bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying Low-keV Beam Damage in Ultrathin MFI Zeolite Nanosheets with an SEM
Authors: Holm Jason 
Published: January 2023

Abstract
This manuscript demonstrates the susceptibility of ultrathin Mobil Five (MFI) zeolite nanosheets to low-keV electron beam damage in a scanning electron microscope (SEM). Beam dose rates and characteristic beam doses are quantified at beam energies from 15 to 30 keV using an on-axis transmission electron detector to measure signal decay times in diffraction patterns and by underfocusing to enable spot size measurement. Characteristic beam doses ranged from approximately 1.9 C/cm2 at 15 keV to 14 C/cm2 at 30 keV, and the damage mechanism was attributable to radiolysis but other processes including electrostatic charging and sputtering could not be ruled out.
Atomic-Scale Determination of Cation and Magnetic Order in the Triple Perovskite Sr3Fe2ReO9
Authors: Ho Ping-Luen , Huang Zhihao , Jin Lei , Choi Si-Young , Dunin-Borkowski Rafal E , Mayer Joachim , Tsang Shik Chi Edman , Zhong Xiaoyan 
Published: January 2023

Abstract
Pseudo-cubic (pc) perovskite oxides (ABO3) that can have different magnetic cations with different types and degrees of order at B sites have attracted considerable interest as a result of their tunable magnetic properties. Nanoscale inhomogeneity in cation order on the B sites can lead to different magnetic ground states and electronic band structures in local sample regions. Here, we determine cation order on the atomic scale in a nanosized Sr3Fe2ReO9 phase that has a 1:2 B-site-ordered triple perovskite structure using aberration-corrected analytical transmission electron microscopy (TEM), revealing that the Fe and Re cations form tripled-layered repeats with –[Fe–Fe–Re]n– sequences along [111]pc and an ordering vector of 1/3[111]*. To the best of our knowledge, this 1:2 B-site-ordered triple perovskite Sr3Fe2ReO9 phase has not been reported before. Based on a relaxed theoretical model that is consistent with the experimental images, density functional theory calculations are performed to determine the magnetic ground states and exchange parameters of the newly discovered Sr3Fe2ReO9 phase, in which nearest-neighbour Fe and Re cations are coupled antiferromagnetically. This combination of aberration-corrected analytical TEM and ab initio calculations provides physical insight into cation order and magnetic coupling in perovskite oxides at the atomic level.
Large-Area and High-Precision Milling of Focused Ion Beam Based on the Integration of Nanoscale Machine Vision and Compensation Control
Authors: Guo Dengji , Fan Shihao , Yang Yandong , Chen Zhang , Huang Haijun , Wen Pinjin , Lin Jianjun , Liu Yuhang , Xu Jiao , Wang Xujin 
Published: January 2023

Abstract
Focused ion beam (FIB) is a high-precision technology for micro/nanofabrication that can be used to fabricate micro/nanoscale structures and electronic devices, such as waveguide gratings, resonators, and photonic crystals. In this study, a novel FIB processing system was developed using machine vision coupled with a piezoelectric motor, which compensates the process periodically and automatically. The FIB system is controlled by a computer program that enables automatic processing, automatic recognition, and provides feedback to control the movement of the stage. The results show that ring arrays with a diameter of 2 μm can be detected automatically under the field of view (FOV) of 114 × 114 μm2 with relative errors of less than 6%. The FOV can be larger than 400 × 400 μm2 after the splicing function of automatic compensation control is applied to the same ring arrays. Structurally, the average splicing errors in the X- and Y-directions decreased one order of magnitude, which are from 1.49 to 0.15 μm and 1.47 to 0.37 μm, respectively. This paves the way for the mass production of nanoholes in a large area with high precision and high speed for semiconductor manufacturing and research.
Multimodal STEM Investigation of Polymer Damage Processes Induced by Electron Beam Irradiation
Authors: Lescott Chamille , Bobbala Sharan , Modak Mallika , dos Reis Roberto , Scott Evan A , Dravid Vinayak P 
Published: January 2023

Abstract
Self-assembled polymer nanostructures are useful for many applications, including biomedicine, energy, and sensing, often presenting a more stable and customizable alternative for drug delivery than lipid-based assemblies, like liposomes. Polyethylene glycol-b-poly(propylene sulfide) (PEG-b-PPS) nanostructures are an example of a cutting-edge self-assembled polymer system. Here, to better understand the impact of electron irradiation on the molecular and macroscale structure, we utilize analytical scanning transmission electron microscopy. Through electron energy-loss spectroscopy (EELS), we access information regarding the degradation of PEG-b-PPS self-assembled polymers under the electron beam. By coupling the spatial and temporal resolution afforded by EELS, we describe the movement of elements in the polymer system during radiolysis and propose a mechanism for sample degradation. We believe this work will serve as a blueprint to determine the effects of electron irradiation on polymer architectures via spectroscopy.
Statistical Determination of Atomic-Scale Characteristics of Au Nanocrystals Based on Correlative Multiscale Transmission Electron Microscopy
Authors: Neumann Stefan , Rezvani Azita , Barasinski Matthäus , Garnweitner Georg , Segets Doris , Rafaja David 
Published: January 2023

Abstract
Atomic-scale characteristics of individual nanocrystals (NCs), such as the crystallographic orientation of their facets and the kind and density of crystal structure defects, play a tremendous role for the functionality and performance of the whole NC population. However, these features are usually quantified only for a small number of individual particles, and thus with limited statistical relevance. In the present work, we developed the multiscale approach available in transmission electron microscopy (TEM) further, and applied it to describe features of different types of Au NCs in a statistical and scale-bridging manner. This approach combines high-resolution TEM, which is capable of describing the characteristics of NCs on atomic scale, with a semi-automatic analysis of low-magnification high-angle annular dark-field scanning TEM images, which reveals the nanoscopic morphological attributes of NCs with good statistics. The results of these complementary techniques are combined and correlated. The potential of this multiscale approach is illustrated on two examples. In the first one, the habitus of Au NCs was classified and assigned to multiply twinned nanoparticles and nanoplates. These classes were quantified and related to different stacking fault densities. The second example demonstrates the statistical determination of crystallographic orientations and configurations of facets in Au nanorods.
Biomimetic Mineralization of Ca-Mg Carbonates: Relevance to Microbial Cells and Extracellular Polymeric Substances
Authors: Zhang Chonghong , Li Fuchun , Lyu Jiejie , Yao Youru 
Published: January 2023

AbstractResearch on Ca-Mg carbonate crystallization and phase transition regulated by microbial cells and extracellular polymeric substances (EPS) is significant for carbon sequestration, remediation of polluted soil and water, and synthesis of functional biomaterials. This study focused on the mineralogical transformation from amorphism to crystal, and interaction among cells, EPS, and minerals. By tracing the law of mineral growth and morphological evolution, the influences of cells and EPS on mineral formation were investigated. The results revealed that calcification and the template of rod-shaped cells of strain HJ-1 were the basis for the formation of dumbbell-shaped particles, and directional aggregation and differential growth were the keys to the development and stability of dumbbells. Cell participation had a noticeable impact on mineral prototypes, instead of determining the polymorphism. EPS contributed to aragonite formation and stability. The acidic amino acids or proteins in EPS were likely to cause an increase in MgCO3 content in Mg-calcite. EPS promoted aggregation of particles and induced spherical formation. Exopolysaccharides and proteins were the main components of EPS that can affect carbonate mineralization. EPS could influence the morphology and polymorphism by providing nucleation sites, interacting with Mg2+, adsorbing or incorporating mineral lattices, and inducing particle aggregation.
Ameliorated Renal Pathological Feature in MRL/MpJ-Faslpr/lprBackground Interleukin-36 Receptor-Deficient Mice
Authors: Namba Takashi , Ichii Osamu , Okamura Tadashi , Nakano Kenta , Nakamura Teppei , Otani Yuki , Kon Yasuhiro 
Published: January 2023

AbstractSystemic autoimmune diseases frequently induce lupus nephritis, causing altered balance and expression of interleukin 36 receptor (IL-36R) ligands, including agonists (IL-36α, β, γ) and antagonists (IL-36Ra, IL-38), in kidneys. Here, we established and analyzed a mouse model of lupus nephritis, MRL/MpJ-Faslpr/lpr with IL-36R-knockout (KO), compared to wild-type (WT) mice. In both genotypes, indices for immune abnormalities and renal functions were comparable, although female WT mice showed higher serum autoantibody levels than males. IL-36R ligand expression did not differ significantly between genotypes at the mRNA level or in IL-36α and IL-38 scores. However, glomerular lesions, especially mesangial matrix expansion, were significantly ameliorated in both sexes of IL-36R-KO mice compared to WT mice. Cell infiltration into the tubulointerstitium with the development of tertiary lymphoid structures was comparable between genotypes. However, the positive correlation with the IL-36α score in WT mice was not evident in IL-36R-KO mice. Fibrosis was less in female IL-36R-KO mice than in WT mice. Importantly, some IL-36α+ nuclei co-localized with acetylated lysine and GCN5 histone acetyltransferase, in both genotypes. Therefore, IL-36R ligands, especially IL-36α, contribute to the progression of renal pathology in lupus nephritis via IL-36R-dependent and IL-36R-independent pathways.
Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome
Authors: Nissley Amos J , Penev Petar I , Watson Zoe L , Banfield Jillian F , Cate Jamie H D 
Published: January 2023

AbstractThe ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3′-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.
Cold-induced inhibition of photosynthesis-related genes integrated by a TOP6 complex in rice mesophyll cells
Authors: Xu Zhan , Zhang Jianxiang , Wang Xu , Essemine Jemaa , Jin Jing , Qu Mingnan , Xiang Yong , Chen Weixiong 
Published: January 2023

AbstractPhotosynthesis is the most temperature-sensitive process in the plant kingdom, but how the photosynthetic pathway responds during low-temperature exposure remains unclear. Herein, cold stress (4°C) induced widespread damage in the form DNA double-stranded breaks (DSBs) in the mesophyll cells of rice (Oryza sativa), subsequently causing a global inhibition of photosynthetic carbon metabolism (PCM) gene expression. Topoisomerase genes TOP6A3 and TOP6B were induced at 4°C and their encoded proteins formed a complex in the nucleus. TOP6A3 directly interacted with KU70 to inhibit its binding to cold-induced DSBs, which was facilitated by TOP6B, finally blocking the loading of LIG4, a component of the classic non-homologous end joining (c-NHEJ) pathway. The repression of c-NHEJ repair imposed by cold extended DSB damage signaling, thus prolonging the inhibition of photosynthesis in leaves. Furthermore, the TOP6 complex negatively regulated 13 crucial PCM genes by directly binding to their proximal promoter regions. Phenotypically, TOP6A3 overexpression exacerbated the γ-irradiation-triggered suppression of PCM genes and led to the hypersensitivity of photosynthesis parameters to cold stress, dependent on the DSB signal transducer ATM. Globally, the TOP6 complex acts as a signal integrator to control PCM gene expression and synchronize cold-induced photosynthesis inhibition, which modulates carbon assimilation rates immediately in response to changes in ambient temperature.
Impact of different immunosuppressive protocols on clinical outcomes in obese kidney transplant recipients: a propensity score–matched analysis
Authors: Serna-Higuita Lina Maria , Della Penna Andrea , Guthoff Martina , Heyne Nils , Beer-Hammer Sandra , Nadalin Silvio , Martus Peter , Königsrainer Alfred , Quante Markus 
Published: January 2023

ABSTRACT

Background
Although obesity has become a significant problem in transplantation medicine, the impact of different immunosuppressive protocols on clinical outcomes in obese transplant recipients remains unclear.

Methods
We performed an analysis of the Scientific Registry of Transplant Recipients database. Kidney transplant recipients were categorized according to body mass index (BMI) categories and immunosuppressive protocols: (i) tacrolimus/mycophenolate mofetil (Tac-MMF), (ii) mTOR-inhibitor/Tac (mTORi-Tac), (iii) mTORi/cyclosporin (mTORi-Cyc) and (iv) mTORi-MMF.

Results
Graft recipients with advanced obesity (BMI ≥35 kg/m2) exhibited significantly lower rates of acute rejection during the first year after transplantation in the mTORi-Tac (6.4%) group compared with Tac-MMF (11.2%). Obesity class 1 (30 &lt; BMI &lt; 35 kg/m2) was associated with a significant risk of acute rejection for the mTORi-Tac group [obesity class 1 hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.21–2.62, P = .003]. A similar trend was observed in the Tac-MMF group for advanced obesity HR 1.29; 95% CI 0.96–1.73, P = .087). For the Tac-MMF group, recipients with both overweight and obesity had significantly impaired survival due to cardiovascular events and also increased mortality due to infection in advanced obesity. Combination of mTORi and calcineurin inhibitor was associated with lower rejection rates and stable long-term kidney function while reducing cardiovascular side effects linked to calcineurin inhibitors in obese kidney graft recipients.

Conclusion
These results are critical for the growing number of obese graft recipients and warrant prospective evaluation.
Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics
Authors: Kim Tae-Wuk , Park Chan Ho , Hsu Chuan-Chih , Kim Yeong-Woo , Ko Yeong-Woo , Zhang Zhenzhen , Zhu Jia-Ying , Hsiao Yu-Chun , Branon Tess , Kaasik Krista , Saldivar Evan , Li Kevin , Pasha Asher , Provart Nicholas J , Burlingame Alma L , Xu Shou-Ling , Ting Alice Y , Wang Zhi-Yong 
Published: January 2023

Abstract
Elucidating enzyme–substrate relationships in posttranslational modification (PTM) networks is crucial for understanding signal transduction pathways but is technically difficult because enzyme–substrate interactions tend to be transient. Here, we demonstrate that TurboID-based proximity labeling (TbPL) effectively and specifically captures the substrates of kinases and phosphatases. TbPL-mass spectrometry (TbPL-MS) identified over 400 proximal proteins of Arabidopsis thaliana BRASSINOSTEROID-INSENSITIVE2 (BIN2), a member of the GLYCOGEN SYNTHASE KINASE 3 (GSK3) family that integrates signaling pathways controlling diverse developmental and acclimation processes. A large portion of the BIN2-proximal proteins showed BIN2-dependent phosphorylation in vivo or in vitro, suggesting that these are BIN2 substrates. Protein–protein interaction network analysis showed that the BIN2-proximal proteins include interactors of BIN2 substrates, revealing a high level of interactions among the BIN2-proximal proteins. Our proteomic analysis establishes the BIN2 signaling network and uncovers BIN2 functions in regulating key cellular processes such as transcription, RNA processing, translation initiation, vesicle trafficking, and cytoskeleton organization. We further discovered significant overlap between the GSK3 phosphorylome and the O-GlcNAcylome, suggesting an evolutionarily ancient relationship between GSK3 and the nutrient-sensing O-glycosylation pathway. Our work presents a powerful method for mapping PTM networks, a large dataset of GSK3 kinase substrates, and important insights into the signaling network that controls key cellular functions underlying plant growth and acclimation.
BASIC PENTACYSTEINE2 fine-tunes corm dormancy release inGladiolus
Authors: Li Jingru , Pan Wenqiang , Liang Jiahui , Liu Chang , Li Danqing , Yang Yingdong , Qu Lianwei , Gazzarrini Sonia , Yi Mingfang , Wu Jian 
Published: January 2023

AbstractBud dormancy is an important trait in geophytes that largely affects their flowering process and vegetative growth after dormancy release. Compared with seed dormancy, the regulation of bud dormancy is still largely unclear. Abscisic acid (ABA) acts as the predominant hormone that regulates the whole dormancy process. In Gladiolus (Gladiolus hybridus), cold storage promotes corm dormancy release (CDR) by repressing ABA biosynthesis and signaling. However, the mechanisms governing ABA-related processes during CDR via epigenetics are poorly understood. Here, we show that class I BASIC PENTACYSTEINE2, (GhBPC2) directly binds to 9-CIS-EPOXYCAROTENOID DIOXYGENASE (GhNCED) and ABA INSENSITIVE5 (GhABI5) loci and down-regulates their expression to accelerate CDR. During CDR, histone modifications change dramatically at the GhBPC2-binding loci of GhABI5 with an increase in H3K27me3 and a decrease in H3K4me3. GhBPC2 is involved in both H3K27me3 and H3K4me3 and fine-tunes GhABI5 expression by recruiting polycomb repressive complex 2 (PRC2) and the chromatin remodeling factor EARLY BOLTING IN SHORT DAYS (GhEBS). These results show GhBPC2 epigenetically regulates CDR in Gladiolus by mediating GhABI5 expression with PRC2 and GhEBS.
RORγt inhibition ameliorates IL-23 driven experimental psoriatic arthritis by predominantly modulating γδ-T cells
Authors: Mortier Céline , Gracey Eric , Coudenys Julie , Manuello Teddy , Decruy Tine , Maelegheer Margaux , Stappers Flore , Gilis Elisabeth , Gaublomme Djoere , Van Hoorebeke Luc , Van Welden Sophie , Ambler Catherine , Hegen Martin , Symanowicz Peter , Steyn Stefan , Berstein Gabriel , Elewaut Dirk , Venken Koen 
Published: January 2023

Abstract

Objective
Divergent therapeutic outcomes on different disease domains have been noted with IL-23 and IL-17A-blockade in PsA. Therefore, elucidating the role of RORγt, the master regulator of type 17 immune responses, is of potential therapeutic interest. To this end, RORγt inhibition was assessed in combined skin, joint and gut inflammation in vivo, using a PsA model.

Methods
We tested the efficacy of a RORγt antagonist in B10.RIII mice challenged with systemic overexpression of IL-23 by hydrodynamic injection of IL-23 enhanced episomal vector (IL-23 EEV). Clinical outcomes were evaluated by histopathology. Bone density and surface erosions were examined using micro-computed tomography. Cytokine production was measured in serum and by intracellular flow cytometry. Gene expression in PsA-related tissues was analysed by qPCR.

Results
RORγt-blockade significantly ameliorated psoriasis, peripheral arthritis and colitis development in IL-23 EEV mice (improvement of clinical scores and weight loss respectively by 91.8%, 58.2% and 7.0%, P &lt; 0.001), in line with profound suppression of an enhanced type IL-17 immune signature in PsA-affected tissues. Moreover, inflammation-induced bone loss and bone erosions were reduced (P &lt; 0.05 in calcaneus, P &lt; 0.01 in tibia). Sustained IL-23 overexpression resulted in only mild signs of sacroiliitis. Gamma-delta (γδ)-T cells, the dominant source of T cell-derived IL-17A and IL-22, were expanded during IL-23 overexpression, and together with Th17 cells, clearly countered by RORγt inhibition (P &lt; 0.001).

Conclusion
RORγt-blockade shows therapeutic efficacy in a preclinical PsA model with protection towards extra-musculoskeletal manifestations, reflected by a clear attenuation of type 17 cytokine responses by γδ-T cells and Th17 cells.
A new entity in the NARS2 variant: the first reported case of type 1 diabetes mellitus associated with the phenotype
Authors: Cokyaman Turgay , Cetin Huriye , Dogan Durmus , Silan Fatma 
Published: January 2023

Abstract
NARS2 mutations are known to cause various clinical phenotypes such as nonsyndromic hearing loss, Leigh/Alpers syndrome, refractory epilepsy, developmental delay, intellectual disability and myopathy. We presented the first Turkish variant of NASR2 and added type 1 diabetes mellitus (DM), which was not previously described in the phenotype spectrum of this disease. A 4.5-month-old girl presented with hearing loss, hypotonia, refractory myoclonic epilepsy, severe developmental delay and large subdural hemorrhage. In the first year of the follow-up, type 1 DM developed. A homozygous missense mutation, [c.500 A&gt;G, p.H167R] in the NARS2 gene was detected in the trio-based whole-exome sequencing (WES). In this disease, in addition to multi-organ involvement, type 1 DM may also develop, as in our case. Since it is a mitochondrial disease, the decision to treat with valproic acid should be reconsidered. The long diagnostic process can be shortened with WES.