bluuebunny/crossref_metadata_2025 huggingface dataset:
Drawn-out Protests in China's Rustbelt: Land Revenue and the Limits to Bargained Authoritarianism
Authors: Chen Xingyan , Zhan Shaohua
Published: July 2022

The rise of the land revenue regime in China, characterized by land dispossession in the countryside and land redevelopment in the city, has sparked numerous protests. This study draws attention to the paradox that the regime has helped to mitigate labour unrest, at least temporarily, in China's Rustbelt, where millions of workers were laid-off in the 1990s. Based on field research in Anshan, Liaoning province, and data from other cities in the Rustbelt, this article shows that laid-off workers’ protests persisted much longer than previously thought, largely owing to a lack of local fiscal resources to meet workers’ demands. Only with the growing revenue from land sales in the recent decade has the local government finally been able to ease the tension with laid-off workers. The article argues that bargained authoritarianism, or “buying stability,” widely considered to be an effective strategy by the local state to control social unrest, has its limits, mainly owing to its dependence on local fiscal resources. Recent economic downturns and declining land revenue will disrupt this strategy, leading to protracted protests and struggles in future.
Trade vs. Security: Recent Developments of Global Trade Rules and China's Policy and Regulatory Responses from Defensive to Proactive
Authors: Zhou Weihuan , Jiang Huiqin , Chen Zhe
Published: July 2022

This paper provides a systemic study of China's policy and legal responses to security-related actions and disputes in the international trade regime. It starts with a brief review of the law and practices relating to the security exceptions under the World Trade Organization to provide an important context for understanding the recent developments of China's approaches to national security. Based on a detailed discussion of China's approaches at international and domestic levels, we argue that China's security strategy has been shifting from being defensive to proactive: internationally by seeking to influence the development of trade rules and practices, and domestically by expanding national security to cover a wide spectrum of economic security interests and developing a comprehensive regulatory framework to protect such interests. The way in which major trading nations are taking the law into their own hands, based on ever-expanding security interests, does not bode well for the future of the multilateral trading system. There is a pressing need for collective action by all governments involved to re-design security-related rules and exceptions to confine the use of security measures to agreed parameters.
High capacity chipless RFID tags for biomass tracking application
Authors: Ali Amjad , Smartt Christopher , Lester Ed , Williams Orla , Greedy Steve
Published: July 2022

The design of a low-cost, flexible, miniaturized, and a high code density chipless radio-frequency identification (RFID) tag is presented as a solution for tracking the transportation of biomass fuel pellets. The performance of the tag is presented and demonstrates the applicability of the design for different material systems, while maintaining a compact size of 5.06 cm2. The tag consists of nested concentric hexagonal elements and a central spiral resonator suitable for ID encoding. The tag presented demonstrates code density of 3.6-bits/cm2, possesses angular stability up to 60°, and high radar cross section (RCS). The tag performance was also observed for tracking 5 kg of fly-ash biomass. Additionally, as the tag mass mostly consists of FR4, PET, or Taconic TLX-0 with a minute mass of either copper, gold, or silver, the tag can be easily combusted and disposed of during biomass combustion. The novel features of this tag are the combination of hexagonal and spiral shape slots for maximum space utilization thereby achieving high RCS signatures along with high code density. All these properties of the proposed chipless RFID tag provide a pioneering pathway for a real-time biomass tracking application.
Ancient Greek for Kids: From Theory to Praxis
Authors: Manolidou Eugenia , Goula Sophia , Sakka Vicky
Published: July 2022

This essay presents the methods, as well as the pedagogical effects, findings and results of introducing Ancient Greek in the curriculum of children between three and 12 years old as evidenced over 27 years in the method of Elliniki Agogi. Elliniki Agogi is an award-winning private educational institute established in Greece in the mid-1990s at a time when the teaching of Ancient Greek was questioned and dramatically reduced from the public curriculum. Its aim is to safeguard learning that has its roots in Ancient Greek and to continue to introduce students to the Greek civilisation and its language, using effective, entertaining and artistic methods. This endeavour was based on specific pedagogical models; by learning through experience and through a communication-orientated educational process. With concomitant, cautious organisation and preparation of each lesson a diversified educational curriculum is created that connects the students to their distant past while experiencing positive emotions, filled with ethical paradigms that contribute later to master a fully-shaped personality. 27 years later, studies have come to prove the positive influence of learning Ancient Greek in children's linguistic and mental abilities. The following study conducted is distinctive in the detailed pedagogical method it provides and validates the importance of teaching the Ancient Greek language to children as early as possible.
Sewing DEI Into the Fabric of the Geosciences
Authors: Wooden Paige , Ricci Mia , Dzekon Tanya
Published: July 2022

AGU journals host a new living special collection on diversity, equity, and inclusion in the geosciences and invite additional contributions to grow this collection.
Barometric Pumping Through Fractured Rock: A Mechanism for Venting Deep Methane to Mars' Atmosphere
Authors: Ortiz J. P. , Rajaram H. , Stauffer P. H. , Harp D. R. , Wiens R. C. , Lewis K. W.
Published: July 2022

Both the source of methane on Mars and the mechanism for transmission from the subsurface to the atmosphere are not fully understood. Previous seepage simulations have invoked relatively shallow subsurface sources to explain observed methane signatures on Mars. We propose that barometric‐pressure pumping through fracture networks could be an effective mechanism for methane transport from the deep subsurface on Mars. Using atmospheric pressure data gathered by Curiosity as input, we simulate methane gas transport from depths of 200 m to the surface. Even with such a deep source, our model reproduces the observed seasonality of methane, and the simulated surface methane fluxes fall within the range of previous estimates derived from atmospheric observations. Because 200 m is the likely minimum hospitable depth for living methanogenic microbes, our fracture network model indirectly reinvigorates the possibility of a microbial source of methane on Mars.
The Maxwell Effect and the Material Transport by Transient Eddies
Authors: Radko T. , Kamenkovich I.
Published: July 2022

Mesoscale eddies—irregular time‐dependent currents with lateral scales of 10–200 km—are ubiquitous in the World Ocean. They profoundly affect general circulation and actively redistribute oceanic heat, salt, biogeochemical tracers, and pollutants. The development of accurate parameterizations of eddy‐induced transport remains one of the most pressing challenges in physical oceanography. Commonly used mesoscale parameterizations assume that the relation between eddy‐induced fluxes and the large‐scale property gradients is local and instantaneous. The present communication challenges this premise. We consider a closure that incorporates a delay in the adjustment of eddy fluxes to changing ambient distribution of properties. This model is inspired by the century‐and‐a‐half‐old idea of Maxwell, who argued that molecular dispersion necessarily involves a finite relaxation period. In our study, this principle is reinterpreted in the context of the turbulent transport problem. A series of simulations reveal marked improvements in eddy parameterizations brought by the inclusion of Maxwell's effect.
Liquid crystal-templated chiral nanomaterials: from chiral plasmonics to circularly polarized luminescence
Authors: Zhang Xuan , Xu Yiyi , Valenzuela Cristian , Zhang Xinfang , Wang Ling , Feng Wei , Li Quan
Published: July 2022

Chiral nanomaterials with intrinsic chirality or spatial asymmetry at the nanoscale are currently in the limelight of both fundamental research and diverse important technological applications due to their unprecedented physicochemical characteristics such as intense light-matter interactions, enhanced circular dichroism, and strong circularly polarized luminescence. Herein, we provide a comprehensive overview of the state-of-the-art advances in liquid crystal-templated chiral nanomaterials. The chiroptical properties of chiral nanomaterials are touched, and their fundamental design principles and bottom-up synthesis strategies are discussed. Different chiral functional nanomaterials based on liquid-crystalline soft templates, including chiral plasmonic nanomaterials and chiral luminescent nanomaterials, are systematically introduced, and their underlying mechanisms, properties, and potential applications are emphasized. This review concludes with a perspective on the emerging applications, challenges, and future opportunities of such fascinating chiral nanomaterials. This review can not only deepen our understanding of the fundamentals of soft-matter chirality, but also shine light on the development of advanced chiral functional nanomaterials toward their versatile applications in optics, biology, catalysis, electronics, and beyond.
2.7 Å cryo-EM structure of ex vivo RML prion fibrils
Authors: Manka Szymon W. , Zhang Wenjuan , Wenborn Adam , Betts Jemma , Joiner Susan , Saibil Helen R. , Collinge John , Wadsworth Jonathan D. F.
Published: July 2022

Mammalian prions propagate as distinct strains and are composed of multichain assemblies of misfolded host-encoded prion protein (PrP). Here, we present a near-atomic resolution cryo-EM structure of PrP fibrils present in highly infectious prion rod preparations isolated from the brains of RML prion-infected mice. We found that prion rods comprise single-protofilament helical amyloid fibrils that coexist with twisted pairs of the same protofilaments. Each rung of the protofilament is formed by a single PrP monomer with the ordered core comprising PrP residues 94–225, which folds to create two asymmetric lobes with the N-linked glycans and the glycosylphosphatidylinositol anchor projecting from the C-terminal lobe. The overall architecture is comparable to that of recently reported PrP fibrils isolated from the brain of hamsters infected with the 263K prion strain. However, there are marked conformational variations that could result from differences in PrP sequence and/or represent distinguishing features of the distinct prion strains.
Instant diagnosis of gastroscopic biopsy via deep-learned single-shot femtosecond stimulated Raman histology
Authors: Liu Zhijie , Su Wei , Ao Jianpeng , Wang Min , Jiang Qiuli , He Jie , Gao Hua , Lei Shu , Nie Jinshan , Yan Xuefeng , Guo Xiaojing , Zhou Pinghong , Hu Hao , Ji Minbiao
Published: July 2022

Gastroscopic biopsy provides the only effective method for gastric cancer diagnosis, but the gold standard histopathology is time-consuming and incompatible with gastroscopy. Conventional stimulated Raman scattering (SRS) microscopy has shown promise in label-free diagnosis on human tissues, yet it requires the tuning of picosecond lasers to achieve chemical specificity at the cost of time and complexity. Here, we demonstrate that single-shot femtosecond SRS (femto-SRS) reaches the maximum speed and sensitivity with preserved chemical resolution by integrating with U-Net. Fresh gastroscopic biopsy is imaged in <60 s, revealing essential histoarchitectural hallmarks perfectly agreed with standard histopathology. Moreover, a diagnostic neural network (CNN) is constructed based on images from 279 patients that predicts gastric cancer with accuracy >96%. We further demonstrate semantic segmentation of intratumor heterogeneity and evaluation of resection margins of endoscopic submucosal dissection (ESD) tissues to simulate rapid and automated intraoperative diagnosis. Our method holds potential for synchronizing gastroscopy and histopathological diagnosis.
A visible-light activated secondary phosphine oxide ligand enabling Pd-catalyzed radical cross-couplings
Authors: Kuribara Takahito , Nakajima Masaya , Nemoto Tetsuhiro
Published: July 2022

Although transition metal-catalyzed reactions have evolved with ligand development, ligand design for palladium-catalyzed photoreactions remains less explored. Here, we report a secondary phosphine oxide ligand bearing a visible-light sensitization moiety and apply it to Pd-catalyzed radical cross-coupling reactions. The tautomeric phosphinous acid coordinates to palladium in situ, allowing for pseudo-intramolecular single-electron transfer between the ligand and palladium. Molecular design of the metal complexes aided by time-dependent density functional theory calculations enables the involvement of allyl radicals from π-allyl palladium(II) complexes, and alkyl and aryl radicals from the corresponding halides and palladium(0) complex. This complex enables radical cross-couplings by ligand-to-Pd(II) and Pd(0)-to-ligand single-electron transfer under visible-light irradiation.
Prolonging valley polarization lifetime through gate-controlled exciton-to-trion conversion in monolayer molybdenum ditelluride
Authors: Zhang Qiyao , Sun Hao , Tang Jiacheng , Dai Xingcan , Wang Zhen , Ning Cun-Zheng
Published: July 2022

Monolayer 2D semiconductors provide an attractive option for valleytronics due to valley-addressability. But the short valley-polarization lifetimes for excitons have hindered potential valleytronic applications. In this paper, we demonstrate a strategy for prolonging the valley-polarization lifetime by converting excitons to trions through efficient gate control and exploiting the much longer valley-polarization lifetimes for trions than for excitons. At charge neutrality, the valley lifetime of monolayer MoTe2 increases by a factor of 1000 to the order of nanoseconds from excitons to trions. The exciton-to-trion conversion changes the dominant depolarization mechanism from the fast electron-hole exchange for excitons to the slow spin-flip process for trions. Moreover, the degree of valley polarization increases to 38% for excitons and 33% for trions through electrical manipulation. Our results reveal the depolarization dynamics and the interplay of various depolarization channels for excitons and trions, providing an effective strategy for prolonging the valley polarization.
Cell-autonomous Hedgehog signaling controls Th17 polarization and pathogenicity
Authors: Hanna Joachim , Beke Flavio , O’Brien Louise M. , Kapeni Chrysa , Chen Hung-Chang , Carbonaro Valentina , Kim Alexander B. , Kishore Kamal , Adolph Timon E. , Skjoedt Mikkel-Ole , Skjoedt Karsten , de la Roche Marc , de la Roche Maike
Published: July 2022

Th17 cells are key drivers of autoimmune disease. However, the signaling pathways regulating Th17 polarization are poorly understood. Hedgehog signaling regulates cell fate decisions during embryogenesis and adult tissue patterning. Here we find that cell-autonomous Hedgehog signaling, independent of exogenous ligands, selectively drives the polarization of Th17 cells but not other T helper cell subsets. We show that endogenous Hedgehog ligand, Ihh, signals to activate both canonical and non-canonical Hedgehog pathways through Gli3 and AMPK. We demonstrate that Hedgehog pathway inhibition with either the clinically-approved small molecule inhibitor vismodegib or genetic ablation of Ihh in CD4+ T cells greatly diminishes disease severity in two mouse models of intestinal inflammation. We confirm that Hedgehog pathway expression is upregulated in tissue from human ulcerative colitis patients and correlates with Th17 marker expression. This work implicates Hedgehog signaling in Th17 polarization and intestinal immunopathology and indicates the potential therapeutic use of Hedgehog inhibitors in the treatment of inflammatory bowel disease.
Identifying multicellular spatiotemporal organization of cells with SpaceFlow
Authors: Ren Honglei , Walker Benjamin L. , Cang Zixuan , Nie Qing
Published: July 2022

One major challenge in analyzing spatial transcriptomic datasets is to simultaneously incorporate the cell transcriptome similarity and their spatial locations. Here, we introduce SpaceFlow, which generates spatially-consistent low-dimensional embeddings by incorporating both expression similarity and spatial information using spatially regularized deep graph networks. Based on the embedding, we introduce a pseudo-Spatiotemporal Map that integrates the pseudotime concept with spatial locations of the cells to unravel spatiotemporal patterns of cells. By comparing with multiple existing methods on several spatial transcriptomic datasets at both spot and single-cell resolutions, SpaceFlow is shown to produce a robust domain segmentation and identify biologically meaningful spatiotemporal patterns. Applications of SpaceFlow reveal evolving lineage in heart developmental data and tumor-immune interactions in human breast cancer data. Our study provides a flexible deep learning framework to incorporate spatiotemporal information in analyzing spatial transcriptomic data.
Bromodomain factor 5 is an essential regulator of transcription in Leishmania
Authors: Jones Nathaniel G. , Geoghegan Vincent , Moore Gareth , Carnielli Juliana B. T. , Newling Katherine , Calderón Félix , Gabarró Raquel , Martín Julio , Prinjha Rab K. , Rioja Inmaculada , Wilkinson Anthony J. , Mottram Jeremy C.
Published: July 2022

Leishmania are unicellular parasites that cause human and animal diseases. Like other kinetoplastids, they possess large transcriptional start regions (TSRs) which are defined by histone variants and histone lysine acetylation. Cellular interpretation of these chromatin marks is not well understood. Eight bromodomain factors, the reader modules for acetyl-lysine, are found across Leishmania genomes. Using L. mexicana, Cas9-driven gene deletions indicate that BDF1–5 are essential for promastigotes. Dimerisable, split Cre recombinase (DiCre)-inducible gene deletion of BDF5 show it is essential for both promastigotes and murine infection. ChIP-seq identifies BDF5 as enriched at TSRs. XL-BioID proximity proteomics shows the BDF5 landscape is enriched for BDFs, HAT2, proteins involved in transcriptional activity, and RNA processing; revealing a Conserved Regulators of Kinetoplastid Transcription (CRKT) Complex. Inducible deletion of BDF5 causes global reduction in RNA polymerase II transcription. Our results indicate the requirement of Leishmania to interpret histone acetylation marks through the bromodomain-enriched CRKT complex for normal gene expression and cellular viability.
Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer
Authors: Lau Denise , Khare Sonal , Stein Michelle M. , Jain Prerna , Gao Yinjie , BenTaieb Aicha , Rand Tim A. , Salahudeen Ameen A. , Khan Aly A.
Published: July 2022

The efficacy of immune checkpoint blockade (ICB) varies greatly among metastatic non-small cell lung cancer (NSCLC) patients. Loss of heterozygosity at the HLA-I locus (HLA-LOH) has been identified as an important immune escape mechanism. However, despite HLA-I disruptions in their tumor, many patients have durable ICB responses. Here we seek to identify HLA-I-independent features associated with ICB response in NSCLC. We use single-cell profiling to identify tumor-infiltrating, clonally expanded CD4+T cells that express a canonical cytotoxic gene program and NSCLC cells with elevated HLA-II expression. We postulate cytotoxic CD4+T cells mediate anti-tumor activity via HLA-II on tumor cells and augment HLA-I-dependent cytotoxic CD8+T cell interactions to drive ICB response in NSCLC. We show that integrating tumor extrinsic cytotoxic gene expression with tumor mutational burden is associated with longer time to progression in a real-world cohort of 123 NSCLC patients treated with ICB regimens, including those with HLA-LOH.
Microglia coordinate cellular interactions during spinal cord repair in mice
Authors: Brennan Faith H. , Li Yang , Wang Cankun , Ma Anjun , Guo Qi , Li Yi , Pukos Nicole , Campbell Warren A. , Witcher Kristina G. , Guan Zhen , Kigerl Kristina A. , Hall Jodie C. E. , Godbout Jonathan P. , Fischer Andy J. , McTigue Dana M. , He Zhigang , Ma Qin , Popovich Phillip G.
Published: July 2022

Traumatic spinal cord injury (SCI) triggers a neuro-inflammatory response dominated by tissue-resident microglia and monocyte derived macrophages (MDMs). Since activated microglia and MDMs are morphologically identical and express similar phenotypic markers in vivo, identifying injury responses specifically coordinated by microglia has historically been challenging. Here, we pharmacologically depleted microglia and use anatomical, histopathological, tract tracing, bulk and single cell RNA sequencing to reveal the cellular and molecular responses to SCI controlled by microglia. We show that microglia are vital for SCI recovery and coordinate injury responses in CNS-resident glia and infiltrating leukocytes. Depleting microglia exacerbates tissue damage and worsens functional recovery. Conversely, restoring select microglia-dependent signaling axes, identified through sequencing data, in microglia depleted mice prevents secondary damage and promotes recovery. Additional bioinformatics analyses reveal that optimal repair after SCI might be achieved by co-opting key ligand-receptor interactions between microglia, astrocytes and MDMs.
Cluster-type analogue memristor by engineering redox dynamics for high-performance neuromorphic computing
Authors: Kang Jaehyun , Kim Taeyoon , Hu Suman , Kim Jaewook , Kwak Joon Young , Park Jongkil , Park Jong Keuk , Kim Inho , Lee Suyoun , Kim Sangbum , Jeong YeonJoo
Published: July 2022

Memristors, or memristive devices, have attracted tremendous interest in neuromorphic hardware implementation. However, the high electric-field dependence in conventional filamentary memristors results in either digital-like conductance updates or gradual switching only in a limited dynamic range. Here, we address the switching parameter, the reduction probability of Ag cations in the switching medium, and ultimately demonstrate a cluster-type analogue memristor. Ti nanoclusters are embedded into densified amorphous Si for the following reasons: low standard reduction potential, thermodynamic miscibility with Si, and alloy formation with Ag. These Ti clusters effectively induce the electrochemical reduction activity of Ag cations and allow linear potentiation/depression in tandem with a large conductance range (~244) and long data retention (~99% at 1 hour). Moreover, according to the reduction potentials of incorporated metals (Pt, Ta, W, and Ti), the extent of linearity improvement is selectively tuneable. Image processing simulation proves that the Ti4.8%:a-Si device can fully function with high accuracy as an ideal synaptic model.
A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment
Authors: Bernard Clément , Locard-Paulet Marie , Noël Cyril , Duchateau Magalie , Giai Gianetto Quentin , Moumen Bouziane , Rattei Thomas , Hechard Yann , Jensen Lars Juhl , Matondo Mariette , Samba-Louaka Ascel
Published: July 2022

Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae.
Human-type sialic acid receptors contribute to avian influenza A virus binding and entry by hetero-multivalent interactions
Authors: Liu Mengying , Huang Liane Z. X. , Smits Anthony A. , Büll Christian , Narimatsu Yoshiki , van Kuppeveld Frank J. M. , Clausen Henrik , de Haan Cornelis A. M. , de Vries Erik
Published: July 2022

Establishment of zoonotic viruses, causing pandemics like the Spanish flu and Covid-19, requires adaptation to human receptors. Pandemic influenza A viruses (IAV) that crossed the avian-human species barrier switched from binding avian-type α2-3-linked sialic acid (2-3Sia) to human-type 2-6Sia receptors. Here, we show that this specificity switch is however less dichotomous as generally assumed. Binding and entry specificity were compared using mixed synthetic glycan gradients of 2-3Sia and 2-6Sia and by employing a genetically remodeled Sia repertoire on the surface of a Sia-free cell line and on a sialoglycoprotein secreted from these cells. Expression of a range of (mixed) 2-3Sia and 2-6Sia densities shows that non-binding human-type receptors efficiently enhanced avian IAV binding and entry provided the presence of a low density of high affinity avian-type receptors, and vice versa. Considering the heterogeneity of sialoglycan receptors encountered in vivo, hetero-multivalent binding is physiologically relevant and will impact evolutionary pathways leading to host adaptation.
Personality profile and its association with conversion to neurodegenerative disorders in idiopathic REM sleep behavior disorder
Authors: Zhou Li , Chau Steven W. H. , Liu Yaping , Wang Jing , Zhang Jihui , Chan Ngan Yin , Chan Joey W. Y. , Huang Bei , Chen Sijing , Li Shirley Xin , Mok Vincent Chung Tong , Wing Yun Kwok
Published: July 2022

Patients with Parkinson’s disease (PD) were described less extraverted and more neurotic. It remained unclear whether similar personality traits could be found in idiopathic rapid eye movement sleep behavior disorder (iRBD), a prodromal stage of PD, and could predict phenoconversion to neurodegenerative disorders. We aimed to investigate the personality profile and its association with future neurodegenerative phenoconversion in iRBD patients. One hundred and eighty-five video-polysomnography confirmed iRBD patients and 91 age- and sex-matched controls underwent personality assessment using the NEO five-factor inventory, and 171 iRBD patients were followed up. Our results showed that iRBD was marginally negatively associated with extraverted personality trait (B = −0.28, 95% confidence interval (CI) = −0.55, −0.001). During a median follow-up of 5.9 years, 47 iRBD patients (27.5%) had phenoconversion. More neurotic (adjusted hazard ratio (HR) = 2.0, 95% CI = 1.3, 3.1) and less extraverted personality traits (adjusted HR = 0.53, 95% CI = 0.36, 0.77) were associated with an increased risk of phenoconversion in iRBD patients. Our findings suggest that personality profile may be a potential prodromal marker of iRBD.
Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods
Authors: Balzerani Francesco , Hinojosa-Nogueira Daniel , Cendoya Xabier , Blasco Telmo , Pérez-Burillo Sergio , Apaolaza Iñigo , Francino M. Pilar , Rufián-Henares José Ángel , Planes Francisco J.
Published: July 2022

The relevance of phenolic compounds in the human diet has increased in recent years, particularly due to their role as natural antioxidants and chemopreventive agents in different diseases. In the human body, phenolic compounds are mainly metabolized by the gut microbiota; however, their metabolism is not well represented in public databases and existing reconstructions. In a previous work, using different sources of knowledge, bioinformatic and modelling tools, we developed AGREDA, an extended metabolic network more amenable to analyze the interaction of the human gut microbiota with diet. Despite the substantial improvement achieved by AGREDA, it was not sufficient to represent the diverse metabolic space of phenolic compounds. In this article, we make use of an enzyme promiscuity approach to complete further the metabolism of phenolic compounds in the human gut microbiota. In particular, we apply RetroPath RL, a previously developed approach based on Monte Carlo Tree Search strategy reinforcement learning, in order to predict the degradation pathways of compounds present in Phenol-Explorer, the largest database of phenolic compounds in the literature. Reactions predicted by RetroPath RL were integrated with AGREDA, leading to a more complete version of the human gut microbiota metabolic network. We assess the impact of our improvements in the metabolic processing of various foods, finding previously undetected connections with output microbial metabolites. By means of untargeted metabolomics data, we present in vitro experimental validation for output microbial metabolites released in the fermentation of lentils with feces of children representing different clinical conditions.
Using PVA and captive breeding to balance trade-offs in the rescue of the island dibbler onto a new island ark
Authors: Aisya Zahra , White Daniel J. , Thavornkanlapachai Rujiporn , Friend J. Anthony , Rick Kate , Mitchell Nicola J.
Published: July 2022

In the face of the current global extinction crisis, it is critical we give conservation management strategies the best chance of success. Australia is not exempt from global trends with currently the world’s greatest mammal extinction rate (~ 1 per 8 years). Many more are threatened including the dibbler (Parantechinus apicalis) whose remnant range has been restricted to Western Australia at just one mainland site and two small offshore islands—Whitlock Island (5 ha) and Boullanger Island (35 ha). Here, we used 14 microsatellite markers to quantify genetic variation in the remaining island populations from 2013 to 2018 and incorporated these data into population viability analysis (PVA) models, used to assess factors important to dibbler survival and to provide guidance for translocations. Remnant population genetic diversity was low (< 0.3), and populations were highly divergent from each other (pairwise FSTs 0.29–0.52). Comparison of empirical data to an earlier study is consistent with recent declines in genetic diversity and models projected increasing extinction risk and declining genetic variation in the next century. Optimal translocation scenarios recommend 80 founders for new dibbler populations—provided by captive breeding—and determined the proportion of founders from parental populations to maximise genetic diversity and minimise harvesting impact. The goal of our approach is long-term survival of genetically diverse, self-sustaining populations and our methods are transferable. We consider mixing island with mainland dibblers to reinforce genetic variation.
Mapping and determinants of consumption of egg and/or flesh foods and zero vegetables or fruits among young children in SSA
Authors: Hailu Bayuh Asmamaw , Geremew Bisrat Misganew , Liverani Silvia , Abera Kindiye Setargie , Beyene Joseph , Miheretu Birhan Asmame
Published: July 2022

Zero vegetable or fruit and egg and/or flesh foods are the latest indicators for assessing infant and young child feeding practices. Understanding national and subnational heterogeneity and regional clustering in children with SSA is becoming increasingly essential for geographic targeting and policy prioritization. Geographical case identification, determinants, and impacts were all investigated. SSA children's consumption of vegetable or fruit, egg and/or flesh food, and both were low. In SSA, some portions of the Southern, South direction of the Western and Central regions have a lower weight of all bad conditions than others, although children continue to suffer in considerable numbers in all disadvantage circumstances. Children under the age of 1 year, from rural areas, uneducated families, and low income were all disadvantaged by both feeding techniques. To improve child nutrition status, multisectoral collaboration is essential. This framework allows for the tracking, planning, and implementation of nutritional treatments.
Evidence of impaired macroautophagy in human degenerative cervical myelopathy
Authors: Smith Sam S. , Young Adam M. H. , Davies Benjamin M. , Takahashi Hitoshi , Allinson Kieren S. J. , Kotter Mark R. N.
Published: July 2022

Degenerative cervical myelopathy (DCM) is a common progressive disease of the spinal cord which can cause tetraplegia. Despite its prevalence, few studies have investigated the pathophysiology of DCM. Macroautophagy is a cellular process which degrades intracellular contents and its disruption is thought to contribute to many neurodegenerative diseases. The present study tests the hypothesis that macroautophagy is impaired in DCM. To address this, we utilised a collection of post-mortem cervical spinal cord samples and investigated seven DCM cases and five human controls. Immunohistochemical staining was used to visualise proteins involved in autophagy. This demonstrated significantly reduced numbers of LC3 puncta in cases versus controls (p = 0.0424). Consistent with reduced autophagy, we identified large aggregates of p62 in four of seven cases and no controls. Tau was increased in two of five cases compared to controls. BCL-2 was significantly increased in cases versus controls (p = 0.0133) and may explain this reduction in autophagy. Increased BCL-2 (p = 0.0369) and p62 bodies (p = 0.055) were seen in more severe cases of DCM. This is the first evidence that autophagy is impaired in DCM; the impairment appears greater in more severe cases. Further research is necessary to investigate whether macroautophagy has potential as a therapeutic target in DCM.
In situ laboratory for plastic degradation in the Red Sea
Authors: Brümmer Franz , Schnepf Uwe , Resch Julia , Jemmali Raouf , Abdi Rahma , Kamel Hesham Mostafa , Bonten Christian , Müller Ralph-Walter
Published: July 2022

Degradation and fragmentation of plastics in the environment are still poorly understood. This is partly caused by the lack of long-term studies and methods that determine weathering duration. We here present a novel study object that preserves information on plastic age: microplastic (MP) resin pellets from the wreck of the SS Hamada, a ship that foundered twenty-nine years ago at the coast of Wadi el Gemal national park, Egypt. Its sinking date enabled us to precisely determine how long MP rested in the wreck and a nearby beach, on which part of the load was washed off. Pellets from both sampling sites were analyzed by microscopy, X-ray tomography, spectroscopy, calorimetry, gel permeation chromatography, and rheology. Most pellets were made of low-density polyethylene, but a minor proportion also consisted of high-density polyethylene. MP from inside the wreck showed no signs of degradation compared to pristine reference samples. Contrary, beached plastics exhibited changes on all structural levels, which sometimes caused fragmentation. These findings provide further evidence that plastic degradation under saltwater conditions is comparatively slow, whereas UV radiation and high temperatures on beaches are major drivers of that process. Future long-term studies should focus on underlying mechanisms and timescales of plastic degradation.
Mutual synchronization of spin-torque oscillators within a ring array
Authors: Castro M. A. , Mancilla-Almonacid D. , Dieny B. , Allende S. , Buda-Prejbeanu L. D. , Ebels U.
Published: July 2022

An array of spin torque nano-oscillators (STNOs), coupled by dipolar interaction and arranged on a ring, has been studied numerically and analytically. The phase patterns and locking ranges are extracted as a function of the number N, their separation, and the current density mismatch between selected subgroups of STNOs. If $$N\ge 6$$

N
≥
6

for identical current densities through all STNOs, two degenerated modes are identified an in-phase mode (all STNOs have the same phase) and a splay mode (the phase makes a 2$$\pi$$
π
turn along the ring). When inducing a current density mismatch between two subgroups, additional phase shifts occur. The locking range (maximum current density mismatch) of the in-phase mode is larger than the one for the splay mode and depends on the number N of STNOs on the ring as well as on the separation. These results can be used for the development of magnetic devices that are based on STNO arrays.
Network-medicine framework for studying disease trajectories in U.S. veterans
Authors: do Valle Italo Faria , Ferolito Brian , Gerlovin Hanna , Costa Lauren , Demissie Serkalem , Linares Franciel , Cohen Jeremy , Gagnon David R. , Gaziano J. Michael , Begoli Edmon , Cho Kelly , Barabási Albert-László
Published: July 2022

A better understanding of the sequential and temporal aspects in which diseases occur in patient’s lives is essential for developing improved intervention strategies that reduce burden and increase the quality of health services. Here we present a network-based framework to study disease relationships using Electronic Health Records from > 9 million patients in the United States Veterans Health Administration (VHA) system. We create the Temporal Disease Network, which maps the sequential aspects of disease co-occurrence among patients and demonstrate that network properties reflect clinical aspects of the respective diseases. We use the Temporal Disease Network to identify disease groups that reflect patterns of disease co-occurrence and the flow of patients among diagnoses. Finally, we define a strategy for the identification of trajectories that lead from one disease to another. The framework presented here has the potential to offer new insights for disease treatment and prevention in large health care systems.
Mode of action of fluopyram in plant-parasitic nematodes
Authors: Schleker A. Sylvia S. , Rist Marc , Matera Christiane , Damijonaitis Arunas , Collienne Ursel , Matsuoka Koichi , Habash Samer S. , Twelker Katja , Gutbrod Oliver , Saalwächter Corinna , Windau Maren , Matthiesen Svend , Stefanovska Tatyana , Scharwey Melanie , Marx Michael T. , Geibel Sven , Grundler Florian M. W.
Published: July 2022

Plant-parasitic nematodes (PPN) are responsible for severe yield losses in crop production. Management is challenging as effective and safe means are rare. Recently, it has been discovered that the succinate dehydrogenase (SDH) inhibitor fluopyram is highly effective against PPN while accompanying an excellent safety profile. Here we show that fluopyram is a potent inhibitor of SDH in nematodes but not in mammals, insects and earthworm, explaining the selectivity on molecular level. As a consequence of SDH inhibition, fluopyram impairs ATP generation and causes paralysis in PPN and Caenorhabditis elegans. Interestingly, efficacy differences of fluopyram amongst PPN species can be observed. Permanent exposure to micromolar to nanomolar amounts of fluopyram prevents Meloidogyne spp. and Heterodera schachtii infection and their development at the root. Preincubation of Meloidogyneincognita J2 with fluopyram followed by a recovery period effectively reduces gall formation. However, the same procedure does not inhibit H.schachtii infection and development. Sequence comparison of sites relevant for ligand binding identified amino acid differences in SDHC which likely mediate selectivity, coincidently revealing a unique amino acid difference within SDHC conserved among Heterodera spp. Docking and C.elegans mutant studies suggest that this minute difference mediates altered sensitivity of H.schachtii towards fluopyram.
Moving closer to experimental level materials property prediction using AI
Authors: Jha Dipendra , Gupta Vishu , Liao Wei-keng , Choudhary Alok , Agrawal Ankit
Published: July 2022

While experiments and DFT-computations have been the primary means for understanding the chemical and physical properties of crystalline materials, experiments are expensive and DFT-computations are time-consuming and have significant discrepancies against experiments. Currently, predictive modeling based on DFT-computations have provided a rapid screening method for materials candidates for further DFT-computations and experiments; however, such models inherit the large discrepancies from the DFT-based training data. Here, we demonstrate how AI can be leveraged together with DFT to compute materials properties more accurately than DFT itself by focusing on the critical materials science task of predicting “formation energy of a material given its structure and composition”. On an experimental hold-out test set containing 137 entries, AI can predict formation energy from materials structure and composition with a mean absolute error (MAE) of 0.064 eV/atom; comparing this against DFT-computations, we find that AI can significantly outperform DFT computations for the same task (discrepancies of $$>0.076$$

>
0.076

eV/atom) for the first time.
Cabin1 domain-containing gene picd-1 interacts with pry-1/Axin to regulate multiple processes in Caenorhabditis elegans
Authors: Mallick Avijit , Taylor Shane K. B. , Mehta Sakshi , Gupta Bhagwati P.
Published: July 2022

The Axin family of scaffolding proteins control diverse processes, such as facilitating the interactions between cellular components and providing specificity to signaling pathways. While several Axin family members have been discovered in metazoans and shown to play crucial roles, their mechanism of action are not well understood. The Caenorhabditis elegans Axin homolog, pry-1, is a powerful tool for identifying interacting genes and downstream effectors that function in a conserved manner to regulate Axin-mediated signaling. Our lab and others have established pry-1’s essential role in developmental processes that affect the reproductive system, seam cells, and a posterior P lineage cell, P11.p. Additionally, pry-1 is crucial for lipid metabolism, stress responses, and aging. In this study, we expanded on our previous work on pry-1 by reporting a novel interacting gene named picd-1 (pry-1-interacting and Cabin1 domain-containing). PICD-1 protein shares sequence conservation with CABIN1, a component of the HUCA complex. Our findings have revealed that PICD-1 is involved in several pry-1-mediated processes, including stress response and lifespan maintenance. picd-1’s expression overlapped with that of pry-1 in multiple tissues throughout the lifespan. Furthermore, PRY-1 and PICD-1 inhibited CREB-regulated transcriptional coactivator homolog CRTC-1, which promotes longevity in a calcineurin-dependent manner. Overall, our study has demonstrated that picd-1 is necessary for mediating pry-1 function and provides the basis to investigate whether Cabin-1 domain-containing protein plays a similar role in Axin signaling in other systems.
Clustering analysis and prognostic signature of lung adenocarcinoma based on the tumor microenvironment
Authors: Shan Qingqing , Zhang Yifan , Liang Zongan
Published: July 2022

Because of immunotherapy failure in lung adenocarcinoma, we have tried to find new potential biomarkers for differentiating different tumor subtypes and predicting prognosis. We identified two subtypes based on tumor microenvironment-related genes in this study. We used seven methods to analyze the immune cell infiltration between subgroups. Further analysis of tumor mutation load and immune checkpoint expression among different subgroups was performed. The least absolute shrinkage and selection operator Cox regression was applied for further selection. The selected genes were used to construct a prognostic 14-gene signature for LUAD. Next, a survival analysis and time-dependent receiver operating characteristics were performed to verify and evaluate the model. Gene set enrichment analyses and immune analysis in risk groups was also performed. According to the expression of genes related to the tumor microenvironment, lung adenocarcinoma can be divided into cold tumors and hot tumors. The signature we built was able to predict prognosis more accurately than previously known models. The signature-based tumor microenvironment provides further insight into the prediction of lung adenocarcinoma prognosis and may guide individualized treatment.
Admission temperature of very low birth weight infants and outcomes at three years old
Authors: Kato Shin , Iwata Osuke , Iwata Sachiko , Yamada Takaharu , Tsuda Kennosuke , Tanaka Taihei , Saitoh Shinji
Published: July 2022

The lower body temperature of preterm newborns at admission to neonatal intensive care units (NICUs) is inversely associated with their morbidities and mortalities before discharge. This retrospective cohort study aimed to determine whether admission rectal temperature in very low birth weight infants (VLBWIs) is independently associated with a composite outcome of death or moderate-to-severe neurodevelopmental impairments as defined by a performance developmental quotient of < 70 at three years of age. VLBWIs admitted to the NICU between April 2010 and March 2016 were assesed. Developmental assessment was completed in 216 newborns. Nine and two infants died before and after discharge, respectively. A higher admission temperature was associated with a lower incidence of death or moderate-to-severe neurodevelopmental impairments with adjustment for gestational age, sex, antenatal steroid use, Apgar score, severe intraventricular hemorrhage, and severe bronchopulmonary dysplasia (odds ratio [OR] 0.424; 95% confidence interval [CI] 0.250–0.717; p = 0.001). The admission temperature remained as an independent variable of adverse outcome at three years of age even when the study cohort was limited to surviving infants (OR 0.448; 95% CI 0.259–0.774; p = 0.004). Further studies are needed to assess whether avoiding low body temperature at admission results in better long-term neurodevelopmental outcomes in VLBWIs.
A semi-automatic toolbox for markerless effective semantic feature extraction
Authors: Pastore Vito Paolo , Moro Matteo , Odone Francesca
Published: July 2022

VisionTool is an open-source python toolbox for semantic features extraction, capable to provide accurate features detectors for different applications, including motion analysis, markerless pose estimation, face recognition and biological cell tracking. VisionTool leverages transfer-learning with a large variety of deep neural networks allowing high-accuracy features detection with few training data. The toolbox offers a friendly graphical user interface, efficiently guiding the user through the entire process of features extraction. To facilitate broad usage and scientific community contribution, the code and a user guide are available at https://github.com/Malga-Vision/VisionTool.git.