bluuebunny/crossref_metadata_2025 huggingface dataset:
Coastal Upwelling Under Anthropogenic Influence Drives the Community Change, Assembly Process, and Co‐Occurrence Pattern of Coral Associated Microorganisms
Authors: Zhu Wentao , Liu Xiangbo , Zhu Ming , Xia Jingquan , Chen Rouwen , Li Xiubao
Published: February 2023

Summer upwelling areas may serve as a thermal refuge for coral reefs under climate change, and the environmental adaptation of scleractinian coral to upwelling environments remains to be further understood. In this work, we systematically analyzed how the coral holobionts of Galaxea fascicularis respond to different environments between the Qiongdong upwelling and non‐upwelling regions. The presence of colder and more saline water was found in seasonal upwelling region east of Hainan Island. Compared with the corals in the non‐upwelling environment, the corals from the upwelling environment generally had higher Symbiodiniaceae density, tissue biomass, and protein content. Evident spatial differences existed in Symbiodiniaceae composition among different regions, and the corals in the upwelling region had remarkably higher symbiont diversity. Importantly, the coastal upwelling under anthropogenic influence (i.e., nutrient pollution and coastal development) shaped coral bacterial communities significantly and decreased their diversity. Local adaptations of coral to environmental changes can be inferred from the flexibility and ecological functions of the coral core microbiome. In particular, the coastal upwelling environment led assembly of coral‐associated bacteria more deterministic rather than stochastic. In the upwelling region, microbial co‐occurrences had more positive interactions but the ecological network structure had a lower stability. These findings deepen the understanding of the ecological impact of upwelling on coral adaptation in the Anthropocene.
Diffusion of Circumpolar Deep Water Towards Antarctica
Authors: Yamazaki Kaihe , Aoki Shigeru , Mizobata Kohei
Published: February 2023

Warm, salty Circumpolar Deep Water (CDW) is recognized as the primary driver for Antarctic glacial melt, but the mechanism by which it reaches the continental shelves remains highly uncertain from an observational standpoint. With the scarcity of eddy flux estimation in the Antarctic margin, we quantify the isopycnal diffusivity of CDW using hydrographic variability and satellite altimetry under the mixing length framework. For comparison, the spiciness and thickness are used as isopycnal tracers, and the two tracers yield qualitatively similar estimates. Over the Antarctic Circumpolar Current (ACC), variation of mixing length is generally aligned with the jet‐induced mixing suppression, including in areas where topography blocks the jet's influence. In contrast, the mixing length does not depend on the mean flow in the subpolar zone, likely reflecting the relatively quiescent flow regime. The estimated isopycnal diffusivity ranges from 100 to 500 m2 s−1 south of the ACC. The eddy diffusivity tends to be enhanced where the gradient of isopycnal thickness becomes small and CDW intrudes onshore. The cross‐slope eddy CDW flux is estimated, and the associated onshore heat flux across is calculated as ∼3.6 TW in the eastern Indian sector. The eddy heat flux and coastal solar heating are generally balanced with cryospheric heat sinks including glacial melting and surface freezing, suggesting that the eddy advection is substantial for the onshore CDW flux. The thickness field is essential for determining mixing length and eddy fluxes in the subpolar zone, however this is not the case in the ACC domain.
Different Types of Corona Discharges Associated With High‐Altitude Positive Narrow Bipolar Events Nearby Cloud Top
Authors: Li Dongshuai , Luque Alejandro , Gordillo‐Vazquez F. J. , Pérez‐Invernón F. J. , Husbjerg Lasse Skaaning , Neubert Torsten , Chanrion Olivier , Lu Gaopeng , Zhang Hongbo , Han Jing , Lehtinen Nikolai G. , Østgaard Nikolai , Reglero Víctor
Published: February 2023

Single‐ and multi‐pulse blue corona discharges are frequently observed in thunderstorm clouds. Although we know they often correlate with Narrow Bipolar Events (NBEs) in Very Low Frequency/Low Frequency radio signals, their physics is not well understood. Here, we report a detailed analysis of different types of blue corona discharges observed by the Atmosphere‐Space Interactions Monitor during an overpass of a thundercloud cell nearby Malaysia. Both single‐ and multi‐pulse blue corona discharges were associated with positive NBEs at the top of the cloud, reaching about 18 km altitude. We find that the primary pulses of multi‐pulse discharges have weaker current moments than the single‐pulse discharges, suggesting that the multi‐pulse discharges either have shorter vertical channels or have weaker currents than the single‐pulse discharges. The subsequent pulse trains of the multi‐pulse discharges delayed some milliseconds are likely from horizontally oriented electrical discharges, but some NBEs, correlated with both single‐and multi‐pulse discharges, include small‐amplitude oscillations within a few microseconds inside their waveforms, which are unresolved in the optical observation and yet to be understood. Furthermore, by jointly analyzing the optical and radio observations, we estimate the photon free mean path at the cloud top to be ∼6 m.
Processes Controlling Methane Emissions From a Tropical Peatland Drainage Canal
Authors: Somers Lauren D. , Hoyt Alison , Cobb Alexander R. , Isnin Suhailah , Suhip Muhammad Asri Akmal bin Haji , Sukri Rahayu S. , Gandois Laure , Harvey Charles
Published: February 2023

Most peat domes in Southeast Asia are crisscrossed by networks of drainage canals. These canals are a potentially important source of methane to the atmosphere because the groundwater that discharges into them carries high concentrations of dissolved methane that is produced within peat. In this study, we present an isotope‐enabled numerical model that simulates transport, degassing, and oxidation of methane and dissolved inorganic carbon (DIC) along a drainage canal. We then estimate methane fluxes through a 5‐km canal that crosses a disturbed, forested, but undeveloped, peat dome in Brunei Darussalam by applying this model to field data: concentrations and stable carbon isotopic ratios of both methane and dissolved inorganic carbon from both peat porewater and canal water. We estimate that approximately 70% of the methane entering the canal is oxidized within the canal, 26% is degassed to the atmosphere, and 4% is transported toward the ocean, under low to moderate flow conditions. The flux of methane to the atmosphere is lowest at the maximum elevation of the canal, where flow is stagnant and methane concentrations are highest. Downstream, as flow velocity increases, methane emissions plateau even as methane concentrations decrease. The resulting methane emissions from the canal are large compared to emissions from the peat surface and vegetation on a per‐area basis. However, since the canal covers only a small portion of the catchment area, the canal may be a substantial but not dominant source of methane from the peatland.
Multiple measurement analysis of resting-state fMRI for ADHD classification in adolescent brain from the ABCD study
Authors: Wang Zhaobin , Zhou Xiaocheng , Gui Yuanyuan , Liu Manhua , Lu Hui
Published: February 2023

Attention deficit hyperactivity disorder (ADHD) is one of the most common psychiatric disorders in school-aged children. Its accurate diagnosis looks after patients’ interests well with effective treatment, which is important to them and their family. Resting-state functional magnetic resonance imaging (rsfMRI) has been widely used to characterize the abnormal brain function by computing the voxel-wise measures and Pearson’s correlation (PC)-based functional connectivity (FC) for ADHD diagnosis. However, exploring the powerful measures of rsfMRI to improve ADHD diagnosis remains a particular challenge. To this end, this paper proposes an automated ADHD classification framework by fusion of multiple measures of rsfMRI in adolescent brain. First, we extract the voxel-wise measures and ROI-wise time series from the brain regions of rsfMRI after preprocessing. Then, to extract the multiple functional connectivities, we compute the PC-derived FCs including the topographical information-based high-order FC (tHOFC) and dynamics-based high-order FC (dHOFC), the sparse representation (SR)-derived FCs including the group SR (GSR), the strength and similarity guided GSR (SSGSR), and sparse low-rank (SLR). Finally, these measures are combined with multiple kernel learning (MKL) model for ADHD classification. The proposed method is applied to the Adolescent Brain and Cognitive Development (ABCD) dataset. The results show that the FCs of dHOFC and SLR perform better than the others. Fusing multiple measures achieves the best classification performance (AUC = 0.740, accuracy = 0.6916), superior to those from the single measure and the previous studies. We have identified the most discriminative FCs and brain regions for ADHD diagnosis, which are consistent with those of published literature.
Latent class analysis of psychotic-affective disorders with data-driven plasma proteomics
Authors: Rhee Sang Jin , Shin Dongyoon , Shin Daun , Song Yoojin , Joo Eun-Jeong , Jung Hee Yeon , Roh Sungwon , Lee Sang-Hyuk , Kim Hyeyoung , Bang Minji , Lee Kyu Young , Kim Se Hyun , Kim Minah , Lee Jihyeon , Kim Jaenyeon , Kim Yeongshin , Kwon Jun Soo , Ha Kyooseob , Kim Youngsoo , Ahn Yong Min
Published: February 2023

Data-driven approaches to subtype transdiagnostic samples are important for understanding heterogeneity within disorders and overlap between disorders. Thus, this study was conducted to determine whether plasma proteomics-based clustering could subtype patients with transdiagnostic psychotic-affective disorder diagnoses. The study population included 504 patients with schizophrenia, bipolar disorder, and major depressive disorder and 160 healthy controls, aged 19 to 65 years. Multiple reaction monitoring was performed using plasma samples from each individual. Pathologic peptides were determined by linear regression between patients and healthy controls. Latent class analysis was conducted in patients after peptide values were stratified by sex and divided into tertile values. Significant demographic and clinical characteristics were determined for the latent clusters. The latent class analysis was repeated when healthy controls were included. Twelve peptides were significantly different between the patients and healthy controls after controlling for significant covariates. Latent class analysis based on these peptides after stratification by sex revealed two distinct classes of patients. The negative symptom factor of the Brief Psychiatric Rating Scale was significantly different between the classes (t = −2.070, p = 0.039). When healthy controls were included, two latent classes were identified, and the negative symptom factor of the Brief Psychiatric Rating Scale was still significant (t = −2.372, p = 0.018). In conclusion, negative symptoms should be considered a significant biological aspect for understanding the heterogeneity and overlap of psychotic-affective disorders.
Neogenin suppresses tumor progression and metastasis via inhibiting Merlin/YAP signaling
Authors: Hu Xiaohan , Li Li , Li Fang , Yang Yuan , An Jingnan , Zhou Xinghua , Zhang Rui , Shi Lingli , Zhao He , Wang Jian , Hu Yizhou , Xu Yunyun
Published: February 2023

From in situ growth to invasive dissemination is the most lethal attribute of various tumor types. This transition is majorly mediated by the dynamic interplay between two cancer hallmarks, EMT and cell cycle. In this study, we applied nonlinear association analysis in 33 cancer types and found that most signaling receptors simultaneously associating with EMT and cell cycle are potential tumor suppressors. Here we find that a top co-associated receptor, Neogenin (NEO1), inhibits colorectal cancer (CRC) and Glioma in situ growth and metastasis by forming a complex with Merlin (NF2), and subsequent simultaneous promoting the phosphorylation of YAP. Furthermore, Neogenin protein level is associated with good prognosis and correlates with Merlin status in CRC and Glioma. Collectively, our results define Neogenin as a tumor suppressor in CRC and Glioma that acts by restricting oncogenic signaling by the Merlin-YAP pathway, and suggest Neogenin as a candidate therapeutic agent for CRC and Glioma.
Intrinsic macroscale oscillatory modes driving long range functional connectivity in female rat brains detected by ultrafast fMRI
Authors: Cabral Joana , Fernandes Francisca F. , Shemesh Noam
Published: February 2023

Spontaneous fluctuations in functional magnetic resonance imaging (fMRI) signals correlate across distant brain areas, shaping functionally relevant intrinsic networks. However, the generative mechanism of fMRI signal correlations, and in particular the link with locally-detected ultra-slow oscillations, are not fully understood. To investigate this link, we record ultrafast ultrahigh field fMRI signals (9.4 Tesla, temporal resolution = 38 milliseconds) from female rats across three anesthesia conditions. Power at frequencies extending up to 0.3 Hz is detected consistently across rat brains and is modulated by anesthesia level. Principal component analysis reveals a repertoire of modes, in which transient oscillations organize with fixed phase relationships across distinct cortical and subcortical structures. Oscillatory modes are found to vary between conditions, resonating at faster frequencies under medetomidine sedation and reducing both in number, frequency, and duration with the addition of isoflurane. Peaking in power within clear anatomical boundaries, these oscillatory modes point to an emergent systemic property. This work provides additional insight into the origin of oscillations detected in fMRI and the organizing principles underpinning spontaneous long-range functional connectivity.
LSD1/PRMT6-targeting gene therapy to attenuate androgen receptor toxic gain-of-function ameliorates spinobulbar muscular atrophy phenotypes in flies and mice
Authors: Prakasam Ramachandran , Bonadiman Angela , Andreotti Roberta , Zuccaro Emanuela , Dalfovo Davide , Marchioretti Caterina , Tripathy Debasmita , Petris Gianluca , Anderson Eric N. , Migazzi Alice , Tosatto Laura , Cereseto Anna , Battaglioli Elena , Sorarù Gianni , Lim Wooi Fang , Rinaldi Carlo , Sambataro Fabio , Pourshafie Naemeh , Grunseich Christopher , Romanel Alessandro , Pandey Udai Bhan , Contestabile Andrea , Ronzitti Giuseppe , Basso Manuela , Pennuto Maria
Published: February 2023

Spinobulbar muscular atrophy (SBMA) is caused by CAG expansions in the androgen receptor gene. Androgen binding to polyQ-expanded androgen receptor triggers SBMA through a combination of toxic gain-of-function and loss-of-function mechanisms. Leveraging cell lines, mice, and patient-derived specimens, we show that androgen receptor co-regulators lysine-specific demethylase 1 (LSD1) and protein arginine methyltransferase 6 (PRMT6) are overexpressed in an androgen-dependent manner specifically in the skeletal muscle of SBMA patients and mice. LSD1 and PRMT6 cooperatively and synergistically transactivate androgen receptor, and their effect is enhanced by expanded polyQ. Pharmacological and genetic silencing of LSD1 and PRMT6 attenuates polyQ-expanded androgen receptor transactivation in SBMA cells and suppresses toxicity in SBMA flies, and a preclinical approach based on miRNA-mediated silencing of LSD1 and PRMT6 attenuates disease manifestations in SBMA mice. These observations suggest that targeting overexpressed co-regulators can attenuate androgen receptor toxic gain-of-function without exacerbating loss-of-function, highlighting a potential therapeutic strategy for patients with SBMA.
The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition
Authors: Ganji Rakesh , Paulo Joao A. , Xi Yuecheng , Kline Ian , Zhu Jiang , Clemen Christoph S. , Weihl Conrad C. , Purdy John G. , Gygi Steve P. , Raman Malavika
Published: February 2023

The intimate association between the endoplasmic reticulum (ER) and mitochondrial membranes at ER-Mitochondria contact sites (ERMCS) is a platform for critical cellular processes, particularly lipid synthesis. How contacts are remodeled and the impact of altered contacts on lipid metabolism remains poorly understood. We show that the p97 AAA-ATPase and its adaptor ubiquitin-X domain adaptor 8 (UBXD8) regulate ERMCS. The p97-UBXD8 complex localizes to contacts and its loss increases contacts in a manner that is dependent on p97 catalytic activity. Quantitative proteomics and lipidomics of ERMCS demonstrates alterations in proteins regulating lipid metabolism and a significant change in membrane lipid saturation upon UBXD8 deletion. Loss of p97-UBXD8 increased membrane lipid saturation via SREBP1 and the lipid desaturase SCD1. Aberrant contacts can be rescued by unsaturated fatty acids or overexpression of SCD1. We find that the SREBP1-SCD1 pathway is negatively impacted in the brains of mice with p97 mutations that cause neurodegeneration. We propose that contacts are exquisitely sensitive to alterations to membrane lipid composition and saturation.
Microbiota-derived acetate enhances host antiviral response via NLRP3
Authors: Niu Junling , Cui Mengmeng , Yang Xin , Li Juan , Yao Yuhui , Guo Qiuhong , Lu Ailing , Qi Xiaopeng , Zhou Dongming , Zhang Chenhong , Zhao Liping , Meng Guangxun
Published: February 2023

Pathogenic viral infections represent a major challenge to human health. Host immune responses to respiratory viruses are closely associated with microbiome and metabolism via the gut-lung axis. It has been known that host defense against influenza A virus (IAV) involves activation of the NLRP3 inflammasome, however, mechanisms behind the protective function of NLRP3 are not fully known. Here we show that an isolated bacterial strain, Bifidobacterium pseudolongum NjM1, enriched in the gut microbiota of Nlrp3−/− mice, protects wild-type but not Nlrp3 deficient mice against IAV infection. This effect depends on the enhanced production of type I interferon (IFN-I) mediated by NjM1-derived acetate. Application of exogenous acetate reproduces the protective effect of NjM1. Mechanistically, NLRP3 bridges GPR43 and MAVS, and promotes the oligomerization and signalling of MAVS; while acetate enhances MAVS aggregation upon GPR43 engagement, leading to elevated IFN-I production. Thus, our data support a model of NLRP3 mediating enhanced induction of IFN-I via acetate-producing bacterium and suggest that the acetate-GPR43-NLRP3-MAVS-IFN-I signalling axis is a potential therapeutic target against respiratory viral infections.
Pulse-driven self-reconfigurable meta-antennas
Authors: Ushikoshi Daiju , Higashiura Riku , Tachi Kaito , Fathnan Ashif Aminulloh , Mahmood Suhair , Takeshita Hiroki , Homma Haruki , Akram Muhammad Rizwan , Vellucci Stefano , Lee Jiyeon , Toscano Alessandro , Bilotti Filiberto , Christopoulos Christos , Wakatsuchi Hiroki
Published: February 2023

Wireless communications and sensing have notably advanced thanks to the recent developments in both software and hardware. Although various modulation schemes have been proposed to efficiently use the limited frequency resources by exploiting several degrees of freedom, antenna performance is essentially governed by frequency only. Here, we present an antenna design concept based on metasurfaces to manipulate antenna performances in response to the time width of electromagnetic pulses. We numerically and experimentally show that by using a proper set of spatially arranged metasurfaces loaded with lumped circuits, ordinary omnidirectional antennas can be reconfigured by the incident pulse width to exhibit directional characteristics varying over hundreds of milliseconds or billions of cycles, far beyond conventional performance. We demonstrate that the proposed concept can be applied for sensing, selective reception under simultaneous incidence and mutual communications as the first step to expand existing frequency resources based on pulse width.
Machine learning potentials for metal-organic frameworks using an incremental learning approach
Authors: Vandenhaute Sander , Cools-Ceuppens Maarten , DeKeyser Simon , Verstraelen Toon , Van Speybroeck Veronique
Published: February 2023

Computational modeling of physical processes in metal-organic frameworks (MOFs) is highly challenging due to the presence of spatial heterogeneities and complex operating conditions which affect their behavior. Density functional theory (DFT) may describe interatomic interactions at the quantum mechanical level, but is computationally too expensive for systems beyond the nanometer and picosecond range. Herein, we propose an incremental learning scheme to construct accurate and data-efficient machine learning potentials for MOFs. The scheme builds on the power of equivariant neural network potentials in combination with parallelized enhanced sampling and on-the-fly training to simultaneously explore and learn the phase space in an iterative manner. With only a few hundred single-point DFT evaluations per material, accurate and transferable potentials are obtained, even for flexible frameworks with multiple structurally different phases. The incremental learning scheme is universally applicable and may pave the way to model framework materials in larger spatiotemporal windows with higher accuracy.
Million-scale data integrated deep neural network for phonon properties of heuslers spanning the periodic table
Authors: Rodriguez Alejandro , Lin Changpeng , Yang Hongao , Al-Fahdi Mohammed , Shen Chen , Choudhary Kamal , Zhao Yong , Hu Jianjun , Cao Bingyang , Zhang Hongbin , Hu Ming
Published: February 2023

Existing machine learning potentials for predicting phonon properties of crystals are typically limited on a material-to-material basis, primarily due to the exponential scaling of model complexity with the number of atomic species. We address this bottleneck with the developed Elemental Spatial Density Neural Network Force Field, namely Elemental-SDNNFF. The effectiveness and precision of our Elemental-SDNNFF approach are demonstrated on 11,866 full, half, and quaternary Heusler structures spanning 55 elements in the periodic table by prediction of complete phonon properties. Self-improvement schemes including active learning and data augmentation techniques provide an abundant 9.4 million atomic data for training. Deep insight into predicted ultralow lattice thermal conductivity (<1 Wm−1 K−1) of 774 Heusler structures is gained by p–d orbital hybridization analysis. Additionally, a class of two-band charge-2 Weyl points, referred to as “double Weyl points”, are found in 68% and 87% of 1662 half and 1550 quaternary Heuslers, respectively.
A multi-centre polyp detection and segmentation dataset for generalisability assessment
Authors: Ali Sharib , Jha Debesh , Ghatwary Noha , Realdon Stefano , Cannizzaro Renato , Salem Osama E. , Lamarque Dominique , Daul Christian , Riegler Michael A. , Anonsen Kim V. , Petlund Andreas , Halvorsen Pål , Rittscher Jens , de Lange Thomas , East James E.
Published: February 2023

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp’s number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as PolypGen) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation.
Denervation during mandibular distraction osteogenesis results in impaired bone formation
Authors: Tevlin Ruth , Griffin Michelle , Chen Kellen , Januszyk Michael , Guardino Nick , Spielman Amanda , Walters Shannon , Gold Garry Evan , Chan Charles K. F. , Gurtner Geoffrey C. , Wan Derrick C. , Longaker Michael T.
Published: February 2023

Mandibular distraction osteogenesis (DO) is mediated by skeletal stem cells (SSCs) in mice, which enact bone regeneration via neural crest re-activation. As peripheral nerves are essential to progenitor function during development and in response to injury, we questioned if denervation impairs mandibular DO. C57Bl6 mice were divided into two groups: DO with a segmental defect in the inferior alveolar nerve (IAN) at the time of mandibular osteotomy (“DO Den”) and DO with IAN intact (“DO Inn”). DO Den demonstrated significantly reduced histological and radiological osteogenesis relative to DO Inn. Denervation preceding DO results in reduced SSC amplification and osteogenic potential in mice. Single cell RNA sequencing analysis revealed that there was a predominance of innervated SSCs in clusters dominated by pathways related to bone formation. A rare human patient specimen was also analyzed and suggested that histological, radiological, and transcriptional alterations seen in mouse DO may be conserved in the setting of denervated human mandible distraction. Fibromodulin (FMOD) transcriptional and protein expression were reduced in denervated relative to innervated mouse and human mandible regenerate. Finally, when exogenous FMOD was added to DO-Den and DO-Inn SSCs undergoing in vitro osteogenic differentiation, the osteogenic potential of DO-Den SSCs was increased in comparison to control untreated DO-Den SSCs, modeling the superior osteogenic potential of DO-Inn SSCs.
Quantum error mitigation by Pauli check sandwiching
Authors: Gonzales Alvin , Shaydulin Ruslan , Saleem Zain H. , Suchara Martin
Published: February 2023

We describe and analyze an error mitigation technique that uses multiple pairs of parity checks to detect the presence of errors. Each pair of checks uses one ancilla qubit to detect a component of the error operator and represents one layer of the technique. We build on the results on extended flag gadgets and put it on a firm theoretical foundation. We prove that this technique can recover the noiseless state under the assumption of noise not affecting the checks. The method does not incur any encoding overhead and instead chooses the checks based on the input circuit. We provide an algorithm for obtaining such checks for an arbitrary target circuit. Since the method applies to any circuit and input state, it can be easily combined with other error mitigation techniques. We evaluate the performance of the proposed methods using extensive numerical simulations on 1850 random input circuits composed of Clifford gates and non-Clifford single-qubit rotations, a class of circuits encompassing most commonly considered variational algorithm circuits. We observe average improvements in fidelity of 34 percentage points with six layers of checks.
Dual RNA sequencing of group B Streptococcus-infected human monocytes reveals new insights into host–pathogen interactions and bacterial evasion of phagocytosis
Authors: Sullivan Matthew J. , Prince Darren , Goh Kelvin G. K. , Katupitiya Lahiru , Gosling Dean , Crowley Michael R. , Crossman David K. , Ulett Glen C.
Published: February 2023

Streptococcus agalactiae, also known as Group BStreptococcus(GBS) is a frequent cause of infections, including bacteraemia and other acute diseases in adults and immunocompromised individuals. We developed a novel system to study GBS within human monocytes to define the co-transcriptome of intracellular GBS (iGBS) and host cells simultaneously using dual RNA-sequencing (RNA-seq) to better define how this pathogen responds to host cells. Using human U937 monocytes and genome-sequenced GBS reference strain 874,391 in antibiotic protection assays we validated a system for dual-RNA seq based on measures of GBS and monocyte viability to ensure that the bacterial and host cell co-transcriptome reflected mainly intracellular (iGBS) rather than extracellular GBS. Elucidation of the co-transcriptome revealed 1119 dysregulated transcripts iniGBSwith most genes, including several that encode virulence factors (e.g., scpB,hvgA, ribD,pil2b) exhibiting activation by upregulated expression. Infection withiGBSresulted in significant remodelling of the monocyte transcriptome, with 7587 transcripts differentially expressed including 7040 up-regulated and 547 down-regulated. qPCR confirmed that the most strongly activated genes includedsht, encoding Streptococcal Histidine Triad Protein. An isogenic GBS mutant strain deficient inshtrevealed a significant effect of this gene on phagocytosis of GBS and survival of the bacteria during systemic infection in mice. Identification of a novel contribution ofshtto GBS virulence shows the co-transcriptome responses elucidated in GBS-infected monocytes help to shape the host–pathogen interaction and establish a role forshtin the response of the bacteria to phagocytic uptake. This study provides comprehension of concurrent transcriptional responses that occur in GBS and human monocytes that shape the host–pathogen interaction.
In silico and in vitro anti-inflammatory study of phenolic compounds isolated from Eucalyptus maculata resin
Authors: Ali Dalia E. , Gedaily Rania A. El , Ezzat Shahira M. , Sawy Maged A. El , Meselhy Meselhy R. , Abdel-Sattar Essam
Published: February 2023

Plant resins are rich in bioactive compounds with high medicinal values. However, the chemistry and anti-inflammatory activity of the resins produced by trees of the genus Eucalyptus were scarcely investigated. The inflammatory targets cyclooxygenase-1 (COX-1), COX-2, TNF-, NF-B, and NO were significantly inhibited by the methanolic extract of Eucalyptus maculata kino resin (EME) and its CH2Cl2 soluble fraction (MCF). Sakuranetin (C1), (E)-cinnamic acid (C2), kaempferol 7- methyl ether (C3), 7-O-methyl aromadendrin (C4), and 1,6- dicinnamoyl-O-α-D-glucopyranoside (C5) were isolated from MCF. Three compounds (C1, C2, and C4) showed potent in vitro COX-1 inhibition, while C5 inhibited COX-2, TNF-α, NF-κB, and NO significantly. An in-silico study revealed that C5 had the highest binding affinity to the active site in COX-2 with binding energy score (S) of -14.85 kcal/mol, better than celecoxib (COX-2 inhibitor). In conclusion, 1,6-dicinnamoyl-O-α-D-glucopyranoside (C5) could be investigated further in the search for anti-inflammatory agents.
Association between pazopanib exposure and safety in Japanese patients with renal cell carcinoma or soft tissue sarcoma
Authors: Aoyama Takeshi , Nakano Kenji , Yuasa Takeshi , Sugiyama Erika , Okawa Takako , Ito Kazuyuki , Azuma Keiichi , Hashimoto Koki , Furutani Ryota , Hiraide Makoto , Kobayashi Kazuo , Suzuki Kenichi , Tomomatsu Jyunnichi , Tajima Masataka , Sato Hitoshi , Hama Toshihiro , Takahashi Shunji
Published: February 2023

The safety and effectiveness of pazopanib are related to plasma trough concentrations in renal cell carcinoma (RCC); however, data on pazopanib plasma trough concentrations with soft tissue sarcoma (STS) are limited. This study investigated the relationship between plasma trough concentrations and pazopanib safety in 45 Japanese patients with RCC or STS. Among the 33 patients included, the median pazopanib trough concentration was 37.5 (range, 12.1–67.6) µg/mL, which was not significantly different between Japanese RCC and STS patients. The plasma trough concentrations showed significant and positive correlations with aspartate aminotransferase and alanine aminotransferase values in blood samples taken for pharmacokinetic measurements after the administration. The incidence of pazopanib treatment discontinuation were significantly higher in RCC patients (p = 0.027). The primary reason for treatment discontinuation was hepatic dysfunction (5/6, 83.3%). Furthermore, this study revealed that pazopanib trough concentration was affected significantly by proton pump inhibitors but not by histamine 2-receptor blockers. In conclusion, the observed pazopanib trough levels and their safety in the Japanese RCC and STS populations in this study were similar to those of the global population. This is the first study to correlate the hepatotoxicity and pharmacokinetic property of pazopanib plasma trough levels by comparing Japanese patients with RCC or STS.
Time-scale synchronisation of oscillatory responses can lead to non-monotonous R-tipping
Authors: Swierczek-Jereczek Jan , Robinson Alexander , Blasco Javier , Alvarez-Solas Jorge , Montoya Marisa
Published: February 2023

Rate-induced tipping (R-tipping) describes the fact that, for multistable dynamic systems, an abrupt transition can take place not only because of the forcing magnitude, but also because of the forcing rate. In the present work, we demonstrate through the case study of a piecewise-linear oscillator (PLO), that increasing the rate of forcing can make the system tip in some cases but might also prevent it from tipping in others. This counterintuitive effect is further called non-monotonous R-tipping (NMRT) and has already been observed in recent studies. We show that, in the present case, the reason for NMRT is the peak synchronisation of oscillatory responses operating on different time scales. We further illustrate that NMRT can be observed even in the presence of additive white noise of intermediate amplitude. Finally, NMRT is also observed on a van-der-Pol oscillator with an unstable limit cycle, suggesting that this effect is not limited to systems with a discontinuous right-hand side such as the PLO. This insight might be highly valuable, as the current research on tipping elements is shifting from an equilibrium to a dynamic perspective while using models of increasing complexity, in which NMRT might be observed but hard to understand.
Feature-enhanced text-inception model for Chinese long text classification
Authors: Yang Guo , Jiayu Yan , Dongdong Xu , Zelin Guo , Hai Huan
Published: February 2023

To solve the problem regarding unbalanced distribution of multi-category Chinese long texts and improve the classification accuracy thereof, a data enhancement method was proposed. Combined with this method, a feature-enhanced text-inception model for Chinese long text classification was proposed. First, the model used a novel text-inception module to extract important shallow features of the text. Meanwhile, the bidirectional gated recurrent unit (Bi-GRU) and the capsule neural network were employed to form a deep feature extraction module to understand the semantic information in the text; K-MaxPooling was then used to reduce the dimension of its shallow and deep features and enhance the overall features. Finally, the Softmax function was used for classification. By comparing the classification effects with a variety of models, the results show that the model can significantly improve the accuracy of long Chinese text classification and has a strong ability to recognize long Chinese text features. The accuracy of the model is 93.97% when applied to an experimental dataset.
A methodological tool for sustainability and feasibility assessment of indoor vertical farming with artificial lighting in Africa
Authors: Paucek Ivan , Durante Emanuele , Pennisi Giuseppina , Quaini Stefania , Gianquinto Giorgio , Orsini Francesco
Published: February 2023

African agriculture is bound to face challenges for its future food systems development and economic transformation. Indoor vertical farms with artificial lighting represent an opportunity that has been gaining relevance worldwide, thanks to their potential to enable high productivity rates, food quality and safety, year-round production, and more sustainable use of water and mineral nutrients. The present study assesses the potential for vertical farming technology integration within the African continent, targeting the countries where a more sustainable approach could be achieved. A deep analysis of each territory’s major opportunities and challenges was built through an updated database of 147 development indicators from 54 African states. Countries such as South Africa, Seychelles, Egypt, Mauritius, Morocco, Tunisia, Algeria, Cape Verde, and Nigeria showed the best prospective for indoor vertical farming implementation. Moreover, Seychelles, South Africa, and Egypt resulted to be the countries where vertical indoor farming could be more sustainable.
Role of vanadium ions substitution on spinel MnCo2O4 towards enhanced electrocatalytic activity for hydrogen generation
Authors: Mohamed M. J. S. , Slimani Y. , Gondal M. A. , Almessiere M. A. , Baykal A. , Hassan M. , Khan A. Z. , Roy Anurag
Published: February 2023

Improving efficient electrocatalysts (ECs) for hydrogen generation through water splitting is of significant interest in tackling the upcoming energy crisis. Sustainable hydrogen generation is the primary prerequisite to realizing the future hydrogen economy. This work examines the electrocatalytic activity of hydrothermally prepared vanadium doped MnCo spinel oxide microspheres (MC), MnVxCo2−xO4 (Vx-MnCo MC, where x ≤ 0.4) in the HER (hydrogen evolution reaction) process. Magnetization measurements demonstrated a paramagnetic (at high temperatures) to a ferrimagnetic (at low temperatures) transition below the Curie temperature (Tc) in all the samples. The magnetization is found to intensify with the rising vanadium content of MCs. The optimized catalyst Vx-MnCo MCs (x = 0.3) outperformed other prepared ECs with a Tafel slope of 84 mV/dec, a low onset potential of 78.9 mV, and a low overpotential of 85.9 mV at a current density of 10 mA/cm2, respectively. The significantly improved HER performance of hydrothermally synthesized Vx-MnCo MCs (x = 0.3) is principally attributable to many exposed active sites, accelerated electron transport at the EC/electrolyte interface, and remarkable electron spectroscopy for chemical analysis (ECSA) value was found ~ 11.4 cm2. Moreover, the Vx-MnCo MCs (x = 0.3) electrode exhibited outstanding electrocatalytic stability after exposure to 1000 cyclic voltametric cycles and 36 h of chronoamperometric testing. Our results suggest a feasible route for developing earth-abundant transition metal oxide-based EC as a superior electrode for future water electrolysis applications.
Engineered mineralogical interfaces as radionuclide repositories
Authors: Douglas G. B. , Reddy S. M. , Saxey D. W. , MacRae C. M. , Webster N. A. S. , Beeching L. J.
Published: February 2023

Effective capture of fugitive actinides and daughter radionuclides constitutes a major remediation challenge at legacy or nuclear accident sites globally. The ability of double-layered, anionic clay minerals known as hydrotalcites (HTC) to contemporaneously sequester a range of contaminants from solution offers a unique remedy. However, HTC do not provide a robust repository for actinide isolation over the long term. In this study, we formed HTC by in-situ precipitation in a barren lixiviant from a uranium mine and thermally transformed the resulting radionuclide-laden, nanoscale HTC. Atomic-scale forensic examination of the amorphized/recrystallised product reveals segregation of U to nanometre-wide mineral interfaces and the local formation of interface-hosted mineral grains. This U-phase is enriched in rare earth elements, a geochemical analogue of actinides such as Np and Pu, and represents a previously unreported radionuclide interfacial segregation. U-rich phases associated with the mineral interfaces record a U concentration factor of ~ 50,000 relative to the original solute demonstrating high extraction and concentration efficiencies. In addition, the co-existing host mineral suite of periclase, spinel-, and olivine-group minerals that equate to a lower mantle, high P–T mineral assemblage have geochemical and geotechnical properties suitable for disposal in a nuclear waste repository. Our results record the efficient sequestering of radionuclides from contaminated water and this novel, broad-spectrum, nanoscale HTC capture and concentration process constitutes a rapid solute decontamination pathway and solids containment option in perpetuity.
Node-based generalized friendship paradox fails
Authors: Evtushenko Anna , Kleinberg Jon
Published: February 2023

The Friendship Paradox—the principle that “your friends have more friends than you do”—is a combinatorial fact about degrees in a graph; but given that many web-based social activities are correlated with a user’s degree, this fact has been taken more broadly to suggest the empirical principle that “your friends are also more active than you are.” This Generalized Friendship Paradox, the notion that any attribute positively correlated with degree obeys the Friendship Paradox, has been established mathematically in a network-level version that essentially aggregates uniformly over all the edges of a network. Here we show, however, that the natural node-based version of the Generalized Friendship Paradox—which aggregates over nodes, not edges—may fail, even for degree-attribute correlations approaching 1. Whether this version holds depends not only on degree-attribute correlations, but also on the underlying network structure and thus can’t be said to be a universal phenomenon. We establish both positive and negative results for this node-based version of the Generalized Friendship Paradox and consider its implications for social-network data.
Three-dimensional evaluation of the maxillary sinus in patients with different skeletal classes and cranio-maxillary relationships assessed with cone beam computed tomography
Authors: Abate Andrea , Cavagnetto Davide , Lanteri Valentina , Maspero Cinzia
Published: February 2023

The objective was to evaluate the relationship between the dimensions of the maxillary sinuses (MSs) and various cephalometric parameters. MS volume (MSV), MS surface (MSS), linear maximum depth (LMD), linear maximum width (LMW), and linear maximum height (LMH) were calculated on CBCT scans of 99 adults. Two sets of two-way (ANOVA) assessed the influence respectively of ANB and SNA angles and of the gender on MS dimensions. Pearson’s correlation was calculated between MS dimensions and different cephalometric variables. Reliability and accuracy of the proposed method was tested with intra-operator and inter-operator intraclass correlation coefficient (ICC). Two-way ANOVA showed no statistically significant difference in MSV, MSS and LMH between ANB groups, whilst males were associated with bigger sinuses. LMW showed statistically significant difference in both ANB and gender groups. LMD showed no statistically significant difference. The second Two-way ANOVA showed significantly larger MSV, MSS and LMD in patients with increased or reduced SNA angle but not between genders. LMW and LMH also showed a significant difference between genders. All linear measurements showed a significant interaction of the two factors. The intra-observer and inter-observer ICC scored high for all the tested measurements. MSV and MSS showed a positive correlation with S-N, PNS-A, S-Go, N-Me, N-Ans and the distance between Mx points. LMW had a negative correlation with Ba-S-N angle and N-Me, LMH with Ba-S-N angle, S-Go and Mx r-Mx l and LMD with N-Me and N-ANS. LMW had a positive correlation with Mx r-Mx l, LMH with S-N, S-N^Ans-Pns, N-Me, N-Ans and LMD with S-N, Ba-S-N, PNS-A, S-Go and distance between Mx points. In conclusion, MSV and MSS did not differ between the three skeletal classes, males showed significantly larger MS than in females. Concerning the influence of the cranio-maxillary relationship (SNA) and gender on MS dimension, subjects with a retrusion (SNA < 80°) or protusion (SNA > 84°) of the maxillary alveolar bone had larger MSV, MSS, LMW, LMH and LMD than subjects with a normal cranio-maxillary relationship (SNA 82 ± 2°). A statistically significant high positive correlation was observed between S-N, Pns-A, S-Go, Mx-R/Mx-r and MS dimension. Further studies that evaluate similar outcomes in different races may be able to enrich our knowledge on this topic.
Hg(II) immobilization and detection using gel formation with tetra-(4-pyridylphenyl)ethylene and an aggregation-induced luminescence effect
Authors: Hu Bing , Wei Taibao , Cui Yanjun , Xu Xia , Li Qiao
Published: February 2023

Tetra-(4-pyridylphenyl)ethylene (TPPE), featuring an aggregation-induced luminescence effect (AIE), has been synthesized and used for selective detection of Hg2+ in DMF/H2O (3:7, v/v) binary solutions. There was a color change from colorless to yellow in the detection of the Hg2+ ions, in addition to an increased fluorescence emission. This shows that TPPE will function as an excellent “turn-on” fluorescence probe in the detection Hg2+. Moreover, the interference of Al3+, Ba2+, Mn2+, Ca2+, Fe3+, Cu2+, Ag+, Cd2+, Co2+, Ni2+, Mg2+, Pb2+, Zn2+, and Cr3+ ions was found to be negligible under optimized solvent conditions. Cysteine and EDTA were also found to form TPPE-based fluorescent switches with the Hg2+ ions. The practical use of the TPPE sensor was also demonstrated by using a specific test kit. Characterization using FT-IR, NMR titration, UV titration, EDS, and HR-MS techniques showed that Hg2+ will form a 1:1 complex with TPPE. Also, the observation of a Tyndall effect, in addition to UV absorption and fluorescence spectra, did clearly demonstrate the presence of an AIE. More noteworthy, TPPE and Hg2+ were found to form a metal–organic gel (MOG) in the DMF solution. The SEM, TEM, ICP, and Zeta potential analyses confirmed that the fluorescent MOG could further adsorb an excess of Hg2+ ions. The BET analyses revealed that the MOG showed a type IV-H3 hysteresis loop according to the International Union of Pure and Applied Chemistry classification. The results of the XRD analysis and of the spectroscopic titrations show that a π–π stacking may be the auxiliary driving force for the gel formation, after that a coordination has taken place. These results indicate that further research on structurally simple metal ion fluorescent probes, which are based on the AIE, is promising for the achievement of a simultaneous fluorescent detection and adsorption of heavy metal pollutants.