bluuebunny/crossref_metadata_2025 huggingface dataset:
Revealing the tissue-level complexity of endogenous glucagon-like peptide-1 receptor expression and signaling
Authors: Ast Julia , Nasteska Daniela , Fine Nicholas H. F. , Nieves Daniel J. , Koszegi Zsombor , Lanoiselée Yann , Cuozzo Federica , Viloria Katrina , Bacon Andrea , Luu Nguyet T. , Newsome Philip N. , Calebiro Davide , Owen Dylan M. , Broichhagen Johannes , Hodson David J.
Published: January 2023

The glucagon-like peptide-1 receptor (GLP1R) is a class B G protein-coupled receptor (GPCR) involved in glucose homeostasis and food intake. GLP1R agonists (GLP1RA) are widely used in the treatment of diabetes and obesity, yet visualizing the endogenous localization, organization and dynamics of a GPCR has so far remained out of reach. In the present study, we generate mice harboring an enzyme self-label genome-edited into the endogenous Glp1r locus. We also rationally design and test various fluorescent dyes, spanning cyan to far-red wavelengths, for labeling performance in tissue. By combining these technologies, we show that endogenous GLP1R can be specifically and sensitively detected in primary tissue using multiple colors. Longitudinal analysis of GLP1R dynamics reveals heterogeneous recruitment of neighboring cell subpopulations into signaling and trafficking, with differences observed between GLP1RA classes and dual agonists. At the nanoscopic level, GLP1Rs are found to possess higher organization, undergoing GLP1RA-dependent membrane diffusion. Together, these results show the utility of enzyme self-labels for visualization and interrogation of endogenous proteins, and provide insight into the biology of a class B GPCR in primary cells and tissue.
Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma
Authors: Ferguson L. Paige , Gatchalian Jovylyn , McDermott Matthew L. , Nakamura Mari , Chambers Kendall , Rajbhandari Nirakar , Lytle Nikki K. , Rosenthal Sara Brin , Hamilton Michael , Albini Sonia , Wartenberg Martin , Zlobec Inti , Galván José A. , Karamitopoulou Eva , Vavinskaya Vera , Wascher Alexis , Lowy Andrew M. , Schürch Christian M. , Puri Pier Lorenzo , Bruneau Benoit G. , Hargreaves Diana C. , Reya Tannishtha
Published: January 2023

Pancreatic cancer is characterized by extensive resistance to conventional therapies, making clinical management a challenge. Here we map the epigenetic dependencies of cancer stem cells, cells that preferentially evade therapy and drive progression, and identify SWI/SNF complex member SMARCD3 as a regulator of pancreatic cancer cells. Although SWI/SNF subunits often act as tumor suppressors, we show that SMARCD3 is amplified in cancer, enriched in pancreatic cancer stem cells and upregulated in the human disease. Diverse genetic mouse models of pancreatic cancer and stage-specific Smarcd3 deletion reveal that Smarcd3 loss preferentially impacts established tumors, improving survival especially in context of chemotherapy. Mechanistically, SMARCD3 acts with FOXA1 to control lipid and fatty acid metabolism, programs associated with therapy resistance and poor prognosis in cancer. These data identify SMARCD3 as an epigenetic modulator responsible for establishing the metabolic landscape in aggressive pancreatic cancer cells and a potential target for new therapies.
Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration
Authors: Pascual-Carreras Eudald , Marín-Barba Marta , Castillo-Lara Sergio , Coronel-Córdoba Pablo , Magri Marta Silvia , Wheeler Grant N. , Gómez-Skarmeta Jose Luis , Abril Josep F. , Saló Emili , Adell Teresa
Published: January 2023

For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process; the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the Wnt/β-catenin signal specifies anterior versus posterior identity. Initially, bothwnt1andnotum(Wnt inhibitor) are expressed in all wounds, but 48 hours later they are restricted to posterior or anterior facing wounds, respectively, by an unknown mechanism. Here we show that 12 hours after amputation, the chromatin accessibility of cells in the wound region changes according to the polarity of the pre-existing tissue in a Wnt/β-catenin-dependent manner. Genomic analyses suggest that homeobox transcription factors and chromatin-remodeling proteins are direct Wnt/β-catenin targets, which trigger the expression of posterior effectors. Finally, we identify FoxG as awnt1up-stream regulator, probably via binding to its first intron enhancer region.
Construction of angstrom-scale ion channels with versatile pore configurations and sizes by metal-organic frameworks
Authors: Li Xingya , Jiang Gengping , Jian Meipeng , Zhao Chen , Hou Jue , Thornton Aaron W. , Zhang Xinyi , Liu Jefferson Zhe , Freeman Benny D. , Wang Huanting , Jiang Lei , Zhang Huacheng
Published: January 2023

Controllable fabrication of angstrom-size channels has been long desired to mimic biological ion channels for the fundamental study of ion transport. Here we report a strategy for fabricating angstrom-scale ion channels with one-dimensional (1D) to three-dimensional (3D) pore structures by the growth of metal-organic frameworks (MOFs) into nanochannels. The 1D MIL-53 channels of flexible pore sizes around 5.2 × 8.9 Å can transport cations rapidly, with one to two orders of magnitude higher conductivities and mobilities than MOF channels of hybrid pore configurations and sizes, including Al-TCPP with 1D ~8 Å channels connected by 2D ~6 Å interlayers, and 3D UiO-66 channels of ~6 Å windows and 9 − 12 Å cavities. Furthermore, the 3D MOF channels exhibit better ion sieving properties than those of 1D and 2D MOF channels. Theoretical simulations reveal that ion transport through 2D and 3D MOF channels should undergo multiple dehydration-rehydration processes, resulting in higher energy barriers than pure 1D channels. These findings offer a platform for studying ion transport properties at angstrom-scale confinement and provide guidelines for improving the efficiency of ionic separations and nanofluidics.
Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer
Authors: Couturier Agathe , Virolle Chloé , Goldlust Kelly , Berne-Dedieu Annick , Reuter Audrey , Nolivos Sophie , Yamaichi Yoshiharu , Bigot Sarah , Lesterlin Christian
Published: January 2023

Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.
Modern temperatures in central–north Greenland warmest in past millennium
Authors: Hörhold M. , Münch T. , Weißbach S. , Kipfstuhl S. , Freitag J. , Sasgen I. , Lohmann G. , Vinther B. , Laepple T.
Published: January 2023

The Greenland Ice Sheet has a central role in the global climate system owing to its size, radiative effects and freshwater storage, and as a potential tipping point1. Weather stations show that the coastal regions are warming2, but the imprint of global warming in the central part of the ice sheet is unclear, owing to missing long-term observations. Current ice-core-based temperature reconstructions3–5 are ambiguous with respect to isolating global warming signatures from natural variability, because they are too noisy and do not include the most recent decades. By systematically redrilling ice cores, we created a high-quality reconstruction of central and north Greenland temperatures from ﻿ad 1000 until 2011. Here we show that the warming in the recent reconstructed decade exceeds the range of the pre-industrial temperature variability in the past millennium with virtual certainty (P < 0.001) and is on average 1.5 ± 0.4 degrees Celsius (1 standard error) warmer than the twentieth century. Our findings suggest that these exceptional temperatures arise from the superposition of natural variability with a long-term warming trend, apparent since ad 1800. The disproportionate warming is accompanied by enhanced Greenland meltwater run-off, implying that anthropogenic influence has also arrived in central and north Greenland, which might further accelerate the overall Greenland mass loss.
A 1.2 Billion Pixel Human-Labeled Dataset for Data-Driven Classification of Coastal Environments
Authors: Buscombe Daniel , Wernette Phillipe , Fitzpatrick Sharon , Favela Jaycee , Goldstein Evan B. , Enwright Nicholas M.
Published: January 2023

The world’s coastlines are spatially highly variable, coupled-human-natural systems that comprise a nested hierarchy of component landforms, ecosystems, and human interventions, each interacting over a range of space and time scales. Understanding and predicting coastline dynamics necessitates frequent observation from imaging sensors on remote sensing platforms. Machine Learning models that carry out supervised (i.e., human-guided) pixel-based classification, or image segmentation, have transformative applications in spatio-temporal mapping of dynamic environments, including transient coastal landforms, sediments, habitats, waterbodies, and water flows. However, these models require large and well-documented training and testing datasets consisting of labeled imagery. We describe “Coast Train,” a multi-labeler dataset of orthomosaic and satellite images of coastal environments and corresponding labels. These data include imagery that are diverse in space and time, and contain 1.2 billion labeled pixels, representing over 3.6 million hectares. We use a human-in-the-loop tool especially designed for rapid and reproducible Earth surface image segmentation. Our approach permits image labeling by multiple labelers, in turn enabling quantification of pixel-level agreement over individual and collections of images.
Brain activity during a working memory task after daily caffeine intake and caffeine withdrawal: a randomized double-blind placebo-controlled trial
Authors: Lin Yu-Shiuan , Weibel Janine , Landolt Hans-Peter , Santini Francesco , Slawik Helen , Borgwardt Stefan , Cajochen Christian , Reichert Carolin Franziska
Published: January 2023

Acute caffeine intake has been found to increase working memory (WM)-related brain activity in healthy adults without improving behavioral performances. The impact of daily caffeine intake—a ritual shared by 80% of the population worldwide—and of its discontinuation on working memory and its neural correlates remained unknown. In this double-blind, randomized, crossover study, we examined working memory functions in 20 young healthy non-smokers (age: 26.4 ± 4.0 years; body mass index: 22.7 ± 1.4 kg/m2; and habitual caffeine intake: 474.1 ± 107.5 mg/day) in a 10-day caffeine (150 mg × 3 times/day), a 10-day placebo (3 times/day), and a withdrawal condition (9-day caffeine followed by 1-day placebo). Throughout the 10th day of each condition, participants performed four times a working memory task (N-Back, comprising 3- and 0-back), and task-related blood-oxygen-level-dependent (BOLD) activity was measured in the last session with functional magnetic resonance imaging. Compared to placebo, participants showed a higher error rate and a longer reaction time in 3- against 0-back trials in the caffeine condition; also, in the withdrawal condition we observed a higher error rate compared to placebo. However, task-related BOLD activity, i.e., an increased attention network and decreased default mode network activity in 3- versus 0-back, did not show significant differences among three conditions. Interestingly, irrespective of 3- or 0-back, BOLD activity was reduced in the right hippocampus in the caffeine condition compared to placebo. Adding to the earlier evidence showing increasing cerebral metabolic demands for WM function after acute caffeine intake, our data suggest that such demands might be impeded over daily intake and therefore result in a worse performance. Finally, the reduced hippocampal activity may reflect caffeine-associated hippocampal grey matter plasticity reported in the previous analysis. The findings of this study reveal an adapted neurocognitive response to daily caffeine exposure and highlight the importance of classifying impacts of caffeine on clinical and healthy populations.
A rodent model for Dirofilaria immitis, canine heartworm: parasite growth, development, and drug sensitivity in NSG mice
Authors: Hess Jessica A. , Eberhard Mark L. , Segura-Lepe Marcelo , Grundner-Culemann Kathrin , Kracher Barbara , Shryock Jeffrey , Harrington John , Abraham David
Published: January 2023

Heartworm disease, caused by Dirofilaria immitis, remains a significant threat to canines and felines. The development of parasites resistant to macrocyclic lactones (ML) has created a significant challenge to the control of the infection. The goal of this study was to determine if mice lacking a functional immune response would be susceptible to D. immitis. Immunodeficient NSG mice were susceptible to the infection, sustaining parasites for at least 15 weeks, with infective third-stage larvae molting and developing into the late fourth-stage larvae. Proteomic analysis of host responses to the infection revealed a complex pattern of changes after infection, with at least some of the responses directed at reducing immune control mechanisms that remain in NSG mice. NSG mice were infected with isolates of D. immitis that were either susceptible or resistant to MLs, as a population. The susceptible isolate was killed by ivermectin whereas the resistant isolate had improved survivability, while both isolates were affected by moxidectin. It was concluded that D. immitis survives in NSG mice for at least 15 weeks. NSG mice provide an ideal model for monitoring host responses to the infection and for testing parasites in vivo for susceptibility to direct chemotherapeutic activity of new agents.
Hysteroscopic injections of autologous endometrial cells and platelet-rich plasma in patients with thin endometrium: a pilot randomized study
Authors: Efendieva Zulfiia , Vishnyakova Polina , Apolikhina Inna , Artemova Daria , Butov Kirill , Kalinina Elena , Fedorova Tatiana , Tregubova Anna , Asaturova Aleksandra , Fatkhudinov Timur , Sukhikh Gennady
Published: January 2023

The aim of this study was to evaluate the efficacy of hysteroscopically controlled injections of autologous platelet-rich plasma (PRP) and autologous endometrial cells as a treatment for infertile women with thin endometrium. The study enrolled 115 patients with thin endometrium (< 7 mm at implantation window) and infertility, who were divided into groups: Group 1 (the control) underwent conservative therapy; Group 2 received intraendometrial PRP injections instead of the conservative therapy; Group 3 received identical injections after conservative therapy; Group 4 received injections of the autologous endometrial cells suspended in PRP. A single injection dose of PRP contained 0.6–0.7 × 1011of platelets. The levels of PDGF-BB and VEGF in PRP were increased compared with ordinary plasma. The autologous endometrial cells, obtained from pipelle biopsies, constituted heterogeneous cell populations containing stromal and epithelial cells. Intraendometrial PRP injections had significant impact on endometrial thickness and local microcirculation in Group 2 and Group 3. In Group 4, injections of PRP reinforced with endometrial cells also facilitated a significant increase in endometrial thickness. This work describes a novel approach for infertility treatment in patients with refractory thin endometrium. PRP injections and injections of the endometrial cells suspended in PRP into endometrium enhanced cell proliferation and angiogenesis.
Computational analysis of ventricular mechanics in hypertrophic cardiomyopathy patients
Authors: Mojumder Joy , Fan Lei , Nguyen Thuy , Campbell Kenneth S. , Wenk Jonathan F. , Guccione Julius M. , Abraham Theodore , Lee Lik Chuan
Published: January 2023

Hypertrophic cardiomyopathy (HCM) is a genetic heart disease that is associated with many pathological features, such as a reduction in global longitudinal strain (GLS), myofiber disarray and hypertrophy. The effects of these features on left ventricle (LV) function are, however, not clear in two phenotypes of HCM, namely, obstructive and non-obstructive. To address this issue, we developed patient-specific computational models of the LV using clinical measurements from 2 female HCM patients and a control subject. Left ventricular mechanics was described using an active stress formulation and myofiber disarray was described using a structural tensor in the constitutive models. Unloaded LV configuration for each subject was first determined from their respective end-diastole LV geometries segmented from the cardiac magnetic resonance images, and an empirical single-beat estimation of the end-diastolic pressure volume relationship. The LV was then connected to a closed-loop circulatory model and calibrated using the clinically measured LV pressure and volume waveforms, peak GLS and blood pressure. Without consideration of myofiber disarray, peak myofiber tension was found to be lowest in the obstructive HCM subject (60 kPa), followed by the non-obstructive subject (242 kPa) and the control subject (375 kPa). With increasing myofiber disarray, we found that peak tension has to increase in the HCM models to match the clinical measurements. In the obstructive HCM patient, however, peak tension was still depressed (cf. normal subject) at the largest degree of myofiber disarray found in the clinic. The computational modeling workflow proposed here can be used in future studies with more HCM patient data.
Machine learning approach for quantitative biodosimetry of partial-body or total-body radiation exposures by combining radiation-responsive biomarkers
Authors: Shuryak Igor , Nemzow Leah , Bacon Bezalel A. , Taveras Maria , Wu Xuefeng , Deoli Naresh , Ponnaiya Brian , Garty Guy , Brenner David J. , Turner Helen C.
Published: January 2023

During a large-scale radiological event such as an improvised nuclear device detonation, many survivors will be shielded from radiation by environmental objects, and experience only partial-body irradiation (PBI), which has different consequences, compared with total-body irradiation (TBI). In this study, we tested the hypothesis that applying machine learning to a combination of radiation-responsive biomarkers (ACTN1, DDB2, FDXR) and B and T cell counts will quantify and distinguish between PBI and TBI exposures. Adult C57BL/6 mice of both sexes were exposed to 0, 2.0–2.5 or 5.0 Gy of half-body PBI or TBI. The random forest (RF) algorithm trained on ½ of the data reconstructed the radiation dose on the remaining testing portion of the data with mean absolute error of 0.749 Gy and reconstructed the product of dose and exposure status (defined as 1.0 × Dose for TBI and 0.5 × Dose for PBI) with MAE of 0.472 Gy. Among irradiated samples, PBI could be distinguished from TBI: ROC curve AUC = 0.944 (95% CI: 0.844–1.0). Mouse sex did not significantly affect dose reconstruction. These results support the hypothesis that combinations of protein biomarkers and blood cell counts can complement existing methods for biodosimetry of PBI and TBI exposures.
A cross-sectional study of inflammatory markers as determinants of circulating kynurenines in the Lung Cancer Cohort Consortium
Authors: Midttun Øivind , Ulvik Arve , Meyer Klaus , Zahed Hana , Giles Graham G. , Manjer Jonas , Sandsveden Malte , Langhammer Arnulf , Sørgjerd Elin Pettersen , Behndig Annelie F. , Johansson Mikael , Freedman Neal D. , Huang Wen-Yi , Chen Chu , Prentice Ross , Stevens Victoria L. , Wang Ying , Le Marchand Loïc , Weinstein Stephanie J. , Cai Qiuyin , Arslan Alan A. , Chen Yu , Shu Xiao-Ou , Zheng Wei , Yuan Jian-Min , Koh Woon-Puay , Visvanathan Kala , Sesso Howard D. , Zhang Xuehong , Gaziano J. Michael , Fanidi Anouar , Robbins Hilary A. , Brennan Paul , Johansson Mattias , Ueland Per M.
Published: January 2023

Circulating concentrations of metabolites (collectively called kynurenines) in the kynurenine pathway of tryptophan metabolism increase during inflammation, particularly in response to interferon-gamma (IFN-γ). Neopterin and the kynurenine/tryptophan ratio (KTR) are IFN-γ induced inflammatory markers, and together with C-reactive protein (CRP) and kynurenines they are associated with various diseases, but comprehensive data on the strength of associations of inflammatory markers with circulating concentrations of kynurenines are lacking. We measured circulating concentrations of neopterin, CRP, tryptophan and seven kynurenines in 5314 controls from 20 cohorts in the Lung Cancer Cohort Consortium (LC3). The associations of neopterin, KTR and CRP with kynurenines were investigated using regression models. In mixed models, one standard deviation (SD) higher KTR was associated with a 0.46 SD higher quinolinic acid (QA), and 0.31 SD higher 3-hydroxykynurenine (HK). One SD higher neopterin was associated with 0.48, 0.44, 0.36 and 0.28 SD higher KTR, QA, kynurenine and HK, respectively. KTR and neopterin respectively explained 24.1% and 16.7% of the variation in QA, and 11.4% and 7.5% of HK. CRP was only weakly associated with kynurenines in regression models. In summary, QA was the metabolite that was most strongly associated with the inflammatory markers. In general, the inflammatory markers were most strongly related to metabolites located along the tryptophan–NAD axis, which may support suggestions of increased production of NAD from tryptophan during inflammation.
Clustering by antigen-presenting genes reveals immune landscapes and predicts response to checkpoint immunotherapy
Authors: Gong Xutong , Karchin Rachel
Published: January 2023

Immune checkpoint blockade (ICB) has demonstrated efficacy by reinvigorating immune cytotoxicity against tumors. However, the mechanisms underlying how ICB induces responses in a subset of patients remain unclear. Using bulk and single-cell transcriptomic cohorts of melanoma patients receiving ICB, we proposed a clustering model based on the expression of an antigen-presenting machinery (APM) signature consisting of 23 genes in a forward-selection manner. We characterized four APM clusters associated with distinct immune characteristics, cancer hallmarks, and patient prognosis in melanoma. The model predicts differential regulation of APM genes during ICB, which shaped ICB responsiveness. Surprisingly, while immunogenically hot tumors with high baseline APM expression prior to treatment are correlated with a better response to ICB than cold tumors with low APM expression, a subset of hot tumors with the highest pre-ICB APM expression fail to upregulate APM expression during treatment. In addition, they undergo immunoediting and display infiltration of exhausted T cells. In comparison, tumors associated with the best patient prognosis demonstrate significant APM upregulation and immune infiltration following ICB. They also show infiltration of tissue-resident memory T cells, shaping prolonged antitumor immunity. Using only pre-treatment transcriptomic data, our model predicts the dynamic APM-mediated tumor-immune interactions in response to ICB and provides insights into the immune escape mechanisms in hot tumors that compromise the ICB efficacy. We highlight the prognostic value of APM expression in predicting immune response in chronic diseases.
Long distance entanglement and high-dimensional quantum teleportation in the Fermi–Hubbard model
Authors: Abaach Sanaa , Mzaouali Zakaria , El Baz Morad
Published: January 2023

The long distance entanglement in finite size open Fermi–Hubbard chains, together with the end-to-end quantum teleportation are investigated. We show the peculiarity of the ground state of the Fermi–Hubbard model to support maximum long distance entanglement, which allows it to operate as a quantum resource for high fidelity long distance quantum teleportation. We determine the physical properties and conditions for creating scalable long distance entanglement and analyze its stability under the effect of the Coulomb interaction and the hopping amplitude. Furthermore, we show that the choice of the measurement basis in the protocol can drastically affect the fidelity of quantum teleportation and we argue that perfect information transfer can be attained by choosing an adequate basis reflecting the salient properties of the quantum channel, i.e. Hubbard projective measurements.
Impact of physiological parameters on the parotid gland fat fraction in a normal population
Authors: Lee Ari , Choi Yoon Joo , Jeon Kug Jin , Han Sang-Sun , Lee Chena
Published: January 2023

Quantifying physiological fat tissue in the organs is important to further assess the organ’s pathologic status. This study aimed to investigate the impact of body mass index (BMI), age, and sex on the fat fraction of normal parotid glands. Patients undergoing magnetic resonance imaging (MRI) of iterative decomposition of water and fat with echo asymmetry and least squares estimation (IDEAL-IQ) due to non-salivary gland-related disease were reviewed. Clinical information of individual patients was categorized into groups based on BMI (under/normal/overweight), age (age I/age II/age III), and sex (female/male) and an inter-group comparison of the fat fraction values of both parotid glands was conducted. Overall, in the 626 parotid glands analyzed, the fat fraction of the gland was 35.80%. The mean fat fraction value increased with BMI (30.23%, 35.74%, and 46.61% in the underweight, normal and overweight groups, respectively [p < 0.01]) and age (32.42%, 36.20%, and 41.94% in the age I, II, and III groups, respectively [p < 0.01]). The fat content of normal parotid glands varies significantly depending on the body mass and age regardless of sex. Therefore, the patient’s age and body mass should be considered when evaluating fatty change in the parotid glands in imaging results.
The impact of industrial agglomeration on urban green land use efficiency in the Yangtze River Economic Belt
Authors: Wang Jingtong , Han Ping
Published: January 2023

At present, the insufficient supply of land resources has seriously hindered the sustainable development of regional economy. Improving the urban green land use efficiency (UGLUE) has become a key issue on the road to sustainable development. As an important feature of economic development, industrial agglomeration has an impact on the UGLUE that cannot be ignored. This paper uses the Global Malmquist–Luenberger Index (GMLI) to measure UGLUE of 107 cities in the Yangtze River Economic Belt (YREB) from 2007 to 2016, and uses a dynamic panel model (DPM) to empirically analyze the effects of industrial specialization agglomeration and diversification agglomeration on UGLUE. On this basis, the heterogeneous impact of industrial agglomeration in different regions on UGLUE is further discussed. The results illustrate that: (1) The UGLUE shows a general downward trend. (2) Different modes of industrial agglomeration have different impacts on UGLUE. The impact of industrial specialization agglomeration on UGLUE was inverted U-shaped. Industrial diversification agglomeration has a positive effect on UGLUE. (3) The impact of industrial agglomeration in different regions on UGLUE is heterogeneous. The relationship between the industrial agglomeration and UGLUE in the YREB revealed in this paper will provide a reference for promoting UGLUE.
Synthesis and characterization of Se doped Fe3O4 nanoparticles for catalytic and biological properties
Authors: Ahghari Mohammad Reza , Amiri-khamakani Zeinab , Maleki Ali
Published: January 2023

In this study, Se-doped Fe3O4 with antibacterial properties was synthesized using by a coprecipitation method. The chemistry and morphology of the Se doped Fe3O4 nanocomposite were characterized by energy-dispersive X-ray spectroscopy, field-emission scanning electron microscopy, X-ray diffraction, vibrating sample magnetometry, and Brunauer–Emmett–Teller spectroscopy. The antibacterial activity of the Fe3O4/Se nanocomposite was examined against G+ (Gram-positive) and G− (Gram-negative) bacteria, in the order Staphylococcusaureus, Staphylococcussaprophyticus, Pseudomonasaeruginosa, Klebsiellapneumonia, and Escherichiacoli, which are the most harmful and dangerous bacteria. Fe3O4/Se, as a heterogeneous catalyst, was successfully applied to the synthesis of pyrazolopyridine and its derivatives via a one-pot four-component reaction of ethyl acetoacetate, hydrazine hydrate, ammonium acetate, and various aromatic aldehydes. Fe3O4/Se was easily separated from the bacteria-containing solution using a magnet. Its admissible magnetic properties, crystalline structure, antibacterial activity, mild reaction conditions, and green synthesis are specific features that have led to the recommendation of the use of Fe3O4/Se in the water treatment field and medical applications. Direct Se doping of Fe3O4 was successfully realized without additional complicated procedures.
Sign change in c-axis thermal expansion constant and lattice collapse by Ni substitution in transition-metal zirconide superconductor Co1−xNixZr2
Authors: Watanabe Yuto , Arima Hiroto , Usui Hidetomo , Mizuguchi Yoshikazu
Published: January 2023

Recently, c-axis negative thermal expansion (NTE) was observed in a CoZr2 superconductor and related transition-metal zirconides. Here, we investigated the structural, electronic, and superconducting properties of Co1−xNixZr2 to achieve systematic control of c-axis NTE and switching from NTE to positive thermal expansion (PTE) by Ni substitution. At x ≤ 0.3, c-axis NTE was observed, and the thermal expansion constant αc approached zero with increasing x. At x = 0.4–0.6, c-axis thermal expansion close to zero thermal expansion (ZTE) was observed, and PTE appeared for x ≥ 0.7. On the superconducting properties, we observed bulk superconductivity for x ≤ 0.6, and bulk nature of superconductivity is suppressed by Ni heavy doping (x ≥ 0.7). For x ≤ 0.6, the evolution of the electronic density of states well explains the change in the superconducting transition temperature (Tc), which suggests conventional phonon-mediated superconductivity in the system. By analyzing the c/a ratio, we observed a possible collapsed transition in the tetragonal lattice at around x = 0.6–0.8. The lattice collapse would be the cause of the suppression of superconductivity in Ni-rich Co1−xNixZr2 and the switching from NTE to PTE.
4,4′-Biphenyldisulfonic acid induced coordination polymers of symmetrical tetramethyl cucurbit[6]uril with alkaline-earth metals for detection of antibiotics
Authors: Chen Kai , Zhu Zhao-Qiang , Zhang Ming-Hui , Yang Xiang , Li Jie , Chen Chen , Redshaw Carl
Published: January 2023

Three new 3D TMeQ[6]-based coordination polymers of alkali-earth metal ions (Ca2+, Sr2+ and Ba2+) were characterized, and one can highly selectively detect NFX (norfloxacin) molecules via a fluorescence quenching effect.
Photorefraction of uranium-doped lithium niobate crystals at multiple visible wavelengths
Authors: Tian Tian , Chen Yuheng , Zhang Jie , Wang Shuolin , Yuan Wen , Liu Hongde , Chu Yaoqing , Mao Chengling , Xu Wenjie , Zheng Dahuai , Xu Jiayue
Published: January 2023

Holographic storage with fast response speed, high saturation diffraction efficiency and high sensitivity are realized in LN:U at multiple visible wavelengths.
Integrated in situ spectroscopic studies on syngas production from partial oxidation of methane catalyzed by atomically dispersed rhodium cations on ceria
Authors: Opalade Adedamola A. , Tang Yu , Tao Franklin (Feng)
Published: January 2023

Single-atom catalyst Rh1/CeO2 was synthesized. Its single-atom Rh coordinates with 4–5 oxygen atoms on average. It exhibits high activity and selectivity for producing syngas from partial oxidation of methane at 500–700 °C.
Polypropylene carbonate-based electrolytes as model for a different approach towards improved ion transport properties for novel electrolytes
Authors: Gerlitz Anna I. , Diddens Diddo , Grünebaum Mariano , Heuer Andreas , Winter Martin , Wiemhöfer Hans-Dieter
Published: January 2023

Polycarbonate-based electrolytes allow for high lithium transference numbers. Through a combination of various experimental techniques and MD simulations, we unravel the interplay between ion coordination and dynamics for different lithium salts.
A study of the thermodynamics and mechanisms of the atmospherically relevant reaction dimethyl sulphide (DMS) with atomic chlorine (Cl) in the absence and presence of water, using electronic structure methods
Authors: Rhyman Lydia , Lee Edmond P. F. , Ramasami Ponnadurai , Dyke John M.
Published: January 2023

The figure shows the TS, formed from DMS·H2O + Cl, that corresponds to the pathway with the largest rate coefficient in the presence of water.
Lanthanide oxide supported Ni nanoparticles for the selective hydrogenation of cinnamaldehyde
Authors: Xin Huiyue , Li Mengnan , Chen Li , Zhao Chen , Wu Peng , Li Xiaohong
Published: January 2023

The Ni/La2O3catalyst, derived from the perovskite LaNiO3precursor with more weak and medium-strong basic sites, displayed better performance in the selective hydrogenation of the CC bond of cinnamaldehyde than that supported on CeO2or Pr6O11.
Core–shell-structured Mn2SnO4@Void@C as a stable anode material for lithium-ion batteries with long cycle life
Authors: Tong Yuanlin , Xu Xiangyang , Liu Yanru , Yao Yunfei , Chen Dongsheng , Huang Chenyu
Published: January 2023

Assembled by adopting a flowsheet comprising SiO2 templating, carbon encapsulation and alkali etching, is a core–shell-structured and void-rich Mn2SnO4 anode exhibiting upgraded capacity and long cycling stability.
Surface engineering of colloidal nanoparticles
Authors: Jing Xinxin , Zhang Yueyue , Li Min , Zuo Xiaolei , Fan Chunhai , Zheng Junhua
Published: January 2023

Synthesis of engineered colloidal nanoparticles (NPs) with delicate surface characteristics leads to well-defined physicochemical properties and contributes to multifunctional applications.
Effects of chemical composition and vacant oxygen defects on the performance of Ni(OH)2–Ni0.85Se heterostructure nanowires as supercapacitor electrodes
Authors: Wang Ziwei , Zheng Yongjie , Song Kun , Xin Jianjiao , Yin Guangming , Chen Guoli
Published: January 2023

The research focus of supercapacitors is the composition and structural design of electrode materials.
Emerging materials for electrochemical CO2reduction: progress and optimization strategies of carbon-based single-atom catalysts
Authors: Qu Guangfei , Wei Kunling , Pan Keheng , Qin Jin , Lv Jiaxin , Li Junyan , Ning Ping
Published: January 2023

This review highlights the synthesis, characterization and optimization strategies for improving the performance of SACs for CO2RR.
Does interfacial exciton quenching exist in high-performance quantum dot light-emitting diodes?
Authors: Qu Xiangwei , Liu Wenbo , Li Depeng , Ma Jingrui , Gu Mi , Jia Siqi , Xiang Guohong , Sun Xiao Wei
Published: January 2023

Exciton quenching at the QD–ETL interface is unintentionally avoided, which bridges interfacial exciton quenching and high performance in a quantum dot light-emitting diode.
Surface reconstructing hierarchical structures as robust sulfion oxidation catalysts to produce hydrogen with ultralow energy consumption
Authors: Gao Taotao , Tang Xiangmin , Li Xiaoqin , Lan Hai , Yu Shumin , Wu Shuaiwei , Yue Qu , Xiao Dan
Published: January 2023

The Ni-Co-S/NF electrode derived from surface activation of Ni-doped cobalt carbonate hydroxide shows high SOR catalytic activity, and is applied in a dissymmetrical acid–base coupled system to obtain H2 and S8 with ultralow energy consumption.
Durable composites by vulcanization of oleyl-esterified lignin
Authors: Karunarathna Menisha S. , Maladeniya Charini P. , Lauer Moira K. , Tennyson Andrew G. , Smith Rhett C.
Published: January 2023

Oleic acid is used to esterify lignin and the esterified lignin reacts with elemental sulfur and different temperatures to produce composites with compressional and flexural strength that can exceed that of traditional Portland cement.
Manipulating D–A interaction to achieve stable photoinduced organic radicals in triphenylphosphine crystals
Authors: Tang Chunlin , Song Lijuan , Zhou Kang , Ren Peng , Zhao Engui , He Zikai
Published: January 2023

Herein, we realized the quick generation of stable photoinduced radicals in donor–acceptor triarylphosphines with associated color changes of emission and absorption, which was deciphered by the electron paramagnetic resonance (EPR) spectra.
The buckling-condensation mechanism driving gas vesicle collapse
Authors: Zhao Tom Y. , Dunbar Martha , Keten Sinan , Patankar Neelesh A.
Published: January 2023

Gas vesicles (GVs) are protein shells that perform superbly as ultrasound contrast agents due to their tunable collapse pressure. Here, the roles of condensation and shell buckling in triggering and controlling final GV collapse are examined.
Efficient two-dimensional Cs2PbI2(SCN)2 perovskite solar cells via intermediate-modulated crystallization
Authors: Xu Jia , Wu Qiaohui , He Yiwu , Cui Meina , Han Huifang , Liu Huijing , Yao Jianxi
Published: January 2023

All-inorganic two-dimensional Cs2PbI2(SCN)2 perovskite films with improved photoelectric properties were fabricated by adding FACl to precursor solutions. A champion efficiency of 4.7% was achieved in solar cells based on those films.
Modulation of the morphology and electronic structure of Ni3S2 nano-forests via P and Mo co-doping in polyoxometalates to promote the urea oxidation reaction
Authors: Zhang Yao , Guo Haoran , Song Ming , Sun Limei , Song Rui
Published: January 2023

The P–Mo–Ni3S2@NF electrode with nanoforest morphology is synthesized and analyzed by systematic experiments and DFT calculations, which shows superior electrocatalytic activity toward the urea oxidation reaction.
Tunable Janus geometric morphology from aqueous two-phase systems on a superhydrophobic substrate
Authors: Cheng Quanyong , Chen Jingyi , Song Yuhang , Yu Xiang , Guan Chengshu , Wan Chuchu , Tan Xuemei , Huang Caili
Published: January 2023

Precise manipulation of the morphologies of aqueous Janus droplets by leveraging the PEG/DEX ATPS on a superhydrophobic surface.
Enabling interfacial stability of LiCoO2 batteries at an ultrahigh cutoff voltage ≥ 4.65 V via a synergetic electrolyte strategy
Authors: Fu Ang , Xu Chuanjing , Lin Jiande , Su Yu , Zhang Haitang , Wu De-Yin , Zhang Xiaozheng , Xia Meng , Zhang Zhongru , Zheng Jianming , Yang Yong
Published: January 2023

A 3-dimethylmaleic anhydride (DMMA) additive is proposed to reconcile CEIs, and H2O/HF in electrolytes is well scavenged. Moreover, a synergetic electrolyte strategy is applied to push the cutoff voltage of LiCoO2 batteries up to 4.7 V.
In situconstruction of graphdiyne based heterojunctions by a deprotection-free approach for photocatalytic hydrogen generation
Authors: Wang Cong , Han Xu , Xu Qian , Sun Yi-Ning , Arbiol Jordi , Ghazzal Mohamed Nawfal , Li Jian
Published: January 2023

A facile deprotection-free method toin situgrow GDY on a C3N4surface is developed. This straightforward strategy enables the formation of an integral GDY@C3N4heterojunction, leading to an enhanced photocatalytic activity.
Oral administration of silver nanomaterials affects the gut microbiota and metabolic profile altering the secretion of 5-HT in mice
Authors: Wang Xiaoyu , Cui Xuejing , Wu Junguang , Bao Lin , Chen Chunying
Published: January 2023

A working model of the effect of silver nanomaterials on the gut microbiota and the secretion of 5-HT by regulating gut metabolites.
Blue-light-excitable pure and efficient short-wave infrared luminescenceviaCr3+→ Yb3+energy transfer in a KYbP2O7:Cr3+phosphor
Authors: Shi Ruiqi , Miao Shihai , Zhang Yi , Lv Xulong , Chen Dongxun , Liang Yanjie
Published: January 2023

A novel KYbP2O7:Cr3+inorganic phosphor that emits pure and efficient SWIR photoluminescence upon blue light excitation has been developed, and can be used as a stable luminescence converter for a SWIR emitter.
Correction: Chemical space: limits, evolution and modelling of an object bigger than our universal library
Authors: Restrepo Guillermo
Published: January 2023

Correction for ‘Chemical space: limits, evolution and modelling of an object bigger than our universal library’ by Guillermo Restrepo et al., Digital Discovery, 2022, 1, 568–585, https://doi.org/10.1039/D2DD00030J.
Comparative genomics and interactomics of polyadenylation factors for the prediction of new parasite targets: Entamoeba histolytica as a working model
Authors: Avila-Bonilla Rodolfo Gamaliel , Velazquez-Guzman Jorge Antonio , Reyes-Zepeda Eimy Itzel , Gutierrez-Avila Jorge Luis , Reyes-López César A , Cisneros-Sarabia Alondra , Saavedra Emma , Lopéz-Sandoval Angel , Ramírez-Moreno Esther , López-Camarillo César , Marchat Laurence A.
Published: January 2023

Protein–protein interactions (PPI) play a key role in predicting the function of a target protein and drug ability to affect an entire biological system. Prediction of PPI networks greatly contributes to determine a target protein and signal pathways related to its function. Polyadenylation of mRNA 3′-end is essential for gene expression regulation and several polyadenylation factors have been shown as valuable targets for controlling protozoan parasites that affect human health. Here, by using a computational strategy based on sequence-based prediction approaches, phylogenetic analyses, and computational prediction of PPI networks, we compared interactomes of polyadenylation factors in relevant protozoan parasites and the human host, to identify key proteins and define potential targets for pathogen control. Then, we used Entamoeba histolytica as a working model to validate our computational results. RT-qPCR assays confirmed the coordinated modulation of connected proteins in the PPI network and evidenced that silencing of the bottleneck protein EhCFIm25 affects the expression of interacting proteins. In addition, molecular dynamics simulations and docking approaches allowed to characterize the relationships between EhCFIm25 and Ehnopp34, two connected bottleneck proteins. Interestingly, the experimental identification of EhCFIm25 interactome confirmed the close relationships among proteins involved in gene expression regulation and evidenced new links with moonlight proteins in E. histolytica, suggesting a connection between RNA biology and metabolism as described in other organisms. Altogether, our results strengthened the relevance of comparative genomics and interactomics of polyadenylation factors for the prediction of new targets for the control of these human pathogens.
The TFIIS N-terminal domain (TND): a transcription assembly module at the interface of order and disorder
Authors: Cermakova Katerina , Veverka Vaclav , Hodges H. Courtney
Published: January 2023

Interaction scaffolds that selectively recognize disordered protein strongly shape protein interactomes. An important scaffold of this type that contributes to transcription is the TFIIS N-terminal domain (TND). The TND is a five-helical bundle that has no known enzymatic activity, but instead selectively reads intrinsically disordered sequences of other proteins. Here, we review the structural and functional properties of TNDs and their cognate disordered ligands known as TND-interacting motifs (TIMs). TNDs or TIMs are found in prominent members of the transcription machinery, including TFIIS, super elongation complex, SWI/SNF, Mediator, IWS1, SPT6, PP1-PNUTS phosphatase, elongin, H3K36me3 readers, the transcription factor MYC, and others. We also review how the TND interactome contributes to the regulation of transcription. Because the TND is the most significantly enriched fold among transcription elongation regulators, TND- and TIM-driven interactions have widespread roles in the regulation of many transcriptional processes.
Glucuronoyl esterases – enzymes to decouple lignin and carbohydrates and enable better utilization of renewable plant biomass
Authors: Larsbrink Johan , Lo Leggio Leila
Published: January 2023

Glucuronoyl esterases (GEs) are microbial enzymes able to cleave covalent linkages between lignin and carbohydrates in the plant cell wall. GEs are serine hydrolases found in carbohydrate esterase family 15 (CE15), which belongs to the large α/β hydrolase superfamily. GEs have been shown to reduce plant cell wall recalcitrance by hydrolysing the ester bonds found between glucuronic acid moieties on xylan polysaccharides and lignin. In recent years, the exploration of CE15 has broadened significantly and focused more on bacterial enzymes, which are more diverse in terms of sequence and structure to their fungal counterparts. Similar to fungal GEs, the bacterial enzymes are able to improve overall biomass deconstruction but also appear to have less strict substrate preferences for the uronic acid moiety. The structures of bacterial GEs reveal that they often have large inserts close to the active site, with implications for more extensive substrate interactions than the fungal GEs which have more open active sites. In this review, we highlight the recent work on GEs which has predominantly regarded bacterial enzymes, and discuss similarities and differences between bacterial and fungal enzymes in terms of the biochemical properties, diversity in sequence and modularity, and structural variations that have been discovered thus far in CE15.