bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Seepage Velocity on Pore Clogging Growth Behavior and Its Effect on Permeability Reduction During Fines Migration in Porous Media
Authors: Han Gyeol , Kwon Tae‐Hyuk
Published: February 2023

Fines migration driven by fluid flows often causes pore clogging in porous media and thus reduces the permeability of the porous media. The clogging can pose serious problems in various practices, such as formation damage in hydrocarbon reservoirs, degradation of fluid withdrawal or injection efficiency, particle‐induced fouling in filtration membranes, or even a risk of sediment failure with geostructures. However, the effect of seepage flow velocity on the spatial growth pattern of fines‐induced pore clogging remains poorly identified. This study explores the pore clogging growth behaviors caused by flow‐driven fines migration and accumulation in porous media and the associated permeability reductions through a series of column experiments and concurrent X‐ray computed tomography imaging. Particularly, the X‐ray image analysis captures the spatial distributions of fines, and thus the homogeneous or heterogeneous (localized) clogging growth pattern under various seepage velocities. Our results reveal that an increase in the seepage flow velocity increases the likelihood of localized clogging growth, attributable to the direct interception of fines by the sand grains. The localized clogging growth causes a faster reduction in permeability than the homogeneous clogging growth. The presented study provides well‐controlled experiment data on fines distribution and associated permeability change, which gives insights into fines‐induced clogging behavior in porous media.
Impact of Matrix Diffusion on Heat Transport Through Heterogeneous Fractured Aquifers
Authors: De Simone Silvia , Bour Olivier , Davy Philippe
Published: February 2023

Heat transport in fractured aquifers is determined by the combined effects of flow velocity heterogeneity in the fracture system, and diffusive exchange between the fluid in the fractures and the rock matrix, which can be assumed as impervious. We analyze the impacts of this diffusive exchange on the response to heat transport, as opposite to the pure advective displacement, which governs solute transport. We focus on the post‐peak behavior where we observe pre‐asymptotic regimes with slopes that differ from the signature of matrix diffusion, which exhibits a decay rate of −3/2. This deviation is driven by the variability of both velocity field and fracture aperture field. We derive theoretical models that predict these pre‐asymptotic tails under three extreme cases that can be related with specific network structures, that is, networks dominated by large or small fractures, networks with highly or poorly channelized flow. These theoretical predictions are compared with results from numerical simulations in different sets of three‐dimensional discrete fracture networks. We determine that the combined observation of solute and heat transport responses allows classifying the network in terms of connectivity structure, and partially characterizing the fracture aperture variability in terms of upscaled parameters.
Wind Could Power Future Settlements on Mars
Authors: Dasgupta Alakananda
Published: February 2023

Using a sophisticated global climate model adapted to Mars, space scientists explore the hidden potential of wind energy on the Red Planet.
Activating transcription factor-2 supports the antioxidant capacity and ability of human mesenchymal stem cells to prevent asthmatic airway inflammation
Authors: Ju Hyein , Yun HongDuck , Kim YongHwan , Nam Yun Ji , Lee Seungun , Lee Jinwon , Jeong Seon Min , Heo Jinbeom , Kwon Hyungu , Cho You Sook , Jeong Gowun , Ryu Chae-Min , Shin Dong-Myung
Published: February 2023

Glutathione (GSH), an abundant nonprotein thiol antioxidant, participates in several biological processes and determines the functionality of stem cells. A detailed understanding of the molecular network mediating GSH dynamics is still lacking. Here, we show that activating transcription factor-2 (ATF2), a cAMP-response element binding protein (CREB), plays a crucial role in maintaining the level and activity of GSH in human mesenchymal stem cells (MSCs) by crosstalking with nuclear factor erythroid-2 like-2 (NRF2), a well-known master regulator of cellular redox homeostasis. Priming with ascorbic acid 2-glucoside (AA2G), a stable vitamin C derivative, increased the expression and activity of ATF2 in MSCs derived from human embryonic stem cells and umbilical cord. Subsequently, activated ATF2 crosstalked with the CREB1-NRF2 pathway to preserve the GSH dynamics of MSCs through the induction of genes involved in GSH synthesis (GCLC and GCLM) and redox cycling (GSR and PRDX1). Accordingly, shRNA-mediated silencing of ATF2 significantly impaired the self-renewal, migratory, proangiogenic, and anti-inflammatory capacities of MSCs, and these defects were rescued by supplementation of the cells with GSH. In addition, silencing ATF2 attenuated the ability of MSCs to alleviate airway inflammatory responses in an ovalbumin-induced mouse model of allergic asthma. Consistently, activation of ATF2 by overexpression or the AA2G-based priming procedure enhanced the core functions of MSCs, improving the in vivo therapeutic efficacy of MSCs for treating asthma. Collectively, our findings suggest that ATF2 is a novel modulator of GSH dynamics that determines the core functionality and therapeutic potency of MSCs used to treat allergic asthma.
Nuclear receptor 5A2 regulation of Agrp underlies olanzapine-induced hyperphagia
Authors: Zapata Rizaldy C. , Zhang Dinghong , Libster Avraham , Porcu Alessandra , Montilla-Perez Patricia , Nur Aisha , Xu Baijie , Zhang Zhi , Correa Stephanie M. , Liu Chen , Telese Francesca , Osborn Olivia
Published: February 2023

Antipsychotic (AP) drugs are efficacious treatments for various psychiatric disorders, but excessive weight gain and subsequent development of metabolic disease remain serious side effects of their use. Increased food intake leads to AP-induced weight gain, but the underlying molecular mechanisms remain unknown. In previous studies, we identified the neuropeptide Agrp and the transcription factor nuclear receptor subfamily 5 group A member 2 (Nr5a2) as significantly upregulated genes in the hypothalamus following AP-induced hyperphagia. While Agrp is expressed specifically in the arcuate nucleus of the hypothalamus and plays a critical role in appetite stimulation, Nr5a2 is expressed in both the CNS and periphery, but its role in food intake behaviors remains unknown. In this study, we investigated the role of hypothalamic Nr5a2 in AP-induced hyperphagia and weight gain. In hypothalamic cell lines, olanzapine treatment resulted in a dose-dependent increase in gene expression of Nr5a2 and Agrp. In mice, the pharmacological inhibition of NR5A2 decreased olanzapine-induced hyperphagia and weight gain, while the knockdown of Nr5a2 in the arcuate nucleus partially reversed olanzapine-induced hyperphagia. Chromatin-immunoprecipitation studies showed for the first time that NR5A2 directly binds to the Agrp promoter region. Lastly, the analysis of single-cell RNA seq data confirms that Nr5a2 and Agrp are co-expressed in a subset of neurons in the arcuate nucleus. In summary, we identify Nr5a2 as a key mechanistic driver of AP-induced food intake. These findings can inform future clinical development of APs that do not activate hyperphagia and weight gain.
O-GlcNAcylation of YTHDF2 promotes HBV-related hepatocellular carcinoma progression in an N6-methyladenosine-dependent manner
Authors: Yang Yang , Yan Yu , Yin Jiaxin , Tang Ni , Wang Kai , Huang Luyi , Hu Jie , Feng Zhongqi , Gao Qingzhu , Huang Ailong
Published: February 2023

Hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC), but its pathogenic mechanism remains to be explored. The RNA N6-methyladenosine (m6A) reader, YTH (YT521-B homology) domain 2 (YTHDF2), plays a critical role in the HCC progression. However, the function and regulatory mechanisms of YTHDF2 in HBV-related HCC remain largely elusive. Here, we discovered that YTHDF2 O-GlcNAcylation was markedly increased upon HBV infection. O-GlcNAc transferase (OGT)-mediated O-GlcNAcylation of YTHDF2 on serine 263 enhanced its protein stability and oncogenic activity by inhibiting its ubiquitination. Mechanistically, YTHDF2 stabilized minichromosome maintenance protein 2 (MCM2) and MCM5 transcripts in an m6A-dependent manner, thus promoting cell cycle progression and HBV-related HCC tumorigenesis. Moreover, targeting YTHDF2 O-GlcNAcylation by the OGT inhibitor OSMI-1 significantly suppressed HCC progression. Taken together, our findings reveal a new regulatory mechanism for YTHDF2 and highlight an essential role of YTHDF2 O-GlcNAcylation in RNA m6A methylation and HCC progression. Further description of the molecular pathway has the potential to yield therapeutic targets for suppression of HCC progression due to HBV infection.
The phosphorylation of PHF5A by TrkA-ERK1/2-ABL1 cascade regulates centrosome separation
Authors: Song Chen , Zhang Yu , Li Yutong , Bie Juntao , Wang Zhe , Yang Xin , Li Haishuang , Zhu Liangyi , Zhang Tianzhuo , Chang Qing , Luo Jianyuan
Published: February 2023

During interphase, the newly duplicated pairs of centrosomes are held together by a centrosome linker, and the centrosome separation needs the disruption of this linker to induce the duplicated centrosomes separating into two distinct microtubule organization centers. The mechanism of regulating centrosome separation is however poorly understood. Here, we demonstrated that the phosphorylation of PHF5A at Y36 by the TrkA-ERK1/2-ABL1 cascade plays a critical role in regulating centrosome separation. PHF5A, a well-characterized spliceosome component, is enriched in the centrosome. The pY36-PHF5A promotes the interaction between CEP250 and Nek2A in a spliceosomal-independent manner, which leads to premature centrosome separation. Furthermore, the unmatured centrosome remodels the microtubule and subsequently regulates cell proliferation and migration. Importantly, we found that the phosphorylation cascade of TrkA-ERK1/2-ABL1-PHF5A is hyper-regulated in medulloblastoma. The inhibition of this cascade can induce senescence and restrict the proliferation of medulloblastoma. Our findings on this phosphorylation cascade in regulating centrosome separation could provide a series of potential targets for restricting the progress of medulloblastoma.
MLKL deficiency attenuated hepatocyte oxidative DNA damage by activating mitophagy to suppress macrophage cGAS-STING signaling during liver ischemia and reperfusion injury
Authors: Xu Jian , Wu Dongming , Zhou Shun , Hu Haoran , Li Fei , Guan Zhu , Zhan Xinyu , Gao Yiyun , Wang Ping , Rao Zhuqing
Published: February 2023

Mixed-lineage kinase domain-like protein (MLKL)-mediated necroptosis has been implicated in aggravating liver ischemia and reperfusion (IR) injury. However, the precise role and mechanism of MLKL in regulating oxidative DNA damage of hepatocytes and subsequent activation of macrophage stimulator of interferon genes (STING) signaling remains unclear. In this study, we investigated the role of MLKL in regulating the interplay between hepatocyte injury and macrophage pro-inflammatory responses during liver IR injury. We found that IR increased MLKL expression in liver tissues of wild type (WT) mice. MLKL knockout (KO) attenuated liver IR injury and suppressed the activation of cGAS-STING signaling in intrahepatic macrophages, which was abrogated by STING activation with its agonist. Mechanistically, IR induced oxidative DNA damage in hepatocytes, leading to cGAS-STING activation in macrophages, which was suppressed by MLKL KO. Moreover, increased PTEN-induced kinase 1 (PINK1)-mediated mitophagy contributed to reduced oxidative DNA damage in hepatocytes and subsequent decreased activation of STING signaling in macrophages in MLKL KO mice. Our findings demonstrated a non-canonical role of MLKL in the pathogenesis of liver IR. MLKL deficiency significantly promoted PINK1-mediated mitophagy activation to inhibit oxidative DNA damage in hepatocytes, which in turn suppressed macrophage cGAS-STING activation and inflammatory liver IR injury.
Human epidermal growth factor receptor 3 serves as a novel therapeutic target for acral melanoma
Authors: Tanaka Yuka , Ito Takamichi , Kaku-Ito Yumiko , Tanegashima Keiko , Tsuji Gaku , Kido-Nakahara Makiko , Oda Yoshinao , Nakahara Takeshi
Published: February 2023

Acral melanoma (AM) is a rare, life-threatening skin cancer. Since AM bears unique features, existing therapies for other types of malignant melanomas have limited effects and the establishment of effective treatments for AM is strongly desired. Human epidermal growth factor receptor 3 (HER3) is a receptor tyrosine kinase that is frequently elevated in tumors and contributes to tumor progression, so it is considered a promising therapeutic target for tumors. This study was established to evaluate the potential of HER3-targeted therapy to treat AM by investigating the expression and function of HER3. HER3 expression was immunohistochemically analyzed in AM lesions of 72 patients and in AM cell lines. To investigate function of HER3, effects of HER3 inhibition on cell proliferation, apoptosis/survival, anchorage-independent growth, and underlying signals were assessed. HER3 was expressed in patients’ AM tissues with various intensities and HER3 expression was significantly correlated with patient’s disease-free survival. In vitro analyses revealed that HER3 is more highly expressed in AM cells than in normal epidermal melanocytes. AM cells were also shown to be sensitive to the cytotoxic part of a HER3-targeted antibody-drug conjugate. Inhibition of HER3 did not affect cell proliferation, whereas it decreased the anchorage-independent growth of AM cells likely through affecting the nuclear translocation of Yes-associated protein. It is implied that HER3 may serve as a novel therapeutic target for AM.
Silver lining to a climate crisis in multiple prospects for alleviating crop waterlogging under future climates
Authors: Liu Ke , Harrison Matthew Tom , Yan Haoliang , Liu De Li , Meinke Holger , Hoogenboom Gerrit , Wang Bin , Peng Bin , Guan Kaiyu , Jaegermeyr Jonas , Wang Enli , Zhang Feng , Yin Xiaogang , Archontoulis Sotirios , Nie Lixiao , Badea Ana , Man Jianguo , Wallach Daniel , Zhao Jin , Benjumea Ana Borrego , Fahad Shah , Tian Xiaohai , Wang Weilu , Tao Fulu , Zhang Zhao , Rötter Reimund , Yuan Youlu , Zhu Min , Dai Panhong , Nie Jiangwen , Yang Yadong , Zhang Yunbo , Zhou Meixue
Published: February 2023

Extreme weather events threaten food security, yet global assessments of impacts caused by crop waterlogging are rare. Here we first develop a paradigm that distils common stress patterns across environments, genotypes and climate horizons. Second, we embed improved process-based understanding into a farming systems model to discern changes in global crop waterlogging under future climates. Third, we develop avenues for adapting cropping systems to waterlogging contextualised by environment. We find that yield penalties caused by waterlogging increase from 3–11% historically to 10–20% by 2080, with penalties reflecting a trade-off between the duration of waterlogging and the timing of waterlogging relative to crop stage. We document greater potential for waterlogging-tolerant genotypes in environments with longer temperate growing seasons (e.g., UK, France, Russia, China), compared with environments with higher annualised ratios of evapotranspiration to precipitation (e.g., Australia). Under future climates, altering sowing time and adoption of waterlogging-tolerant genotypes reduces yield penalties by 18%, while earlier sowing of winter genotypes alleviates waterlogging by 8%. We highlight the serendipitous outcome wherein waterlogging stress patterns under present conditions are likely to be similar to those in the future, suggesting that adaptations for future climates could be designed using stress patterns realised today.
Shape-memory effect in twisted ferroic nanocomposites
Authors: Kim Donghoon , Kim Minsoo , Reidt Steffen , Han Hyeon , Baghizadeh Ali , Zeng Peng , Choi Hongsoo , Puigmartí-Luis Josep , Trassin Morgan , Nelson Bradley J. , Chen Xiang-Zhong , Pané Salvador
Published: February 2023

The shape recovery ability of shape-memory alloys vanishes below a critical size (~50 nm), which prevents their practical applications at the nanoscale. In contrast, ferroic materials, even when scaled down to dimensions of a few nanometers, exhibit actuation strain through domain switching, though the generated strain is modest (~1%). Here, we develop freestanding twisted architectures of nanoscale ferroic oxides showing shape-memory effect with a giant recoverable strain (>8%). The twisted geometrical design amplifies the strain generated during ferroelectric domain switching, which cannot be achieved in bulk ceramics or substrate-bonded thin films. The twisted ferroic nanocomposites allow us to overcome the size limitations in traditional shape-memory alloys and open new avenues in engineering large-stroke shape-memory materials for small-scale actuating devices such as nanorobots and artificial muscle fibrils.
Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches
Authors: Cheng Xiaolong , Li Zexu , Shan Ruocheng , Li Zihan , Wang Shengnan , Zhao Wenchang , Zhang Han , Chao Lumen , Peng Jian , Fei Teng , Li Wei
Published: February 2023

A major challenge in the application of the CRISPR-Cas13d system is to accurately predict its guide-dependent on-target and off-target effect. Here, we perform CRISPR-Cas13d proliferation screens and design a deep learning model, named DeepCas13, to predict the on-target activity from guide sequences and secondary structures. DeepCas13 outperforms existing methods to predict the efficiency of guides targeting both protein-coding and non-coding RNAs. Guides targeting non-essential genes display off-target viability effects, which are closely related to their on-target efficiencies. Choosing proper negative control guides during normalization mitigates the associated false positives in proliferation screens. We apply DeepCas13 to the guides targeting lncRNAs, and identify lncRNAs that affect cell viability and proliferation in multiple cell lines. The higher prediction accuracy of DeepCas13 over existing methods is extensively confirmed via a secondary CRISPR-Cas13d screen and quantitative RT-PCR experiments. DeepCas13 is freely accessible via http://deepcas13.weililab.org.
Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length
Authors: Ng Sheung Chun , Biswas Abin , Huyton Trevor , Schünemann Jürgen , Reber Simone , Görlich Dirk
Published: February 2023

Nup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We show that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier - all consistent with a sieve-like phase. Phase separation tolerates mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remains preserved. NTR-entry, however, is sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we observed that arginines promote FG-phase-entry apparently also by hydrophobic interactions/ hydrogen-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displays remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations make the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxes this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
Application of high-throughput single-nucleus DNA sequencing in pancreatic cancer
Authors: Zhang Haochen , Karnoub Elias-Ramzey , Umeda Shigeaki , Chaligné Ronan , Masilionis Ignas , McIntyre Caitlin A. , Sashittal Palash , Hayashi Akimasa , Zucker Amanda , Mullen Katelyn , Hong Jungeui , Makohon-Moore Alvin , Iacobuzio-Donahue Christine A.
Published: February 2023

Despite insights gained by bulk DNA sequencing of cancer it remains challenging to resolve the admixture of normal and tumor cells, and/or of distinct tumor subclones; high-throughput single-cell DNA sequencing circumvents these and brings cancer genomic studies to higher resolution. However, its application has been limited to liquid tumors or a small batch of solid tumors, mainly because of the lack of a scalable workflow to process solid tumor samples. Here we optimize a highly automated nuclei extraction workflow that achieves fast and reliable targeted single-nucleus DNA library preparation of 38 samples from 16 pancreatic ductal adenocarcinoma patients, with an average library yield per sample of 2867 single nuclei. We demonstrate that this workflow not only performs well using low cellularity or low tumor purity samples but reveals genomic evolution patterns of pancreatic ductal adenocarcinoma as well.
A conserved tooth resorption mechanism in modern and fossil snakes
Authors: LeBlanc A. R. H. , Palci A. , Anthwal N. , Tucker A. S. , Araújo R. , Pereira M. F. C. , Caldwell M. W.
Published: February 2023

Whether snakes evolved their elongated, limbless bodies or their specialized skulls and teeth first is a central question in squamate evolution. Identifying features shared between extant and fossil snakes is therefore key to unraveling the early evolution of this iconic reptile group. One promising candidate is their unusual mode of tooth replacement, whereby teeth are replaced without signs of external tooth resorption. We reveal through histological analysis that the lack of resorption pits in snakes is due to the unusual action of odontoclasts, which resorb dentine from within the pulp of the tooth. Internal tooth resorption is widespread in extant snakes, differs from replacement in other reptiles, and is even detectable via non-destructive μCT scanning, providing a method for identifying fossil snakes. We then detected internal tooth resorption in the fossil snake Yurlunggur, and one of the oldest snake fossils, Portugalophis, suggesting that it is one of the earliest innovations in Pan-Serpentes, likely preceding limb loss.
FGL2-targeting T cells exhibit antitumor effects on glioblastoma and recruit tumor-specific brain-resident memory T cells
Authors: Zhao Qingnan , Hu Jiemiao , Kong Lingyuan , Jiang Shan , Tian Xiangjun , Wang Jing , Hashizume Rintaro , Jia Zhiliang , Fowlkes Natalie Wall , Yan Jun , Xia Xueqing , Yi Sofia F. , Dao Long Hoang , Masopust David , Heimberger Amy B. , Li Shulin
Published: February 2023

Although tissue-resident memory T (TRM) cells specific for previously encountered pathogens have been characterized, the induction and recruitment of brain TRM cells following immune therapy has not been observed in the context of glioblastoma. Here, we show that T cells expressing fibrinogen-like 2 (FGL2)–specific single-chain variable fragments (T-αFGL2) can induce tumor-specific CD8+ TRM cells that prevent glioblastoma recurrence. These CD8+ TRM cells display a highly expanded T cell receptor repertoire distinct from that found in peripheral tissue. When adoptively transferred to the brains of either immunocompetent or T cell-deficient naïve mice, these CD8+ TRM cells reject glioma cells. Mechanistically, T-αFGL2 cell treatment increased the number of CD69+CD8+ brain-resident memory T cells in tumor-bearing mice via a CXCL9/10 and CXCR3 chemokine axis. These findings suggest that tumor-specific brain-resident CD8+ TRM cells may have promising implications for the prevention of brain tumor recurrence.
H2B ubiquitination recruits FACT to maintain a stable altered nucleosome state for transcriptional activation
Authors: Luo Anfeng , Kong Jingwei , Chen Jun , Xiao Xue , Lan Jie , Li Xiaorong , Liu Cuifang , Wang Peng-Ye , Li Guohong , Li Wei , Chen Ping
Published: February 2023

Histone H2B mono-ubiquitination at lysine 120 (ubH2B) has been found to regulate transcriptional elongation by collaborating with the histone chaperone FACT (Facilitates Chromatin Transcription) and plays essential roles in chromatin-based transcriptional processes. However, the mechanism of how ubH2B directly collaborates with FACT at the nucleosome level still remains elusive. In this study, we demonstrate that ubH2B impairs the mechanical stability of the nucleosome and helps to recruit FACT by enhancing the binding of FACT on the nucleosome. FACT prefers to bind and deposit H2A-ubH2B dimers to form an intact nucleosome. Strikingly, the preferable binding of FACT on ubH2B-nucleosome greatly enhances nucleosome stability and maintains its integrity. The stable altered nucleosome state obtained by ubH2B and FACT provides a key platform for gene transcription, as revealed by genome-wide and time-course ChIP-qPCR analyses. Our findings provide mechanistic insights of how ubH2B directly collaborates with FACT to regulate nucleosome dynamics for gene transcription.
Miniaturized multicolor fluorescence imaging system integrated with a PDMS light-guide plate for biomedical investigation
Authors: Shin Hyogeun , Yoon Gun-Wook , Choi Woongsun , Lee Donghwan , Choi Hoyun , Jo Deok Su , Choi Nakwon , Yoon Jun-Bo , Cho Il-Joo
Published: February 2023

Miniaturized fluorescence imaging systems are promising platforms that overcome the limited use of conventional microscopes in the biomedical field. However, there are physical limitations for multicolor fluorescence imaging in existing miniaturized imaging systems because multiple filters have to be integrated into a small structure. Here, we present a miniaturized multicolor fluorescence imaging system integrated with single polydimethylsiloxane (PDMS) light-guide plate (LGP) for multicolor fluorescence imaging. The PDMS LGP allows guiding the transmitted light from the light source only to the fluorescent samples regardless of the wavelength of the light source. Thus, our system is capable of multicolor fluorescence imaging without multiple filters that block the excitation light. We demonstrated the usability of our system in the biomedical field by observing green- and red-labeled cells in the incubator. Our proposed system can be used in a wide range of applications for studies that require multicolor fluorescence imaging in the biomedical field.
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer
Authors: Li Xiong , Meng Xu , Chen Haowen , Fu Xiangzheng , Wang Peng , Chen Xia , Gu Changlong , Zhou Juan
Published: February 2023

A deep understanding of the complex interaction mechanism between the various cellular components in tumor microenvironment (TME) of lung adenocarcinoma (LUAD) is a prerequisite for understanding its drug resistance, recurrence, and metastasis. In this study, we proposed two complementary computational frameworks for integrating multi-source and multi-omics data, namely ImmuCycReg framework (single sample level) and L0Reg framework (population or subtype level), to carry out difference analysis between the normal population and different LUAD subtypes. Then, we aimed to identify the possible immune escape pathways adopted by patients with different LUAD subtypes, resulting in immune deficiency which may occur at different stages of the immune cycle. More importantly, combining the research results of the single sample level and population level can improve the credibility of the regulatory network analysis results. In addition, we also established a prognostic scoring model based on the risk factors identified by Lasso-Cox method to predict survival of LUAD patients. The experimental results showed that our frameworks could reliably identify transcription factor (TF) regulating immune-related genes and could analyze the dominant immune escape pathways adopted by each LUAD subtype or even a single sample. Note that the proposed computational framework may be also applicable to the immune escape mechanism analysis of pan-cancer.
Trait biases in microbial reference genomes
Authors: Albright Sage , Louca Stilianos
Published: February 2023

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
Metabolome-wide association study on physical activity
Authors: Kojouri Maedeh , Pinto Rui , Mustafa Rima , Huang Jian , Gao He , Elliott Paul , Tzoulaki Ioanna , Dehghan Abbas
Published: February 2023

The underlying mechanisms linking physical activity to better health are not fully understood. Here we examined the associations between physical activity and small circulatory molecules, the metabolome, to highlight relevant biological pathways. We examined plasma metabolites associated with self-reported physical activity among 2217 participants from the Airwave Health Monitoring Study. Metabolic profiling was conducted using the mass spectrometry-based Metabolon platform (LC/GC–MS), measuring 828 known metabolites. We replicated our findings in an independent subset of the study (n = 2971) using untargeted LC–MS. Mendelian randomisation was carried out to investigate potential causal associations between physical activity, body mass index, and metabolites. Higher vigorous physical activity was associated (P < 0.05/828 = 6.03 × 10–5) with circulatory levels of 28 metabolites adjusted for age, sex and body mass index. The association was inverse for glutamate and diacylglycerol lipids, and direct for 3–4-hydroxyphenyllactate, phenyl lactate (PLA), alpha-hydroxy isovalerate, tiglylcarnitine, alpha-hydroxyisocaproate, 2-hydroxy-3-methylvalerate, isobutyrylcarnitine, imidazole lactate, methionine sulfone, indole lactate, plasmalogen lipids, pristanate and fumarate. In the replication panel, we found 23 untargeted LC–MS features annotated to the identified metabolites, for which we found nominal associations with the same direction of effect for three features annotated to 1-(1-enyl-palmitoyl)-2-oleoyl-GPC (P-16:0/18:1), 1-(1-enyl-palmitoyl)-2-linoleoyl-GPC (P-16:0/18:2), 1-stearoyl-2-dihomo-linolenoyl-GPC (18:0/20:3n3 or 6). Using Mendelian randomisation, we showed a potential causal relationship between body mass index and three identified metabolites. Circulatory metabolites are associated with physical activity and may play a role in mediating its health effects.
Dynamics of volcanic vortex rings
Authors: Pulvirenti Fabio , Scollo Simona , Ferlito Carmelo , Schwandner Florian M.
Published: February 2023

Vortex rings can easily be generated in the laboratory or with homemade devices, but they have also been observed on volcanoes, since the eighteenth century. However, the physical conditions under which volcanic vortex rings form are still unknown. In order to better understand this phenomenon and provide clues on the dynamics of the volcanic vortex rings, we performed a series of finite element simulations to investigate which model configuration leads to the rings formation that best matches the field observations. Results show that the formation of volcanic vortex rings requires a combination of fast gas release from gas bubbles (slugs) at the top of the magma conduit and regularity in the shape of the emitting vent. Our findings offer important insights into the geometry of the uppermost portion of vortex-forming volcanic conduits. Volcanic vortex ring studies may form the basis for a cross-disciplinary assessment of the upper conduit dynamics of volcanic vents.
Effects of continuous straw returning on bacterial community structure and enzyme activities in rape-rice soil aggregates
Authors: Yuan Luhong , Gao Yue , Mei Ying , Liu Jiaren , Kalkhajeh Yusef Kianpoor , Hu Hongxiang , Huang Jieying
Published: February 2023

Straw returning is an effective management measure to improve or maintain soil fertility in agricultural ecosystems. This study investigated the effects of straw returning combined with compound fertilizer on the bacterial community, enzyme activities, and soil nutrients’ contents in a rape-rice rotation soil aggregates. To do so, a 5-year field trial (November 2016 to October 2021) was carried out in a paddy soil with three treatments: no straw + no fertilization (CK), compound fertilizer (F), and straw returning + compound fertilizer (SF). Soil aggregates were classified into mega-aggregates (> 2 mm), macro-aggregates (0.25–2 mm), micro-aggregates (0.053–0.25 mm), and silt–clay (< 0.053 mm) using the wet sieve method. High-throughput sequencing was employed to characterize the bacterial community, and Pearson correlation coefficient was used to identify the relationships among bacterial community, organic carbon, nitrogen, phosphorus, and enzyme activities in soil aggregates. Compared with F, the results showed that straw returning increased the content of > 2 mm aggregates by 3.17% and significantly decreased the content of 0.053–0.25 mm aggregates by 20.27%. The contents of organic carbon and total nitrogen in > 0.053 mm straw amended aggregates increased by 15.29 and 18.25%, respectively. Straw returning significantly increased the urease activity of > 0.053 mm aggregates with an average of 43.08%, while it decreased the phosphatase and invertase activities of soil aggregates by 7.71–40.66%. The Shannon indices of the bacterial community in each particle sizes soil aggregates decreased by an average of 1.16% and the Chao indices of the bacterial community in < 2 mm aggregates increased by an average of 3.90% in straw amended soils. Nevertheless, the relative abundances of Chloroflexi and Nitrospirotain in all soil aggregates increased by 6.17–71.77% in straw amended soils. Altogether, our findings suggest that straw returning is an efficient approach to enhance soil structure, carbon and nitrogen contents, and the richness of soil bacterial diversity.
Diagnosis of coronary layered plaque by deep learning
Authors: Araki Makoto , Park Sangjoon , Nakajima Akihiro , Lee Hang , Ye Jong Chul , Jang Ik-Kyung
Published: February 2023

Healed coronary plaques, morphologically characterized by a layered phenotype, are signs of previous plaque destabilization and healing. Recent optical coherence tomography (OCT) studies demonstrated that layered plaque is associated with higher levels of local and systemic inflammation and rapid plaque progression. However, the diagnosis of layered plaque needs expertise in OCT image analysis and is susceptible to inter-observer variability. We developed a deep learning (DL) model for an accurate diagnosis of layered plaque. A Visual Transformer (ViT)-based DL model that integrates information from adjacent frames emulating the cardiologists who review consecutive OCT frames to make a diagnosis was developed and compared with the standard convolutional neural network (CNN) model. A total of 237,021 cross-sectional OCT images from 581 patients collected from 8 sites were used for training and internal validation, and 65,394 images from 292 patients collected from another site were used for external validation. In the five-fold cross-validation, the ViT-based model provided better performance (area under the curve [AUC]: 0.860; 95% confidence interval [CI]: 0.855–0.866) than the standard CNN-based model (AUC: 0.799; 95% CI: 0.792–0.805). The ViT-based model (AUC: 0.845; 95% CI: 0.837–0.853) also surpassed the standard CNN-based model (AUC: 0.791; 95% CI: 0.782–0.800) in the external validation. The ViT-based DL model can accurately diagnose a layered plaque, which could help risk stratification for cardiac events.
Phenotype alteration causes long-term changes to the social strategies of victimised birds
Authors: Liste Guiomar , Estevez Inma
Published: February 2023

Phenotype alterations can occur naturally during the life span of the domestic fowl. These alterations increase the risk to become a target of aggression and may cause a severe impact on the welfare of affected birds. We analysed the behavioural consequences of sequential phenotype alterations and their long-term effects within stable social groups of adult birds differing in group size. Phenotypically homogeneous groups, with 100% or 0% marked individuals, and heterogeneous groups, with 70%, 50% or 30% marked birds, were housed at constant density in groups of 10, 20 or 40. We applied sequential phenotype alterations to homogeneous groups (by marking or unmarking birds) and compared their behavioural response to heterogeneous groups considered controls. Results show that aggression was greatly affected by phenotype alteration but, unexpectedly, group size did not play any relevant role modulating social responses. Aggression was directed towards the first altered birds and was significantly higher than in control groups. Long term effects were detected, as victimized individuals failed to engage in aggression at any time and adapted their behaviour to minimize aggressive encounters (e.g. high perch use). Therefore, we provide evidence of long-lasting submissive strategies in stable groups of adult domestic fowl, highlighting the relevance of phenotype alteration on the social dynamics of affected birds. Phenotype alterations could help explain much of the targeted aggression observed in producing flocks which severely affects animal welfare.
A cost-effectiveness evaluation of latent tuberculosis infection screening of a migrant population in Malaysia
Authors: Barker Erin , Moss Joe , Holmes Hayden , Bowe Catherine , Suryaprakash Vinay , Alagna Riccardo , Nikolayevskyy Vladyslav , Destito Marc , Manissero Davide
Published: February 2023

To estimate the costs and benefits of screening for latent tuberculosis infection (LTBI) in a migrant population in Malaysia. An economic model was developed from a Malaysian healthcare perspective to compare QuantiFERON-TB Gold Plus (QuantiFERON) with the tuberculin skin test (TST). A decision tree was used to capture outcomes relating to LTBI screening followed by a Markov model that simulated the lifetime costs and benefits of the patient cohort. The Markov model did not capture the impact of secondary infections. The model included an R shiny interactive interface to allow adaptation to other scenarios and settings. QuantiFERON is both more effective and less costly than TST (dominant). Compared with QuantiFERON, the lifetime risk of developing active TB increases by approximately 40% for TST due to missed LTBI cases during screening (i.e. a higher number of false negative cases for TST). For a migrant population in Malaysia, QuantiFERON is cost-effective when compared with TST. Further research should consider targeted LTBI screening for migrants in Malaysia based on common risk factors.
What Is Caiman latirostris Teaching Us About Endocrine Disruptors?
Authors: Durando M. , Galoppo G. H. , Tavalieri Y. E. , Zanardi M. V. , Muñoz-de-Toro M.
Published: February 2023

Endocrine-disrupting chemicals (EDCs), which include a large variety of man-made chemicals frequently used around the world, are substances that behave as endogenous hormones or as inhibitors of their actions. The negative impact of EDCs on laboratory rodents, humans and aquatic and avian species has been deeply studied for years. The aim of this chapter is to highlight the huge value of the native South American crocodilian species Caiman latirostris as a sentinel species of EDC pollution and to summarize how much we have learned from this caiman in the past two decades. We expect that the results described here can contribute not only to the knowledge of the effects of EDCs on wild species but also to warning government control agencies and EDC users and producers for their responsible use as a tool for the preservation of natural ecosystems.
From an aluminum oxo cluster to an aluminum oxo cluster organic cage
Authors: Zhang Yi , Chen Ran-Qi , Wang San-Tai , Liu Ya-Jie , Fang Wei-Hui , Zhang Jian
Published: February 2023

Presented herein is an example of the assembly of a tetrahedral metal–organic cage compound from a trinuclear Al(iii) cluster. Such a synthetic method can be applied to the construction of cluster-based porous materials.
Synthesis and crystal structure of Fe[SeO4]OH and prediction of polytypes in the extended R[MO4]Z family
Authors: Arakcheeva Alla , Maamouri Noémie , Bi Wen Hua , Truc Benoît , Magrez Arnaud
Published: February 2023

The newly synthesized compound Fe[SeO4]OH belongs to the kieserite-like structure. Using the superspace approach, possible polytypes are predicted for R[MO4]Z, where R = Mg, Fe, Ni, Co, Zn, Mn, Al, V, Sb, Y; M = S, Se, P, As; Z = OH, H2O, F, O.
New types of complex motion of a simple camphor boat
Authors: Löffler Richard J.G. , Roliński Tomasz , Kitahata Hiroyuki , Koyano Yuki , Górecki Jerzy
Published: February 2023

Experiments with rotating camphor boats revealed a new type of boat motion characterized by oscillating speed.
Magnetic boron nitride adorned with Pd nanoparticles: an efficient catalyst for the reduction of nitroarenes in aqueous media
Authors: Wang Jinghan , Cheon Woo Seok , Lee Ju-Yong , Yan Wenqian , Jung Sunghoon , Jang Ho Won , Shokouhimehr Mohammadreza
Published: February 2023

Hexagonal boron nitride (h-BN) is an excellent support material for nanocatalysts due to its two-dimensional (2D) architectural morphology and physicochemical stability.
Sequential speciation analysis of heavy metals on suspended particulate matter in water using electrochemical mass spectrometry
Authors: Zhang Xinglei , Xu Yuan , Li Ting , Li Hui , Yu Zhendong , Song Lili , Xu Jiaquan
Published: February 2023

An electrochemical mass spectrometry method was developed for speciation analysis of heavy metals in suspended particulate matter in lake water.
Eco-friendly inorganic molecular novel antiperovskites for light-emitting application
Authors: Luo Jiawei , Ji Qun , Wu Yilei , Gao Xinying , Wang Jinlan , Ju Ming-Gang
Published: February 2023

The novel antiperovskites exhibit a low dimensional electronic structure, making them a potential luminous material. Herein, our study explored the new and ecofriendly antiperovskites to identify six promising luminous candidates.
New functionalized thioxanthone derivatives as type I photoinitiators for polymerization under UV-Vis LEDs
Authors: Wang Yu , Chen Rao , Liu Dongmei , Peng Chaofei , Wang Junwei , Dong Xiaoqing
Published: February 2023

Thioxanthone derivatives, well known as type II photoinitiators, can perform as type I photoinitiators to efficiently induce polymerization under visible LEDs, owing to the advantages of photodecarboxylation reaction and photolysis of oxime-esters.
Self-poled and transparent polyvinylidene fluoride-co-hexafluoropropylene-based piezoelectric devices for printable and flexible electronics
Authors: Li Hai , Lim Sooman
Published: February 2023

This article reports the novel self-poled and highly transparent piezoelectric nanogenerators (ST-PENGs) based on 1H,1H,2H,2H-perfluorodecyltriethoxysilane and polyvinylidene fluoride-co-hexafluoropropylene composite filmsviaextrusion printing.
Unveiling growth and dynamics of liposomes by graphene liquid cell-transmission electron microscopy
Authors: Jabbari Vahid , Sawczyk Michal , Amiri Azadeh , Král Petr , Shahbazian-Yassar Reza
Published: February 2023

Real-time TEM images of evolution of the liposomes formed via self-assembly of phosphatidylcholine lipids in liquid pockets of GLC shows three stages of fast initial growth, slow growth and stabilization, and formation of stable liposomes.
Frontier nanoarchitectonics of graphitic carbon nitride based plasmonic photocatalysts and photoelectrocatalysts for energy, environment and organic reactions
Authors: Kumar Ajay , Choudhary Priyanka , Chhabra Tripti , Kaur Harpreet , Kumar Ashish , Qamar Mohammad , Krishnan Venkata
Published: February 2023

Plasmonic photocatalysis for effective charge carrier separation and tuning of optical response is very much desired. In this review, the recent advances in plasmon mediated graphitic carbon nitride materials for photocatalysis and photoelectrocatalysis are summarized.
Nano-polyaniline enables highly efficient electrocatalytic reduction of CO2 to methanol in supporting electrolyte-free media and the detection of free-radical signals
Authors: Mu Shaolin , Shi Qiaofang , Chen Chong , Gong Xiangxiang , Xue Huaiguo
Published: February 2023

Metals and metal oxides are widely used as catalysts for the electrochemical reduction of CO2.
Perfect absorption based on a ceramic anapole metamaterial
Authors: Luo Weijia , Wang Xubin , Chen Xingcong , Zheng Siyong , Zhao Shiqiang , Wen Yongzheng , Li Lingxia , Zhou Ji
Published: February 2023

Perfect absorption is realized by an anapole metamaterial composed only of oxide ceramics. The tolerance limits of metamaterial devices to an extreme environment, especially in a high-temperature oxidation environment, are being broken.
A detection of the layered structure of nearby open clusters
Authors: Hu Qingshun , Zhang Yu , Esamdin Ali , Wang Hong , Qin Mingfeng
Published: February 2023

We applied the newly developed rose diagram overlay method to detect the layered structure of 88 nearby open clusters (≤500 pc) on the three projections after the distance correction of their member stars, based on the catalog in literature. The results show that with the rose diagram overlay method, a total of 74 clusters in our sample have a layered structure, while the remaining clusters are without a clear layered structure. We for the first time defined the layered structure parameters for the sample clusters. Meanwhile, we found that the layered circle core area (s) has a strong positive correlation with the number of cluster members, while the kernel instability index (η) has a strong negative correlation with the number of cluster members. Our study provides a novel perspective for the detection of the layered structure of open clusters.