bluuebunny/crossref_metadata_2025 huggingface dataset:
Middle Pleistocene re-organization of Australian Monsoon
Authors: Gong Li , Holbourn Ann , Kuhnt Wolfgang , Opdyke Bradley , Zhang Yan , Ravelo Ana Christina , Zhang Peng , Xu Jian , Matsuzaki Kenji , Aiello Ivano , Beil Sebastian , Andersen Nils
Published: April 2023

The sensitivity of the Australian Monsoon to changing climate boundary conditions remains controversial due to limited understanding of forcing processes and past variability. Here, we reconstruct austral summer monsoonal discharge and wind-driven winter productivity across the Middle Pleistocene Transition (MPT) in a sediment sequence drilled off NW Australia. We show that monsoonal precipitation and runoff primarily responded to precessional insolation forcing until ~0.95 Ma, but exhibited heightened sensitivity to ice volume andpCO2related feedbacks following intensification of glacial-interglacial cycles. Our records further suggest that summer monsoon variability at the precessional band was closely tied to the thermal evolution of the Indo-Pacific Warm Pool and strength of the Walker circulation over the past ~1.6 Myr. By contrast, productivity proxy records consistently tracked glacial-interglacial variability, reflecting changing rhythms in polar ice fluctuations and Hadley circulation strength. We conclude that the Australian Monsoon underwent a major re-organization across the MPT and that extratropical feedbacks were instrumental in driving short- and long-term variability.
Active and durable R2MnRuO7 pyrochlores with low Ru content for acidic oxygen evolution
Authors: Galyamin Dmitry , Torrero Jorge , Rodríguez Isabel , Kolb Manuel J. , Ferrer Pilar , Pascual Laura , Salam Mohamed Abdel , Gianolio Diego , Celorrio Verónica , Mokhtar Mohamed , Garcia Sanchez Daniel , Gago Aldo Saul , Friedrich Kaspar Andreas , Peña Miguel A. , Alonso José Antonio , Calle-Vallejo Federico , Retuerto María , Rojas Sergio
Published: April 2023

The production of green hydrogen in water electrolyzers is limited by the oxygen evolution reaction (OER). State-of-the-art electrocatalysts are based on Ir. Ru electrocatalysts are a suitable alternative provided their performance is improved. Here we show that low-Ru-content pyrochlores (R2MnRuO7, R = Y, Tb and Dy) display high activity and durability for the OER in acidic media. Y2MnRuO7 is the most stable catalyst, displaying 1.5 V at 10 mA cm−2 for 40 h, or 5000 cycles up to 1.7 V. Computational and experimental results show that the high performance is owed to Ru sites embedded in RuMnOx surface layers. A water electrolyser with Y2MnRuO7 (with only 0.2 mgRu cm−2) reaches 1 A cm−2 at 1.75 V, remaining stable at 200 mA cm−2 for more than 24 h. These results encourage further investigation on Ru catalysts in which a partial replacement of Ru by inexpensive cations can enhance the OER performance.
A cationic motif upstream Engrailed2 homeodomain controls cell internalization through selective interaction with heparan sulfates
Authors: Cardon Sébastien , Hervis Yadira P. , Bolbach Gérard , Lopin-Bon Chrystel , Jacquinet Jean-Claude , Illien Françoise , Walrant Astrid , Ravault Delphine , He Bingwei , Molina Laura , Burlina Fabienne , Lequin Olivier , Joliot Alain , Carlier Ludovic , Sagan Sandrine
Published: April 2023

Engrailed2 (En2) is a transcription factor that transfers from cell to cell through unconventional pathways. The poorly understood internalization mechanism of this cationic protein is proposed to require an initial interaction with cell-surface glycosaminoglycans (GAGs). To decipher the role of GAGs in En2 internalization, we have quantified the entry of its homeodomain region in model cells that differ in their content in cell-surface GAGs. The binding specificity to GAGs and the influence of this interaction on the structure and dynamics of En2 was also investigated at the amino acid level. Our results show that a high-affinity GAG-binding sequence (RKPKKKNPNKEDKRPR), upstream of the homeodomain, controls En2 internalization through selective interactions with highly-sulfated heparan sulfate GAGs. Our data underline the functional importance of the intrinsically disordered basic region upstream of En2 internalization domain, and demonstrate the critical role of GAGs as an entry gate, finely tuning homeoprotein capacity to internalize into cells.
Tenascin C+ papillary fibroblasts facilitate neuro-immune interaction in a mouse model of psoriasis
Authors: Cai Xiaojie , Han Maoying , Lou Fangzhou , Sun Yang , Yin Qianqian , Sun Libo , Wang Zhikai , Li Xiangxiao , Zhou Hong , Xu Zhenyao , Wang Hong , Deng Siyu , Zheng Xichen , Zhang Taiyu , Li Qun , Zhou Bin , Wang Honglin
Published: April 2023

Dermal fibroblasts and cutaneous nerves are important players in skin diseases, while their reciprocal roles during skin inflammation have not been characterized. Here we identify an inflammation-induced subset of papillary fibroblasts that promotes aberrant neurite outgrowth and psoriasiform skin inflammation by secreting the extracellular matrix protein tenascin-C (TNC). Single-cell analysis of fibroblast lineages reveals aTnc+papillary fibroblast subset with pro-axonogenesis and neuro-regulation transcriptomic hallmarks. TNC overexpression in fibroblasts boosts neurite outgrowth in co-cultured neurons, while fibroblast-specific TNC ablation suppresses hyperinnervation and alleviates skin inflammation in male mice modeling psoriasis. Dermal γδT cells, the main producers of type 17 pathogenic cytokines, frequently contact nerve fibers in mouse psoriasiform lesions and are likely modulated by postsynaptic signals. Overall, our results highlight the role of an inflammation-responsive fibroblast subset in facilitating neuro-immune synapse formation and suggest potential avenues for future therapeutic research.
Encoding reprogrammable properties into magneto-mechanical materials via topology optimization
Authors: Zhao Zhi , Zhang Xiaojia Shelly
Published: April 2023

The properties of materials and structures typically remain fixed after being designed and manufactured. There is a growing interest in systems with the capability of altering their behaviors without changing geometries or material constitutions, because such reprogrammable behaviors could unlock multiple functionalities within a single design. We introduce an optimization-driven approach, based on multi-objective magneto-mechanical topology optimization, to design magneto-active metamaterials and structures whose properties can be seamlessly reprogrammed by switching on and off the external stimuli fields. This optimized material system exhibits one response under pure mechanical loading, and switches to a distinct response under joint mechanical and magnetic stimuli. We discover and experimentally demonstrate magneto-mechanical metamaterials and metastructures that realize a wide range of reprogrammable responses, including multi-functional actuation responses, adaptable snap-buckling behaviors, switchable deformation modes, and tunable bistability. The proposed approach paves the way for promising applications such as magnetic actuators, soft robots, and energy harvesters.
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome
Authors: Russell Seongmi K. , Harrison Jessica K. , Olson Benjamin S. , Lee Hyung Joo , O’Brien Valerie P. , Xing Xiaoyun , Livny Jonathan , Yu Lu , Roberson Elisha D. O. , Bomjan Rajdeep , Fan Changxu , Sha Marina , Estfanous Shady , Amer Amal O. , Colonna Marco , Stappenbeck Thaddeus S. , Wang Ting , Hannan Thomas J. , Hultgren Scott J.
Published: April 2023

Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding—responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection.
Maximum likelihood pandemic-scale phylogenetics
Authors: De Maio Nicola , Kalaghatgi Prabhav , Turakhia Yatish , Corbett-Detig Russell , Minh Bui Quang , Goldman Nick
Published: April 2023

Phylogenetics has a crucial role in genomic epidemiology. Enabled by unparalleled volumes of genome sequence data generated to study and help contain the COVID-19 pandemic, phylogenetic analyses of SARS-CoV-2 genomes have shed light on the virus’s origins, spread, and the emergence and reproductive success of new variants. However, most phylogenetic approaches, including maximum likelihood and Bayesian methods, cannot scale to the size of the datasets from the current pandemic. We present ‘MAximum Parsimonious Likelihood Estimation’ (MAPLE), an approach for likelihood-based phylogenetic analysis of epidemiological genomic datasets at unprecedented scales. MAPLE infers SARS-CoV-2 phylogenies more accurately than existing maximum likelihood approaches while running up to thousands of times faster, and requiring at least 100 times less memory on large datasets. This extends the reach of genomic epidemiology, allowing the continued use of accurate phylogenetic, phylogeographic and phylodynamic analyses on datasets of millions of genomes.
Comparison of transformations for single-cell RNA-seq data
Authors: Ahlmann-Eltze Constantin , Huber Wolfgang
Published: April 2023

The count table, a numeric matrix of genes × cells, is the basic input data structure in the analysis of single-cell RNA-sequencing data. A common preprocessing step is to adjust the counts for variable sampling efficiency and to transform them so that the variance is similar across the dynamic range. These steps are intended to make subsequent application of generic statistical methods more palatable. Here, we describe four transformation approaches based on the delta method, model residuals, inferred latent expression state and factor analysis. We compare their strengths and weaknesses and find that the latter three have appealing theoretical properties; however, in benchmarks using simulated and real-world data, it turns out that a rather simple approach, namely, the logarithm with a pseudo-count followed by principal-component analysis, performs as well or better than the more sophisticated alternatives. This result highlights limitations of current theoretical analysis as assessed by bottom-line performance benchmarks.
Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape
Authors: Ren Jingyi , Zhou Haowen , Zeng Hu , Wang Connie Kangni , Huang Jiahao , Qiu Xiaojie , Sui Xin , Li Qiang , Wu Xunwei , Lin Zuwan , Lo Jennifer A. , Maher Kamal , He Yichun , Tang Xin , Lam Judson , Chen Hongyu , Li Brian , Fisher David E. , Liu Jia , Wang Xiao
Published: April 2023

Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA remain obscured due to the limitations of existing transcriptomics methods. Here, we report TEMPOmap—a method that uncovers subcellular RNA profiles across time and space at the single-cell level. TEMPOmap integrates pulse-chase metabolic labeling with highly multiplexed three-dimensional in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape in various human cells from transcription and translocation to degradation. Clustering analysis of RNA kinetic parameters across single cells revealed ‘kinetic gene clusters’ whose expression patterns were shaped by multistep kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated in a cell-state- and cell-type-dependent manner. Spatiotemporally resolved transcriptomics provides a gateway to uncovering new spatiotemporal gene regulation principles.
A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation
Authors: Sanghai Zahra A. , Piwowarczyk Rafal , Broeck Arnaud Vanden , Klinge Sebastian
Published: April 2023

During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the formation of an early large subunit assembly checkpoint precedes the separation of small and large subunit maturation, its mechanism of action and function remain unknown. Here, we report the cryo-electron microscopy structure of the yeast co-transcriptional large ribosomal subunit assembly intermediate that serves as a checkpoint. The structure provides the mechanistic basis for how quality-control pathways are established through co-transcriptional ribosome assembly factors, that structurally interrogate, remodel and, together with ribosomal proteins, cooperatively stabilize correctly folded pre-ribosomal RNA. Our findings thus provide a molecular explanation for quality control during eukaryotic ribosome assembly in the nucleolus.
AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap
Authors: Parejo M. , Talenti A. , Richardson M. , Vignal A. , Barnett M. , Wragg D.
Published: April 2023

Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Thus the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.
New insights into how popular electronic cigarette aerosols and aerosol constituents affect SARS-CoV-2 infection of human bronchial epithelial cells
Authors: Phandthong Rattapol , Wong Man , Song Ann , Martinez Teresa , Talbot Prue
Published: April 2023

The relationship between the use of tobacco products and SARS-CoV-2 infection is poorly understood and controversial. Few studies have examined the effect of electronic cigarettes (ECs) on SARS-CoV-2 infection. We tested the hypothesis that EC fluids and aerosols with nicotine promote SARS-COV-2 infection by increasing viral entry into human respiratory epithelial cells. Responses of BEAS-2B cells to JUUL aerosols or their individual constituents were compared using three exposure platforms: submerged culture, air–liquid-interface (ALI) exposure in a cloud chamber, and ALI exposure in a Cultex system, which produces authentic heated EC aerosols. In general, nicotine and nicotine + propylene glycol/vegetable glycerin aerosols increased ACE2 (angiotensin converting enzyme 2) levels, the SARS-CoV-2 receptor; and increased the activity of TMPRSS2 (transmembrane serine protease 2), an enzyme essential for viral entry. Lentivirus pseudoparticles with spike protein were used to test viral penetration. Exposure to nicotine, EC fluids, or aerosols altered the infection machinery and increased viral entry into cells. While most data were in good agreement across the three exposure platforms, cells were more responsive to treatments when exposed at the ALI in the Cultex system, even though the exposures were brief and intermittent. While both nicotine and JUUL aerosols increased SARS-CoV-2 infection, JUUL significantly decreased the effect of nicotine alone. These data support the idea that vaping can increase the likelihood of contracting COVID-19 and that e-liquid composition may modulate this effect.
Cerebral hypoperfusion in post-COVID-19 cognitively impaired subjects revealed by arterial spin labeling MRI
Authors: Ajčević Miloš , Iscra Katerina , Furlanis Giovanni , Michelutti Marco , Miladinović Aleksandar , Buoite Stella Alex , Ukmar Maja , Cova Maria Assunta , Accardo Agostino , Manganotti Paolo
Published: April 2023

Cognitive impairment is one of the most prevalent symptoms of post Severe Acute Respiratory Syndrome COronaVirus 2 (SARS-CoV-2) state, which is known as Long COVID. Advanced neuroimaging techniques may contribute to a better understanding of the pathophysiological brain changes and the underlying mechanisms in post-COVID-19 subjects. We aimed at investigating regional cerebral perfusion alterations in post-COVID-19 subjects who reported a subjective cognitive impairment after a mild SARS-CoV-2 infection, using a non-invasive Arterial Spin Labeling (ASL) MRI technique and analysis. Using MRI-ASL image processing, we investigated the brain perfusion alterations in 24 patients (53.0 ± 14.5 years, 15F/9M) with persistent cognitive complaints in the post COVID-19 period. Voxelwise and region-of-interest analyses were performed to identify statistically significant differences in cerebral blood flow (CBF) maps between post-COVID-19 patients, and age and sex matched healthy controls (54.8 ± 9.1 years, 13F/9M). The results showed a significant hypoperfusion in a widespread cerebral network in the post-COVID-19 group, predominantly affecting the frontal cortex, as well as the parietal and temporal cortex, as identified by a non-parametric permutation testing (p < 0.05, FWE-corrected with TFCE). The hypoperfusion areas identified in the right hemisphere regions were more extensive. These findings support the hypothesis of a large network dysfunction in post-COVID subjects with cognitive complaints. The non-invasive nature of the ASL-MRI method may play an important role in the monitoring and prognosis of post-COVID-19 subjects.
The efficacy of a range of hygiene measures for boot cleaning to protect natural vegetation from Phytophthora cinnamomi
Authors: Liew Edward C. Y. , Phelan Maureen , McDougall Keith L.
Published: April 2023

Phytophthora cinnamomiis an oomycete found in the soil and capable of invading the roots of a wide range of host plants globally, potentially killing them and affecting the ecosystems they inhabit. This pathogen is often inadvertently dispersed in natural vegetation on the footwear of humans. A range of equipment is often provided or recommended to be carried for cleaning footwear in places whereP. cinnamomiposes a threat to biodiversity. These are typically a brush for mechanically removing soil and/or a disinfectant for killing the pathogen. Despite their widespread use, to our knowledge, the majority of hygiene measures have not been experimentally tested for their efficacy. In the current study, we tested whether two types of brush and the two most widely used disinfectants (70% methylated spirits and benzalkonium chloride) were effective in removing the pathogen from boots. We tested the brushes and disinfectants in two soil types and two moisture levels. All hygiene measures were found to be better than doing nothing, although some were only effective with sandy or dry soils. Benzalkonium chloride was largely ineffective as a spray but highly effective when used in a footbath. Brushing did not improve cleaning when used with 70% methylated spirits. None of the hygiene measures was completely effective for cleaning boots that had been in wet loamy soil. Our findings have important implications for management of this threat because some recommended hygiene practices are not doing what they claim.
Application of a novel deep eutectic solvent as a capable and new catalyst for the synthesis of tetrahydropyridines and 1,3-thiazolidin-4-ones
Authors: Goudarzi Hadis , Habibi Davood , Monem Arezo
Published: April 2023

A novel deep eutectic solvent (ETPP-Br/THF-TCA-DES) was prepared by a mixture of ethyl triphenylphosphonium bromide (ETPP-Br) and tetrahydrofuran-2,3,4,5-tetra-carboxylic acid (THF-TCA, mole ratio 7:3), characterized by FT-IR, TGA/DTA, densitometer, eutectic point, and 1H NMR techniques and used as a capable and new catalyst for the synthesis of two sets of compounds: (1) the four new [a(1–4)] and the eleven [a(5–15)] known alkyl 1,2,6-trisubstituted-4-[(hetero)arylamino]-1,2,5,6-tetrahydropyridine-3-carboxylates and (2) the two new [b(1–2)] and the eight [b(3–10)] known 1,3-thiazolidin-4-ones in DES with short reaction time, high yields, and easy recycling and separation of the DES catalyst. There is a nice consistency between the proposed structure of the DES compound, the integration values of the 1H NMR peaks and the ratio of ETPP-Br to THF-TCA obtained from the eutectic point phase diagram. Also, the decrease in splitting patterns of the peaks in DES, compared to the two starting materials can be the good evidence of the hydrogen bond formation between the two components.
Exogenous lactate augments exercise-induced improvement in memory but not in hippocampal neurogenesis
Authors: Hwang Deunsol , Kim Jisu , Kyun Sunghwan , Jang Inkwon , Kim Taeho , Park Hun-Young , Lim Kiwon
Published: April 2023

Adult hippocampal neurogenesis (AHN), the lifelong process of formation of new neurons in the mammalian brain, plays an important role in learning and memory. Exercise is an effective enhancer of AHN; however, the molecular mediators of exercise-induced AHN are unknown. Recently, lactate was considered as an important mediator of exercise-induced AHN. Therefore, we hypothesized that exercise with lactate intake could augment exercise-induced AHN. This study was conducted for 5 weeks with 7-week-old ICR male mice that performed mild-intensity exercise (just below lactate threshold, 55–60%VO2max) with or without oral administration of lactate 5 days/week. Cell proliferation, neuronal differentiation, neurogenesis-relevant factors, reference and retention memory, and spatial working memory were evaluated at the end of the experiment. The results showed that AHN was enhanced by lactate intake, but exercise-induced AHN was not augmented by exercise with lactate intake. Nevertheless, exercise-induced improvement in reference and retention memory was augmented by exercise with lactate intake. And spatial working memory was promoted by the co-treatment, also protein expression of hippocampal FNDC5, BDNF, PGC1α, and MCT2 were elevated by the co-treatment. Therefore, our findings suggest that lactate has a potential to be developed as a novel supplement that improves the positive effects of exercise on the hippocampus and its cognitive function.
Using inertial measurement units for quantifying the most intense jumping movements occurring in professional male volleyball players
Authors: Lima Ricardo Franco , Silva Ana Filipa , Matos Sérgio , de Oliveira Castro Henrique , Rebelo André , Clemente Filipe Manuel , Nobari Hadi
Published: April 2023

The purpose of this study was to use an inertial measurement unit (IMU) to analyze variations in the jump outcomes concerning weekly training days, and the dependencies between the number of jumps per minute and the jump height. An experimental research design was adopted across three weeks of the final play-off of a volleyball championship. Through an IMU, the external load of seven male elite volleyball athletes of a top rating team from Portuguese 1st Division (age: 30.5 ± 3.5 years; height: 200.2 ± 6.3 cm; body mass: 93.0 ± 8.1 kg; BMI: 23.1 ± 2.3 kg/m2) was monitored. Repeated measures ANOVA was executed to compare the outcomes between training days. It was observed a similar density of jumps during the week. However, when comparing MD-1 to MD-2, a more significant average number of jumps per minute was observed in MD-1 (1.3 ± 0.2 vs. 1.0 ± 0.2). Additionally, a positive, large and significant correlation was registered between the number of jumps and the height of the jump. Those results highlight the benefits of the specific training, leading to greater stimulation and improvement, in a game-like context, of the stretching-shortening cycle, observed in every jump action in volleyball.
PDLIM1 inhibits cell migration and invasion in diabetic retinopathy via negatively regulating Wnt3a
Authors: Xie Pinxue , You Qisheng , Zhu Jiang , Xie Wuxiang , Wei Ping , Zhu Siquan , Du Yunhui , Gao Xinxiao
Published: April 2023

The injury of vascular endothelial cells is a crucial factor in the development of diabetic retinopathy (DR). PDLIM1 (a member of the PDZ and LIM protein family) has been reported to exert an essential function in vascular diseases. This study aimed to elucidate the role of PDLIM1 on retinal vascular endothelial cells in DR. Immunofluorescence staining was used to localize the expression of PDLIM1 in the mouse retina. In some tumor diseases, PDLIM1 has been reported to play a key role in regulating the Wnt pathway. However, no in-depth reports have been found in DR. Retinal capillary endothelial cells (RCECs) were treated with high-glucose and high-lipid (HG/HL) culture medium, and siRNA transfection to investigate the role of PDLIM1 in DR. PDLIM1 and Wnt3a expression was confirmed by qRT-PCR and western blotting. Flow cytometry, Transwell assay, and scratch assay were used to test the ability of cell apoptosis, migration, and invasion. PDLIM1 was mainly expressed in the retinal pigment epithelium (RPE), ganglion cell layer (GCL), inner plexus layer (IPL), and outer plexus layer (OPL). HG/HL increased Wnt3a levels and promoted cell’s ability of apoptosis, migration, and invasion, which were reversed by the knockdown of PDLIM1. PDLIM1 was found to play a protective role in diabetic retinopathy by counter-regulating Wnt3a. PDLIM1 ameliorates cell apoptosis, migration, and invasion by negatively regulating Wnt3a in RCECs of DR, which suggests that PDLIM1 might be a promising therapeutic target for DR treatment.
A mathematical model for supercooling process and its application to frazil ice evolution
Authors: Yang Deming , Lian Jijian , Zhao Xin , Hou Qingzhi , Chen Yunfei , Zhang Yue
Published: April 2023

The calculation of the number of ice crystals for the model of frazil ice evolution is very important and affects the whole frazil events. In this paper, the general formula for the number of frazil ice crystals was established considering secondary nucleation, flocculation, gravity and turbulent entrainment, and ice crystals by melting. Meanwhile, two physical processes of secondary nucleation and flocculation were expressed by introducing critical impact velocity and the probability of flocculation from previous models. It has been found that the simulation results of frazil ice evolution are in good agreement with the experimental data and actual project. Then, Sobol method is carried out to judge parameters’ influence degree, which found the number of nuclei produced $$E$$
E
is the most sensitive and has the greatest influence on the model results. In addition, sensitivity analysis of these parameters shows that they can affect the maximum supercooling and the period of supercooling. Therefore, the calculation method of the number of ice crystals is applied, which provides technical support for exploring the water temperature and internal relationship of frazil ice evolution.
Mechanism of bubbles formation and anomalous phase separation in the CoNiP system
Authors: Panasyuk Maria I. , Zubar Tatiana I. , Usovich Tatsiana I. , Tishkevich Daria I. , Kanafyev Oleg D. , Fedkin Vladimir A. , Kotelnikova Anna N. , Trukhanov Sergei V. , Michels Dominik , Lyakhov Dmitry , Vershinina Tatiana N. , Fedosyuk Valery M. , Trukhanov Alex V.
Published: April 2023

This study announces the anomalous phase separation in CoNiP alloy electroplating. The observed phenomenon of the formation of magnetic bubbles was described for the first time for this triple CoNiP system. This study briefly covers all stages of magnetic bubble formation, starting from the formation of an amorphous phosphor-rich sublayer, followed by nucleation centers, and finally cobalt-rich bubbles. An explanation for the anomalous mechanism of bubble formation was found in the effects of additives and the phenomena of depolarization and superpolarization.
Comparative study on landslide susceptibility mapping based on unbalanced sample ratio
Authors: Tang Li , Yu Xianyu , Jiang Weiwei , Zhou Jianguo
Published: April 2023

The Zigui–Badong section of the Three Gorges Reservoir area is used as the research area in this study to research the impact of unbalanced sample sets on Landslide Susceptibility Mapping (LSM) and determine the sample ratio interval with the best performance for different models. We employ 12 LSM factors, five training sample sets with different sample ratios (1:1, 1:2, 1:4, 1:8, and 1:16), and C5.0, Support Vector Machine (SVM), Logistic Regression (LR), and one-dimensional Convolution Neural Network (CNN) models are used to obtain landslide susceptibility index and landslide susceptibility zoning in the study area, respectively. The prediction performance of the model is evaluated by the receiver operating characteristic curve area under the curve value, five statistical methods, and specific category precision. The results show that the CNN, SVM, and LR models in the sample ratio of 1:2 achieve better performance than on the balanced sample set, which indicates the importance of the unbalanced sample set in training the LSM modeling. The C5.0 model is always in a state of overfitting in this study and needs to be further studied. The conclusions put forward in this study help improve the scientificity and reliability of LSM.
LCRMP-1 is required for spermatogenesis and stabilises spermatid F-actin organization via the PI3K-Akt pathway
Authors: Chang Jung-Hsuan , Chou Chia-Hua , Wu Jui-Ching , Liao Keng-Mao , Luo Wei-Jia , Hsu Wei-Lun , Chen Xuan-Ren , Yu Sung-Liang , Pan Szu-Hua , Yang Pan-Chyr , Su Kang-Yi
Published: April 2023

Long-form collapsin response mediator protein-1 (LCRMP-1) belongs to the CRMP family which comprises brain-enriched proteins responsible for axon guidance. However, its role in spermatogenesis remains unclear. Here we find that LCRMP-1 is abundantly expressed in the testis. To characterize its physiological function, we generate LCRMP-1-deficient mice (Lcrmp-1−/−). These mice exhibit aberrant spermiation with apoptotic spermatids, oligospermia, and accumulation of immature testicular cells, contributing to reduced fertility. In the seminiferous epithelial cycle, LCRMP-1 expression pattern varies in a stage-dependent manner. LCRMP-1 is highly expressed in spermatids during spermatogenesis and especially localized to the spermiation machinery during spermiation. Mechanistically, LCRMP-1 deficiency causes disorganized F-actin due to unbalanced signaling of F-actin dynamics through upregulated PI3K-Akt-mTOR signaling. In conclusion, LCRMP-1 maintains spermatogenesis homeostasis by modulating cytoskeleton remodeling for spermatozoa release.
Machine learning-enabled globally guaranteed evolutionary computation
Authors: Li Bin , Wei Ziping , Wu Jingjing , Yu Shuai , Zhang Tian , Zhu Chunli , Zheng Dezhi , Guo Weisi , Zhao Chenglin , Zhang Jun
Published: April 2023

Evolutionary computation, for example, particle swarm optimization, has impressive achievements in solving complex problems in science and industry; however, an important open problem in evolutionary computation is that there is no theoretical guarantee of reaching the global optimum and general reliability; this is due to the lack of a unified representation of diverse problem structures and a generic mechanism by which to avoid local optima. This unresolved challenge impairs trust in the applicability of evolutionary computation to a variety of problems. Here we report an evolutionary computation framework aided by machine learning, named EVOLER, which enables the theoretically guaranteed global optimization of a range of complex non-convex problems. This is achieved by: (1) learning a low-rank representation of a problem with limited samples, which helps to identify an attention subspace; and (2) exploring this small attention subspace via the evolutionary computation method, which helps to reliably avoid local optima. As validated on 20 challenging benchmarks, this method finds the global optimum with a probability approaching 1. We use EVOLER to tackle two important problems: power grid dispatch and the inverse design of nanophotonics devices. The method consistently reached optimal results that were challenging to achieve with previous state-of-the-art methods. EVOLER takes a leap forwards in globally guaranteed evolutionary computation, overcoming the uncertainty of data-driven black-box methods, and offering broad prospects for tackling complex real-world problems.
Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab
Authors: Nabbi Arash , Danesh Arnavaz , Espin-Garcia Osvaldo , Pedersen Stephanie , Wellum Johanna , Fu Lingyan Helen , Paulson Joseph N. , Geoerger Birgit , Marshall Lynley V. , Trippett Tanya , Rossato Gianluca , Pugh Trevor J. , Hutchinson Katherine E.
Published: April 2023

We report herein an exploratory biomarker analysis of refractory tumors collected from pediatric patients before atezolizumab therapy (iMATRIX-atezolizumab, NCT02541604). Elevated levels of CD8+ T cells and PD-L1 were associated with progression-free survival and a diverse baseline infiltrating T-cell receptor repertoire was prognostic. Differential gene expression analysis revealed elevated expression of CALCA (preprocalcitonin) and CCDC183 (highly expressed in testes) in patients who experienced clinical activity, suggesting that tumor neoantigens from these genes may contribute to immune response. In patients who experienced partial response or stable disease, elevated Igα2 expression correlated with T- and B-cell infiltration, suggesting that tertiary lymphoid structures existed in these patients’ tumors. Consensus gene co-expression network analysis identified core cellular pathways that may play a role in antitumor immunity. Our study uncovers features associated with response to immune-checkpoint inhibition in pediatric patients with cancer and provides biological and translational insights to guide prospective biomarker profiling in future clinical trials.
PD-L1 blockade in combination with carboplatin as immune induction in metastatic lobular breast cancer: the GELATO trial
Authors: Voorwerk Leonie , Isaeva Olga I. , Horlings Hugo M. , Balduzzi Sara , Chelushkin Maksim , Bakker Noor A. M. , Champanhet Elisa , Garner Hannah , Sikorska Karolina , Loo Claudette E. , Kemper Inge , Mandjes Ingrid A. M. , de Maaker Michiel , van Geel Jasper J. L. , Boers Jorianne , de Boer Maaike , Salgado Roberto , van Dongen Marloes G. J. , Sonke Gabe S. , de Visser Karin E. , Schumacher Ton N. , Blank Christian U. , Wessels Lodewyk F. A. , Jager Agnes , Tjan-Heijnen Vivianne C. G. , Schröder Carolien P. , Linn Sabine C. , Kok Marleen
Published: April 2023

Invasive lobular breast cancer (ILC) is the second most common histological breast cancer subtype, but ILC-specific trials are lacking. Translational research revealed an immune-related ILC subset, and in mouse ILC models, synergy between immune checkpoint blockade and platinum was observed. In the phase II GELATO trial (NCT03147040), patients with metastatic ILC were treated with weekly carboplatin (area under the curve 1.5 mg ml–1 min–1) as immune induction for 12 weeks and atezolizumab (PD-L1 blockade; triweekly) from the third week until progression. Four of 23 evaluable patients had a partial response (17%), and 2 had stable disease, resulting in a clinical benefit rate of 26%. From these six patients, four had triple-negative ILC (TN-ILC). We observed higher CD8+ T cell infiltration, immune checkpoint expression and exhausted T cells after treatment. With this GELATO trial, we show that ILC-specific clinical trials are feasible and demonstrate promising antitumor activity of atezolizumab with carboplatin, particularly for TN-ILC, and provide insights for the design of highly needed ILC-specific trials.
Quantitative characterization of orogens through isotopic mapping
Authors: Wang Tao , Xiao Wenjiao , Collins William J. , Tong Ying , Hou Zengqian , Huang He , Wang Xiaoxia , Lin Shoufa , Seltmann Reimar , Wang Chaoyang , Han Baofu
Published: April 2023

The relationship between orogens and crustal growth is a fundamental issue in the Earth sciences. Here we present Nd isotope mapping results of felsic and intermediate igneous rocks from eight representative and well-studied Phanerozoic orogens. The results illustrate the distribution of isotopic domains that reflect the compositional architecture of the orogens. We calculated the areal proportion of juvenile crust and divided the orogens into five types: (i) highly juvenile (with >70% juvenile crust); (ii) moderately juvenile (70–50%; e.g., the Altaids with ~58% and the North American Cordillera with ~54%); (iii) mixed juvenile and reworked (50–30%; e.g., the Newfoundland Appalachians with ~40% and the Lachlan Orogen with ~31%); (iv) reworked (30–10%); (v) highly reworked (<10%; e.g., the Tethyan Tibet (~3%), Caledonides (~1%), Variscides (~1%), and the Qinling-Dabie Orogen (<1%)). This study presents an approach for quantitatively characterizing orogens based on compositional architecture through isotope mapping, and for investigating the relationships between orogenesis and continental growth.
Rapid and quantitative detection of the inflammatory marker neopterin based on a visible luminescent Zn(ii)–Eu(iii) nanocluster
Authors: Zhao Jinni , Leng Xilong , Lin Jiazhao , Yang Xiaoping , Lv Xiaoli , Huang Xianfeng , Yang Zhi , Schipper Desmond
Published: April 2023

A 48-metal Zn(ii)–Eu(iii) nanocluster (molecular sizes: 1.3 × 2.8 × 3.1 nm) was constructed for the rapid and quantitative luminescence detection of neopterin as an inflammatory marker.
Folate modified dual pH/reduction-responsive mixed micelles assembled using FA-PEG-PDEAEMA and PEG-SS-PCL for doxorubicin delivery
Authors: Yang Chufen , Wang Delin , Liu Wenyao , Yang Zexiong , He Teng , Chen Fang , Lin Wenjing
Published: April 2023

Superiority of FA-PEG112-PDEAEMA40/PEG112-SS-PCL70 mixed micelles with high loading capacity, well controlled release, and active targeting-enhanced inhibitory effects on HepG2 cells was found.
Coumarin-based derivatives targetingTrypanosoma cruzicruzain andTrypanosoma bruceicathepsin L-like proteases
Authors: Nunes Jéssica Alves , Silva Fabrícia Nunes da , Silva Elany Barbosa da , Costa Clara Andrezza Crisóstomo Bezerra , Freitas Johnnatan Duarte de , Mendonça-Junior Francisco Jaime Bezerra , Giardini Miriam Aparecida , Siqueira-Neto Jair Lage de , McKerrow James H. , Rodrigues Teixeira Thaiz , Odeesho Louis William , Caffrey Conor R. , Cardoso Sílvia Helena , Silva-Júnior Edeildo Ferreira da
Published: April 2023

Trypanosoma cruzi(Chagas diseases – also named American trypanosomiasis) andT. brucei(human African trypanosomiasis – HAT) negatively impact public health, being endemic in several countries and leading to thousands of deaths per year.
Microkinetic insights into the role of catalyst and water activity on the nucleation, growth, and dissolution during COF-5 synthesis
Authors: Dighe Anish V. , Bhawnani Rajan R. , Podupu Prem K.R. , Dandu Naveen K. , Ngo Anh T. , Chaudhuri Santanu , Singh Meenesh R.
Published: April 2023

The time-resolved in situ Fourier transform infrared spectroscopy coupled with a large-scale microkinetic model unravel the roles of catalyst pKa on the yield of covalent-organic framework and the effect of water on growth rate and size distribution.
Molecular understanding of Eubacterium limosum chemostat methanol metabolism
Authors: Wood Jamin C. , Gonzalez-Garcia R. Axayacatl , Daygon Dara , Talbo Gert , Plan Manuel R. , Marcellin Esteban , Virdis Bernardino
Published: April 2023

Methanol is a promising renewable energy carrier that can be used as a favourable substrate for biotechnology, due to its high energy efficiency conversion and ease of integration within existing infrastructure.
An in silico osmotic pressure approach allows characterization of pressure–area isotherms of lipid monolayers at low molecular areas
Authors: Prabhu Janak , Singh Akhil Pratap , Vanni Stefano
Published: April 2023

We present an improved computational methodology to characterise surface pressure–area (Π–A) isotherms for Langmuir monolayers. Our approach is particularly suited to the study of Π–A isotherms at low molecular areas.
Metric-based analysis of FTIR data to discriminate tissue types in oral cancer
Authors: Ellis Barnaby G. , Ingham James , Whitley Conor A. , Al Jedani Safaa , Gunning Philip J. , Gardner Peter , Shaw Richard J. , Barrett Steve D. , Triantafyllou Asterios , Risk Janet M. , Smith Caroline I. , Weightman Peter
Published: April 2023

Comparison of (a) H&E image of oral squamous cell carcinoma with (b) ratio of absorbance at 1252 cm−1/1285 cm−1 and (c) pseudo-coloured labelled image of seven types of tissue found in oral tissue.
Using a biphasic system and digital imaging analysis with chemometric tools for simultaneous determination of Cu2+ and furfural in cachaça
Authors: de O.K. Franco Mathews , Cardoso Wilson J. , Vilanculo Castelo B. , dos Santos Vagner B. , de Almeida João Paulo B. , Capitán-Vallvey Luis Fermin , Suarez Willian T.
Published: April 2023

The present study reports, for the first time, the development and application of a method based on digital imaging analysis for the simultaneous determination of Cu2+ and furfural in cachaça samples using a two-phase system and chemometrics tools.
Metal-rich cascade nanosystem for dual-pathway ferroptosis resistance regulation and photothermal effect for efficient tumor combination therapy
Authors: Liu Xinran , Guan Ping , Mu Jiaxiang , Meng Zhaoxu , Lian He
Published: April 2023

Mechanism of the Simva-HMPB-Mn@GOx nanosystem in both classical and non-classical ferroptosis pathways in tumors under the NIR laser irradiation.
Guanidine-based biomimetic hydrides for carbon dioxide reduction
Authors: Chen Junbo , Yu Haibo , Tan Davin , Lee Richmond
Published: April 2023

The feasibility of various bespoke guanidine-based compounds as electrochemically regenerative biomimetic hydrides for reduction of carbon dioxide to formate were assessed by Density Functional Theory (DFT).
N-Heterocyclic carbene catalyzed desymmetrization of diols: access to enantioenriched oxindoles having a C3-quaternary stereocenter
Authors: Dutta Sourav , Porey Arka , Guin Joyram
Published: April 2023

Herein, we describe an effective strategy for enantioselective synthesis of oxindoles having a C3-quaternary stereocenterviaN-heterocyclic carbene (NHC) catalyzed desymmetrization of diols.
An amplified logic gate driven by in situ synthesis of silver nanoclusters for identification of biomarkers
Authors: Shen Hui , Li Zhimin , Dou Baoting , Feng Qiumei , Wang Po
Published: April 2023

An amplified logic gate driven by in situ synthesis of silver nanoclusters was developed for the accurate identification of biomarkers.
Electrochemical site-selective direct C–H sulfenylation and selenylation of a chromone-fused-indolizine (CFI) skeleton
Authors: Jat Pooja Kumari , Yadav Lalit , Chouhan Amreen , Ucheniya Kusum , Badsara Satpal Singh
Published: April 2023

For the first time, we report the transition metal-free electrochemical site-selective direct C–H sulfenylation/selenylation of chromone-fused indolizine compounds (CFIs) to afford the corresponding CFIs thioethers and selenoethers in 58–96% yields.
Rational optimization of siRNA to ensure strand bias in the interaction with the RNA-induced silencing complex
Authors: Datta Dhrubajyoti , Theile Christopher S. , Wassarman Kelly , Qin June , Racie Tim , Schmidt Karyn , Jiang Yongfeng , Sigel Rachel , Janas Maja M. , Egli Martin , Manoharan Muthiah
Published: April 2023

A new class of 5′-morpholino modified nucleoside building blocks was synthesized. Among them, Mo2 exhibited better off-target mitigation for RNAi compared to other analogues Pip and Mo3 and the previously reported morpholino derivative Mo1.
Endogenous glutathione-activated DNA nanoprobes for spatially controllable imaging of microRNA in living cells
Authors: Li Yuyan , Zhang Fanghua , Liu Wendong , Shao Mingzheng , Hao Zhe , Zhang Hongyan , Zhang Ruizhong , Li Xiyan , Zhang Libing
Published: April 2023

A DNA nanoprobe, activated by glutathione (GSH), was designed to enable spatially selective sensing and imaging of miRNA in living cells.
Dichloromethanol but not difluoromethanol as a viable surrogate of carbon monoxide for prodrug design
Authors: Liu Miao , Li Zhang , Hu Ziwei , Yan ZhiCheng , Min Qingqiang , Peng Wei , Ji Xingyue
Published: April 2023

Herein, we demonstrate that dichloromethanol but not difluoromethanol is a viable surrogate of carbon monoxide for prodrug design.
Topochemical 1,3-dipolar cycloaddition polymerization assisted by non-covalent interactions
Authors: Meng Xiao , Xu Shu , Chen Changqing , Guo Lihui , Ma Yuguo
Published: April 2023

An efficient topochemical azide–alkyne cycloaddition polymerization of monomers, which comprised phenylene and tetrafluorophenylene units linked by alkylene linkers and terminated by azide and alkyne groups, was achieved through a supramolecular approach.
Four isostructural lanthanide metal–organic frameworks: luminescence properties and fluorescence sensing for Fe3+and Cr2O72−ions
Authors: Zhao Li-Juan , Li Bin , Yong Guo-Ping
Published: April 2023

The isostructural 3D lanthanide metal–organic frameworks reveal better luminescence sensing properties for the detection of Fe3+ions and Cr2O72−anions.
The role of the A monovalent cation in the AVF3 perovskite series. A quantum mechanical investigation
Authors: Pascale Fabien , Atallah Neveen I. , El-Kelany Khaled E. , Doll Klaus , Dovesi Roberto
Published: April 2023

The relative stability of various phases of five AVF3 compounds (A = Li, Na, K, Rb and Cs) is investigated starting from the cubic (C) Pm3̄m (221) prototype structure, with five atoms (one formula unit) in the primitive cell.
A controllable nanoscale telescopic arm designed by encoding the nested multi-walled carbon nanotubes
Authors: Si Wei , Wang Liwei , Lin Xiaojing , Wu Gensheng , Zhang Yin , Sha Jingjie
Published: April 2023

A nanoscale telescopic arm composed of nested carbon nanotubes was designed in this work, the encoding manipulation of it was precisely realized by well controlling the surface charge density, electric double layer and external electric field.
Insight into the role of excess hydroxide ions in silicate condensation reactions
Authors: Do Tuong Ha , Tong Hien Duy , Tran Khanh-Quang , Meijer Evert Jan , Trinh Thuat T.
Published: April 2023

This paper describes the formation of silicate species, from dimers to 4-membered rings, using ab initio molecular dynamics simulations in explicit water molecules with an excess hydroxide ion.
Transparent spacecraft smart thermal control device based on VO2 and hyperbolic metamaterials
Authors: Wu Biyuan , Zhang Derui , Wang Cunhai , Zhang Kaihua , Wu Xiaohu
Published: April 2023

We demonstrate a transparent spacecraft smart radiation device based on vanadium dioxide (VO2) and a hyperbolic metamaterial (HMM) structure. The solar absorption, emission modulation and visible transmission are 0.25, 0.44 and 0.7, respectively.