bluuebunny/crossref_metadata_2025 huggingface dataset:
MXene-Graphene Composites: A Perspective on Biomedical Potentials
Authors: Mostafavi Ebrahim , Iravani Siavash
Published: June 2022

MXenes, transition metal carbides and nitrides with graphene-like structures, have received considerable attention since their first discovery. On the other hand, Graphene has been extensively used in biomedical and medicinal applications. MXene and graphene, both as promising candidates of two-dimensional materials, have shown to possess high potential in future biomedical applications due to their unique physicochemical properties such as superior electrical conductivity, high biocompatibility, large surface area, optical and magnetic features, and extraordinary thermal and mechanical properties. These special structural, functional, and biological characteristics suggest that the hybrid/composite structure of MXene and graphene would be able to meet many unmet needs in different fields; particularly in medicine and biomedical engineering, where high-performance mechanical, electrical, thermal, magnetic, and optical requirements are necessary. However, the hybridization and surface functionalization should be further explored to obtain biocompatible composites/platforms with unique physicochemical properties, high stability, and multifunctionality. In addition, toxicological and long-term biosafety assessments and clinical translation evaluations should be given high priority in research. Although very limited studies have revealed the excellent potentials of MXene/graphene in biomedicine, the next steps should be toward the extensive research and detailed analysis in optimizing the properties and improving their functionality with a clinical and industrial outlook. Herein, different synthesis/fabrication methods and performances of MXene/graphene composites are discussed for potential biomedical applications. The potential toxicological effects of these composites on human cells and tissues are also covered, and future perspectives toward more successful translational applications are presented. The current state-of-the-art biotechnological advances in the use of MXene-Graphene composites, as well as their developmental challenges and future prospects are also deliberated. Due to the superior properties and multifunctionality of MXene-graphene composites, these hybrid structures can open up considerable new horizons in future of healthcare and medicine.
Time evolution of plasma parameters in the jet of a low-power vacuum arc thruster
Authors: Michaux Etienne , Mazouffre Stéphane , Blanchet Antoine
Published: June 2022

The plasma parameters temporal evolution of a 30 W-class Vacuum Arc Thruster equipped with a Ni-Cr cathode is examined in the far-field region of the plasma jet. Measurements have been performed 20 cm downstream of the arc region where the plasma is created. The thruster operated at 1 Hz with 25 μs duration current pulses. The maximum current intensity reaches 4000 A about 8 μs after the discharge ignition. The change in the electron density, electron temperature and plasma potential during the short high-current pulse has been obtained by means of time-resolved Langmuir probe measurements. A time-of-flight technique based on a planar probe has been used to determine the mean ion velocity in the plasma jet. In addition, a Faraday cup allowed the determination of the ion current density. The electron density peaks at ∼ 8×1017 m−3 at 12 μs. The electron temperature is above 25 eV at 7 μs and then it stabilizes around 5 eV. Several ion populations are identified. The lowest ion mean velocity amounts to 20 km/s. Interestingly, combining all data allows to assess the ion mean electrical charge and its temporal behavior. The mean charge reaches 12 a few μs after ignition. It decays quickly afterwards and stays unchanged at 2 beyond 10 μs. Analysis of all the results support the idea of two distinct plasma discharge regimes.
On Arash Abazari's Hegel's Ontology of Power
Authors: de Laurentiis Allegra
Published: June 2022

If one's goal as a scholar is neither rejection nor embrace, whether piecemeal or wholesale, of a classical text, but rather the clarification of its key concepts, arguments and intellectual context, in order to show where those concepts and arguments lead—possibly to conclusions beyond those made explicit in the text itself—then Arash Abazari's Hegel's Ontology of Power: The Structure of Social Domination in Capitalism leads by example. The general premise of this study is that Hegel's philosophy of the real is grounded in the prima philosophia of the system, the Science of Logic. The specific task of the investigation is the uncovering of the foundations of the philosophy of objective spirit, as embodied in the 1820 Outlines of the Philosophy of Right, in pivotal categories of the Logic's Doctrine of Essence. But the ultimate goal of Abazari's work is to disclose how the radically critical potential of these same categories and their relations finds its actualization in Marx's account of the process of capital as the real bedrock of bourgeois society (bürgerliche Gesellschaft).
Fibonacci spirals may not need the Golden Angle
Authors: Yin Xiaofeng , Tsukaya Hirokazu
Published: June 2022

Phyllotaxis, the regular arrangement of plant lateral organs, is an important aspect of quantitative plant biology. Some models relying on the geometric relationship of the shoot apex and organ primordia focus mainly on spiral phyllotaxis, a common phyllotaxis mode. While these models often predict the dependency of Fibonacci spirals on the Golden Angle, other models do not emphasise such a relation. Phyllotactic patterning in Asteraceae is one such example. Recently, it was revealed that auxin dynamics and the expansion and contraction of the active ring of the capitulum (head) are the key processes to guide Fibonacci spirals in gerbera (Gerbera hybrida). In this Insights paper, we discuss the importance of auxin dynamics, distinct phases of phyllotactic patterning, and the transition of phyllotaxis modes. These findings signify the local interaction among primordia in phyllotactic patterning and the notion that Fibonacci spirals may not need the Golden Angle.
US Anti-Dumping Practices Evolving against Market Economies
Authors: Kim Kyounghwa , Roh Jaeyoun
Published: June 2022

This study examines how US discretionary practices developed in the past decade have affected antidumping duty rates against exporters. Using the most recent data on dumping margin calculations, we find that the US Department of Commerce (DOC) has developed discretionary practices in a more nuanced manner to inflate dumping margins, which have primarily targeted market economy exporters. Our case studies document that practices known as targeted dumping and particular market situations appear to serve as trade protectionism for market economy exporters, especially those who could otherwise have received a negative determination without such practices. Furthermore, the DOC has brought an apparent change in its application of discretionary practices after the Trade Extension Preferences Act of 2015, leading to much higher dumping margins for the market economy. Along with empirical and case analyses, we further examine the World Trade Organization (WTO) jurisprudence concerning the extent to which the discretion of an investigating authority in anti-dumping proceedings can be condoned in the WTO.
Turkish validity and reliability of the Cancer Stigma Scale (CASS-T)
Authors: Çevik Banu , Kav Sultan , Kaynar Pelinsu , Sahin Zeynep Kübra , Tekcan Büşra , Ülker Şeymanur
Published: June 2022

Objectives

This study is aimed to evaluate the validity and reliability of the Cancer Stigma Scale for the Turkish population (CASS-T).

Methods

The sample of the study consisted of 412 students of a foundation university located in Ankara, Turkey. The reliability of the CASS was evaluated using the Cronbach alpha reliability coefficient and item-total score correlations. Exploratory factor analyses were applied to examine the factor structure of the scale and its construct validity. To test the time invariance of the scale, the relationships between the scores obtained from the first and second applications were examined using the intraclass correlation coefficient (ICC).

Results

The Cronbach's alpha coefficient of CASS-T was 0.83. In the factor analysis, it was confirmed that the scale has a six-dimensional structure in parallel to original version, namelyAvoidance,Severity,Responsibility,Policy opposition,Awkwardness,and Discrimination. The ICC values all remained in the range that indicates the reliability of the 0.63–0.71 to be substantial. The contribution of the six factors of the CASS-T scale to the variance is 57.8.

Significance in results

The Turkish version of the CASS was confirmed to have good reliability and validity for evaluating stigma toward cancer in Turkish society.
Children and Youth in Strategic Climate Litigation: Advancing Rights through Legal Argument and Legal Mobilization
Authors: Donger Elizabeth
Published: June 2022

Children and young people constitute more than one quarter of all plaintiffs in rights-based strategic climate litigation cases filed globally up to 2021. This article examines the implications of this development for children's environmental rights inside and outside the courtroom, relying on the analysis of case documents, media coverage, and the broader literature on strategic climate litigation and children's rights. The article finds that children are well placed to make powerful arguments for intergenerational justice. Conversely, children's rights arguments that address their current-day grievances are under-utilized. More consistent inclusion of these types of claim could strengthen children's environmental rights, clarifying and enforcing legal obligations towards children in the context of the climate crisis as it unfolds. The involvement of children in strategic climate litigation, moreover, can advance the critical role of this demographic as stakeholder in climate solutions. However, the participation of children also raises ethical and practical dilemmas, which are currently poorly understood and only haphazardly addressed.
Exploring the Deep Ocean Single‐Frequency Microseisms Southwest of Japan in Northern Philippine Sea
Authors: Huang Bin , Xue Mei , Guo Zhen , Song Wenkai
Published: June 2022

Single‐frequency microseisms (SFMs) have been revealed to be only generated in shallow water for decades, while some recent studies reported them in a deep ocean. Using the continuous waveform data recorded by ocean bottom seismometers, we investigate the deep ocean SFMs in the northern Philippine Sea. Based on the spectrum analysis, we find that the SFMs can be detected in deep ocean and the detection is time variable. To determine the source locations of SFMs, we perform polarization analysis and calculate the cross‐correlation coefficients between SFMs on vertical components and ocean wave energy spectra considering the attenuation of SFMs. Both the polarization and correlation results show that the sources nearby stations dominate the observed Rayleigh‐wave SFMs though distant sources also contribute. Our investigation suggests that the SFMs can be generated in a deep ocean likely by infragravity ocean waves interacting with seafloor topography, which is strengthened by strong ocean storms.
The Overlooked Role of the Stratosphere Under a Solar Constant Reduction
Authors: Bednarz Ewa M. , Visioni Daniele , Banerjee Antara , Braesicke Peter , Kravitz Ben , MacMartin Douglas G.
Published: June 2022

Modeling experiments reducing surface temperatures via an idealized reduction of the solar constant have often been used as analogs for Stratospheric Aerosol Injection (SAI), thereby implicitly assuming that solar dimming captures the essential physical mechanism through which SAI influences surface climate. While the omission of some important processes that otherwise operate under SAI was identified before, here we demonstrate that the imposed reduction in the incoming solar radiation also induces a different stratospheric dynamical response, manifested through a weakening of the polar vortex, that propagates from the upper stratosphere down to the troposphere. The coupled stratospheric‐tropospheric response exerts a previously overlooked first‐order influence on southern hemispheric surface climate in the solar dimming experiments, including on the position of the tropospheric jet and Hadley Circulation and thus, ultimately, precipitation patterns. This perturbation, opposite to that expected under SAI, highlights the need for caution when attributing responses in idealized experiments.
Stress Map of Japan: Detailed Nationwide Crustal Stress Field Inferred From Focal Mechanism Solutions of Numerous Microearthquakes
Authors: Uchide Takahiko , Shiina Takahiro , Imanishi Kazutoshi
Published: June 2022

Crustal stress is a crucial parameter for understanding tectonics and assessing the occurrence of large earthquakes. Stress at seismogenic depths over a wide area has been inferred from focal mechanism solutions. The existence of focal mechanism solutions determines the area that can be potentially studied. Therefore, we studied the crustal stress orientations in Japan from focal mechanism solutions of small earthquakes. First, we obtained about 220,000 focal mechanisms using the P‐wave first‐motion polarities picked by a deep learning model. Next, we performed a linearized inversion on the nationwide stress orientation model at a grid of 0.2‐degree intervals. The estimation errors reflect the quality and quantity of focal mechanism solutions. Overall, the results indicate that Japanese islands are under an east–west compressional stress, whereas some areas along the Pacific coast of northeast Japan are under east–west extensional stress. A closer look shows the spatial trends of stress orientation may vary near the geological borders, including the Hinagu and Futagawa faults in Kumamoto Prefecture (Kyushu Island) and the Median Tectonic Line in Shikoku Island. Our stress model also revealed the existence of stress anomalies around Cape Shionomisaki in the Kii peninsula. Most of the active faults are at approximately optimal orientation for the derived stress orientation and stress ratio, although uncertainties in the fault geometry, particularly the dip angle, substantially affect this evaluation. The stress map helps understand the overall vision of the crustal stress in Japan and further study the local stress distribution.
On the Noise Estimation in Super Dual Auroral Radar Network Data
Authors: Ponomarenko P. V. , Bland E. C. , McWilliams K. A. , Nishitani N.
Published: June 2022

The Super Dual Auroral Radar Network (SuperDARN) currently consists of more than thirty high‐frequency (HF, 3–30 MHz) radars covering mid‐latitude to polar regions in both hemispheres. Their major task is to map ionospheric plasma circulation which provides information about the interactions between the solar wind and the near‐Earth's space plasma environment. One of the major factors defining radar data quality is the signal‐to‐noise ratio (SNR), which requires an accurate characterization of the HF noise. The standard SuperDARN data analysis software uses the SNR as part of a set of empirical procedures designed to remove low‐quality data from further analysis. In this study we found that the currently used empirical algorithm systematically underestimates the noise level by up to 40%. Based on comparison of theoretical and observational noise statistics, we resolve this issue by designing and validating a procedure for accurate background noise level estimation. We then propose a simple SNR threshold to replace the existing criteria for excluding low‐quality data. In addition, we show that several aspects of the radar operational regime design, as well as short‐lived anthropogenic radio interference, can adversely affect the quality of the noise estimates at selected radar sites, and we propose ways to mitigate these problems.
Unmet need in Sierra Leone: a national oral health survey of schoolchildren
Authors: Ghotane S. G. , Challacombe S. J. , Don-Davis P. , Kamara D. , Gallagher J. E.
Published: June 2022

Objective

Sierra Leone (SL), in West Africa, with a population of over 7.5 million people has suffered the effects of a civil war previously, and more recently Ebola & Covid-19. Dental care is very limited, mostly in the capital Freetown and the private sector. No dental education is available in the country. The objective of this research was to investigate the oral health needs of schoolchildren at key ages, to inform future action.

Materials and methods

This first national oral health survey of schoolchildren at 6-, 12- and 15-years was conducted in urban and rural settings across all four regions using a multi-stage cluster sampling in line with the WHO guidelines, adapted according to contemporary survey methods to include ‘International Caries Detection and Assessment System (ICDAS)’. Whilst parents were invited to complete a questionnaire for 6-year-old children, 12- and 15-year-olds self-completed a questionnaire. Data were weighted according to age and regional population and analysed using STATA v.15 and SPSS v.22.

Results

A total of 1174 children participated across 22 schools from all four regions. Dental caries was prevalent (over 80% of all age-groups having clinical decay; ICDAS score ≥ 2) and largely untreated. No children had fillings and only 4% had missing teeth. Amongst 6, 12 and 15-year-olds, average decay levels at ICDAS > 3 threshold was 3.47 (primary teeth), 2.94 and 4.30 respectively. Almost, 10% (n = 119) of all children reported experiencing pain in their teeth with 7% (n = 86) children having PUFA lesions present. At least one in five children required one or more dental extractions. ‘Age’ was a significant predictor of dental caries experience and the odds of having dental caries experience was higher in rural areas at D3–6MFT (p < 0.05).

Conclusion

The findings demonstrate a vast unmet oral health need in the children of SL. Using ICDAS as an epidemiological tool in a low-income country provides valuable insight to the pattern of oral disease to inform health service planning. Urgent action is required to address this silent epidemic.
Climatic and tectonic drivers shaped the tropical distribution of coral reefs
Authors: Jones Lewis A. , Mannion Philip D. , Farnsworth Alexander , Bragg Fran , Lunt Daniel J.
Published: June 2022

Today, warm-water coral reefs are limited to tropical-to-subtropical latitudes. These diverse ecosystems extended further poleward in the geological past, but the mechanisms driving these past distributions remain uncertain. Here, we test the role of climate and palaeogeography in shaping the distribution of coral reefs over geological timescales. To do so, we combine habitat suitability modelling, Earth System modelling and the ~247-million-year geological record of scleractinian coral reefs. A broader latitudinal distribution of climatically suitable habitat persisted throughout much of the Mesozoic–early Paleogene due to an expanded tropical belt and more equable distribution of shallow marine substrate. The earliest Cretaceous might be an exception, with reduced shallow marine substrate during a ‘cold-snap’ interval. Climatically suitable habitat area became increasingly skewed towards the tropics from the late Paleogene, likely steepening the latitudinal biodiversity gradient of reef-associated taxa. This was driven by global cooling and increases in tropical shallow marine substrate resulting from the tectonic evolution of the Indo-Australian Archipelago. Although our results suggest global warming might permit long-term poleward range expansions, coral reef ecosystems are unlikely to keep pace with the rapid rate of anthropogenic climate change.
Proposed energy-metabolisms cannot explain the atmospheric chemistry of Venus
Authors: Jordan Sean , Shorttle Oliver , Rimmer Paul B.
Published: June 2022

Life in the clouds of Venus, if present in sufficiently high abundance, must be affecting the atmospheric chemistry. It has been proposed that abundant Venusian life could obtain energy from its environment using three possible sulfur energy-metabolisms. These metabolisms raise the possibility of Venus’s enigmatic cloud-layer SO2-depletion being caused by life. We here couple each proposed energy-metabolism to a photochemical-kinetics code and self-consistently predict the composition of Venus’s atmosphere under the scenario that life produces the observed SO2-depletion. Using this photo-bio-chemical kinetics code, we show that all three metabolisms can produce SO2-depletions, but do so by violating other observational constraints on Venus’s atmospheric chemistry. We calculate the maximum possible biomass density of sulfur-metabolising life in the clouds, before violating observational constraints, to be ~10−5 − 10−3 mg m−3. The methods employed are equally applicable to aerial biospheres on Venus-like exoplanets, planets that are optimally poised for atmospheric characterisation in the near future.
Evidence of water on the lunar surface from Chang’E-5 in-situ spectra and returned samples
Authors: Liu Jianjun , Liu Bin , Ren Xin , Li Chunlai , Shu Rong , Guo Lin , Yu Songzheng , Zhou Qin , Liu Dawei , Zeng Xingguo , Gao Xingye , Zhang Guangliang , Yan Wei , Zhang Hongbo , Jia Lihui , Jin Shifeng , Xu Chunhua , Deng Xiangjin , Xie Jianfeng , Yang Jianfeng , Huang Changning , Zuo Wei , Su Yan , Wen Weibin , Ouyang Ziyuan
Published: June 2022

The distribution range, time-varying characteristics, and sources of lunar water are still controversial. Here we show the Chang’E-5 in-situ spectral observations of lunar water under Earth’s magnetosphere shielding and relatively high temperatures. Our results show the hydroxyl contents of lunar soils in Chang’E-5 landing site are with a mean value of 28.5 ppm, which is on the weak end of lunar hydration features. This is consistent with the predictions from remote sensing and ground-based telescopic data. Laboratory analysis of the Chang’E-5 returned samples also provide critical clues to the possible sources of these hydroxyl contents. Much less agglutinate glass contents suggest a weak contribution of solar wind implantation. Besides, the apatite present in the samples can provide hydroxyl contents in the range of 0 to 179 ± 13 ppm, which shows compelling evidence that, the hydroxyl-containing apatite may be an important source for the excess hydroxyl observed at this young mare region.
A framework for the general design and computation of hybrid neural networks
Authors: Zhao Rong , Yang Zheyu , Zheng Hao , Wu Yujie , Liu Faqiang , Wu Zhenzhi , Li Lukai , Chen Feng , Song Seng , Zhu Jun , Zhang Wenli , Huang Haoyu , Xu Mingkun , Sheng Kaifeng , Yin Qianbo , Pei Jing , Li Guoqi , Zhang Youhui , Zhao Mingguo , Shi Luping
Published: June 2022

There is a growing trend to design hybrid neural networks (HNNs) by combining spiking neural networks and artificial neural networks to leverage the strengths of both. Here, we propose a framework for general design and computation of HNNs by introducing hybrid units (HUs) as a linkage interface. The framework not only integrates key features of these computing paradigms but also decouples them to improve flexibility and efficiency. HUs are designable and learnable to promote transmission and modulation of hybrid information flows in HNNs. Through three cases, we demonstrate that the framework can facilitate hybrid model design. The hybrid sensing network implements multi-pathway sensing, achieving high tracking accuracy and energy efficiency. The hybrid modulation network implements hierarchical information abstraction, enabling meta-continual learning of multiple tasks. The hybrid reasoning network performs multimodal reasoning in an interpretable, robust and parallel manner. This study advances cross-paradigm modeling for a broad range of intelligent tasks.
Morphological pseudotime ordering and fate mapping reveal diversification of cerebellar inhibitory interneurons
Authors: Wang Wendy Xueyi , Lefebvre Julie L.
Published: June 2022

Understanding how diverse neurons are assembled into circuits requires a framework for describing cell types and their developmental trajectories. Here we combine genetic fate-mapping, pseudotemporal profiling of morphogenesis, and dual morphology and RNA labeling to resolve the diversification of mouse cerebellar inhibitory interneurons. Molecular layer interneurons (MLIs) derive from a common progenitor population but comprise diverse dendritic-, somatic-, and axon initial segment-targeting interneurons. Using quantitative morphology from 79 mature MLIs, we identify two discrete morphological types and presence of extensive within-class heterogeneity. Pseudotime trajectory inference using 732 developmental morphologies indicate the emergence of distinct MLI types during migration, before reaching their final positions. By comparing MLI identities from morphological and transcriptomic signatures, we demonstrate the dissociation between these modalities and that subtype divergence can be resolved from axonal morphogenesis prior to marker gene expression. Our study illustrates the utility of applying single-cell methods to quantify morphology for defining neuronal diversification.
Accelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties
Authors: Xie Tian , France-Lanord Arthur , Wang Yanming , Lopez Jeffrey , Stolberg Michael A. , Hill Megan , Leverick Graham Michael , Gomez-Bombarelli Rafael , Johnson Jeremiah A. , Shao-Horn Yang , Grossman Jeffrey C.
Published: June 2022

Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous systems: the amorphous structure of polymers requires multiple, repeated sampling to reduce noise and the slow relaxation requires long simulation time for convergence. Here, we accelerate the screening with a multi-task graph neural network that learns from a large amount of noisy, unconverged, short MD data and a small number of converged, long MD data. We achieve accurate predictions of 4 different converged properties and screen a space of 6247 polymers that is orders of magnitude larger than previous computational studies. Further, we extract several design principles for polymer electrolytes and provide an open dataset for the community. Our approach could be applicable to a broad class of material discovery problems that involve the simulation of complex, amorphous materials.
Brain-wide reconstruction of inhibitory circuits after traumatic brain injury
Authors: Frankowski Jan C. , Tierno Alexa , Pavani Shreya , Cao Quincy , Lyon David C. , Hunt Robert F.
Published: June 2022

Despite the fundamental importance of understanding the brain’s wiring diagram, our knowledge of how neuronal connectivity is rewired by traumatic brain injury remains remarkably incomplete. Here we use cellular resolution whole-brain imaging to generate brain-wide maps of the input to inhibitory neurons in a mouse model of traumatic brain injury. We find that somatostatin interneurons are converted into hyperconnected hubs in multiple brain regions, with rich local network connections but diminished long-range inputs, even at areas not directly damaged. The loss of long-range input does not correlate with cell loss in distant brain regions. Interneurons transplanted into the injury site receive orthotopic local and long-range input, suggesting the machinery for establishing distant connections remains intact even after a severe injury. Our results uncover a potential strategy to sustain and optimize inhibition after traumatic brain injury that involves spatial reorganization of the direct inputs to inhibitory neurons across the brain.
A westerly wind dominated Puna Plateau during deposition of upper Pleistocene loessic sediments in the subtropical Andes, South America
Authors: Pullen Alex , Barbeau David L. , Leier Andrew L. , Abell Jordan T. , Ward Madison , Bruner Austin , Fidler Mary Kate
Published: June 2022

The Tafí del Valle depression (~27° S) in the eastern Andes of Argentina provides a record of late Pleistocene dust deposition in the subtropics of South America. We present large-nU-Pb geochronology data for detrital zircons from upper Pleistocene loess-paleosol deposits. When compared to regional data, the age spectra from the Tafí del Valle samples are most like the southern Puna Plateau, supporting derivation largely from the west and northwest. This runs counter to hypotheses suggesting these loessic sediments were derived from the low elevation plains to the east or extra-Andean Patagonia. Mapping of linear wind erosion features on the Puna Plateau yield a mean orientation of 125.7° (1 s.d. = 12.4°). These new data and existing records are consistent with a westerly-northwesterly dominated (upper- and lower-level) wind system over the southern Puna Plateau (to at least ~27° S) during periods of high dust accumulation in Tafí del Valle.
Structural remodeling of ribosome associated Hsp40-Hsp70 chaperones during co-translational folding
Authors: Chen Yan , Tsai Bin , Li Ningning , Gao Ning
Published: June 2022

Ribosome associated complex (RAC), an obligate heterodimer of HSP40 and HSP70 (Zuo1 and Ssz1 in yeast), is conserved in eukaryotes and functions as co-chaperone for another HSP70 (Ssb1/2 in yeast) to facilitate co-translational folding of nascent polypeptides. Many mechanistic details, such as the coordination of one HSP40 with two HSP70s and the dynamic interplay between RAC-Ssb and growing nascent chains, remain unclear. Here, we report three sets of structures of RAC-containing ribosomal complexes isolated from Saccharomyces cerevisiae. Structural analyses indicate that RAC on the nascent-chain-free ribosome is in an autoinhibited conformation, and in the presence of a nascent chain at the peptide tunnel exit (PTE), RAC undergoes large-scale structural remodeling to make Zuo1 J-Domain more accessible to Ssb. Our data also suggest a role of Zuo1 in orienting Ssb-SBD proximal to the PTE for easy capture of the substrate. Altogether, in accordance with previous data, our work suggests a sequence of structural remodeling events for RAC-Ssb during co-translational folding, triggered by the binding and passage of growing nascent chain from one to another.
CXCL4 synergizes with TLR8 for TBK1-IRF5 activation, epigenomic remodeling and inflammatory response in human monocytes
Authors: Yang Chao , Bachu Mahesh , Du Yong , Brauner Caroline , Yuan Ruoxi , Ah Kioon Marie Dominique , Chesi Giancarlo , Barrat Franck J. , Ivashkiv Lionel B.
Published: June 2022

Regulation of endosomal Toll-like receptor (TLR) responses by the chemokine CXCL4 is implicated in inflammatory and fibrotic diseases, with CXCL4 proposed to potentiate TLR responses by binding to nucleic acid TLR ligands and facilitating their endosomal delivery. Here we report that in human monocytes/macrophages, CXCL4 initiates signaling cascades and downstream epigenomic reprogramming that change the profile of the TLR8 response by selectively amplifying inflammatory gene transcription and interleukin (IL)−1β production, while partially attenuating the interferon response. Mechanistically, costimulation by CXCL4 and TLR8 synergistically activates TBK1 and IKKε, repurposes these kinases towards an inflammatory response via coupling with IRF5, and activates the NLRP3 inflammasome. CXCL4 signaling, in a cooperative and synergistic manner with TLR8, induces chromatin remodeling and activates de novo enhancers associated with inflammatory genes. Our findings thus identify new regulatory mechanisms of TLR responses relevant for cytokine storm, and suggest targeting the TBK1-IKKε-IRF5 axis may be beneficial in inflammatory diseases.
Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks
Authors: Amato Katherine A. , Haddock Luis A. , Braun Katarina M. , Meliopoulos Victoria , Livingston Brandi , Honce Rebekah , Schaack Grace A. , Boehm Emma , Higgins Christina A. , Barry Gabrielle L. , Koelle Katia , Schultz-Cherry Stacey , Friedrich Thomas C. , Mehle Andrew
Published: June 2022

Transmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The bottlenecks within hosts and their potential impacts on evolutionary pathways taken during infection are poorly understood. To address this, we created highly diverse IAV libraries bearing molecular barcodes on two gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in “islands” of infection in lung lobes, each with genetically distinct populations. We perform site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and track viral diversity as infection spreads to the trachea and lungs. We detect extensive compartmentalization of discrete populations within lung lobes. Bottleneck events and localized replication stochastically sample individual viruses from the upper respiratory tract or the trachea that become the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with limited evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation.
Programmable probiotics modulate inflammation and gut microbiota for inflammatory bowel disease treatment after effective oral delivery
Authors: Zhou Jun , Li Maoyi , Chen Qiufang , Li Xinjie , Chen Linfu , Dong Ziliang , Zhu Wenjun , Yang Yang , Liu Zhuang , Chen Qian
Published: June 2022

Reactive oxygen species (ROS) play vital roles in intestinal inflammation. Therefore, eliminating ROS in the inflammatory site by antioxidant enzymes such as catalase and superoxide dismutase may effectively curb inflammatory bowel disease (IBD). Here, Escherichia coli Nissle 1917 (ECN), a kind of oral probiotic, was genetically engineered to overexpress catalase and superoxide dismutase (ECN-pE) for the treatment of intestinal inflammation. To improve the bioavailability of ECN-pE in the gastrointestinal tract, chitosan and sodium alginate, effective biofilms, were used to coat ECN-pE via a layer-by-layer electrostatic self-assembly strategy. In a mouse IBD model induced by different chemical drugs, chitosan/sodium alginate coating ECN-pE (ECN-pE(C/A)2) effectively relieved inflammation and repaired epithelial barriers in the colon. Unexpectedly, such engineered EcN-pE(C/A)2 could also regulate the intestinal microbial communities and improve the abundance of Lachnospiraceae_NK4A136 and Odoribacter in the intestinal flora, which are important microbes to maintain intestinal homeostasis. Thus, this study lays a foundation for the development of living therapeutic proteins using probiotics to treat intestinal-related diseases.
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas
Authors: Walzer Mathias , García-Seisdedos David , Prakash Ananth , Brack Paul , Crowther Peter , Graham Robert L. , George Nancy , Mohammed Suhaib , Moreno Pablo , Papatheodorou Irene , Hubbard Simon J. , Vizcaíno Juan Antonio
Published: June 2022

The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.
A global database for conducting systematic reviews and meta-analyses in innovation and quality management
Authors: Csizmadia Tibor , Katona Attila Imre
Published: June 2022

Innovation and quality management are two fundamental business orientations that complement each other in improving performance and are important drivers of long-term economic growth. These themes have generated widespread attention in the literature; however, most of these studies mainly focused on a narrow area and only in a short term. No systematic effort has been made to build an extended bibliometric database regarding these research areas, which can be immediately used to conduct literature reviews. This study presents a complete (from 1975–2021), up-to-date, preprocessed and geocoded bibliometric database combining published articles of the two themes. The data collection was performed following the PRISMA methodology. The database consists of seven data tables, including one core dataset with 59,231 records and six citation network-related tables, including latitude and longitude values of the affiliations. These data will benefit researchers conducting comparative and in-depth analyses, such as gaining an overview of relevant existing studies, identifying relevant trends and gaining opportunities for a variety of geographic analyses.
Novel inorganic crystal structures predicted using autonomous simulation agents
Authors: Ye Weike , Lei Xiangyun , Aykol Muratahan , Montoya Joseph H.
Published: June 2022

We report a dataset of 96640 crystal structures discovered and computed using our previously published autonomous, density functional theory (DFT) based, active-learning workflow named CAMD (Computational Autonomy for Materials Discovery). Of these, 894 are within 1 meV/atom of the convex hull and 26826 are within 200 meV/atom of the convex hull. The dataset contains DFT-optimized pymatgen crystal structure objects, DFT-computed formation energies and phase stability calculations from the convex hull. It contains a variety of spacegroups and symmetries derived from crystal prototypes derived from known experimental compounds, and was generated from active learning campaigns of various chemical systems. This dataset can be used to benchmark future active-learning or generative efforts for structure prediction, to seed new efforts of experimental crystal structure discovery, or to construct new models of structure-property relationships.
A map of bat virus receptors derived from single-cell multiomics
Authors: Lv Tianhang , Wang Xiaoshan , Yu Chao , Wang Zhifeng , Xiang Rong , Li Linmiao , Yuan Yue , Wang Yuhang , Wei Xiaoyu , Yu Yeya , He Xiangyang , Zhang Libiao , Deng Qiuting , Wu Peiying , Hou Yong , Chen Jinping , Liu Chuanyu , Wong Gary , Liu Longqi
Published: June 2022

Bats are considered reservoirs of many lethal zoonotic viruses and have been implicated in several outbreaks of emerging infectious diseases, such as SARS-CoV, MERS-CoV, and SARS-CoV-2. It is necessary to systematically derive the expression patterns of bat virus receptors and their regulatory features for future research into bat-borne viruses and the prediction and prevention of pandemics. Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) of major organ samples collected from Chinese horseshoe bats (Rhinolophus affinis) and systematically checked the expression pattern of bat-related virus receptors and chromatin accessibility across organs and cell types, providing a valuable dataset for studying the nature of infection among bat-borne viruses.
The ERP and psychophysical changes related to facial emotion perception by expertise in Japanese hospitality, “OMOTENASHI”
Authors: Miki Kensaku , Takeshima Yasuyuki , Kida Tetsuo , Kakigi Ryusuke
Published: June 2022

We investigated the emotion perception process based on hospitality expertise. Forty subjects were divided into the OMOTENASHI group working at inns considered to represent the spirit of hospitality, OMOTENASHI in Japan, and CONTROL group without experience in the hospitality industry. We presented neutral, happy, and angry faces to investigate P100 and N170 by these faces, and psychophysical changes by the favor rating test to evaluate emotional perception. In the favor rating test, the score was significantly smaller (less favorable) in OMOTENASHI than in CONTROL. Regarding event-related potential components, the maximum amplitude of P100 was significantly larger for a neutral face at the right occipital electrode in OMOTENASHI than in CONTROL, and it was significantly larger for an angry face at both occipital electrodes in OMOTENASHI than in CONTROL. However, the peak latency and maximum amplitude of N170 were not significantly different between OMOTENASHI and CONTROL at both temporal electrodes for each emotion condition. Differences on the favor rating test and P100 in OMOTENASHI suggested that workers at inns may more quickly notice and be more sensitive to the facial emotion of guests due to hospitality training, and/or that hospitality expertise may increase attention to emotion by top-down and/or bottom-up processing.
Exogenous human α-Synuclein acts in vitro as a mild platelet antiaggregant inhibiting α-thrombin-induced platelet activation
Authors: Acquasaliente Laura , Pontarollo Giulia , Radu Claudia Maria , Peterle Daniele , Artusi Ilaria , Pagotto Anna , Uliana Federico , Negro Alessandro , Simioni Paolo , De Filippis Vincenzo
Published: June 2022

α-Synuclein (αSyn) is a small disordered protein, highly conserved in vertebrates and involved in the pathogenesis of Parkinson’s disease (PD). Indeed, αSyn amyloid aggregates are present in the brain of patients with PD. Although the pathogenic role of αSyn is widely accepted, the physiological function of this protein remains elusive. Beyond the central nervous system, αSyn is expressed in hematopoietic tissue and blood, where platelets are a major cellular host of αSyn. Platelets play a key role in hemostasis and are potently activated by thrombin (αT) through the cleavage of protease-activated receptors. Furthermore, both αT and αSyn could be found in the same spatial environment, i.e. the platelet membrane, as αT binds to and activates platelets that can release αSyn from α-granules and microvesicles. Here, we investigated the possibility that exogenous αSyn could interfere with platelet activation induced by different agonists in vitro. Data obtained from distinct experimental techniques (i.e. multiple electrode aggregometry, rotational thromboelastometry, immunofluorescence microscopy, surface plasmon resonance, and steady-state fluorescence spectroscopy) on whole blood and platelet-rich plasma indicate that exogenous αSyn has mild platelet antiaggregating properties in vitro, acting as a negative regulator of αT-mediated platelet activation by preferentially inhibiting P-selectin expression on platelet surface. We have also shown that both exogenous and endogenous (i.e. cytoplasmic) αSyn preferentially bind to the outer surface of activated platelets. Starting from these findings, a coherent model of the antiplatelet function of αSyn is proposed.
Removal of chemical and microbial water pollutants by cold plasma combined with Ag/TiO2-rGO nanoparticles
Authors: Abdel-Wahed Mahmoud S. , Hefny Mohamed Mokhtar , Abd-Elmaksoud Sherif , El-Liethy Mohamed A. , Kamel Marwa A. , El-Kalliny Amer S. , Hamza Ibrahim Ahmed
Published: June 2022

This study aimed to investigate the synergistic effect of the cold atmospheric plasma (CAP) and heterogeneous photocatalytic processes in an aqueous solution to enhance water purification efficacy and reduce the energy cost required by CAP. 0.1% Ag/TiO2-reduced graphene oxide (rGO) nanoparticles (NPs) photo-composite were prepared and fully characterized. Data showed that Ag nanoparticles and the rGO play an important role in increasing the efficiency of the whole treatment process and the photo-composite (0.1% Ag/TiO2-1% rGO at 400 °C) revealed the highest phenol removal rate with excellent reusability. Also, complete inactivation (~ 5log10 reduction) of both E. coli and S. aureus by NPs was observed without CAP exposure, whereas a minimal effect (0.1–0.5 log10) on viruses (Adenovirus (AdV), rotavirus, and ɸX174) was observed after 10 min incubation. Interestingly, the photocatalytic virus inactivation test was promising, as it resulted in > 4.7log10 reduction of AdV at 2 min treatment, whereas < 1log10 could be reduced using only CAP at the same treatment time. Accordingly, we believe that this work could provide new insights into how the synergy between CAP and 0.1% Ag/TiO2-1% rGO photo-composite in aqueous media imposes a great potential for environmental applications, such as water purification and microbial inactivation.
Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study
Authors: Ruiz-Rodriguez Alicia , Lusarreta-Parga Paula , de Steenhuijsen Piters Wouter A. A. , Koppensteiner Lilian , Balcazar-Lopez Carlos E. , Campbell Robyn , Dewar Rebecca , McHugh Martin P. , Dockrell David , Templeton Kate E. , Bogaert Debby
Published: June 2022

Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.
Molecular dynamics study of lithium intercalation into –OH functionalized carbon nanotube bundle
Authors: Zheng Bin , Dong Huaze , Zhu Jinmiao , Wang Yanping
Published: June 2022

The influence of hydroxyl group (–OH) on carbon nanotube (CNT) interacting with lithium (Li) ions has been investigated via ab initio molecular dynamic (MD) simulations. Compared with the pure CNT, a higher efficiency has been observed for lithium intercalating into CNT-OH bundle. At lower Li ion density and CNT bundle density, CNT-OH exhibits higher intercalation efficiency than the pristine and ammonium functionalized CNTs. As the increasing of Li ion densities and CNT bundle densities, Li ions tend to intercalate into the interlayer between CNT-OH tubes instead of the interior of CNT-OH tubes. We also observe the destruction of hydroxyl groups during the intercalation of Li ions into interlayer of CNT-OH bundle. It is therefore suggested that eliminating the intercalation of Li ions into interlayer between tubes is important for the design of Li ion batteries.