bluuebunny/crossref_metadata_2025 huggingface dataset:
Technical development and validation of a clinically applicable microenvironment classifier as a biomarker of tumour hypoxia for soft tissue sarcoma
Authors: Forker Laura J. , Bibby Becky , Yang Lingjian , Lane Brian , Irlam Joely , Mistry Hitesh , Khan Mairah , Valentine Helen , Wylie James , Shenjere Patrick , Leahy Michael , Gaunt Piers , Billingham Lucinda , Seddon Beatrice M. , Grimer Rob , Robinson Martin , Choudhury Ananya , West Catharine
Published: April 2023

Background

Soft tissue sarcomas (STS) are rare, heterogeneous tumours and biomarkers are needed to inform management. We previously derived a prognostic tumour microenvironment classifier (24-gene hypoxia signature). Here, we developed/validated an assay for clinical application.

Methods

Technical performance of targeted assays (Taqman low-density array, nanoString) was compared in 28 prospectively collected formalin-fixed, paraffin-embedded (FFPE) biopsies. The nanoString assay was biologically validated by comparing to HIF-1α/CAIX immunohistochemistry (IHC) in clinical samples. The Manchester (n = 165) and VORTEX Phase III trial (n = 203) cohorts were used for clinical validation. The primary outcome was overall survival (OS).

Results

Both assays demonstrated excellent reproducibility. The nanoString assay detected upregulation of the 24-gene signature under hypoxia in vitro, and 16/24 hypoxia genes were upregulated in tumours with high CAIX expression in vivo. Patients with hypoxia-high tumours had worse OS in the Manchester (HR 3.05, 95% CI 1.54–5.19, P = 0.0005) and VORTEX (HR 2.13, 95% CI 1.19–3.77, P = 0.009) cohorts. In the combined cohort, it was independently prognostic for OS (HR 2.24, 95% CI 1.42–3.53, P = 0.00096) and associated with worse local recurrence-free survival (HR 2.17, 95% CI 1.01–4.68, P = 0.04).

Conclusions

This study comprehensively validates a microenvironment classifier befitting FFPE STS biopsies. Future uses include: (1) selecting high-risk patients for perioperative chemotherapy; and (2) biomarker-driven trials of hypoxia-targeted therapies.
Downregulation of the Rho GTPase pathway abrogates resistance to ionizing radiation in wild-type p53 glioblastoma by suppressing DNA repair mechanisms
Authors: Magalhaes Yuli Thamires , Boell Viktor Kalbermatter , Cardella Giovanna Duo , Forti Fabio Luis
Published: April 2023

Glioblastoma (GBM), the most common aggressive brain tumor, is characterized by rapid cellular infiltration and is routinely treated with ionizing radiation (IR), but therapeutic resistance inevitably recurs. The actin cytoskeleton of glioblastoma cells provides their high invasiveness, but it remains unclear whether Rho GTPases modulate DNA damage repair and therapeutic sensitivity. Here, we irradiated glioblastoma cells with different p53 status and explored the effects of Rho pathway inhibition to elucidate how actin cytoskeleton disruption affects the DNA damage response and repair pathways. p53-wild-type and p53-mutant cells were subjected to Rho GTPase pathway modulation by treatment with C3 toxin; knockdown of mDia-1, PFN1 and MYPT1; or treatment with F-actin polymerization inhibitors. Rho inhibition increased the sensitivity of glioma cells to IR by increasing the number of DNA double-strand breaks and delaying DNA repair by nonhomologous end-joining in p53-wild-type cells. p53 knockdown reversed this phenotype by reducing p21 expression and Rho signaling activity, whereas reactivation of p53 in p53-mutant cells by treatment with PRIMA-1 reversed these effects. The interdependence between p53 and Rho is based on nuclear p53 translocation facilitated by G-actin and enhanced by IR. Isolated IR-resistant p53-wild-type cells showed an altered morphology and increased stress fiber formation: inhibition of Rho or actin polymerization decreased cell viability in a p53-dependent manner and reversed the resistance phenotype. p53 silencing reversed the Rho inhibition-induced sensitization of IR-resistant cells. Rho inhibition also impaired the repair of IR-damaged DNA in 3D spheroid models. Rho GTPase activity and actin cytoskeleton dynamics are sensitive targets for the reversal of acquired resistance in GBM tumors with wild-type p53.
Higher-order mesoscopic self-assembly of fluorinated surfactants on water surfaces
Authors: Tanaka Motomu , Krafft Marie Pierre , Pasc Andreea
Published: April 2023

Surfactants containing fluorocarbon chains have been increasingly studied because they self-assemble into a variety of microscopic and mesoscopic domains and tend to form highly ordered patterns at the air/water interface; these patterns are clearly different from those formed by their hydrocarbon analogs. Focusing on the fluorinated surfactants possessing unique physical characteristics, this review describes the relationship between the line tension and dipole interaction, which is the comprehensive principle governing the pattern formation of two-dimensional self-assemblies. This review further discusses several key experimental and analytical techniques that are useful for characterizing the shape, size, correlation, and viscoelasticity of hierarchical self-assemblies on water surfaces. Finally, several biomedical applications, including biomimetic surface coating, multimodal contrast agents in medical diagnostics, and controlled delivery of gases (O2 and NO) for oxygenation and antimicrobial effects, are introduced to highlight how the unique physicochemical properties of fluorinated self-assemblies can be applied in materials science.
Fabricating higher-order functional DNA origami structures to reveal biological processes at multiple scales
Authors: Zhou Yihao , Dong Jinyi , Wang Qiangbin
Published: April 2023

DNA origami technology enables the precise assembly of well-defined two-dimensional and three-dimensional nanostructures with DNA, an inherently biocompatible material. Given their modularity and addressability, DNA origami objects can be used as scaffolds to fabricate larger higher-order structures with other functional biomolecules and engineer these molecules with nanometer precision. Over the past decade, these higher-order functional structures have shown potential as powerful tools to study the function of various bio-objects, revealing the corresponding biological processes, from the single-molecule level to the cell level. To inspire more creative and fantastic research, herein, we highlight seminal works in four emerging areas of bioapplications of higher-order DNA origami structures: (1) assisting in single-molecule studies, including protein structural analysis, biomolecule interaction analysis, and protein functional analysis, (2) manipulating lipid membranes, (3) directing cell behaviors, and (4) delivering drugs as smart nanocarriers. Finally, current challenges and opportunities in the fabrication and application of DNA origami-based functional structures are discussed.
Toward the production of renewable diesel over robust Ni nanoclusters highly dispersed on a two-dimensional zeolite
Authors: Pang Hao , Yang Guoju , Li Lin , Yu Jihong
Published: April 2023

Deoxygenation of bioderived lipids into renewable transportation fuels is a promising route to decreasing the dependence on fossil sources. Ni-based catalysts are high performing and cost-effective in deoxygenation reactions but suffer from severe sintering and aggregation. Herein, a ligand-chelating impregnation method was used to prepare highly dispersed Ni nanoclusters on a two-dimensional (2D) ITQ-2 zeolite. Comprehensive characterization was utilized to monitor the changes in the organometallic precursors during activation and to investigate their impact on the dispersion of the Ni nanoclusters on the ITQ-2 zeolite. The high external surface area and abundant surface defects of the 2D support enhanced the dispersion and immobilization of the Ni nanoclusters and outperformed conventional zeolites. The protection of the Ni2+ cations by the organic ligand suppressed the aggregation of Ni species during the activation processes, thereby leading to the formation of uniformly distributed Ni nanoclusters on the ITQ-2 zeolite. Due to the highly dispersed Ni nanoclusters and immobilization on the 2D zeolite, the Ni/ITQ-2-co material prepared by the ligand-chelating impregnation approach showed outstanding activity and stability for conversions of stearic acid or palm oil to diesel range alkanes. This work provides a rational design and precise modulation of metal-based catalysts for the production of renewable diesel.
Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers
Authors: Brase Logan , You Shih-Feng , D’Oliveira Albanus Ricardo , Del-Aguila Jorge L. , Dai Yaoyi , Novotny Brenna C. , Soriano-Tarraga Carolina , Dykstra Taitea , Fernandez Maria Victoria , Budde John P. , Bergmann Kristy , Morris John C. , Bateman Randall J. , Perrin Richard J. , McDade Eric , Xiong Chengjie , Goate Alison M. , Farlow Martin ,   Dominantly Inherited Alzheimer Network (DIAN), Sutherland Greg T. , Kipnis Jonathan , Karch Celeste M. , Benitez Bruno A. , Harari Oscar
Published: April 2023

Genetic studies of Alzheimer disease (AD) have prioritized variants in genes related to the amyloid cascade, lipid metabolism, and neuroimmune modulation. However, the cell-specific effect of variants in these genes is not fully understood. Here, we perform single-nucleus RNA-sequencing (snRNA-seq) on nearly 300,000 nuclei from the parietal cortex of AD autosomal dominant (APP and PSEN1) and risk-modifying variant (APOE, TREM2 and MS4A) carriers. Within individual cell types, we capture genes commonly dysregulated across variant groups. However, specific transcriptional states are more prevalent within variant carriers. TREM2 oligodendrocytes show a dysregulated autophagy-lysosomal pathway, MS4A microglia have dysregulated complement cascade genes, and APOEε4 inhibitory neurons display signs of ferroptosis. All cell types have enriched states in autosomal dominant carriers. We leverage differential expression and single-nucleus ATAC-seq to map GWAS signals to effector cell types including the NCK2 signal to neurons in addition to the initially proposed microglia. Overall, our results provide insights into the transcriptional diversity resulting from AD genetic architecture and cellular heterogeneity. The data can be explored on the online browser (http://web.hararilab.org/SNARE/).
Microbial biomanufacturing for space-exploration—what to take and when to make
Authors: Averesch Nils J. H. , Berliner Aaron J. , Nangle Shannon N. , Zezulka Spencer , Vengerova Gretchen L. , Ho Davian , Casale Cameran A. , Lehner Benjamin A. E. , Snyder Jessica E. , Clark Kevin B. , Dartnell Lewis R. , Criddle Craig S. , Arkin Adam P.
Published: April 2023

As renewed interest in human space-exploration intensifies, a coherent and modernized strategy for mission design and planning has become increasingly crucial. Biotechnology has emerged as a promising approach to increase resilience, flexibility, and efficiency of missions, by virtue of its ability to effectively utilize in situ resources and reclaim resources from waste streams. Here we outline four primary mission-classes on Moon and Mars that drive a staged and accretive biomanufacturing strategy. Each class requires a unique approach to integrate biomanufacturing into the existing mission-architecture and so faces unique challenges in technology development. These challenges stem directly from the resources available in a given mission-class—the degree to which feedstocks are derived from cargo and in situ resources—and the degree to which loop-closure is necessary. As mission duration and distance from Earth increase, the benefits of specialized, sustainable biomanufacturing processes also increase. Consequentially, we define specific design-scenarios and quantify the usefulness of in-space biomanufacturing, to guide techno-economics of space-missions. Especially materials emerged as a potentially pivotal target for biomanufacturing with large impact on up-mass cost. Subsequently, we outline the processes needed for development, testing, and deployment of requisite technologies. As space-related technology development often does, these advancements are likely to have profound implications for the creation of a resilient circular bioeconomy on Earth.
The small and large intestine contain related mesenchymal subsets that derive from embryonic Gli1+ precursors
Authors: Pærregaard Simone Isling , Wulff Line , Schussek Sophie , Niss Kristoffer , Mörbe Urs , Jendholm Johan , Wendland Kerstin , Andrusaite Anna T. , Brulois Kevin F. , Nibbs Robert J. B. , Sitnik Katarzyna , Mowat Allan McI , Butcher Eugene C. , Brunak Søren , Agace William W.
Published: April 2023

The intestinal lamina propria contains a diverse network of fibroblasts that provide key support functions to cells within their local environment. Despite this, our understanding of the diversity, location and ontogeny of fibroblasts within and along the length of the intestine remains incomplete. Here we show that the small and large intestinal lamina propria contain similar fibroblast subsets that locate in specific anatomical niches. Nevertheless, we find that the transcriptional profile of similar fibroblast subsets differs markedly between the small intestine and colon suggesting region specific functions. We perform in vivo transplantation and lineage-tracing experiments to demonstrate that adult intestinal fibroblast subsets, smooth muscle cells and pericytes derive from Gli1-expressing precursors present in embryonic day 12.5 intestine. Trajectory analysis of single cell RNA-seq datasets of E12.5 and adult mesenchymal cells suggest that adult smooth muscle cells and fibroblasts derive from distinct embryonic intermediates and that adult fibroblast subsets develop in a linear trajectory from CD81+ fibroblasts. Finally, we provide evidence that colonic subepithelial PDGFRαhi fibroblasts comprise several functionally distinct populations that originate from an Fgfr2-expressing fibroblast intermediate. Our results provide insights into intestinal stromal cell diversity, location, function, and ontogeny, with implications for intestinal development and homeostasis.
Error-related signaling in nucleus accumbens D2 receptor-expressing neurons guides inhibition-based choice behavior in mice
Authors: Nishioka Tadaaki , Attachaipanich Suthinee , Hamaguchi Kosuke , Lazarus Michael , de Kerchove d’Exaerde Alban , Macpherson Tom , Hikida Takatoshi
Published: April 2023

Learned associations between environmental cues and the outcomes they predict (cue-outcome associations) play a major role in behavioral control, guiding not only which responses we should perform, but also which we should inhibit, in order to achieve a specific goal. The encoding of such cue-outcome associations, as well as the performance of cue-guided choice behavior, is thought to involve dopamine D1 and D2 receptor-expressing medium spiny neurons (D1-/D2-MSNs) of the nucleus accumbens (NAc). Here, using a visual discrimination task in male mice, we assessed the role of NAc D1-/D2-MSNs in cue-guided inhibition of inappropriate responding. Cell-type specific neuronal silencing and in-vivo imaging revealed NAc D2-MSNs to contribute to inhibiting behavioral responses, with activation of NAc D2-MSNs following response errors playing an important role in optimizing future choice behavior. Our findings indicate that error-signaling by NAc D2-MSNs contributes to the ability to use environmental cues to inhibit inappropriate behavior.
Geometric fluctuation of conformal Hilbert spaces and multiple graviton modes in fractional quantum Hall effect
Authors: Yuzhu Wang , Bo Yang
Published: April 2023

Neutral excitations in fractional quantum Hall (FQH) fluids define the incompressibility of topological phases, a species of which can show graviton-like behaviors and are thus called the graviton modes (GMs). Here, we develop the microscopic theory for multiple GMs in FQH fluids and show explicitly that they are associated with the geometric fluctuation of well-defined conformal Hilbert spaces (CHSs), which are hierarchical subspaces within a single Landau level, each with emergent conformal symmetry and continuously parameterized by a unimodular metric. This leads to several statements about the number and the merging/splitting of GMs, which are verified numerically with both model and realistic interactions. We also discuss how the microscopic theory can serve as the basis for the additional Haldane modes in the effective field theory description and their experimental relevance to realistic electron-electron interactions.
Oxidative dissolution of (U,Ce)O2 materials in aqueous solutions containing H2O2
Authors: Montaigne Théo , Szenknect Stéphanie , Broudic Véronique , Imbert Paul-Henri , Tocino Florent , Martin Christelle , Miserque Frédéric , Jégou Christophe , Dacheux Nicolas
Published: April 2023

Homogeneous and heterogeneous U1-xCexO2 (with 0≤ x≤ 0.25) materials were prepared via wet and dry chemistry routes, respectively before being submitted to dynamic leaching experiments. The feeding solution containing 0.20 mmol.L−1 H2O2 was kept under air and renewed to guarantee the stability of H2O2 during the experiment. Normalized alteration rates were determined from U concentration in the leachates. For homogeneous (U,Ce)O2 materials, the dissolution rate was divided by a factor of 3 when increasing the Ce content from 0.08 to 0.25. Surface characterizations revealed that studtite precipitated all over UO2 pellet surface and only on the UO2 grains of heterogeneous U0.92Ce0.08O2 samples. The behaviour of this heterogeneous material was similar to that observed for (U,Pu)O2 in the same conditions, which revealed the reliability of cerium as a plutonium analogue.
The potential of bamboo seeds for natural biofortification of dietary zinc and iron
Authors: Hu Qifang , Wang Rong , Hu Lin , Chen Rong , Yu Xuejun , Shao Ji Feng
Published: April 2023

Moso bamboo has been shown to accumulate high concentrations of iron and zinc in the seeds. However, the bioavailablity of iron and zinc in bamboo seeds is poorly understood. Here, we evaluated the bioaccessibility and bioavailability of iron and zinc in bamboo seeds by using an in vitro digestion protocol. Our evaluations revealed that values of bioaccessibility and bioavailability of iron were 25 and 21 mg kg−1in bamboo seeds which were 1.6- and 1.7- fold higher than in rice, respectively. Also, values of bioaccessibility and bioavailability of zinc were 20 and 13 mg kg−1in bamboo seeds which were 1.9- and 2.6- fold higher than in rice, respectively. Boiling process reduced both the bioaccessibility and bioavailability of iron and zinc. In addition, phytic acid concentration in bamboo seeds was only 0.42 times higher than in rice. By contrast, the tannins concentration in bamboo seeds was 2.2 times higher than in rice. Cellular localization results showed that iron and zinc were mainly concentrated in the embryo and the aleurone layer. These results clearly suggest that Moso bamboo seeds are rich in iron and zinc and have potential as a food for iron and zinc biofortification.
On enabling collaborative non-intrusive load monitoring for sustainable smart cities
Authors: Shi Yunchuan , Li Wei , Chang Xiaomin , Yang Ting , Sun Yaojie , Zomaya Albert Y.
Published: April 2023

Improving energy efficiency is a crucial aspect of building a sustainable smart city and, more broadly, relevant for improving environmental, economic, and social well-being. Non-intrusive load monitoring (NILM) is a computing technique that estimates energy consumption in real-time and helps raise energy awareness among users to facilitate energy management. Most NILM solutions are still a single machine approach and do not fit well in smart cities. This work proposes a model-agnostic hybrid federated learning framework to collaboratively train NILM models for city-wide energy-saving applications. The framework supports both centralised and decentralised training modes to provide a cluster-based, customisable and optimal learning solution for users. The proposed framework is evaluated on a real-world energy disaggregation dataset. The results show that all NILM models trained in our proposed framework outperform the locally trained ones in accuracy. The results also suggest that the NILM models trained in our framework are resistant to privacy leakage.
Clinical and microbiological characteristics of bloodstream infection caused by Klebsiella pneumoniae harboring rmpA in Japanese adults
Authors: Kikuchi Shota , Kosai Kosuke , Ota Kenji , Mitsumoto-Kaseida Fujiko , Sakamoto Kei , Hasegawa Hiroo , Izumikawa Koichi , Mukae Hiroshi , Yanagihara Katsunori
Published: April 2023

We investigated the clinical features of bloodstream infections (BSIs) caused by Klebsiella pneumoniae harboring rmpA and molecular characteristics of the bacteria. We retrospectively investigated adult patients with K. pneumoniae BSI from January 2010 to March 2021 at Nagasaki University Hospital. A matched case–control study in a 1:3 ratio was conducted to clarify the clinical and bacterial characteristics of BSI caused by rmpA-positive K. pneumoniae compared with those caused by rmpA-negative isolates. Antimicrobial susceptibility testing and multilocus sequence typing (MLST) were performed for rmpA-positive isolates. The rmpA was detected in 36 (13.4%) of the 268 isolates. Of these 36 isolates, 31 (86.1%) harbored iucA and 35 (97.2%) each possessed peg-344 and iroB; capsular types were identified as K1 in 9 (25.0%) and K2 in 10 isolates (27.8%). Contrarily, of the 108 rmpA-negative isolates, which were matched for case–control studies, 5 isolates (4.6%) harbored iucA and 1 (0.9%) each possessed peg-344 and iroB; 2 (1.9%) and 3 isolates (2.8%) had K1 and K2 capsular types, respectively. Among the rmpA-positive isolates, ST23/K1 (eight isolates) was the most frequent, followed by ST412/non-K1/K2 (seven isolates), ST86/K2 (five isolates), and ST268/non-K1/K2 (four isolates). In a multivariate analysis using clinical factors, liver abscess positively correlated with rmpA-positive isolates, whereas biliary tract infection and use of anticancer drugs negatively correlated with rmpA-positive isolates in patients with K. pneumoniae BSI. Considering the correlation between rmpA-positive isolates and clinical features, rmpA can be used as a marker for understanding the pathophysiology of K. pneumoniae BSI.
Exploration on ability of printable modified papers for the application in heat sublimation transfer printing of polyester fabric
Authors: Adel Abeer M. , Ahmed Nivin M. , Diab Mohamed A. , El-Shall Fatma N. , El-Shinnawy Nabila
Published: April 2023

In this work heat transfer papers were loaded with a new core–shell pigment based on precipitating thin shell of titanium dioxide on a core of rice husk silica ash TiO2/RHSA to be applied in dye sublimation printing of textile fabrics. Besides, 0.1% (w/w) cationic polyacrylamide (CPAM) and 1% (w/w) bentonite (Bt) were also added sequentially to improve drainage and filler retention of the paper hand-sheets made from bleached kraft bagasse pulps. The effect of the new core–shell pigment on the mechanical and barrier properties, thermal stability and surface morphology of modified paper sheets were investigated. In addition, the study of transfer printability and ease of dye release from paper to fabric in this heat transfer printing of polyester fabrics using silk-screen printing under different transfer parameters were studied. Also, fastness measurements including washing, light and perspiration of printing polyester fabric were also estimated.
The screening method for use of wild pheasant feathers in the monitoring of environmental pollution with heavy metals
Authors: Tajchman Katarzyna , Drabik Kamil , Ukalska-Jaruga Aleksandra , Janiszewski Paweł , Spustek Damian , Wengerska Karolina
Published: April 2023

It has been shown that some species of birds, especially herbivorous and territorial ones, are more sensitive to the effects of toxic substances compared to mammals. This allows for taking integrated actions in the area of environmental protection and monitoring in a holistic sense (at various trophic levels). Therefore, this study aimed to assess the possibility of using pheasant feathers (Phasianuscolchicus) as a potential bioindicator ofenvironmental contamination, and thus to determine the concentration of heavy metals (lead—Pb, arsenic—As, cadmium—Cd, chromium—Cr, nickel—Ni, and zinc—Zn) in the analyzed tissue of animals inhabiting the forest districts of the Lubartów, Tomaszów, Skierniewice, and Ostrowiec Świętokrzyski areas. The chemical analysis used to determine the concentration of toxic elements in pheasant feathers was carried out by inductively coupled plasma mass spectrometry. The highest concentrations of Cr and Zn were found in birds from the Lubartów Forest District (1.93 mg/kg and 120.63 mg/kg, respectively), As and Ni in the Tomaszów Forest District (0.55 mg/kg and 1.60 mg/kg, respectively), Cd in the Lubartów Forest District and Skierniewice (0.04 mg/kg), and Pb in the Skierniewice Forest Distict (6.79 mg/kg). The observed results were strongly related to soil contamination and urbanization index, as key environmental factors which significantly determine the metal content in pheasant feathers. Therefore, proposed non-invasive measurements of the elemental composition of feathers of birds living in specific areas may be an important indicator of environmental pollution in relation to the high impact of anthropopressure.
Influence of lateral single jets for thermal protection of reentry nose cone with multi-row disk spike at hypersonic flow: computational study
Authors: Shi Yunbin , Cheng Qiong , Alizadeh As’ad , Yan Hongbo , Choubey Gautam , Fallah K. , Shamsborhan Mahmoud
Published: April 2023

The main challenge for the advancement of current high-speed automotives is aerodynamic heating. In this study, the application of lateral jet for thermal protection of the high-speed automotives is extensively studied. The simulation of the lateral coolant jet is done via Computational fluid dynamic at high-velocity condition. Finding optimum jet configuration for reduction of the aerodynamic heating is the main goal of this research. Two different coolant jets (Helium and Carbon dioxide) are investigated as coolant jet and flow study and fuel penetration mechanism are fully presented. In addition, the thermal load on the main body of nose cone is compared for different configurations. Our results specify that the injection of lateral jet near the tip of spike is effective for thermal protection of main body via deflection of bow shock. Also, Carbon dioxide jet with lower diffusivity is more effective for the protection of forebody with multi-row disk from sever aerodynamic heating.
Automated cornea diagnosis using deep convolutional neural networks based on cornea topography maps
Authors: Fassbind Benjamin , Langenbucher Achim , Streich Andreas
Published: April 2023

Cornea topography maps allow ophthalmologists to screen and diagnose cornea pathologies. We aim to automatically identify any cornea abnormalities based on such cornea topography maps, with focus on diagnosing keratoconus. To do so, we represent the OCT scans as images and apply Convolutional Neural Networks (CNNs) for the automatic analysis. The model is based on a state-of-the-art ConvNeXt CNN architecture with weights fine-tuned for the given specific application using the cornea scans dataset. A set of 1940 consecutive screening scans from the Saarland University Hospital Clinic for Ophthalmology was annotated and used for model training and validation. All scans were recorded with a CASIA2 anterior segment Optical Coherence Tomography (OCT) scanner. The proposed model achieves a sensitivity of 98.46% and a specificity of 91.96% when distinguishing between healthy and pathological corneas. Our approach enables the screening of cornea pathologies and the classification of common pathologies like keratoconus. Furthermore, the approach is independent of the topography scanner and enables the visualization of those scan regions which drive the model’s decisions.
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome
Authors: Nilsson Jonas Birkelund , Kaabinejadian Saghar , Yari Hooman , Peters Bjoern , Barra Carolina , Gragert Loren , Hildebrand William , Nielsen Morten
Published: April 2023

Human leukocyte antigen (HLA) class II antigen presentation is key for controlling and triggering T cell immune responses. HLA-DQ molecules, which are believed to play a major role in autoimmune diseases, are heterodimers that can be formed as both cis and trans variants depending on whether the α- and β-chains are encoded on the same (cis) or opposite (trans) chromosomes. So far, limited progress has been made for predicting HLA-DQ antigen presentation. In addition, the contribution of trans-only variants (i.e. variants not observed in the population as cis) in shaping the HLA-DQ immunopeptidome remains largely unresolved. Here, we seek to address these issues by integrating state-of-the-art immunoinformatics data mining models with large volumes of high-quality HLA-DQ specific mass spectrometry immunopeptidomics data. The analysis demonstrates highly improved predictive power and molecular coverage for models trained including these novel HLA-DQ data. More importantly, investigating the role of trans-only HLA-DQ variants reveals a limited to no contribution to the overall HLA-DQ immunopeptidome. In conclusion, this study furthers our understanding of HLA-DQ specificities and casts light on the relative role of cis versus trans-only HLA-DQ variants in the HLA class II antigen presentation space. The developed method, NetMHCIIpan-4.2, is available at https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.2.
Lunar gravity prevents skeletal muscle atrophy but not myofiber type shift in mice
Authors: Hayashi Takuto , Fujita Ryo , Okada Risa , Hamada Michito , Suzuki Riku , Fuseya Sayaka , Leckey James , Kanai Maho , Inoue Yuri , Sadaki Shunya , Nakamura Ayano , Okamura Yui , Abe Chikara , Morita Hironobu , Aiba Tatsuya , Senkoji Teruhiro , Shimomura Michihiko , Okada Maki , Kamimura Daisuke , Yumoto Akane , Muratani Masafumi , Kudo Takashi , Shiba Dai , Takahashi Satoru
Published: April 2023

Skeletal muscle is sensitive to gravitational alterations. We recently developed a multiple artificial-gravity research system (MARS), which can generate gravity ranging from microgravity to Earth gravity (1 g) in space. Using the MARS, we studied the effects of three different gravitational levels (microgravity, lunar gravity [1/6 g], and 1 g) on the skeletal muscle mass and myofiber constitution in mice. All mice survived and returned to Earth, and skeletal muscle was collected two days after landing. We observed that microgravity-induced soleus muscle atrophy was prevented by lunar gravity. However, lunar gravity failed to prevent the slow-to-fast myofiber transition in the soleus muscle in space. These results suggest that lunar gravity is enough to maintain proteostasis, but a greater gravitational force is required to prevent the myofiber type transition. Our study proposes that different gravitational thresholds may be required for skeletal muscle adaptation.
RAB35 is required for murine hippocampal development and functions by regulating neuronal cell distribution
Authors: Maejima Ikuko , Hara Taichi , Tsukamoto Satoshi , Koizumi Hiroyuki , Kawauchi Takeshi , Akuzawa Tomoko , Hirai Rika , Kobayashi Hisae , Isobe Inoya , Emoto Kazuo , Kosako Hidetaka , Sato Ken
Published: April 2023

RAB35 is a multifunctional small GTPase that regulates endocytic recycling, cytoskeletal rearrangement, and cytokinesis. However, its physiological functions in mammalian development remain unclear. Here, we generatedRab35-knockout mice and found that RAB35 is essential for early embryogenesis. Interestingly, brain-specificRab35-knockout mice displayed severe defects in hippocampal lamination owing to impaired distribution of pyramidal neurons, although defects in cerebral cortex formation were not evident. In addition,Rab35-knockout mice exhibited defects in spatial memory and anxiety-related behaviors. Quantitative proteomics indicated that the loss of RAB35 significantly affected the levels of other RAB proteins associated with endocytic trafficking, as well as some neural cell adhesion molecules, such as contactin-2. Collectively, our findings revealed that RAB35 is required for precise neuronal distribution in the developing hippocampus by regulating the expression of cell adhesion molecules, thereby influencing spatial memory.
A data-driven crop model for maize yield prediction
Authors: Chang Yanbin , Latham Jeremy , Licht Mark , Wang Lizhi
Published: April 2023

Accurate estimation of crop yield predictions is of great importance for food security under the impact of climate change. We propose a data-driven crop model that combines the knowledge advantage of process-based modeling and the computational advantage of data-driven modeling. The proposed model tracks the daily biomass accumulation process during the maize growing season and uses daily produced biomass to estimate the final grain yield. Computational studies using crop yield, field location, genotype and corresponding environmental data were conducted in the US Corn Belt region from 1981 to 2020. The results suggest that the proposed model can achieve an accurate prediction performance with a 7.16% relative root-mean-square-error of average yield in 2020 and provide scientifically explainable results. The model also demonstrates its ability to detect and separate interactions between genotypic parameters and environmental variables. Additionally, this study demonstrates the potential value of the proposed model in helping farmers achieve higher yields by optimizing seed selection.
Search for ferromagnetism in Mn-doped lead halide perovskites
Authors: Sajedi Maryam , Luo Chen , Siemensmeyer Konrad , Krivenkov Maxim , Chen Kai , Taylor James M. , Flatken Marion A. , Radu Florin , Rader Oliver
Published: April 2023

Lead halide perovskites are new key materials in various application areas such as high efficiency photovoltaics, lighting, and photodetectors. Doping with Mn, which is known to enhance the stability, has recently been reported to lead to ferromagnetism below 25 K in methylammonium lead iodide (MAPbI3) mediated by superexchange. Two most recent reports confirm ferromagnetism up to room temperature but mediated by double exchange between Mn2+ and Mn3+ ions. Here we investigate a wide concentration range of MAMnxPb1−xI3 and Mn-doped triple-cation thin films by soft X-ray absorption, X-ray magnetic circular dichroism, and quantum interference device magnetometry. The X-ray absorption lineshape shows clearly an almost pure Mn2+ configuration, confirmed by a sum-rule analysis of the dichroism spectra. A remanent magnetization is not observed down to 2 K. Curie-Weiss fits to the magnetization yield negative Curie temperatures. All data show consistently that significant double exchange and ferromagnetism do not occur. Our results show that Mn is not suitable for creating ferromagnetism in lead halide perovskites.
Deep anoxic aquifers could act as sinks for uranium through microbial-assisted mineral trapping
Authors: Pidchenko Ivan N. , Christensen John N. , Kutzschbach Martin , Ignatyev Konstantin , Puigdomenech Ignasi , Tullborg Eva-Lena , Roberts Nick M. W. , Rasbury E. Troy , Northrup Paul , Tappero Ryan , Kvashnina Kristina O. , Schäfer Thorsten , Suzuki Yohey , Drake Henrik
Published: April 2023

Uptake of uranium (U) by secondary minerals, such as carbonates and iron (Fe)-sulfides, that occur ubiquitously on Earth, may be substantial in deep anoxic environments compared to surficial settings due to different environment-specific conditions. Yet, knowledge of U reductive removal pathways and related fractionation between 238U and 235U isotopes in deep anoxic groundwater systems remain elusive. Here we show bacteria-driven degradation of organic constituents that influences formation of sulfidic species facilitating reduction of geochemically mobile U(VI) with subsequent trapping of U(IV) by calcite and Fe-sulfides. The isotopic signatures recorded for U and Ca in fracture water and calcite samples provide additional insights on U(VI) reduction behaviour and calcite growth rate. The removal efficiency of U from groundwater reaching 75% in borehole sections in fractured granite, and selective U accumulation in secondary minerals in exceedingly U-deficient groundwater shows the potential of these widespread mineralogical sinks for U in deep anoxic environments.
Multidimensional economic complexity and inclusive green growth
Authors: Stojkoski Viktor , Koch Philipp , Hidalgo César A.
Published: April 2023

To achieve inclusive green growth, countries need to consider a multiplicity of economic, social, and environmental factors. These are often captured by metrics of economic complexity derived from the geography of trade, thus missing key information on innovative activities. To bridge this gap, we combine trade data with data on patent applications and research publications to build models that significantly and robustly improve the ability of economic complexity metrics to explain international variations in inclusive green growth. We show that measures of complexity built on trade and patent data combine to explain future economic growth and income inequality and that countries that score high in all three metrics tend to exhibit lower emission intensities. These findings illustrate how the geography of trade, technology, and research combine to explain inclusive green growth.
Fragmentation and release of pristine and functionalized carbon nanotubes from epoxy-nanocomposites during accelerated weathering
Authors: Sahle-Demessie Endalkachew , Han Changseok , Varughese Eunice , Acrey Brad , Zepp Richard
Published: April 2023

Nano-enabled consumer materials could degrade during their use or end-of-life disposal due to weathering. Understanding the potential risks from the release and the toxicity of embedded nanomaterial is needed.
Health risks due to intrusion into the drinking water distribution network: hydraulic modelling and quantitative microbial risk assessment
Authors: Odhiambo Michael , Viñas Victor , Sokolova Ekaterina , Pettersson Thomas J. R.
Published: April 2023

This work provides a valuable application of the QMRA framework in a real distribution network, using available data from the water supplier and validated with other readily available sources.
Efficient detection ofl-aspartic acid andl-glutamic acid by self-assembled fluorescent microparticles with AIE and FRET activities
Authors: Qu Wen-Juan , Liu Tingting , Chai Yongping , Ji Dongyan , Che Yu-Xin , Hu Jian-Peng , Yao Hong , Lin Qi , Wei Tai-Bao , Shi Bingbing
Published: April 2023

The detection ofl-aspartic acid andl-glutamic acid was tackled using fluorescent microparticles constructed by the combination of aggregation-induced emission and self-assembly-induced Förster resonance energy transfer.
Activation of peroxymonosulfate by palygorskite supported Co–Fe for water treatment
Authors: Xia Wenxiang , Wu Qianqian , Huang Rui , Tao Yinglu , Wang Kaimei , Wu Shuxiao , Wang Songxue , Wang Mingli , Li Qingsheng
Published: April 2023

In the present work, palygorskite (PAL) supported Co–Fe oxides (CoFe@PAL) were prepared and used as a peroxymonosulfate (PMS) activator for removal of rhodamine B (RhB) in water.
Ex vivo activation of dendritic cells via coacervate-mediated exogenous tumor cell lysate delivery
Authors: Seong Jihyun , Jeong Sehwan , Kim Sungjun , Yun Seojeong , Baek Yujin , Kim Kyobum
Published: April 2023

Coacervate-mediated exogenous tumor cell lysate (TCL) delivery for effective ex vivo dendritic cell (DC) activation.
A Cu medium designed Z-scheme ZnO–Cu–CdS heterojunction photocatalyst for stable and excellent H2 evolution, methylene blue degradation, and CO2 reduction
Authors: Ahmad Irshad , Shukrullah Shazia , Naz Muhammad Yasin , Bhatti Haq Nawaz
Published: April 2023

A ZnO–Cu–CdS Z-scheme heterojunction system was prepared by a sol–gel process and its photocatalytic activity was evaluated for H2 evolution, methylene blue degradation, and CO2 reduction under visible light illumination.
High Mg2+ conduction in three-dimensional pores of a metal–organic framework under organic vapors
Authors: Aoki Kouhei , Kato Kenichi , Sadakiyo Masaaki
Published: April 2023

A Mg2+-conductive MOF was created with small-sized three-dimensional pores. The sample showed superionic conductivity at room temperature under guest vapors.
Aqueous solutions of super reduced polyoxotungstates as electron storage systems
Authors: Zhao Tingting , Bell Nicola L. , Chisholm Greig , Kandasamy Balamurugan , Long De-Liang , Cronin Leroy
Published: April 2023

The cation/proton exchange illustration during the reduction/reoxidation process of {P5W30}.
Asymmetric aldol reaction catalyzed by amino acid tetrapeptides (l-Pro-l-Pro-l-Phe-l-Phe-OMe)
Authors: Wang Yaodong , Wang Yudan , Liu Lijia , Sang Kexiao , Zhang Chunhong , Satoh Toshifumi
Published: April 2023

The heterogeneous oligopeptide catalyst l-Pro-l-Pro-l-Phe-l-Phe-OMe was synthesized using aromatic amino acids and proline dipeptides. The product has a high ee value (up to 98%) in catalyzing the aldol reaction.
How can you trust what you read?
Authors: Copsey May C. , Cooper Andrew I.
Published: April 2023

Chemical Science is introducing the option of transparent peer-review for authors. Editor-in-Chief Andy Cooper and Executive Editor May Copsey take a look at the reasons why, and how this will work.
A surface-grafted hydrogel demonstrating thermoresponsive adhesive strength change
Authors: Akimoto Aya M. , Ohta Yuji , Koizumi Yuki , Ishii Taichi , Endo Masaru , Enomoto Takafumi , Nishimoto Taihei , Yoshida Ryo
Published: April 2023

We designed a poly(N-isopropylacrylamide) (PNIPAAm) surface-grafted hydrogel (SG gel) exhibiting thermoresponsive adhesive changes to a Bakelite plate owing to the control of hydrophobic interactions.
Unraveling the origin of improved photovoltaic performance in acceptor–acceptor-structured perylene-diimide-based polymeric acceptors through partially fluorinating benzo[c][1,2,5]thiadiazole
Authors: Tong Junfeng , Liu Wuyan , Huang Yubo , Li Zheyu , Wang Yan , Bai Suiyan , Liang Zezhou , Yan Lihe , Li Jianfeng , Xia Yangjun
Published: April 2023

PPDI-DTFBT not only possessed better molecular planarity and lower exciton binding energy (Eb) but also exhibited faster and efficient exciton dissociation and transfer, leading to an increased PCE of 6.04%.
Side-chain modification of non-fullerene acceptors for organic solar cells with efficiency over 18%
Authors: Li Zhixiang , Jiang Changzun , Chen Xin , Song Guangkun , Wan Xiangjian , Kan Bin , Duan Tainan , Knyazeva Ekaterina A. , Rakitin Oleg A. , Chen Yongsheng
Published: April 2023

A new synthetic route to realize efficient screening of aryl side chains on the Y6 skeleton was reported, and then three acceptors with different side chains were synthesized. Among them, the BTP-OC6-based device exhibits the best PCE and stability.
60 years of the Colworth Medal
Authors: Ollett Lucy
Published: April 2023

The Colworth Medal is an esteemed annual award for outstanding research by a young biochemist of any nationality who has carried out the majority of their work in the UK or Republic of Ireland. Donated in 1963 by Unilever Research Colworth Laboratory, the award is made to an early-career scientist who is within 10 years of receiving their highest qualification. Interviews with past winners from 1963 to 2013 were previously published throughout 2013. To celebrate the 60th anniversary of the Colworth Medal, interviews with our latest winners will appear in The Biochemist throughout 2023. In this issue, we will hear from Professor David Grainger (2016) and Professor Matt Johnson (2018).
Discrete‐time modelling methodology of networked control systems under packet delay and dropout
Authors: Mohajeri Kamran , Madadi Ali , Tavassoli Babak , Rahiman Wan
Published: April 2023

Models and control techniques for networked control systems (NCSs) can be divided into continuous‐time and discrete‐time types. Unlike the continuous‐time analysis, literature on discrete‐time analysis and control of NCSs under packet delay and dropout shows a variety of different models. However, a systematic study of these models is absent in the literature. This article is a methodology for these models. Different factors involved in making this variety are discussed. The models are described and it is shown how they are different or related to each other. The models are from the existing literature. However, to complete the methodology some of the models are introduced by the authors. Furthermore, the concept of sequence matrix is introduced which helps to differentiate some models and should be considered when NCS is analysed as a switched linear system. This methodology can be used as a basis for selecting the suitable model in analysis and design of NCSs. Denial of service (DoS) attack and time delay switch (TDS) attack can be considered as packet dropout and packet delay respectively. Thus, this methodology can also be used in analysis and design of NCS under these cyber‐physical attacks.
X-ray flashes from the low-mass X-ray binary IGR J17407−2808
Authors: Ducci L. , Malacaria C. , Romano P. , Bozzo E. , Berton M. , Santangelo A. , Congiu E.
Published: April 2023

IGR J17407−2808 is an enigmatic and poorly studied X-ray binary that was recently observed quasi-simultaneously with NuSTAR and XMM-Newton. In this paper we report the results of this observational campaign. During the first 60 ks of observation, the source was caught in a relatively low emission state characterised by a modest variability and an average flux of ∼8.3 × 10−13 erg cm−2 s−1 (4−60 keV). Subsequently, IGR J17407−2808 entered a significantly more active emission state that persisted for the remaining ∼40 ks of the NuSTAR observation. During this state, IGR J17407−2808 displayed several fast X-ray flares of ∼1 − 100 s in duration and featuring profiles with either single or multiple peaks. The source flux in the flaring state reached values as high as ∼2 × 10−9 erg cm−2 s−1 (4−60 keV), leading to a measured dynamic range during the NuSTAR and XMM-Newton campaign of ≳103. We also analysed available archival photometric near-infrared data for IGR J17407−2808 in order to improve the constraints available so far on the nature of the donor star hosted in this system. Our analysis shows that the donor star can be either a rare K or M-type sub-subgiant, a K-type main sequence or subgiant star. Our findings support the classification of IGR J17407−2808 as a low-mass X-ray binary. We discuss the X-ray behaviour of the source as recorded by NuSTAR and XMM-Newton in view of this revised classification.
Study on the Emergence and Audience Preference of Chinese Drama Costume Revised by Network Novels
Authors: Wu Dongyi
Published: April 2023

Recently, TV dramas reedited by network novels have become the main content of Chinese popular culture. Based on analyzing the phenomenon of its high communication influence, the cross-media narration of the works greatly affects its communication. This study adopts the case study method, combined with the text analysis of TV dramas. This paper finds that the adaptation of online novels to film and television works is more prominent in artistic expression. This paper depicts that online novels adapt film and television works, as it may focus on the diversity of media texts through cross-media narration study.
Disney IP derivative product marketing--A case study of LinaBell
Authors: Chai Yaxin
Published: April 2023

In recent years, the culture of “cute things” has blossomed everywhere. People use cute things to cure their inner stress. Disney’s doll LinaBell has been widely spread for her cute appearance. Behind the popularity of LinaBell is the deep grasp of people’s inner emotions and the precise implementation of marketing strategy. As the derivative of Disney IP, how did LinaBell develop her own marketing strategy in the background with the characteristics of The Times and achieve success?