bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic DNA-based measurable residual disease monitoring in pediatric acute myeloid leukemia: unselected consecutive cohort study
Authors: Zaliova Marketa , Zuna Jan , Winkowska Lucie , Janotova Iveta , Skorepova Justina , Lukes Julius , Meyer Claus , Marschalek Rolf , Novak Zbynek , Domansky Jiri , Stary Jan , Sramkova Lucie , Trka Jan 
Published: November 2023

AbstractMeasurable residual disease (MRD) monitoring in childhood acute myeloid leukemia (AML) is used to assess response to treatment and for early detection of imminent relapse. In childhood AML, MRD is typically evaluated using flow cytometry, or by quantitative detection of leukemia-specific aberrations at the mRNA level. Both methods, however, have significant limitations. Recently, we demonstrated the feasibility of MRD monitoring in selected subgroups of AML at the genomic DNA (gDNA) level. To evaluate the potential of gDNA-based MRD monitoring across all AML subtypes, we conducted a comprehensive analysis involving 133 consecutively diagnosed children. Integrating next-generation sequencing into the diagnostic process, we identified (presumed) primary genetic aberrations suitable as MRD targets in 97% of patients. We developed patient-specific quantification assays and monitored MRD in 122 children. The gDNA-based MRD monitoring via quantification of primary aberrations with a sensitivity of at least 10−4 was possible in 86% of patients; via quantification with sensitivity of 5 × 10−4, of secondary aberrations, or at the mRNA level in an additional 8%. Importantly, gDNA-based MRD exhibited independent prognostic value at early time-points in patients stratified to intermediate-/high-risk treatment arms. Our study demonstrates the broad applicability, feasibility, and clinical significance of gDNA-based MRD monitoring in childhood AML.
Wavefront control of subcycle vortex pulses via carrier-envelope-phase tailoring
Authors: Lin Yu-Chieh , Midorikawa Katsumi , Nabekawa Yasuo 
Published: November 2023

AbstractThe carrier-envelope phase (CEP) of an ultrashort laser pulse is becoming more crucial to specify the temporal characteristic of the pulse’s electric field when the pulse duration becomes shorter and attains the subcycle regime; here, the pulse duration of the intensity envelope is shorter than one cycle period of the carrier field oscillation. When this subcycle pulse involves a structured wavefront as is contained in an optical vortex (OV) pulse, the CEP has an impact on not only the temporal but also the spatial characteristics owing to the spatiotemporal coupling in the structured optical pulse. However, the direct observation of the spatial effect of the CEP control has not yet been demonstrated. In this study, we report on the measurement and control of the spatial wavefront of a subcycle OV pulse by adjusting the CEP. To generate subcycle OV pulses, an optical parametric amplifier delivering subcycle Gaussian pulses and a Sagnac interferometer as a mode converter were integrated and provided an adequate spectral adaptability. The pulse duration of the generated OV pulse was 4.7 fs at a carrier wavelength of 1.54 µm. To confirm the wavefront control with the alteration of the CEP, we developed a novel $$f$$
f
-2$$f$$
f
interferometer that exhibited spiral fringes originating from the spatial interference between the subcycle OV pulse and the second harmonic of the subcycle Gaussian pulse producing a parabolic wavefront as a reference; this resulted in the successful observation of the rotation of spiral interference fringes during CEP manipulation.
Antisecretory factor in breastmilk is associated with reduced incidence of sepsis in preterm infants
Authors: Gustafsson Anna , Johansson Ewa , Henckel Ewa , Olin Axel , Rodriguez Lucie , Brodin Petter , Lange Stefan , Bohlin Kajsa 
Published: November 2023

Abstract
Background
Antisecretory Factor (AF) is a protein present in breastmilk that regulates inflammatory processes. We aimed to investigate the level of AF in mothers’ own milk (MOM) in relation to sepsis and other neonatal morbidities in preterm infants.

Methods
Samples of breastmilk and infant plasma were collected at 1, 4, and 12 weeks after birth from 38 mothers and their 49 infants born before 30 weeks gestation. AF-compleasome in MOM was determined by a sandwich enzyme-linked immunosorbent assay (ELISA) and inflammatory markers in infant plasma by a panel of 92 inflammatory proteins. Neonatal treatments and outcomes were recorded.

Results
The level of AF in MOM week 1 was lower for infants with later sepsis compared to no sepsis (p = 0.005). Corrected for nutritional intake of MOM, higher levels of AF decreased the risk for sepsis, OR 0.24. AF in MOM week 1 was negatively correlated to inflammatory proteins in infant plasma week 4, markedly IL-8, which was also associated with infant sepsis. Overall, higher AF levels in MOM was associated with fewer major morbidities of prematurity.

Conclusion
Mother’s milk containing high levels of antisecretory factor is associated with reduced risk for sepsis and inflammation in preterm infants.

Impact

High level of antisecretory factor (AF) in mothers’ own milk is associated with less risk for later sepsis in preterm infants.

Receiving mothers’ milk with low AF levels during the first week after birth is correlated with more inflammatory proteins in infant’s plasma 2–4 weeks later.

Human breastmilk has anti-inflammatory properties, and antisecretory factor in mothers’ own milk is a component of potential importance for infants born preterm.

The findings suggest that food supplementation with AF to mothers of preterm infants to increase AF-levels in breastmilk may be a means to decrease the risk of inflammatory morbidities of prematurity.
3D-printed TCP-HA scaffolds delivering MicroRNA-302a-3p improve bone regeneration in a mouse calvarial model
Authors: Limlawan Pirawish , Insin Numpon , Marger Laurine , Freudenreich Mélanie , Durual Stéphane , Vacharaksa Anjalee 
Published: November 2023

Abstract
Objective
To demonstrate hydroxyapatite nanoparticles modified with cationic functional molecules. 3-aminopropyltriethoxysilane (HA-NPs-APTES) carrying microRNA-302a-3p (miR) in the 3D-printed tricalcium phosphate/Hydroxyapatite (TCP/HA) scaffold can increase healing of the critical-sized bone defect.

Materials and methods
3D-printed TCP/HA were modified with HA-NPs-APTES by two methods (M1, M2). The dispersion of particles was visualized by fluorescent microscopy. Biocompatibility of the scaffolds was tested by alizarin assay. Delivery of miR to the cells and osteogenic gene expression were evaluated by qPCR. After selecting best method (M2), scaffolds, scaffolds+HA-NPs-APTES with or without miR were implanted in 4 mm mouse calvarium defect (n = 4 per group). After 2,4 and 6 weeks, bone regeneration were evaluated by microCT and histology sections.

Results
Both M1 and M2 scaffolds were biocompatible with cell adhesion on its surface. M2 scaffold showed significant increase of miR, suggesting successful delivery, resulted in downregulation of its target mRNA COUP-TFII, and upregulation of RUNX2 mRNA. Calvarium defect with M2 scaffold also showed significantly higher BV/TV and higher number of filled spaces at all time points. Histomorphometry demonstrated new bone formed at the center of the HA-NPs-APTES-miR scaffold earlier than controls.

Conclusion
TCP/HA scaffold modified with HA-NPs-APTES facilitated delivery of miR and enhanced bone regeneration.
Izod impact resistance of 3D printed discontinuous fibrous composites with Bouligand structure
Authors: Guan Lizhi , Peng Weixiang , Wen Rachel Ng Jing , Fan Jingbo , Le Ferrand Hortense 
Published: November 2023

AbstractThe Bouligand structure found in the dactyl club of mantis shrimps is known for its impact resistance. However, Bouligand-inspired reinforced composites with 3D shapes and impact resistance characteristics have not yet been demonstrated. Herein, direct ink writing was used to 3D print composites reinforced with glass microfibers assembled into Bouligand structures with controllable pitch angles. The energy absorption levels of the Bouligand composites under impact were found to surpass those of composites with unidirectional microfiber alignment. Additionally, the Bouligand composites with a pitch angle of 40° exhibited a maximum energy absorption of 2.4 kJ/m2, which was 140% higher than that of the unidirectional composites. Furthermore, the characterization of the topography of the fractured surface, supplemented with numerical simulations, revealed a combination of crack twisting and crack bridging mechanisms. Flexural tests conducted on the composites with a pitch angle of 40° revealed that these composites had the strongest properties, including a flexural strength of 36.9 MPa, a stiffness of 2.26 GPa, and energy absorption of 8 kJ/m2. These findings are promising for the microstructural design of engineered composites using direct ink writing for applications in aerospace, transportation, and defense.
Paired single-cell multi-omics data integration with Mowgli
Authors: Huizing Geert-Jan , Deutschmann Ina Maria , Peyré Gabriel , Cantini Laura 
Published: November 2023

AbstractThe profiling of multiple molecular layers from the same set of cells has recently become possible. There is thus a growing need for multi-view learning methods able to jointly analyze these data. We here present Multi-Omics Wasserstein inteGrative anaLysIs (Mowgli), a novel method for the integration of paired multi-omics data with any type and number of omics. Of note, Mowgli combines integrative Nonnegative Matrix Factorization and Optimal Transport, enhancing at the same time the clustering performance and interpretability of integrative Nonnegative Matrix Factorization. We apply Mowgli to multiple paired single-cell multi-omics data profiled with 10X Multiome, CITE-seq, and TEA-seq. Our in-depth benchmark demonstrates that Mowgli’s performance is competitive with the state-of-the-art in cell clustering and superior to the state-of-the-art once considering biological interpretability. Mowgli is implemented as a Python package seamlessly integrated within the scverse ecosystem and it is available at http://github.com/cantinilab/mowgli.
The unusual quadruple bonding of nitrogen in ThN
Authors: Fei Zejie , Wang Jia-Qi , Tang Rulin , Lu Yuzhu , Han Changcai , Wang Yongtian , Hong Jing , Dong Changwu , Hu Han-Shi , Xiong Xiao-Gen , Ning Chuangang , Liu Hongtao , Li Jun 
Published: November 2023

AbstractNitrogen has five valence electrons and can form a maximum of three shared electron-pair bonds to complete its octet, which suggests that its maximum bond order is three. With a joint anion photoelectron spectroscopy and quantum chemistry investigation, we report herein that nitrogen presents a quadruple bonding interaction with thorium in ThN. The quadruple Th≣N bond consists of two electron-sharing Th-N π bonds formed between the Th-6dxz/6dyz and N 2px/2py orbitals, one dative Th←N σ bond and one weak Th←N σ bonding interaction formed between Th-6dz2 and N 2s/2pz orbitals. The ThC molecule has also been investigated and proven to have a similar bonding pattern as ThN. Nonetheless, due to one singly occupied σ-bond, ThC is assigned a bond order of 3.5. Moreover, ThC has a longer bond length as well as a lower vibrational frequency in comparison with ThN.
All electromagnetic scattering bodies are matrix-valued oscillators
Authors: Zhang Lang , Monticone Francesco , Miller Owen D. 
Published: November 2023

AbstractScattering theory is the basis of all linear optical and photonic devices, whose spectral response underpins wide-ranging applications from sensing to energy conversion. Unlike the Shannon theory for communication channels, or the Fano theory for electric circuits, understanding the limits of spectral wave scattering remains a notoriously challenging open problem. We introduce a mathematical scattering representation that inherently embeds fundamental principles of causality and passivity into its elemental degrees of freedom. We use this representation to reveal strong constraints in the mathematical structure of scattered fields, and to develop a general theory of the maximum radiative heat transfer in the near field, resolving a long-standing open question. Our approach can be seamlessly applied to high-interest applications across nanophotonics, and appears extensible to general classical and quantum scattering theory.
Autophagy drives the conversion of developmental neural stem cells to the adult quiescent state
Authors: Calatayud-Baselga Isabel , Casares-Crespo Lucía , Franch-Ibáñez Carmina , Guijarro-Nuez José , Sanz Pascual , Mira Helena 
Published: November 2023

AbstractNeurogenesis in the adult mammalian brain relies on the lifelong persistence of quiescent neural stem cell (NSC) reservoirs. Little is known about the mechanisms that lead to the initial establishment of quiescence, the main hallmark of adult stem cells, during development. Here we show that protein aggregates and autophagy machinery components accumulate in developmental radial glia-like NSCs as they enter quiescence and that pharmacological or genetic blockade of autophagy disrupts quiescence acquisition and maintenance. Conversely, increasing autophagy through AMPK/ULK1 activation instructs the acquisition of the quiescent state without affecting BMP signaling, a gatekeeper of NSC quiescence during adulthood. Selective ablation of Atg7, a critical gene for autophagosome formation, in radial glia-like NSCs at early and late postnatal stages compromises the initial acquisition and maintenance of quiescence during the formation of the hippocampal dentate gyrus NSC niche. Therefore, we demonstrate that autophagy is cell-intrinsically required to establish NSC quiescence during hippocampal development. Our results uncover an important role of autophagy in the transition of developmental NSCs into their dormant adult form, paving the way for studies directed at further understanding the mechanisms of stem cell niche formation and maintenance in the mammalian brain.
Cu-mediated enantioselective C–H alkynylation of ferrocenes with chiral BINOL ligands
Authors: Kuang Xin , Li Jian-Jun , Liu Tao , Ding Chang-Hua , Wu Kevin , Wang Peng , Yu Jin-Quan 
Published: November 2023

AbstractA wide range of Cu(II)-catalyzed C–H activation reactions have been realized since 2006, however, whether a C–H metalation mechanism similar to Pd(II)-catalyzed C–H activation reaction is operating remains an open question. To address this question and ultimately develop ligand accelerated Cu(II)-catalyzed C–H activation reactions, realizing the enantioselective version and investigating the mechanism is critically important. With a modified chiral BINOL ligand, we report the first example of Cu-mediated enantioselective C–H activation reaction for the construction of planar chiral ferrocenes with high yields and stereoinduction. The key to the success of this reaction is the discovery of a ligand acceleration effect with the BINOL-based diol ligand in the directed Cu-catalyzed C–H alkynylation of ferrocene derivatives bearing an oxazoline-aniline directing group. This transformation is compatible with terminal aryl and alkyl alkynes, which are incompatible with Pd-catalyzed C–H activation reactions. This finding provides an invaluable mechanistic information in determining whether Cu(II) cleaves C–H bonds via CMD pathway in analogous manner to Pd(II) catalysts.
Extent of carbon nitride photocharging controls energetics of hydrogen transfer in photochemical cascade processes
Authors: Savateev Oleksandr , Nolkemper Karlo , Kühne Thomas D. , Shvalagin Vitaliy , Markushyna Yevheniia , Antonietti Markus 
Published: November 2023

AbstractGraphitic carbon nitride is widely studied in organic photoredox catalysis. Reductive quenching of carbon nitride excited state is postulated in many photocatalytic transformations. However, the reactivity of this species in the turn over step is less explored. In this work, we investigate electron and proton transfer from carbon nitride that is photocharged to a various extent, while the negative charge is compensated either by protons or ammonium cations. Strong stabilization of electrons by ammonium cations makes proton-coupled electron transfer uphill, and affords air-stable persistent carbon nitride radicals. In carbon nitrides, which are photocharged to a smaller extent, protons do not stabilize electrons, which results in spontaneous charge transfer to oxidants. Facile proton-coupled electron transfer is a key step in the photocatalytic oxidative-reductive cascade – tetramerization of benzylic amines. The feasibility of proton-coupled electron transfer is modulated by adjusting the extent of carbon nitride photocharging, type of counterion and temperature.
The genomic epidemiology of shigellosis in South Africa
Authors: Stenhouse George E. , Keddy Karen H. , Bengtsson Rebecca J. , Hall Neil , Smith Anthony M. , Thomas Juno , Iturriza-Gómara Miren , Baker Kate S. 
Published: November 2023

AbstractShigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.
Stepwise differentiation of follicular helper T cells reveals distinct developmental and functional states
Authors: Podestà Manuel A. , Cavazzoni Cecilia B. , Hanson Benjamin L. , Bechu Elsa D. , Ralli Garyfallia , Clement Rachel L. , Zhang Hengcheng , Chandrakar Pragya , Lee Jeong-Mi , Reyes-Robles Tamara , Abdi Reza , Diallo Alos , Sen Debattama R. , Sage Peter T. 
Published: November 2023

AbstractFollicular helper T (Tfh) cells are essential for the formation of high affinity antibodies after vaccination or infection. Although the signals responsible for initiating Tfh differentiation from naïve T cells have been studied, the signals controlling sequential developmental stages culminating in optimal effector function are not well understood. Here we use fate mapping strategies for the cytokine IL-21 to uncover sequential developmental stages of Tfh differentiation including a progenitor-like stage, a fully developed effector stage and a post-effector Tfh stage that maintains transcriptional and epigenetic features without IL-21 production. We find that progression through these stages are controlled intrinsically by the transcription factor FoxP1 and extrinsically by follicular regulatory T cells. Through selective deletion of Tfh stages, we show that these cells control antibody dynamics during distinct stages of the germinal center reaction in response to a SARS-CoV-2 vaccine. Together, these studies demonstrate the sequential phases of Tfh development and how they promote humoral immunity.
Occlusive membranes for guided regeneration of inflamed tissue defects
Authors: Choi Woojin , Mangal Utkarsh , Park Jin-Young , Kim Ji-Yeong , Jun Taesuk , Jung Ju Won , Choi Moonhyun , Jung Sungwon , Lee Milae , Na Ji-Yeong , Ryu Du Yeol , Kim Jin Man , Kwon Jae-Sung , Koh Won-Gun , Lee Sangmin , Hwang Patrick T. J. , Lee Kee-Joon , Jung Ui-Won , Cha Jae-Kook , Choi Sung-Hwan , Hong Jinkee 
Published: November 2023

AbstractGuided bone regeneration aided by the application of occlusive membranes is a promising therapy for diverse inflammatory periodontal diseases. Symbiosis, homeostasis between the host microbiome and cells, occurs in the oral environment under normal, but not pathologic, conditions. Here, we develop a symbiotically integrating occlusive membrane by mimicking the tooth enamel growth or multiple nucleation biomineralization processes. We perform human saliva and in vivo canine experiments to confirm that the symbiotically integrating occlusive membrane induces a symbiotic healing environment. Moreover, we show that the membrane exhibits tractability and enzymatic stability, maintaining the healing space during the entire guided bone regeneration therapy period. We apply the symbiotically integrating occlusive membrane to treat inflammatory-challenged cases in vivo, namely, the open and closed healing of canine premolars with severe periodontitis. We find that the membrane promotes symbiosis, prevents negative inflammatory responses, and improves cellular integration. Finally, we show that guided bone regeneration therapy with the symbiotically integrating occlusive membrane achieves fast healing of gingival soft tissue and alveolar bone.
Autonomous nanorobots with powerful thrust under dry solid-contact conditions by photothermal shock
Authors: Gu Zhaoqi , Zhu Runlin , Shen Tianci , Dou Lin , Liu Hongjiang , Liu Yifei , Liu Xu , Liu Jia , Zhuang Songlin , Gu Fuxing 
Published: November 2023

AbstractNanorobotic motion on solid substrates is greatly hindered by strong nanofriction, and powerful nanomotors‒the core components for nanorobotic motion‒are still lacking. Optical actuation addresses power and motion control issues simultaneously, while conventional technologies with small thrust usually apply to fluid environments. Here, we demonstrate micronewton-thrust nanomotors that enable the autonomous nanorobots working like conventional robots with precise motion control on dry surfaces by a photothermal-shock technique. We build a pulsed laser-based actuation and trapping platform, termed photothermal-shock tweezers, for general motion control of metallic nanomaterials and assembled nanorobots with nanoscale precision. The thrust-to-weight ratios up to 107 enable nanomotors output forces to interact with external micro/nano-objects. Leveraging machine vision and deep learning technologies, we assemble the nanomotors into autonomous nanorobots with complex structures, and demonstrate multi-degree-of-freedom motion and sophisticated functions. Our photothermal shock-actuation concept fundamentally addresses the nanotribology challenges and expands the nanorobotic horizon from fluids to dry solid surfaces.