biogenesis is precisely controlled through modulating the activity of microprocessor. Here, we report that CWC15, a spliceosome-associated protein, acts as a positive regulator of miRNA biogenesis. CWC15 binds the promoters of genes encoding miRNAs (MIRs), promotes their activity, and increases the occupancy of DNA-dependent RNA polymerases at MIR promoters, suggesting that CWC15 positively regulates the transcription of primary miRNA transcripts (pri-miRNAs). In addition, CWC15 interacts with Serrate (SE) and HYL1, two key components of microprocessor, and is required for efficient pri-miRNA processing and the HYL1-pri-miRNA interaction. Moreover, CWC15 interacts with the 20 S proteasome and PRP4KA, facilitating SE phosphorylation by PRP4KA, and subsequent non-functional SE degradation by the 20 S proteasome. These data reveal that CWC15 ensures optimal miRNA biogenesis by maintaining proper SE levels and by modulating pri-miRNA levels. Taken together, this study uncovers the role of a conserved splicing-related protein in miRNA biogenesis.
Universal growth of perovskite thin monocrystals from high solute flux for sensitive self-driven X-ray detection
Authors: Liu Da , Zheng Yichu , Sui Xin Yuan , Wu Xue Feng , Zou Can , Peng Yu , Liu Xinyi , Lin Miaoyu , Wei Zhanpeng , Zhou Hang , Yao Ye-Feng , Dai Sheng , Yuan Haiyang , Yang Hua Gui , Yang Shuang , Hou Yu 
Published: March 2024

AbstractMetal-halide perovskite thin monocrystals featuring efficient carrier collection and transport capabilities are well suited for radiation detectors, yet their growth in a generic, well-controlled manner remains challenging. Here, we reveal that mass transfer is one major limiting factor during solution growth of perovskite thin monocrystals. A general approach is developed to overcome synthetic limitation by using a high solute flux system, in which mass diffusion coefficient is improved from 1.7×10–10 to 5.4×10–10 m2 s–1 by suppressing monomer aggregation. The generality of this approach is validated by the synthesis of 29 types of perovskite thin monocrystals at 40–90 °C with the growth velocity up to 27.2 μm min–1. The as-grown perovskite monocrystals deliver a high X-ray sensitivity of 1.74×105 µC Gy−1 cm−2 without applied bias. The findings regarding limited mass transfer and high-flux crystallization are crucial towards advancing the preparation and application of perovskite thin monocrystals.
Structural basis for autoinhibition by the dephosphorylated regulatory domain of Ycf1
Authors: Khandelwal Nitesh Kumar , Tomasiak Thomas M. 
Published: March 2024

AbstractYeast Cadmium Factor 1 (Ycf1) sequesters glutathione and glutathione-heavy metal conjugates into yeast vacuoles as a cellular detoxification mechanism. Ycf1 belongs to the C subfamily of ATP Binding Cassette (ABC) transporters characterized by long flexible linkers, notably the regulatory domain (R-domain). R-domain phosphorylation is necessary for activity, whereas dephosphorylation induces autoinhibition through an undefined mechanism. Because of its transient and dynamic nature, no structure of the dephosphorylated Ycf1 exists, limiting understanding of this R-domain regulation. Here, we capture the dephosphorylated Ycf1 using cryo-EM and show that the unphosphorylated R-domain indeed forms an ordered structure with an unexpected hairpin topology bound within the Ycf1 substrate cavity. This architecture and binding mode resemble that of a viral peptide inhibitor of an ABC transporter and the secreted bacterial WXG peptide toxins. We further reveal the subset of phosphorylation sites within the hairpin turn that drive the reorganization of the R-domain conformation, suggesting a mechanism for Ycf1 activation by phosphorylation-dependent release of R-domain mediated autoinhibition.
Light and matter co-confined multi-photon lithography
Authors: Guan Lingling , Cao Chun , Liu Xi , Liu Qiulan , Qiu Yiwei , Wang Xiaobing , Yang Zhenyao , Lai Huiying , Sun Qiuyuan , Ding Chenliang , Zhu Dazhao , Kuang Cuifang , Liu Xu 
Published: March 2024

AbstractMask-free multi-photon lithography enables the fabrication of arbitrary nanostructures low cost and more accessible than conventional lithography. A major challenge for multi-photon lithography is to achieve ultra-high precision and desirable lateral resolution due to the inevitable optical diffraction barrier and proximity effect. Here, we show a strategy, light and matter co-confined multi-photon lithography, to overcome the issues via combining photo-inhibition and chemical quenchers. We deeply explore the quenching mechanism and photoinhibition mechanism for light and matter co-confined multiphoton lithography. Besides, mathematical modeling helps us better understand that the synergy of quencher and photo-inhibition can gain a narrowest distribution of free radicals. By using light and matter co-confined multiphoton lithography, we gain a 30 nm critical dimension and 100 nm lateral resolution, which further decrease the gap with conventional lithography.
Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport
Authors: Watanabe Satoshi , Kise Yoshiaki , Yonezawa Kento , Inoue Mariko , Shimizu Nobutaka , Nureki Osamu , Inaba Kenji 
Published: March 2024

AbstractERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn2+-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.
Poincaré sphere trajectory encoding metasurfaces based on generalized Malus’ law
Authors: Deng Zi-Lan , Hu Meng-Xia , Qiu Shanfeng , Wu Xianfeng , Overvig Adam , Li Xiangping , Alù Andrea 
Published: March 2024

AbstractAs a fundamental property of light, polarization serves as an excellent information encoding carrier, playing significant roles in many optical applications, including liquid crystal displays, polarization imaging, optical computation and encryption. However, conventional polarization information encoding schemes based on Malus’ law usually consider 1D polarization projections on a linear basis, implying that their encoding flexibility is largely limited. Here, we propose a Poincaré sphere (PS) trajectory encoding approach with metasurfaces that leverages a generalized form of Malus’ law governing universal 2D projections between arbitrary elliptical polarization pairs spanning the entire PS. Arbitrary polarization encodings are realized by engineering PS trajectories governed by either arbitrary analytic functions or aligned modulation grids of interest, leading to versatile polarization image transformation functionalities, including histogram stretching, thresholding and image encryption within non-orthogonal PS loci. Our work significantly expands the encoding dimensionality of polarization information, unveiling new opportunities for metasurfaces in polarization optics for both quantum and classical regimes.
Data-driven prediction of colonization outcomes for complex microbial communities
Authors: Wu Lu , Wang Xu-Wen , Tao Zining , Wang Tong , Zuo Wenlong , Zeng Yu , Liu Yang-Yu , Dai Lei 
Published: March 2024

AbstractMicrobial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria speciesEnterococcus faeciumandAkkermansia muciniphilain hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g.,Enterococcus faecalisinhibits the invasion ofE. faeciuminvasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.
Architecture of symbiotic dinoflagellate photosystem I–light-harvesting supercomplex in Symbiodinium
Authors: Zhao Long-Sheng , Wang Ning , Li Kang , Li Chun-Yang , Guo Jian-Ping , He Fei-Yu , Liu Gui-Ming , Chen Xiu-Lan , Gao Jun , Liu Lu-Ning , Zhang Yu-Zhong 
Published: March 2024

AbstractSymbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI–AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI–AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI–AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI–LHCI among various photosynthetic organisms.
Improving the degradation and magnetization performance of FePC amorphous alloys by annealing treatment
Authors: Qi Z. G. , Chen Q. , Wang Z. X. , Song Z. Q. , Kim K. B. , Pang J. , Zhang X. H. , Wang W. M. 
Published: March 2024

AbstractThe Fe80PxC20-x ingots and amorphous ribbons (4.5 ≤ x ≤ 6.5) are arc melted and melt spun respectively. The Rhodamine B degradation performance of as spun and annealed ribbons are investigated with various methods. In present alloys, increasing P content (cP) can inhibit the precipitation of primary α-Fe and graphite phases, and promote the formation of eutectic α-Fe + Fe3C + Fe3P phases in ingots and annealed ribbons. With increasing annealing temperature (Tan), the primary α-Fe grain size of the ribbons with cP = 4.5 at.% increases gradually and that of the ribbons with cP = 6.5 at.% increases firstly and then decreases. The degradation performance and reusability of the ribbons show a similar Tan-dependent behavior, which can be explained by the size effect of the galvanic cells. Meanwhile, the saturation magnetisation Bs and coercivity Hc of the ribbons with cP = 4.5 and 6.5 at.% increase with increasing Tan, showing a near-linear change of the reaction rate constant k against ln (Bs·Hc). This work not only studies the mechanism of improving degradation performance for FePC amorphous alloys by annealing treatment, but also reveals a correlation between degradation performance and magnetization performance of FePC alloys.
Advanced brain aging in Parkinson’s disease with cognitive impairment
Authors: Chen Chang-Le , Cheng Shao-Ying , Montaser-Kouhsari Leila , Wu Wen-Chao , Hsu Yung-Chin , Tai Chun-Hwei , Tseng Wen-Yih Isaac , Kuo Ming-Che , Wu Ruey-Meei 
Published: March 2024

AbstractPatients with Parkinson’s disease and cognitive impairment (PD-CI) deteriorate faster than those without cognitive impairment (PD-NCI), suggesting an underlying difference in the neurodegeneration process. We aimed to verify brain age differences in PD-CI and PD-NCI and their clinical significance. A total of 94 participants (PD-CI, n = 27; PD-NCI, n = 34; controls, n = 33) were recruited. Predicted age difference (PAD) based on gray matter (GM) and white matter (WM) features were estimated to represent the degree of brain aging. Patients with PD-CI showed greater GM-PAD (7.08 ± 6.64 years) and WM-PAD (8.82 ± 7.69 years) than those with PD-NCI (GM: 1.97 ± 7.13, Padjusted = 0.011; WM: 4.87 ± 7.88, Padjusted = 0.049) and controls (GM: -0.58 ± 7.04, Padjusted = 0.004; WM: 0.88 ± 7.45, Padjusted = 0.002) after adjusting demographic factors. In patients with PD, GM-PAD was negatively correlated with MMSE (Padjusted = 0.011) and MoCA (Padjusted = 0.013) and positively correlated with UPDRS Part II (Padjusted = 0.036). WM-PAD was negatively correlated with logical memory of immediate and delayed recalls (Padjusted = 0.003 and Padjusted < 0.001). Also, altered brain regions in PD-CI were identified and significantly correlated with brain age measures, implicating the neuroanatomical underpinning of neurodegeneration in PD-CI. Moreover, the brain age metrics can improve the classification between PD-CI and PD-NCI. The findings suggest that patients with PD-CI had advanced brain aging that was associated with poor cognitive functions. The identified neuroimaging features and brain age measures can serve as potential biomarkers of PD-CI.
Mapping of secondary forest age in China using stacked generalization and Landsat time series
Authors: Zhang Shaoyu , Xu Hanzeyu , Liu Aixia , Qi Shuhua , Hu Bisong , Huang Min , Luo Jin 
Published: March 2024

AbstractA national distribution of secondary forest age (SFA) is essential for understanding the forest ecosystem and carbon stock in China. While past studies have mainly used various change detection algorithms to detect forest disturbance, which cannot adequately characterize the entire forest landscape. This study developed a data-driven approach for improving performances of the Vegetation Change Tracker (VCT) and Continuous Change Detection and Classification (CCDC) algorithms for detecting the establishment of forest stands. An ensemble method for mapping national-scale SFA by determining the establishment time of secondary forest stands using change detection algorithms and dense Landsat time series was proposed. A dataset of national secondary forest age for China (SFAC) for 1 to 34 and with a 30-m spatial resolution was produced from the optimal ensemble model. This dataset provides national, continuous spatial SFA information and can improve understanding of secondary forests and the estimation of forest carbon storage in China.
The safety and efficacy of clevidipine for blood pressure management in neurocritical patients: a systematic review and meta-analysis
Authors: Widiastuti Monika , Bisri Dewi Yulianti , Rachman Iwan Abdul 
Published: March 2024

AbstractWe aim to determine the safety and efficacy of clevidipine for neurocritical patients. To comprehensively identify relevant studies, a systematic search strategy was employed using the following keywords: “clevidipine”, “high blood pressure”, “hypertension”, “Neuroscience Intensive Care”, “neuro critical”, and “neurosurgical patients”. Searches were conducted in the Clinicaltrials.gov, PubMed, and EuroPMC databases, with the search extending until September 1, 2023. The primary outcomes of interest were the time needed to achieve the target systolic blood pressure (SBP) and the percentage of time a patient remained within the targeted SBP range. Secondary outcomes included SBP values, duration of intensive care unit (ICU) stay in days, rates of hypotension, and rates of tachycardia. We included five retrospective cohort studies (n = 443), utilizing nicardipine as the primary comparator. Comparison of the time to reach target systolic blood pressure (SBP) revealed no significant difference between medications (SMD = − 1.09, p = 0.33). Likewise, the achieved SBP target showed no notable distinction (RR = 1.15, p = 0.81). However, clevidipine exhibited a slightly higher percentage of time within the target SBP range (SMD = 0.33, p = 0.04), albeit with moderate heterogeneity. Importantly, all included studies were retrospective cohort studies, underscoring the methodological context of the investigation. Clevidipine and the control group were found to be comparable in terms of achieving target SBP. Clevidipine may have a slight advantage in maintaining blood pressure within the desired range, but further research is needed to confirm this finding.
Mechanical behavior of hot extruded aluminum 6082 chip
Authors: Mahmoud Seif El Din , El-Gamasy Ramadan , El-Wahab Ayman A. Abd 
Published: March 2024

AbstractIn a bid to address the energy-intensive nature of primary aluminum production, this study explores the solid-state recycling of aluminum alloy 6082 chips through direct hot extrusion. Compacted at room temperature, chips were extruded at temperatures (350, 425, and 500 °C) and reduction ratios (6, 8.5, and 11) to optimize mechanical properties. Extensive analyses, including ANOVA and linear regressions, of strength, density, and microstructure revealed significant influences of those extrusion parameters. Optimizing these parameters within the study's aforementioned working ranges can impact the recycled material's strength; with a 36% reduction ratio increase and 20% temperature increase modestly reducing ultimate strength (2%), while a 20% temperature increase alone lowers yield strength more noticeably (9%). These findings highlight the potential for enhanced recycling and sustainable manufacturing.
Application of 32 factorial design for loratadine-loaded nanosponge in topical gel formulation: comprehensive in-vitro and ex vivo evaluations
Authors: Sivadasan Durgaramani , Venkatesan Krishnaraju , Mohamed Jamal Moideen Muthu , Alqahtani Saud , Asiri Yahya I. , Faisal Mennatullah M. , Ibrahim Adel Ehab , Alrashdi Yahya Bin Abdullah , Menaa Farid , Deeb Sami El 
Published: March 2024

AbstractLoratadine (LoR) is a highly lipophilic and practically insoluble in water, hence having a low oral bioavailability. As it is formulated as topical gel, it competitively binds with the receptors, thus reducing the side-effects. The objective of this study was to prepare LoR loaded nanosponge (LoR-NS) in gel for topical delivery. Nine different formulations of emulsion were prepared by solvent evaporation method with polyvinyl alcohol (PVA), ethyl cellulose (EC), and dichloromethane (DCM). Based on 32 Full Factorial Design (FFD), optimization was carried out by varying the concentration of LOR:EC ratio and stirring rate. The preparations were subjected for the evaluation of particle size (PS), in vitro release, zeta potential (ZP) and entrapment efficiency (EE). The results revealed that the NS dispersion was nanosized with sustained release profiles and significant PS. The optimised formulation was formulated and incorporated into carbopol 934P hydrogel. The formulation was then examined to surface morphological characterizations using scanning electron microscopy (SEM) which depicted spherical NS. Stability studies, undertaken for 2 months at 40 ± 2 °C/75 ± 5% RH, concluded to the stability of the formulation. The formulation did not cause skin irritation. Therefore, the prepared NS hydrogel proved to be a promising applicant for LoR as a novel drug delivery system (NDDS) for safe, sustained and controlled topical application.
Animal-borne soundscape logger as a system for edge classification of sound sources and data transmission for monitoring near-real-time underwater soundscape
Authors: Noda Takuji , Koizumi Takuya , Yukitake Naoto , Yamamoto Daisuke , Nakaizumi Tetsuro , Tanaka Kotaro , Okuyama Junichi , Ichikawa Kotaro , Hara Takeshi 
Published: March 2024

AbstractThe underwater environment is filled with various sounds, with its soundscape composed of biological, geographical, and anthropological sounds. Our work focused on developing a novel method to observe and classify these sounds, enriching our understanding of the underwater ecosystem. We constructed a biologging system allowing near-real-time observation of underwater soundscapes. Utilizing deep-learning-based edge processing, this system classifies the sources of sounds, and upon the tagged animal surfacing, it transmits positional data, results of sound source classification, and sensor readings such as depth and temperature. To test the system, we attached the logger to sea turtles (Chelonia mydas) and collected data through a cellular network. The data provided information on the location-specific sounds detected by the sea turtles, suggesting the possibility to infer the distribution of specific species of organisms over time. The data showed that not only biological sounds but also geographical and anthropological sounds can be classified, highlighting the potential for conducting multi-point and long-term observations to monitor the distribution patterns of various sound sources. This system, which can be considered an autonomous mobile platform for oceanographic observations, including soundscapes, has significant potential to enhance our understanding of acoustic diversity.