bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of narrow-wide row planting patterns on canopy photosynthetic characteristics, bending resistance and yield of soybean in maize‒soybean intercropping systems
Authors: Gu Yan , Zheng Haoyuan , Li Shuang , Wang Wantong , Guan Zheyun , Li Jizhu , Mei Nan , Hu Wenhe
Published: April 2024

With the improvements in mechanization levels, it is difficult for the traditional intercropping planting patterns to meet the needs of mechanization. In the traditional maize‒soybean intercropping, maize has a shading effect on soybean, which leads to a decrease in soybean photosynthetic capacity and stem bend resistance, resulting in severe lodging, which greatly affects soybean yield. In this study, we investigated the effects of three intercropping ratios (four rows of maize and four rows of soybean; four rows of maize and six rows of soybean; six rows of maize and six rows of soybean) and two planting patterns (narrow-wide row planting pattern of 80–50 cm and uniform-ridges planting pattern of 65 cm) on soybean canopy photosynthesis, stem bending resistance, cellulose, hemicellulose, lignin and related enzyme activities. Compared with the uniform-ridge planting pattern, the narrow-wide row planting pattern significantly increased the LAI, PAR, light transmittance and compound yield by 6.06%, 2.49%, 5.68% and 5.95%, respectively. The stem bending resistance and cellulose, hemicellulose, lignin and PAL, TAL and CAD activities were also significantly increased. Compared with those under the uniform-ridge planting pattern, these values increased by 7.74%, 3.04%, 8.42%, 9.76%, 7.39%, 10.54% and 8.73% respectively. Under the three intercropping ratios, the stem bending resistance, cellulose, hemicellulose, lignin content and PAL, TAL, and CAD activities in the M4S6 treatment were significantly greater than those in the M4S4 and M6S6 treatments. Compared with the M4S4 treatment, these variables increased by 12.05%, 11.09%, 21.56%, 11.91%, 18.46%, 16.1%, and 16.84%, respectively, and compared with the M6S6 treatment, they increased by 2.06%, 2.53%, 2.78%, 2.98%, 8.81%, 4.59%, and 4.36%, respectively. The D-M4S6 treatment significantly improved the lodging resistance of soybean and weakened the negative impact of intercropping on soybean yield. Therefore, based on the planting pattern of narrow-wide row maize‒soybean intercropping planting pattern, four rows of maize and six rows of soybean were more effective at improving the lodging resistance of soybean in the semiarid region of western China.
A dense matching method for remote sensing images fused with CPS denoising
Authors: Zhu Bo , Tan Xiao , Li Houpu
Published: April 2024

Dense matching of remote sensing images is crucial for 3D reconstruction. This study proposes an enhanced dense matching method employing the CPS image denoising algorithm, aiming to boost the SGM algorithm's accuracy and efficiency in remote sensing image matching. The stereo image pair's quality is evaluated using the PSNR index, and a decision-making criterion based on the CPS algorithm is incorporated to determine the need for denoising. Preprocessing steps, including image cropping and pixel coordinate transformation, significantly reduce computational requirements. An epipolar line model, minimizing the disparity between two pixels, is used for calculations. This model is employed to construct an epipolar image, enhancing the accuracy and efficiency of the process. The study conducted experimental validation and analysis of the mismatch rate, running time, and denoising effect of the algorithm using the Middlebury 2021 stereo datasets. Additionally, the matching results of the World-View3 satellite stereo image pairs were visualized and analyzed. The experimental results indicate that the proposed algorithm reduces the average mismatch rate by 13.1% and increases the running speed by about 3 to 4 times compared to the SGBM algorithm. Specifically, the denoising effect reduces the mismatch rate of the reconstructed image by an average of 8.97%. The results indicate that the CPS method effectively addresses dense matching challenges in the presence of image blur and noise, thereby improving the operational efficiency and accuracy of the dense matching algorithm.
Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data
Authors: Schultheis Hendrik , Bentsen Mette , Heger Vanessa , Looso Mario
Published: April 2024

Transcription factors (TFs) are crucial epigenetic regulators, which enable cells to dynamically adjust gene expression in response to environmental signals. Computational procedures like digital genomic footprinting on chromatin accessibility assays such as ATACseq can be used to identify bound TFs in a genome-wide scale. This method utilizes short regions of low accessibility signals due to steric hindrance of DNA bound proteins, called footprints (FPs), which are combined with motif databases for TF identification. However, while over 1600 TFs have been described in the human genome, only ~ 700 of these have a known binding motif. Thus, a substantial number of FPs without overlap to a known DNA motif are normally discarded from FP analysis. In addition, the FP method is restricted to organisms with a substantial number of known TF motifs. Here we present DENIS (DE Novo motIf diScovery), a framework to generate and systematically investigate the potential of de novo TF motif discovery from FPs. DENIS includes functionality (1) to isolate FPs without binding motifs, (2) to perform de novo motif generation and (3) to characterize novel motifs. Here, we show that the framework rediscovers artificially removed TF motifs, quantifies de novo motif usage during an early embryonic development example dataset, and is able to analyze and uncover TF activity in organisms lacking canonical motifs. The latter task is exemplified by an investigation of a scATAC-seq dataset in zebrafish which covers different cell types during hematopoiesis.
Integrating tumor and healthy epithelium in a micro-physiology multi-compartment approach to study renal cell carcinoma pathophysiology
Authors: Somova Maryna , Simm Stefan , Padmyastuti Adventina , Ehrhardt Jens , Schoon Janosch , Wolff Ingmar , Burchardt Martin , Roennau Cindy , Pinto Pedro Caetano
Published: April 2024

The advent of micro-physiological systems (MPS) in biomedical research has enabled the introduction of more complex and relevant physiological into in vitro models. The recreation of complex morphological features in three-dimensional environments can recapitulate otherwise absent dynamic interactions in conventional models. In this study we developed an advanced in vitro Renal Cell Carcinoma (RCC) that mimics the interplay between healthy and malignant renal tissue. Based on the TissUse Humimic platform our model combines healthy renal proximal tubule epithelial cells (RPTEC) and RCC. Co-culturing reconstructed RPTEC tubules with RCC spheroids in a closed micro-perfused circuit resulted in significant phenotypical changes to the tubules. Expression of immune factors revealed that interleukin-8 (IL-8) and tumor necrosis factor-alfa (TNF-α) were upregulated in the non-malignant cells while neutrophil gelatinase-associated lipocalin (NGAL) was downregulated in both RCC and RPTEC. Metabolic analysis showed that RCC prompted a shift in the energy production of RPTEC tubules, inducing glycolysis, in a metabolic adaptation that likely supports RCC growth and immunogenicity. In contrast, RCC maintained stable metabolic activity, emphasizing their resilience to external factors. RNA-seq and biological process analysis of primary RTPTEC tubules demonstrated that the 3D tubular architecture and MPS conditions reverted cells to a predominant oxidative phosphorylate state, a departure from the glycolytic metabolism observed in 2D culture. This dynamic RCC co-culture model, approximates the physiology of healthy renal tubules to that of RCC, providing new insights into tumor-host interactions. Our approach can show that an RCC-MPS can expand the complexity and scope of pathophysiology and biomarker studies in kidney cancer research.
Optimization of hepatological clinical guidelines interpretation by large language models: a retrieval augmented generation-based framework
Authors: Kresevic Simone , Giuffrè Mauro , Ajcevic Milos , Accardo Agostino , Crocè Lory S. , Shung Dennis L.
Published: April 2024

Large language models (LLMs) can potentially transform healthcare, particularly in providing the right information to the right provider at the right time in the hospital workflow. This study investigates the integration of LLMs into healthcare, specifically focusing on improving clinical decision support systems (CDSSs) through accurate interpretation of medical guidelines for chronic Hepatitis C Virus infection management. Utilizing OpenAI’s GPT-4 Turbo model, we developed a customized LLM framework that incorporates retrieval augmented generation (RAG) and prompt engineering. Our framework involved guideline conversion into the best-structured format that can be efficiently processed by LLMs to provide the most accurate output. An ablation study was conducted to evaluate the impact of different formatting and learning strategies on the LLM’s answer generation accuracy. The baseline GPT-4 Turbo model’s performance was compared against five experimental setups with increasing levels of complexity: inclusion of in-context guidelines, guideline reformatting, and implementation of few-shot learning. Our primary outcome was the qualitative assessment of accuracy based on expert review, while secondary outcomes included the quantitative measurement of similarity of LLM-generated responses to expert-provided answers using text-similarity scores. The results showed a significant improvement in accuracy from 43 to 99% (p < 0.001), when guidelines were provided as context in a coherent corpus of text and non-text sources were converted into text. In addition, few-shot learning did not seem to improve overall accuracy. The study highlights that structured guideline reformatting and advanced prompt engineering (data quality vs. data quantity) can enhance the efficacy of LLM integrations to CDSSs for guideline delivery.
Detection of ribonucleotides embedded in DNA by Nanopore sequencing
Authors: Grasso Lavinia , Fonzino Adriano , Manzari Caterina , Leonardi Tommaso , Picardi Ernesto , Gissi Carmela , Lazzaro Federico , Pesole Graziano , Muzi-Falconi Marco
Published: April 2024

Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome instability and human pathologies are not fully understood. The available sequencing technologies only allow to indirectly deduce the genomic location of rNMPs. Oxford Nanopore Technologies (ONT) may overcome such limitation, revealing the sites of rNMPs incorporation in genomic DNA directly from raw sequencing signals. We synthesized two types of DNA molecules containing rNMPs at known or random positions and we developed data analysis pipelines for DNA-embedded ribonucleotides detection by ONT. We report that ONT can identify all four ribonucleotides incorporated in DNA by capturing rNMPs-specific alterations in nucleotide alignment features, current intensity, and dwell time. We propose that ONT may be successfully employed to directly map rNMPs in genomic DNA and we suggest a strategy to build an ad hoc basecaller to analyse native genomes.
Multiscale X-ray phase-contrast CT unveils the evolution of bile infarct in obstructive biliary disease
Authors: Xin Xiaohong , Jian Jianbo , Fan Xu , Qi Beining , Zhao Yuanyuan , Lv Wenjuan , Zhao Yuqing , Zhao Xinyan , Hu Chunhong
Published: April 2024

Bile infarct is a pivotal characteristic of obstructive biliary disease, but its evolution during the disease progression remains unclear. Our objective, therefore, is to explore morphological alterations of the bile infarct in the disease course by means of multiscale X-ray phase-contrast CT. Bile duct ligation is performed in mice to mimic the obstructive biliary disease. Intact liver lobes of the mice are scanned by phase-contrast CT at various resolution scales. Phase-contrast CT clearly presents three-dimensional (3D) images of the bile infarcts down to the submicron level with good correlation with histological images. The CT data illustrates that the infarct first appears on day 1 post-BDL, while a microchannel between the infarct and hepatic sinusoids is identified, the number of which increases with the disease progression. A 3D model of hepatic acinus is proposed, in which the infarct starts around the portal veins (zone I) and gradually progresses towards the central veins (zone III) during the disease process. Multiscale phase-contrast CT offers the comprehensive analysis of the evolutionary features of the bile infarct in obstructive biliary disease. During the course of the disease, the bile infarcts develop infarct-sinusoidal microchannels and gradually occupy the whole liver, promoting the disease progression.
Spatial partitioning of terrestrial precipitation reveals varying dataset agreement across different environments
Authors: Markonis Yannis , Vargas Godoy Mijael Rodrigo , Pradhan Rajani Kumar , Pratap Shailendra , Thomson Johanna Ruth , Hanel Martin , Paschalis Athanasios , Nikolopoulos Efthymios , Papalexiou Simon Michael
Published: April 2024

The study of the water cycle at planetary scale is crucial for our understanding of large-scale climatic processes. However, very little is known about how terrestrial precipitation is distributed across different environments. In this study, we address this gap by employing a 17-dataset ensemble to provide, for the first time, precipitation estimates over a suite of land cover types, biomes, elevation zones, and precipitation intensity classes. We estimate annual terrestrial precipitation at approximately 114,000 ± 9400 km3, with about 70% falling over tropical, subtropical and temperate regions. Our results highlight substantial inconsistencies, mainly, over the arid and the mountainous areas. To quantify the overall discrepancies, we utilize the concept of dataset agreement and then explore the pairwise relationships among the datasets in terms of “genealogy”, concurrency, and distance. The resulting uncertainty-based partitioning demonstrates how precipitation is distributed over a wide range of environments and improves our understanding on how their conditions influence observational fidelity.
Rapid diagnosis of bloodstream infections using a culture-free phenotypic platform
Authors: Shi Xuyang , Sharma Shivani , Chmielewski Richard A. , Markovic Mario J. , VanEpps J. Scott , Yau Siu-Tung
Published: April 2024

Background

Bloodstream infections (BSIs) are a life-threatening acute medical condition and current diagnostics for BSIs suffer from long turnaround time (TAT). Here we show the validation of a rapid detection-analysis platform (RDAP) for the diagnosis of BSIs performed on clinical blood samples

Methods

The validation was performed on a cohort of 59 clinical blood samples, including positive culture samples, which indicated confirmed bloodstream infections, and negative culture samples. The bacteria in the positive culture samples included Gram-positive and Gram-negative pathogenic species. RDAP is based on an electrochemical sandwich immunoassay with voltage-controlled signal amplification, which provides an ultra-low limit of detection (4 CFU/mL), allowing the platform to detect and identify bacteria without requiring culture and perform phenotypic antibiotic susceptibility testing (AST) with only 1–2 h of antibiotic exposure. The preliminary diagnostic performance of RDAP was compared with that of standard commercial diagnostic technologies.

Results

Using a typical clinical microbiology laboratory diagnostic workflow that involved sample culture, agar plating, bacteria identification using matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry, and AST using MicroScan as a clinical diagnostic reference, RDAP showed diagnostic accuracy of 93.3% and 95.4% for detection-identification and AST, respectively. However, RDAP provided results at least 15 h faster.

Conclusions

This study shows the preliminary feasibility of using RDAP to rapidly diagnose BSIs, including AST. Limitations and potential mitigation strategies for clinical translation of the present RDAP prototype are discussed. The results of this clinical feasibility study indicate an approach to provide near real-time diagnostic information for clinicians to significantly enhance the treatment outcome of BSIs.
Mechanochemical synthesis of zinc-doped hydroxyapatite for tunable micronutrient release
Authors: Ammar Mohamed , Bortoletto-Santos Ricardo , Ribeiro Caue , Zhang Lihua , Baltrusaitis Jonas
Published: April 2024

Mechanochemical synthesis using ZnCO3 and monetite/brushite precursors afforded Zn-incorporated hydroxyapatite with tunable Zn concentration-dependent dissolution properties.
Anomalous spectral shift of localized surface plasmon resonance
Authors: Kosame Saikiran , Josline Mukkath Joseph , Lee Jae-Hyun , Ju Heongkyu
Published: April 2024

We report the first observation of abnormal spectral shift of plasmon resonance of silver nanoparticles (AgNPs) due to a negative optical nonlinearity of a local ambient medium.
Enzyme-loaded rod-like microgel shapes: a step towards the creation of shape-specific microreactors for blood detoxification purposes
Authors: Bishnoi Shahana , Jansman Michelle Maria Theresia , Chen Jiantao , Thulstrup Peter Waaben , Keller Stephan Sylvest , Hosta-Rigau Leticia
Published: April 2024

We report shape-specific hydrogel microparticles acting as enzymatic microreactors by encapsulating the enzyme β-lactamase that catalyzes the conversion of nitrocefin into the hydrolyzed red product.
A dual emitting CsPbBr3/Eu-BDC composite as a ratiometric photoluminescent turn-on probe for aliphatic amine sensing
Authors: Ahmed Shahnaz , Dolui Swapan Kumar
Published: April 2024

A dual emissive ratiometric fluorescent probe sensor made of a CsPbBr3/Eu-BDC perovskite composite was prepared for the sensing of aliphatic amine derivatives. A visual color change was observed on exposure to volatile amines.
An ALP-responsive, anionic iridium complex for specific recognition of osteosarcoma cells
Authors: Shen Shuang , Nong Shuli , Zhang Xianpeng , Song Jiaqi , Meng Caiting , Liu Xinling , Shao Liang , Li Guanying , Xu Li
Published: April 2024

Through the hydrolysis by alkaline phosphatase, an anionic Ir(iii) complex is converted into cationic complex with increased lipophilicity, subsequently enhancing cell internalization and specifically staining osteosarcoma cells.
A sustainable strategic approach for N-alkylation of amines with activation of alcohols triggered via a hydrogen auto-transfer reaction using a Pd(ii) complex: evidence for metal–ligand cooperativity
Authors: Kumar Chaudhary Virendra , Kukreti Prashant , Sharma Keshav , Kumar Kapil , Singh Sain , Kumari Sheela , Ghosh Kaushik
Published: April 2024

Palladium complex containing pincer bisazo-amine ligand was synthesized and characterized with various techniques. Complex was utilized to study the catalytic activity for the synthesis of amine derivatives via a hydrogen borrowing strategy.
Correction: Preferred planar crystal growth and uniform solid electrolyte interfaces enabled by anion receptors for stable aqueous Zn batteries
Authors: Wang Xinyu , Ying Yiran , Li Xiaomin , Chen Shengmei , Gao Guowei , Huang Haitao , Ma Longtao
Published: April 2024

Correction for ‘Preferred planar crystal growth and uniform solid electrolyte interfaces enabled by anion receptors for stable aqueous Zn batteries’ by Xinyu Wang et al., Energy Environ. Sci., 2023, 16, 4572–4583, https://doi.org/10.1039/D3EE01580G.
On synergy between ultrahigh throughput screening and machine learning in biocatalyst engineering
Authors: Gantz Maximilian , Mathis Simon V. , Nintzel Friederike E. H. , Lio Pietro , Hollfelder Florian
Published: April 2024

We explore strategies for drawing-up ‘fitness landscapes’ in sequence space with ultrahigh throughput (uHT) droplet microfluidics, review the current state of AI/ML in enzyme engineering and discuss how uHT datasets may be combined with AI/ML.
Correction: Pickering emulsions stabilized with a spirulina protein–chitosan complex for astaxanthin delivery
Authors: Liu Ronggang , Li Yu , Zhou Chengfu , Tan Mingqian
Published: April 2024

Correction for ‘Pickering emulsions stabilized with a spirulina protein–chitosan complex for astaxanthin delivery’ by Ronggang Liu et al., Food Funct., 2023, 14, 4254–4266, https://doi.org/10.1039/D3FO00092C.
Green and sustainable in situ water treatment: a review of noble-free catalysts for electrochemical oxygen reduction to hydrogen peroxide
Authors: Liu Jiahao , Li Cheng , Zhang Zhaorui , Wang Jiacheng , Yang Minghui
Published: April 2024

Water treatment is an essential process for ensuring access to clean and safe drinking water.
Drug testing of monodisperse arrays of live microdissected tumors using a valved multiwell microfluidic platform
Authors: Lockhart Ethan J. , Horowitz Lisa F. , Rodríguez Adán , Zhu Songli , Nguyen Tran , Mehrabi Mehdi , Gujral Taranjit S. , Folch Albert
Published: April 2024

A microfluidic platform was developed that hydrodynamically traps microdissected cuboids for selective drug treatments and isolates conditions with thermoplastic valves.
Electrodeposited Ni–Fe alloy as a cost-effective material for harnessing hydrogen via the oxygen evolution and urea oxidation reactions
Authors: Venkatachalam Ananth , Senthilnathan Venkatesan , Veerapandian Murugan , Rajasekaran N.
Published: April 2024

Electrochemical energy conversion for hydrogen production is a crucial method to address the global energy demand.
Sulfonic group modified carbon nanotubes: the decorative strategy for enhancing the performance of lithium-sulfur batteries
Authors: Yang Chensong , Tang Yakun , Zhang Yue , Zeng Xingyan , Dai Mengyao , Liu Lang
Published: April 2024

Sulfonic group-modified thin-walled porous CNTs are successfully designed by reacting with sulfuric acid, and enhance the electrochemical performance of lithium-sulfur batteries by dispersing sulfur and adsorbing polysulfides.
Medium-sized peptides from microbial sources with potential for antibacterial drug development
Authors: Chen Jianwei , Wang Wei , Hu Xubin , Yue Yujie , Lu Xingyue , Wang Chenjie , Wei Bin , Zhang Huawei , Wang Hong
Published: April 2024

This review summarizes the medium-sized antimicrobial peptides discovered in the last three decades (1993 to the end of 2022) and highlights the novel antibacterial mechanisms as well as part of the structure–activity relationships.
Visible light-mediated synthesis of quinazolinones and benzothiadiazine-1,1-dioxides utilizing aliphatic alcohols
Authors: Kumari Saloni , Roy Souvik , Arora Pragya , Kundu Sabuj
Published: April 2024

The activation and utilization of challenging aliphatic alcohols like methanol and ethanol is a very appealing approach to synthesize valuable organic molecules.
In situ interfacial reactions in hydride–oxide composite electrolytes for stable all-solid-state Li–metal batteries
Authors: Zeng Shunqin , Zhao Meinan , Xie Chen , Li Jianhui , Ding Xiaoli , He Liqing , Li Yongtao , Zhang Qingan , Li Hai-Wen
Published: April 2024

Mechanochemical formation of hydride–oxide dual core–shell composite electrolytes is demonstrated for stable all-solid-state Li–metal batteries.
NaVSeO5: synergistic combinations to synthesize excellent birefringent materials
Authors: Feng Qiuyuan , Wang Jialong , Liu Changyou , Jing Qun , Dong Xiaoyu
Published: April 2024

Enhancing the birefringence of compounds by “two steps in one”: a synergistic strategy of stereochemically active lone pairs [SeO3] and distorted [VO6] polyhedra.
The role of optical fiber sensors in the new generation of healthcare devices: a review
Authors: Leal-Junior Arnaldo , Silva Jussara , Macedo Leandro , Marchesi Arthur , Morau Samilly , Valentino Janine , Valentim Fabricya , Costa Magno
Published: April 2024

This paper presents a review of optical sensor systems for wearable applications aiming at the new demands on healthcare motivated by the new paradigms in internet of things, photonics development and artificial intelligence.
A layering technique for achieving pinhole-free organic–inorganic halide perovskite thin films through the vapor–solid reaction
Authors: Zhang Lixin , Zhong Jialing , Kong Anqi , Chen Yuanyuan , Fan Junshuai , Tan Qiang , Peng Yong , Liang Guijie , Ku Zhiliang
Published: April 2024

A multi-stage vapor–solid reaction technique was introduced to form segmented perovskite thin films. The triple-layer film exhibited a dense, pinhole-free structure. Solar cells made from it achieved a champion power conversion efficiency of 21.09%.
A highly selective and high-performance sulfonated poly(ether ether ketone)-based hybrid membrane enabled by complexed UiO-66-NH2 and sulfonated graphitic carbon nitride for vanadium flow batteries
Authors: Zhao Caiyuan , Wang Haixia , Li Lang , Liu Liping , Cui Xinrui , Shi Haifeng
Published: April 2024

Complexed UiO-66-NH2 and s-g-C3N4 nanofillers contribute ultralow permeability and ultrahigh selectivity to SPEEK/NF-1 : 1 and ensure outstanding VFB efficiencies owing to manipulated acid–base interactions and synergistic ion barriers.
Lithiophilic interlayer driven ‘bottom-up’ metal infilling in high current density Li-metal anodes
Authors: Abdul Ahad Syed , Drews Janina , Danner Timo , Latz Arnulf , Geaney Hugh
Published: April 2024

A functional interlayer is designed to inhibit dendrite formation in Li metal anodes. The single-sided lithiophilic germanium nanowire layer on carbon cloth promotes bottom-up Li infilling during the plating process.
Toward record high Zn2+ storage in carbon electrodes via pore confinement engineering
Authors: Zhang Xiubo , Yu Chang , Xie Yuanyang , Yu Jinhe , Liu Yingbin , Yang Yi , Wang Jianjian , Lan Shuqin , Hou Siyi , Liu Kunlun , Qiu Jieshan
Published: April 2024

The effective specific surface area is proposed and well correlated with Zn2+ storage, guiding maximum Zn2+ storage within carbon. Multiple in situ spectroscopy techniques clarify the co-adsorption mechanism of hydrated Zn2+, SO42−, and H+.
Light-degradable nanocomposite hydrogels for antibacterial wound dressing applications
Authors: Fang Changhao , Shen Qiming , Zhang Yingnan , Kanemaru Karen , Serpe Michael J.
Published: April 2024

We developed a light-degradable nanocomposite hydrogel to achieve both controlled antibiotic delivery and hydrogel degradation using light as the sole stimulus. They could serve as novel materials for antibacterial wound dressing applications.
Bioprinted biomimetic hydrogel matrices guiding stem cell aggregates for enhanced chondrogenesis and cartilage regeneration
Authors: Liu Yuetian , Du Lijuan , Zhang Hua , Li Guanrong , Luo Yang , Hu Zeming , Xu Rong , Yao Jie , Shi Zheyuan , Chen Yige , Zhang Chi , Jin Zhanping , Zhang Caihua , Xie Chanchan , Fu Jun , Zhu Yabin , Zhu Yingchun
Published: April 2024

A bioprinted hydrogel matrix exhibiting superior cellular adhesion and aggregation characteristics was engineered to enhance cartilage repair by finely tuning biochemical stimuli and mechanical stability.
A 20 kiloparsec bipolar Lyman α outflow from a radio galaxy at z = 2.95
Authors: Puga M. Coloma , Balmaverde B. , Capetti A. , Almeida C. Ramos , Massaro F. , Venturi G.
Published: April 2024

The study of ionized gas kinematics in high-z active galaxies plays a key part in our understanding of galactic evolution, in an age where nuclear activity was widespread and star formation close to its peak. We present a study of TXS 0952−217, a radio galaxy at z = 2.95, using VLT/MUSE integral field optical spectroscopy as part of a project aimed studying of the properties of ionized gas in high redshift radio galaxies (HzRGs). The Lyα line profile of this object presents various emission and absorption components. By utilizing Voronoi binning, we obtained a comprehensive map of the kinematic properties of these components. These observations revealed the presence of a redshifted, high velocity (v ∼ 500 km s−1) bipolar structure of Lyα emission, most likely corresponding to an outflow of ionized gas. The outflow extends beyond the compact radio source on both sides, with a total size of ∼21 kpc. Its kinetic power (1042.1 erg s−1) is about five orders of magnitude smaller than its radio power. Additional ionized lines, including HeIIλ1640, CIVλ1550 and CIII]λ1908 were detected and their line flux ratios determined. The presence of HeII allowed for a precise redshift measurement (z = 2.945 ± 0.002). Along with the recent discovery of a similar structure in TN J1049−1258, another HzRG, it displays the feasibility of using Lyα as a tracer of outflowing gas in high redshift sources, and particularly so when supported by non-resonant ionized lines such as HeII, which allow for accurate redshift and velocity measurements.
Spectroflat: A generic spectrum and flat-field calibration library for spectro-polarimetric data
Authors: Hölken J. , Doerr H.-P. , Feller A. , Iglesias F. A.
Published: April 2024

Context. Flat-fielding spectro-polarimetric data with one spatial and one spectral dimension is inherently difficult as the imprint of the spectral lines needs to be separated from other wavelength-dependent instrumental effect (e.g., fringes or prefilter profiles) and wavelength-independent effects (e.g., dust and sensor response). Current approaches for spectrometers are often based on moving the grating or they depend on optical models and/or on lab calibration data. They are also limited to small spectral regions and are instrument-specific. Approaches that would be suitable for polarimeters have not been reported yet.

Aims. We present an approach that allows for flat-field calibration data to be to obtained for diffraction-grating-based, long-slit spec-trographs combined with temporally modulated polarimetry from high-resolution solar telescopes. This approach is based on nominal flat-fielding procedures performed during the instrument’s science operations.

Methods. We performed a precise and field-dependent correction of the spectrographic distortion effect (resulting in curved spectral lines, typically denoted as a “smile” effect) to ensure the orthogonality of the spectral and spatial dimensions. We identified distortions by tracking the position of multiple spectral lines within the full spectral field of view. From the raw modulated flats, we then removed the solar line imprints and derived separate flat-fields for sensor and slit dust features. Optionally, wavelength calibration and continuum correction can be included in this process.

Results. We have created generic Python libraries that can be plugged into existing Python-based data reduction pipelines or used as a standalone calibration tool. We show that for spectrographs covering many spectral lines, a correction of the smile distortion based on optical models alone is not sufficient. Our results demonstrate a suppression of fringes, sensor artifacts, and fixed-pattern imprints in demodulated data by one order of magnitude. For intensity images, the photon noise level can be closely attained after calibration. Our correction works across the full spectral range. The algorithm was tested for different wavelength regimes with emission (EUV range) or absorption (near-UV, VIS, IR range) spectra, on data acquired with ground-based (SST/TRIPPLE-SP, GREGOR/GRIS), balloon-borne (SUNRISE-III/SUSI), and space-based (SolO/SPICE) instruments. The data calibrated with our method offer robust and precise inversion results.

Conclusions. We have extended existing spectroscopic flat-field techniques to modern instruments with large imaging sensors covering many spectral lines simultaneously, and with polarimetric capabilities, where methods described so far are not adequate. We believe that our method is applicable as a standard calibration approach for most modern high resolution large-FOV, long-slit spectrographs – both with and without polarimetric capabilities.
The VELOCE modulation zoo
Authors: Netzel H. , Anderson R. I. , Viviani G.
Published: April 2024

Context. The photometric observations from the recent decade revolutionized our view on classical pulsators. Low-amplitude signals have been detected photometrically in addition to the dominant high-amplitude radial mode pulsations in many RR Lyrae stars and classical Cepheids. First-overtone pulsators with an additional low-amplitude signal at a period ratio of around 0.61 with the main mode, the so-called 0.61 stars, form the most populous group among these stars. The nature of this signal has been attributed to non-radial pulsations. Another mysterious group are stars in which the additional signal forms a period ratio of around 0.68. These are the 0.68 stars. The origin of the signal remains unknown.

Aims. Here, we search for similar phenomena in spectroscopic observations of first-overtone classical Cepheids collected as part of the VELOCE project.

Methods. We performed a frequency analysis of several parameters derived from cross-correlation functions (CCFs), including radial velocity, the full width at half maximum, the bisector inverse span, and the CCF depth (contrast). Using standard pre-whitening, we searched for additional low-amplitude signals. We identified the location of these stars in various sequences of the Petersen diagram.

Results. We detect additional signals in four first-overtone classical Cepheids: BG Cru, QZ Nor, V0391 Nor, and V0411 Lac. We classified BG Cru, QZ Nor, and V0391 Nor as 0.61 stars based on their period ratios. V0411 Lac, however, exhibits a ratio of 0.68 between the two modes, and the additional signal has a longer period. This type of multi-periodicity remains unexplained.

Conclusions. VELOCE CCFs yield the first spectroscopic detections of non-radial pulsation modes in classical Cepheids. This opens an asteroseismic window for pursuing a more detailed understanding of these important stars. While the 0.61 signal of BG Cru, QZ Nor, and V0391 Nor is understood to originate from non-radial modes of moderate degrees, the 0.68 signal of V0411 Lac still lacks a physical explanation.
Gray two-moment neutrino transport: Comprehensive tests and improvements for supernova simulations
Authors: Andresen Haakon , O’Connor Evan P. , Andersen Oliver Eggenberger , Couch Sean M.
Published: April 2024

Aims. In this work we extended an energy-integrated neutrino transport method to facilitate efficient, yet precise, modeling of compact astrophysical objects. We particularly focus on core-collapse supernovae.

Methods. We implemented a gray neutrino-transport framework from the literature into FLASH and performed a detailed evaluation of its accuracy in core-collapse supernova simulations. Based on comparisons with results from simulations using energy-dependent neutrino transport, we incorporated several improvements to the original scheme.

Results. Our analysis shows that our gray neutrino transport method successfully reproduces key aspects from more complex energy-dependent transport across a variety of progenitors and equations of state. We find both qualitative and reasonable quantitative agreement with multi-group M1 transport simulations. However, the gray scheme tends to slightly favor shock revival. In terms of gravitational wave and neutrino signals, there is a good alignment with the energy-dependent transport, although we find 15–30% discrepancies in the average energy and luminosity of heavy-lepton neutrinos. Simulations using the gray transport are around four times faster than those using energy-dependent transport.
Étude du comportement thermodynamique du CO2 en stockage en cavité saline
Authors: Soubeyran Aurélien , Rouabhi Ahmed , Coquelet Christophe
Published: April 2024

Dans le contexte actuel de la transition énergétique, le besoin de développer des solutions permettant de stocker temporairement l’énergie pousse à étendre les applications de stockage souterrain en cavité saline à de nouveaux fluides (parmi eux notamment l’hydrogène ou le dioxyde de carbone). Cependant, ces derniers fluides présentent des particularités thermodynamiques qu’il est important de bien caractériser et dont il faut anticiper l’impact sur le comportement global du stockage. Dans le cas du dioxyde de carbone, pris comme exemple d’application dans cet article, ces spécificités concernent l’état physique sous lequel il peut être stocké et sa forte solubilité dans la saumure également présente au fond de la cavité. Un modèle global de stockage est établi, permettant le couplage des comportements thermodynamique des fluides contenus et thermomécanique du massif salin, ainsi qu’une adaptation à chaque fluide pouvant être stocké. Ce modèle est ici étendu pour prendre en compte les nouveaux phénomènes liés au stockage de dioxyde de carbone, et tout particulièrement afin d’observer l’impact des échanges de matière avec la saumure sur les conditions de stockage. À cette fin, on compare les résultats de deux déclinaisons du modèle de stockage (à savoir prendre en compte ou non les transferts de masse) appliquées à différents scénarii d’opération : remplissage de la cavité, injection et extraction selon que le dioxyde de carbone est stocké sous forme liquide ou gazeuse. L’étude souligne l’intérêt d’appliquer le modèle étendu à toutes les modélisations d’opération impliquant un transfert de saumure. Enfin, une étude expérimentale et numérique portant sur la cinétique de dissolution du dioxyde de carbone dans la saumure a été menée. Celle-ci, bien qu’encore sujette à développement et principalement qualitative, confirme la nécessité d’intégrer un tel phénomène au modèle.
How the Earth’s upper crust deforms in a viscous or brittle manner and how these behaviors interact and evolve over time: the crucial role of pressure solution creep and sealing processes1
Authors: Gratier Jean-Pierre
Published: April 2024

Observations of the geological deformation of the Earth’s upper crust show both brittle behavior (faults) and viscous behavior (folds, shear zones). This paper explains the crucial role of pressure solution creep and sealing processes in these contrasting behaviors and in their evolutions over time. A description of natural deformation by pressure solution shows that the pressure solution creep process can accommodate large ductile deformation without any faults. This process can also accommodate near-stable ductile deformation through the coupling of pressure solution and fracturing. Even if pressure solution creep cannot accommodate the tectonic loading rate and earthquakes consequently occur, the post-seismic evolution is largely controlled by pressure solution processes such as post-seismic creep and fault healing and sealing. Some key experiments are presented that allow evaluating the thermodynamics and kinetics of these processes. Various models are then presented that could help engineers integrate pressure solution creep and sealing processes into predictions of the long-term behavior of rock deformation in underground storage and geo-energy facilities.
Explicit stabilized multirate methods for the monodomain model in cardiac electrophysiology
Authors: de Souza Giacomo Rosilho , Grote Marcus J. , Pezzuto Simone , Krause Rolf
Published: April 2024

Fully explicit stabilized multirate (mRKC) methods are well-suited for the numerical solution of large multiscale systems of stiff ordinary differential equations thanks to their improved stability properties. To demonstrate their efficiency for the numerical solution of stiff, multiscale, nonlinear parabolic PDE’s, we apply mRKC methods to the monodomain equation from cardiac electrophysiology. In doing so, we propose an improved version, specifically tailored to the monodomain model, which leads to the explicit exponential multirate stabilized (emRKC) method. Several numerical experiments are conducted to evaluate the efficiency of both mRKC and emRKC, while taking into account different finite element meshes (structured and unstructured) and realistic ionic models. The new emRKC method typically outperforms a standard implicit-explicit baseline method for cardiac electrophysiology. Code profiling and strong scalability results further demonstrate that emRKC is faster and inherently parallel without sacrificing accuracy.
L’intelligence artificielle, une révolution dans le développement des médicaments
Authors: Moingeon Philippe , Garbay Christiane , Dahan Muriel , Fermont Irène , Benmakhlouf Ali , Gouyette Alain , Poitou Pierre , Saint-Pierre Alain ,   le Groupe de Veille IA et Sciences pharmaceutiques
Published: April 2024

L’intelligence artificielle (IA) et l’apprentissage automatique produisent des modèles prédictifs qui aident à la prise de décisions dans le processus de découverte de nouveaux médicaments. Cette modélisation par ordinateur permet de représenter l’hétérogénéité d’une maladie, d’identifier des cibles thérapeutiques, de concevoir et optimiser des candidats-médicaments et d’évaluer ces médicaments sur des patients virtuels, ou des jumeaux numériques. En facilitant à la fois une connaissance détaillée des caractéristiques des patients et en prédisant les propriétés de multiples médicaments possibles, l’IA permet l’émergence d’une médecine de précision « computationnelle » offrant des traitements parfaitement adaptés aux spécificités des patients.
La cachexie associée au cancer
Authors: Bastin Jean
Published: April 2024

La cachexie est un état caractéristique de nombreux cancers en phase avancée qui se traduit par un amaigrissement extrême lié à une dénutrition, pouvant évoluer vers une issue fatale, sans traitement à l’heure actuelle. Les symptômes de la cachexie incluent une fonte musculaire, souvent accompagnée de perte de la masse grasse, et un ensemble complexe de troubles (inflammation, douleurs, faiblesse générale, anorexie, dépression). L’étiologie de la maladie, encore mal comprise, met en jeu des composantes inflammatoires, métaboliques et neuroendocrines affectant de nombreux organes, qui sont induites par un grand nombre de médiateurs.
Efficacy of Subthreshold Micropulse Laser for Central Serous Chorioretinopathy
Authors: Fasler Katrin , Turgut Ferhat , Gunzinger Jeanne Martine , Sommer Chiara , Muth Daniel Rudolf , Kinzl Stephan , Nilius Henning , Zweifel Sandrine , Somfai Gabor Mark
Published: April 2024

Purpose To evaluate the efficacy of a subthreshold micropulse laser (SML) in patients with central serous chorioretinopathy (CSCR).

Methods Retrospective clinical study conducted at the Departments of Ophthalmology at a university and a municipal hospital in Zurich, Switzerland. We enrolled acute and chronic CSCR patients with persistent subretinal fluid (SRF) treated with SML. Two treatment protocols (fluorescein/indocyanine green angiography or optical coherence tomography guided) were evaluated for efficacy after 3 and 6 months. The primary outcomes of the study were reduction and percentage of eyes with complete resolution of SRF 3 and 6 months after SML treatment. Secondary endpoints included changes in central subfield thickness (CST) and visual acuity (VA) after 3 and 6 months.

Results The study involved 37 eyes (35 patients, 48.6% chronic). A statistically significant reduction in SRF height and CST could be shown, irrespective of SRF duration, type of CSCR, or chosen guidance after 3 and 6 months: SRF − 40 µm (p < 0.01), CST − 52 µm (p < 0.01). Percentage of eyes with complete resolution of fluid at 3 and 6 months after SML were 24.3 and 21.6%, respectively. No statistically significant functional improvement (VA) could be shown. Multivariable regression and linear mixed regression analyses did not identify statistically significant differences in SRF reduction, CMT change, or VA improvement with respect to the type of CSCR or the treatment plan used (p > 0.05).

Conclusion The effectiveness of SML in CSCR is under continuous debate. Our study findings demonstrate structural but only little functional changes with SML. In view of the shortage of verteporfin for photodynamic therapy, SML remains an important therapeutic option for CSCR patients.
OP-Ablauf: Oberschenkelhalsfraktur
Authors: Becker Petra
Published: April 2024

Im vorherigen Artikel haben Sie die unterschiedlichen Versorgungsmethoden der Femurfraktur kennengelernt. Wie eine Oberschenkelhalsfraktur in der Praxis mit einem proximalen Femurnagelsystem versorgt wird, erfahren Sie Schritt für Schritt in diesem OP-Ablauf.
Multi-phased Kinetics and Interaction of Protein Kinase Signaling in Glycoprotein VI-Induced Platelet αIIbβ3 Integrin Activation and Degranulation
Authors: Zhang Pengyu , von Ungern-Sternberg Saskia , Hastenplug Luisa , Solari Fiorella A. , Sickmann Albert , Kuijpers Marijke J. E. , Heemskerk Johan W. M. , Walter Ulrich , Jurk Kerstin
Published: April 2024

Background Platelet glycoprotein VI (GPVI) stimulation activates the tyrosine kinases Syk and Btk, and the effector proteins phospholipase Cγ 2 (PLCγ2) and protein kinase C (PKC). Here, the activation sequence, crosstalk, and downstream effects of this Syk-Btk-PKC signalosome in human platelets were analyzed.

Methods and Results Using immunoblotting, we quantified 14 regulated phospho-sites in platelets stimulated by convulxin with and without inhibition of Syk, Btk, or PKC. Convulxin induced fast, reversible tyrosine phosphorylation (pY) of Syk, Btk, LAT, and PLCγ2, followed by reversible serine/threonine phosphorylation (pS/T) of Syk, Btk, and downstream kinases MEK1/2, Erk1/2, p38, and Akt. Syk inhibition by PRT-060318 abolished all phosphorylations, except Syk pY352. Btk inhibition by acalabrutinib strongly decreased Btk pY223/pS180, Syk pS297, PLCγ2 pY759/Y1217, MEK1/2 pS217/221, Erk1/2 pT202/Y204, p38 pT180/Y182, and Akt pT308/S473. PKC inhibition by GF109203X abolished most pS/T phosphorylations except p38 pT180/Y182 and Akt pT308, but enhanced most Y-phosphorylations. Acalabrutinib, but not GF109203X, suppressed convulxin-induced intracellular Ca2+ mobilization, whereas all three protein kinase inhibitors abolished degranulation and αIIbβ3 integrin activation assessed by flow cytometry. Inhibition of autocrine ADP effects by AR-C669931 partly diminished convulxin-triggered degranulation.

Conclusion Kinetic analysis of GPVI-initiated multisite protein phosphorylation in human platelets demonstrates multiple phases and interactions of tyrosine and serine/threonine kinases with activation-altering feedforward and feedback loops partly involving PKC. The protein kinase inhibitor effects on multisite protein phosphorylation and functional readouts reveal that the signaling network of Syk, Btk, and PKC controls platelet granule exocytosis and αIIbβ3 integrin activation.
Contemporary Management of Pulmonary Embolism: Review of the Inferior Vena Cava ﬁlter and Other Endovascular Devices
Authors: Lei KaChon , DiCaro Michael V. , Tak Nadia , Turnbull Scott , Abdallah Ala , Cyrus Tillman , Tak Tahir
Published: April 2024

Inferior vena cava (IVC) filters and endovascular devices are used to mitigate the risk of pulmonary embolism in patients presenting with lower extremity venous thromboembolism in whom long-term anticoagulation is not a good option. However, the efficacy and beneﬁt of these devices remain uncertain, and controversies exist. This review focuses on the current use of IVC ﬁlters and other endovascular therapies in clinical practice. The indications, risks, and beneﬁts are discussed based on current data. Further research and randomized controlled trials are needed to characterize the patient population that would beneﬁt most from these interventional therapies.