bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bidirectional causality between idiopathic sudden sensorineural hearing loss and depression: a Mendelian randomization study
Authors: Wu Chuanyu , Yu Ya , Zhao Tongtong , Xie Hui 
Published: June 2024

AbstractIdiopathic Sudden Sensorineural Hearing Loss (ISSHL) is a sudden onset, unexplained sensorineural hearing loss. Depression is a common mental disorder and a leading cause of disability. Here, We used a two-sample Mendelian randomization approach using pooled statistics from genome-wide association studies of ISSHL (1491 cases, 196,592 controls) and depression (23,424 cases, 192,220 controls) in European populations. This study investigated the bidirectional relationship between single nucleotide polymorphisms associated with depression and ISSHL using inverse variance weighting.Additional sensitivity analyses, such as Mendelian randomization-Egger (MR-Egger), weighted median estimates, and leave-one-out analysis, were performed to assess the reliability of the findings. Significant causal association between genetic susceptibility to ISSHL and depression in a random-effects IVW approach (OR = 1.037, 95% CI = 1.004–1.072, P = 0.030). In contrast, genetic depression was not risk factors for ISSHL (OR = 1.134, 95% CI = 0.871–1.475, P = 0.350). After validation by different MR methods and the sensitivity analysis, all of the above results are consistent. The evidence we have gathered suggests a causal relationship between ISSHL and depression. The presence of the former induces or further exacerbates the latter, whereas a similar situation does not exist when the latter is an influencing factor.
Variable data structures and customized deep learning surrogates for computationally efficient and reliable characterization of buried objects
Authors: Yurt Reyhan , Torpi Hamid , Kizilay Ahmet , Koziel Slawomir , Mahouti Peyman 
Published: June 2024

AbstractIn this study, in order to characterize the buried object via deep-learning-based surrogate modeling approach, 3-D full-wave electromagnetic simulations of a GPR model have been used. The task is to independently predict characteristic parameters of a buried object of diverse radii allocated at different positions (depth and lateral position) in various dispersive subsurface media. This study has analyzed variable data structures (raw B-scans, extracted features, consecutive A-scans) with respect to computational cost and accuracy of surrogates. The usage of raw B-scan data and the applications for processing steps on B-scan profiles in the context of object characterization incur high computational cost so it can be a challenging issue. The proposed surrogate model referred to as the deep regression network (DRN) is utilized for time frequency spectrogram (TFS) of consecutive A-scans. DRN is developed with the main aim being computationally efficient (about 13 times acceleration) compared to conventional network models using B-scan images (2D data). DRN with TFS is favorably benchmarked to the state-of-the-art regression techniques. The experimental results obtained for the proposed model and second-best model, CNN-1D show mean absolute and relative error rates of 3.6 mm, 11.8 mm and 4.7%, 11.6% respectively. For the sake of supplementary verification under realistic scenarios, it is also applied for scenarios involving noisy data. Furthermore, the proposed surrogate modeling approach is validated using measurement data, which is indicative of suitability of the approach to handle physical measurements as data sources.
Polyphasic identification of Rhizopus oryzae and evaluation of physical fermentation parameters in potato starch processing liquid waste for β-glucan production
Authors: Anchundia Miguel , León-Revelo Gualberto , Santacruz Stalin , Torres Freddy 
Published: June 2024

AbstractΒ-glucans are polysaccharide macromolecules that can be found in the cell walls of molds, such as Rhizopus oryzae. They provide functional properties in food systems and have immunomodulatory activity, anticancer, and prebiotic effects; reduce triglycerides and cholesterol; and prevent obesity, among others benefits. Furthermore, potato starch production requires a large amount of water, which is usually discharged into the environment, creating problems in soils and bodies of water. The physical parameters to produce β-glucans were determined, liquid waste from potato starch processing was used and native Rhizopus oryzae was isolated and identified from cereal grains. The isolates grew quickly on the three types of agars used at 25 °C and 37 °C, and they did not grow at 45 °C. Rhizopus oryzae M10A1 produced the greatest amount of β-glucans after six days of culture at 30 °C, pH 6, a stirring rate of 150 rpm and a fermentation volume of 250 mL. By establishing the physical fermentation parameters and utilizing the liquid waste from potato starch, Rhizopus oryzae M10A1 yielded 397.50 mg/100 g of β-glucan was obtained.
Improving urban emergency medical service systems through brownfield transformation in Huangshi, China
Authors: Liu Zhiping , Feng Yingxue , Li Jing , Tao Haoyu , Liu Zhen , Li Xiaodan 
Published: June 2024

AbstractA comprehensive emergency medical service (EMS) system significantly enhances a city’s capacity to prevent and mitigate disasters. Using Huangshi as a case study, this research evaluated the service radium coverage rate of the current EMS system by examining its transport capacity, population density, and prevalence rate, finding it to be only 61.49% with an inefficient spatial layout. To address this, we proposed transforming urban brownfields into EMS parks. By selecting the most suitable brownfields based on capacity and service radius, we increased the coverage rate to 90.21%. We introduced a new "consultation-referral" model, where existing EMS facilities serve as pre-diagnosis and triage centers, and the urban brownfield EMS parks function as isolation and centralized treatment centers. GIS network analysis confirmed the feasibility, showing all transit times to be under 30 min. The methodology outlined in this study—comprising "demand assessment, supply optimization, and feasibility verification"—not only strengthens the city’s EMS system but also facilitates the renewal of urban brownfields. This approach can serve as a valuable reference for enhancing EMS systems in other cities.
Functional surface expression of immunoglobulin cleavage systems in a candidate Mycoplasma vaccine chassis
Authors: Torres-Puig Sergi , Crespo-Pomar Silvia , Akarsu Hatice , Yimthin Thatcha , Cippà Valentina , Démoulins Thomas , Posthaus Horst , Ruggli Nicolas , Kuhnert Peter , Labroussaa Fabien , Jores Jörg 
Published: June 2024

AbstractThe Mycoplasma Immunoglobulin Binding/Protease (MIB-MIP) system is a candidate ‘virulence factor present in multiple pathogenic species of the Mollicutes, including the fast-growing species Mycoplasma feriruminatoris. The MIB-MIP system cleaves the heavy chain of host immunoglobulins, hence affecting antigen-antibody interactions and potentially facilitating immune evasion. In this work, using -omics technologies and 5’RACE, we show that the four copies of the M. feriruminatoris MIB-MIP system have different expression levels and are transcribed as operons controlled by four different promoters. Individual MIB-MIP gene pairs of M. feriruminatoris and other Mollicutes were introduced in an engineered M. feriruminatoris strain devoid of MIB-MIP genes and were tested for their functionality using newly developed oriC-based plasmids. The two proteins are functionally expressed at the surface of M. feriruminatoris, which confirms the possibility to display large membrane-associated proteins in this bacterium. However, functional expression of heterologous MIB-MIP systems introduced in this engineered strain from phylogenetically distant porcine Mollicutes like Mesomycoplasma hyorhinis or Mesomycoplasma hyopneumoniae could not be achieved. Finally, since M. feriruminatoris is a candidate for biomedical applications such as drug delivery, we confirmed its safety in vivo in domestic goats, which are the closest livestock relatives to its native host the Alpine ibex.
Unveiled reactivity of masked diformylmethane with enamines forming resonance-assisted hydrogen bonding leads to di-meta-substituted pyridines
Authors: Yi Sihyeong , Lee Ji Hyae , Cho Hana , Vaithegi Kannan , Yi Dawon , Noh Sijun , Park Seung Bum 
Published: June 2024

AbstractPyridine, an essential structure in drug development, shows a wide array of bioactivities according to its substitution patterns. Among the bioactive pyridines, meta-substituted pyridines suffer from limited synthetic approaches despite their significance. In this study, we present a condensation-based synthetic method enabling the facile incorporation of biologically relevant functional groups at the meta position of pyridine. This methodology unveiled the concealed reactivity of 3-formyl(aza)indoles as diformylmethane analogs for synthesizing dissymmetric di-meta-substituted pyridines without ortho and para substitutions. Furthermore, we uncovered resonance-assisted hydrogen bonding (RAHB) as the requirement for the in situ generation of enamines, the key intermediates of this transformation. Successful development of the designed methodology linked to wide applications—core remodeling of natural products, drug–natural product conjugation, late-stage functionalization of drug molecules, and synthesis of the regioisomeric CZC24832. Furthermore, we discovered anti-inflammatory agents through the functional evaluation of synthesized bi-heteroaryl analogs, signifying the utility of this methodology.
Competitive protein recruitment in artificial cells
Authors: van Veldhuisen Thijs W. , Verwiel Madelief A. M. , Novosedlik Sebastian , Brunsveld Luc , van Hest Jan C. M. 
Published: June 2024

AbstractLiving cells can modulate their response to environmental cues by changing their sensitivities for molecular signals. Artificial cells are promising model platforms to study intercellular communication, but populations with such differentiated behavior remain underexplored. Here, we show the affinity-regulated exchange of proteins in distinct populations of coacervate-based artificial cells via protein-protein interactions (PPI) of the hub protein 14-3-3. By loading different coacervates with different isoforms of 14-3-3, featuring varying PPI affinities, a client peptide is directed to the more strongly recruiting coacervates. By switching affinity of client proteins through phosphorylation, weaker binding partners can be outcompeted for their 14-3-3 binding, inducing their release from artificial cells. Combined, a communication system between coacervates is constructed, which leads to the transport of client proteins from strongly recruiting coacervates to weakly recruiting ones. The results demonstrate that affinity engineering and competitive binding can provide directed protein uptake and exchange between artificial cells.
Discovery, characterization, and comparative analysis of new UGT72 and UGT84 family glycosyltransferases
Authors: Li Tuo , Borg Annika J. E. , Krammer Leo , Weber Hansjörg , Breinbauer Rolf , Nidetzky Bernd 
Published: June 2024

AbstractGlycosylated derivatives of natural product polyphenols display a spectrum of biological activities, rendering them critical for both nutritional and pharmacological applications. Their enzymatic synthesis by glycosyltransferases is frequently constrained by the limited repertoire of characterized enzyme-catalyzed transformations. Here, we explore the glycosylation capabilities and substrate preferences of newly identified plant uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs) within the UGT72 and UGT84 families, with particular focus on natural polyphenol glycosylation from UDP-glucose. Four UGTs are classified according to their phylogenetic relationships and reaction products, identifying them as biocatalysts for either glucoside (UGT72 enzymes) or glucose ester (UGT84 members) formation from selected phenylpropanoid compounds. Detailed kinetic evaluations expose the unique attributes of these enzymes, including their specific activities and regio-selectivities towards diverse polyphenolic substrates, with product characterizations validating the capacity of UGT84 family members to perform di-O-glycosylation on flavones. Sequence analysis coupled with structural predictions through AlphaFold reveal an unexpected absence of a conserved threonine residue across all four enzymes, a trait previously linked to pentosyltransferases. This comparative analysis broadens the understood substrate specificity range for UGT72 and UGT84 enzymes, enhancing our understanding of their utility in the production of natural phenolic glycosides. The findings from this in-depth characterization provide valuable insights into the functional versatility of UGT-mediated reactions.
The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities
Authors: Ramberger Evelyn , Sapozhnikova Valeriia , Ng Yuen Lam Dora , Dolnik Anna , Ziehm Matthias , Popp Oliver , Sträng Eric , Kull Miriam , Grünschläger Florian , Krüger Josefine , Benary Manuela , Müller Sina , Gao Xiang , Murgai Arunima , Haji Mohamed , Schmidt Annika , Lutz Raphael , Nogai Axel , Braune Jan , Laue Dominik , Langer Christian , Khandanpour Cyrus , Bassermann Florian , Döhner Hartmut , Engelhardt Monika , Straka Christian , Hundemer Michael , Beule Dieter , Haas Simon , Keller Ulrich , Einsele Hermann , Bullinger Lars , Knop Stefan , Mertins Philipp , Krönke Jan 
Published: June 2024

AbstractMultiple myeloma (MM) is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, MM remains incurable, and better risk stratification as well as new therapies are therefore highly needed. The proteome of MM has not been systematically assessed before and holds the potential to uncover insight into disease biology and improved prognostication in addition to genetic and transcriptomic studies. Here we provide a comprehensive multiomics analysis including deep tandem mass tag-based quantitative global (phospho)proteomics, RNA sequencing, and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive MM, plasma cell leukemia and the premalignancy monoclonal gammopathy of undetermined significance, as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells are highly deregulated as compared with healthy plasma cells and is both defined by chromosomal alterations as well as posttranscriptional regulation. A prognostic protein signature was identified that is associated with aggressive disease independent of established risk factors in MM. Integration with functional genetics and single-cell RNA sequencing revealed general and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include potential targets for (immuno)therapies. Our study demonstrates the potential of proteogenomics in cancer and provides an easily accessible resource for investigating protein regulation and new therapeutic approaches in MM.
In vivo organoid growth monitoring by stimulated Raman histology
Authors: Sarri Barbara , Chevrier Véronique , Poizat Flora , Heuke Sandro , Franchi Florence , De Franqueville Louis , Traversari Eddy , Ratone Jean-Philippe , Caillol Fabrice , Dahel Yanis , Hoibian Solène , Giovannini Marc , de Chaisemartin Cécile , Appay Romain , Guasch Géraldine , Rigneault Hervé 
Published: June 2024

AbstractPatient-derived tumor organoids have emerged as a crucial tool for assessing the efficacy of chemotherapy and conducting preclinical drug screenings. However, the conventional histological investigation of these organoids necessitates their devitalization through fixation and slicing, limiting their utility to a single-time analysis. Here, we use stimulated Raman histology (SRH) to demonstrate non-destructive, label-free virtual staining of 3D organoids, while preserving their viability and growth. This novel approach provides contrast similar to conventional staining methods, allowing for the continuous monitoring of organoids over time. Our results demonstrate that SRH transforms organoids from one-time use products into repeatable models, facilitating the efficient selection of effective drug combinations. This advancement holds promise for personalized cancer treatment, allowing for the dynamic assessment and optimization of chemotherapy treatments in patient-specific contexts.
Deep learning-based virtual H& E staining from label-free autofluorescence lifetime images
Authors: Wang Qiang , Akram Ahsan R. , Dorward David A. , Talas Sophie , Monks Basil , Thum Chee , Hopgood James R. , Javidi Malihe , Vallejo Marta 
Published: June 2024

AbstractLabel-free autofluorescence lifetime is a unique feature of the inherent fluorescence signals emitted by natural fluorophores in biological samples. Fluorescence lifetime imaging microscopy (FLIM) can capture these signals enabling comprehensive analyses of biological samples. Despite the fundamental importance and wide application of FLIM in biomedical and clinical sciences, existing methods for analysing FLIM images often struggle to provide rapid and precise interpretations without reliable references, such as histology images, which are usually unavailable alongside FLIM images. To address this issue, we propose a deep learning (DL)-based approach for generating virtual Hematoxylin and Eosin (H&E) staining. By combining an advanced DL model with a contemporary image quality metric, we can generate clinical-grade virtual H&E-stained images from label-free FLIM images acquired on unstained tissue samples. Our experiments also show that the inclusion of lifetime information, an extra dimension beyond intensity, results in more accurate reconstructions of virtual staining when compared to using intensity-only images. This advancement allows for the instant and accurate interpretation of FLIM images at the cellular level without the complexities associated with co-registering FLIM and histology images. Consequently, we are able to identify distinct lifetime signatures of seven different cell types commonly found in the tumour microenvironment, opening up new opportunities towards biomarker-free tissue histology using FLIM across multiple cancer types.
Formation of chirality in propagating spin waves
Authors: Trevillian Cody , Tyberkevych Vasyl 
Published: June 2024

AbstractA general approach to quantify chirality, or absence of parity symmetry, of spin waves has been developed and applied to spin waves propagating in obliquely magnetized ferromagnetic films. Using theoretical arguments and numerical calculations, it is shown that, upon increasing spin wave wavevector, initially achiral spin waves develop chiral properties through the “parity exchange” mechanism, which implies, in particular, that chiral spin waves appear in pairs. The most striking example of the parity exchange mechanism is the simultaneous formation of two chiral waves: the magnetostatic surface wave and the recently discovered heterosymmetric spin wave, which were previously considered independent of each other. Another manifestation of the parity exchange is the formation of strongly chiral waves near the anti-crossings of spin wave branches of unequal symmetry. These findings illustrate viable paths to engineering spin wave systems with prescribed chiral spectra that had not previously been considered.
Pixel-super-resolved lens-free quantitative phase microscopy with partially coherent illumination
Authors: Chen Yang , Wu Xuejuan , Lu Linpeng , Sun Jiasong , Zhang Runnan , Lin Wenhui , Chen Yufan , Trusiak Maciej , Gao Peng , Zuo Chao 
Published: June 2024

AbstractLens-free on-chip microscopy (LFOCM) has been widely utilized in digital pathology, drug screening, point-of-care testing (POCT), and quantitative phase imaging (QPI) due to its high throughput imaging capability and compactness. Initially, coherent laser sources were used in LFOCM to generate interference fringes to reconstruct the intensity and phase information of an object. The use of partially coherent light-emitting diodes (LEDs) in LFOCM offers a more portable and cost-effective alternative to conventional coherent illumination sources. However, the coherence-gating effect from a relatively low degree of coherence may cause a blur of high-frequency information in holograms, leading to an inaccurate object recovery. Thus, we present a pixel-super-resolved lens-free quantitative phase microscopy (PSR-LFQPM) with partially coherent illumination, which not only compensates for the impact of low coherence without increasing the volume of the system but also suppresses the theoretical Nyquist-Shannon sampling resolution limit imposed by the sensor pixel size (0.9 μm). Based on the partially coherent imaging model, we integrate the spatial coherence transfer function (SCTF) obtained from the pre-calibrated LED source distribution during the iteration process to obtain an accurate high-resolution recovery. Applying PSR-LFQPM to image living HeLa cells in vitro, we achieve real-time dynamic high-throughput QPI performance (half-pitch resolution of 780 nm with a 1.41-fold improvement compared to results without considering the effect of coherence) across a wide FOV (19.53 mm2). The proposed method provides a compact, low-cost, and high-throughput lens-free on-chip microscopy system for biomedical and POCT applications.
Advances on broadband and resonant chiral metasurfaces
Authors: Deng Qian-Mei , Li Xin , Hu Meng-Xia , Li Feng-Jun , Li Xiangping , Deng Zi-Lan 
Published: June 2024

AbstractChirality describes mirror symmetry breaking in geometric structures or certain physical quantities. The interaction between chiral structure and chiral light provides a rich collection of means for studying the chirality of substances. Recently, optical chiral metasurfaces have emerged as planar or quasi-planar photonic devices composed of subwavelength chiral unit cells, offering distinct appealing optical responses to circularly polarized light with opposite handedness. The chiroptical effects in optical metasurfaces can be manifested in the absorption, scattering, and even emission spectra under the circular polarization bases. A broadband chiroptical effect is highly desired for many passive chiral applications such as pure circular polarizers, chiral imaging, and chiral holography, in which cases the resonances should be avoided. On the other hand, resonant chiroptical responses are particularly needed in many situations requiring strong chiral field enhancement such as chiral sensing and chiral emission. This article reviews the latest research on both broadband and resonant chiral metasurfaces. First, we discuss the basic principle of different types of chiroptical effects including 3D/2D optical chirality and intrinsic/extrinsic optical chirality. Then we review typical means for broadband chiral metasurfaces, and related chiral photonic devices including broadband circular polarizers, chiral imaging and chiral holography. Then, we discuss the interaction between chiral light and matter enhanced by resonant chiral metasurfaces, especially for the chiral bound states in the continuum metasurfaces with ultra-high quality factors, which are particularly important for chiral molecule sensing, and chiral light sources. In the final section, the review concludes with an outlook on future directions in chiral photonics.