bluuebunny/crossref_metadata_2025 huggingface dataset:
A hybrid full-wave Markov chain approach to calculating radio-frequency wave scattering from scrape-off layer filaments
Authors: Biswas Bodhi , Shiraiwa Syun'ichi , Baek Seung-Gyou , Bonoli Paul , Ram Abhay , White Anne E.
Published: October 2021

The interaction of radio-frequency (RF) waves with edge turbulence modifies the incident wave spectrum, and can significantly affect RF heating and current drive in tokamaks. Previous lower hybrid (LH) scattering models have either used the weak-turbulence approximation, or treated more realistic, filamentary turbulence in the ray tracing limit. In this work, a new model is introduced which retains full-wave effects of RF scattering in filamentary turbulence. First, a Mie-scattering technique models the interaction of an incident wave with a single Gaussian filament. Next, an effective differential scattering width is derived for a statistical ensemble of filaments. Lastly, a Markov chain solves for the transmitted wave spectrum in slab geometry. This model is applied to LH launching for current drive. The resulting wave spectrum is asymmetrically broadened in angular wavenumber space. This asymmetry is not accounted for in previous LH scattering models. The modified wave spectrum is coupled to a ray tracing/Fokker–Planck solver (GENRAY/CQL3D) to study its impact on current drive. The resulting current profile is greatly altered, and there is significant increase in the on-axis current and decrease in the off-axis peaks. This is attributed to a portion of the modified wave spectrum that is strongly dampened on-axis during the first pass.
The Emperor's New Markov Blankets
Authors: Bruineberg Jelle , Dołęga Krzysztof , Dewhurst Joe , Baltieri Manuel
Published: October 2021

The free energy principle, an influential framework in computational neuroscience and theoretical neurobiology, starts from the assumption that living systems ensure adaptive exchanges with their environment by minimizing the objective function of variational free energy. Following this premise, it claims to deliver a promising integration of the life sciences. In recent work, Markov blankets, one of the central constructs of the free energy principle, have been applied to resolve debates central to philosophy (such as demarcating the boundaries of the mind). The aim of this paper is twofold. First, we trace the development of Markov blankets starting from their standard application in Bayesian networks, via variational inference, to their use in the literature on active inference. We then identify a persistent confusion in the literature between the formal use of Markov blankets as an epistemic tool for Bayesian inference, and their novel metaphysical use in the free energy framework to demarcate the physical boundary between an agent and its environment. Consequently, we propose to distinguish between “Pearl blankets” to refer to the original epistemic use of Markov blankets and “Friston blankets” to refer to the new metaphysical construct. Second, we use this distinction to critically assess claims resting on the application of Markov blankets to philosophical problems. We suggest that this literature would do well in differentiating between two different research programmes: “inference with a model” and “inference within a model.” Only the latter is capable of doing metaphysical work with Markov blankets, but requires additional philosophical premises and cannot be justified by an appeal to the success of the mathematical framework alone.
Iron Isotope Biogeochemical Cycling in the Western Arctic Ocean
Authors: Zhang Ruifeng , Jensen Laramie , Fitzsimmons Jessica , Sherrell Robert M. , Lam Phoebe , Xiang Yang , John Seth
Published: October 2021

The Arctic Ocean is unique, connecting the Atlantic and Pacific basins and being especially vulnerable to the impacts of a changing climate. Iron stable isotopes (δ56Fe) provide a unique window into the biogeochemical cycling of Fe in the Arctic. Here we present the first seawater δ56Fe for the Western Arctic Ocean, from the 2015 U.S. GEOTRACES GN01 transect. Samples analyzed for δ56Fe include seawater dissolved (<0.2 μm), soluble (<∼0.003 μm), and leachable particulate phases. Several key processes were explored using Fe isotopes, each characterized by a distinct combination of δ56Fe and Fe concentrations. Input of Fe from reducing continental shelf sediments was characterized by high dissolved Fe concentrations (6.18 ± 4.84 nmol kg−1) and low δ56Fe (−1.57 ± 0.66‰). Riverine Fe input observed in the Transpolar Drift Current was characterized by high Fe concentrations corresponding to a riverine end‐member Fe concentration of 19 nM, and near‐zero δ56Fe (0.02 ± 0.23‰) that was similar to that of average crustal material. The deep Arctic was mostly characterized by low Fe concentrations (0.33 ± 0.14 nmol kg−1) and slightly higher δ56Fe (0.05 ± 0.30‰), except for samples taken near continental slopes that were affected by sedimentary Fe input with lower δ56Fe, and in the Amundsen Basin which showed possible hydrothermal Fe input. Our data thus illuminate Fe biogeochemical cycling processes in the modern Arctic Ocean, and serve as a baseline for understanding how the Arctic Fe cycle responds to climate change.
Modulation of Magnetosonic Waves by Background Plasma Density in a Dipole Magnetic Field: 2‐D PIC Simulation
Authors: Sun Jicheng , Lu Quanming , Wang Xueyi , Liu Xu , Gao Xinliang , Yang Huigen
Published: October 2021

Recent satellite observations, combined with instability analyses, have shown that the background plasma density variation can modulate the magnetosonic (MS) waves by controlling the wave excitation. However, the detailed modulation process needs to be identified since the MS waves propagate nearly perpendicular to the background magnetic field. In this study, we investigate the MS wave modulation by background plasma density using a 2‐D general curvilinear particle‐in‐cell simulation in the meridian plane of a dipole magnetic field. The simulation model consists of three plasma components: the background cold electrons and protons and ring distribution protons. We find that MS waves can be locally generated by ring distribution protons in the low plasma density region, while no MS wave is generated in the high density region. These MS waves are confined near the local source region since they are damped by the background cold plasma. The background protons gain more energy than background electrons, implying the plasmaspheric protons may dominate the modulation of MS waves. Moreover, we have also investigated the generation and propagation of MS waves in the plasmapause density structure. Our simulation results demonstrate that the background plasma density variation can modulate the MS waves and may play an important role in the spatial distribution of MS waves.
Reconstruction of the Electron Diffusion Region With Inertia and Compressibility Effects
Authors: Hasegawa H. , Nakamura T. K. M. , Denton R. E.
Published: October 2021

A method based on electron magnetohydrodynamics (EMHD) for the reconstruction of steady, two‐dimensional plasma and magnetic field structures from data taken by a single spacecraft, first developed by Sonnerup et al. (2016), https://doi.org/10.1002/2016ja022430, is extended to accommodate inhomogeneity of the electron density and temperature, electron inertia effects, and guide magnetic field in and around the electron diffusion region (EDR), the central part of the magnetic reconnection region. The new method assumes that the electron density and temperature are constant along, but may vary across, the magnetic field lines. We present two models for the reconstruction of electron streamlines, one of which is not constrained by any specific formula for the electron pressure tensor term in the generalized Ohm's law that is responsible for electron unmagnetization in the EDR, and the other is a modification of the original model to include the inertia and compressibility effects. Benchmark tests using data from fully kinetic simulations show that our new method is applicable to both antiparallel and guide‐field (component) reconnection, and the electron velocity field can be better reconstructed by including the inertia effects. The new EMHD reconstruction technique has been applied to an EDR of magnetotail reconnection encountered by the Magnetospheric Multiscale spacecraft on 11 July 2017, reported by Torbert et al. (2018), https://doi.org/10.1126/science.aat2998 and reconstructed with the original inertia‐less version by Hasegawa et al. (2019), https://doi.org/10.1029/2018ja026051, which demonstrates that the new method better performs in recovering the electric field and electron streamlines than the original version.
Monthly and Interannual Variations in Winter Positive Surface‐Bottom Temperature Difference in Northeastern Coastal Waters of the Shandong Peninsula in the Yellow Sea
Authors: Zhai Fangguo , Liu Zizhou , Li Peiliang , Gu Yanzhen , Hu Luoyu , Sun Liyuan , Yang Baoqing
Published: October 2021

Traditionally, the Yellow Sea (YS) is believed to be well mixed throughout the water column or to experience significant temperature inversions in winter. Recently, we found a significant positive surface‐bottom temperature difference (SBTD) as large as 3.7°C in northeastern coastal waters of the Shandong Peninsula in the YS in winter. By analyzing 4 years (June 2016–September 2020) of online in situ observations, this study examined monthly and interannual variations in winter positive SBTD and the underlying dynamics. The winter positive SBTD generally formed in November, peaked in December/January, and disappeared in March. At the interannual time scale, this SBTD was strongest in 2018 and weakest in 2020. The underlying dynamics involved the combined effects of prevailing winter monsoon winds and resultant surface heat loss and current heat advection. When the surface northerly wind was strong, strengthened southward advection of cold air over the ocean cooled the water column intensely, whereas wind‐enhanced southward advection of warm surface water partly offset the sea surface cooling and resulted in surface temperature cooling that was considerably slower than bottom temperature or even surface temperature warming. These processes together generated strong positive SBTDs. When the surface northerly wind was weak, all of the above processes became weak and resulted in weak positive SBTDs. The relationship with Yellow River runoff was also discussed. This study enriches our knowledge of winter thermal structure in the YS. More observations and coupled physical‐biogeochemical simulations are needed to further clarify the impacts on climate and marine ecology.
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley
Authors: Mahdi Lisa K , Miyauchi Shingo , Uhlmann Charles , Garrido-Oter Ruben , Langen Gregor , Wawra Stephan , Niu Yulong , Guan Rui , Robertson-Albertyn Senga , Bulgarelli Davide , Parker Jane E , Zuccaro Alga
Published: October 2021

Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.
Circular RNA circUBE2J2 acts as the sponge of microRNA-370-5P to suppress hepatocellular carcinoma progression
Authors: Zhang Lu , Liu Yachong , Tao Haisu , Zhu He , Pan Yonglong , Li Pengcheng , Liang Huifang , Zhang Bixiang , Song Jia
Published: October 2021

Accumulating evidences indicate that circular RNAs (circRNAs), a class of non-coding RNAs, play important roles in tumorigenesis. However, the function of circRNAs in hepatocellular carcinoma is largely unknown. CircRNA microarray was performed to identify abnormally expressed circRNAs in HCC tissue samples. We conducted Kaplan–Meier survival analysis to explore the significance of circUBE2J2 in clinical prognosis. Then, we examined the functions of circUBE2J2 in HCC by cell proliferation, migration, and mouse xenograft assay. We identified miR-370-5P as a circUBE2J2-related microRNA by using biotin-labeled circUBE2J2 probe to perform RNA antisense purification (RAP) assay in HCC cells. The dual luciferase reporter assay and RNA pulldown assays were employed to verify the relationships among circUBE2J2, miRNA-370-5P, and KLF7. Microarray analysis and qRT-PCR verified a circRNA termed circUBE2J2 that was downregulated in HCC. Kaplan–Meier survival analysis showed that downregulated circUBE2J2 was correlated with poorer survival. CircUBE2J2 expression in HCC cells was selectively regulated via luciferase reporter assays; circUBE2J2 and KLF7 were observed to directly bind to miR-370-5P. Furthermore, knockdown of circUBE2J2 in HCC could downregulate KLF7, the target of miR-370-5P, thus promoting the proliferation and migration of HCC cells. Then the related experiment suggested that circUBE2J2 could regulate the expression of KLF7 by sponging miR-370-5p. In summary, we infer that circUBE2J2 may act as a competing endogenous RNA (ceRNA) to regulate KLF7 expression through sponging miR-370-5P and play a regulatory functions in HCC. CircUBE2J2 may be a diagnostic biomarker and potential target for HCC therapy.
Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21
Authors: Liu Jinfeng , Yang Jinrong , Zeng Xiao Cheng , Xantheas Sotiris S. , Yagi Kiyoshi , He Xiao
Published: October 2021

The spectroscopic features of protonated water species in dilute acid solutions have been long sought after for understanding the microscopic behavior of the proton in water with gas-phase water clusters H+(H2O)n extensively studied as bottom-up model systems. We present a new protocol for the calculation of the infrared (IR) spectra of complex systems, which combines the fragment-based Coupled Cluster method and anharmonic vibrational quasi-degenerate perturbation theory, and demonstrate its accuracy towards the complete and accurate assignment of the IR spectrum of the H+(H2O)21 cluster. The site-specific IR spectral signatures reveal two distinct structures for the internal and surface four-coordinated water molecules, which are ice-like and liquid-like, respectively. The effect of inter-molecular interaction between water molecules is addressed, and the vibrational resonance is found between the O-H stretching fundamental and the bending overtone of the nearest neighboring water molecule. The revelation of the spectral signature of the excess proton offers deeper insight into the nature of charge accommodation in the extended hydrogen-bonding network underpinning this aqueous cluster.
Geophysical constraints on the reliability of solar and wind power worldwide
Authors: Tong Dan , Farnham David J. , Duan Lei , Zhang Qiang , Lewis Nathan S. , Caldeira Ken , Davis Steven J.
Published: October 2021

If future net-zero emissions energy systems rely heavily on solar and wind resources, spatial and temporal mismatches between resource availability and electricity demand may challenge system reliability. Using 39 years of hourly reanalysis data (1980–2018), we analyze the ability of solar and wind resources to meet electricity demand in 42 countries, varying the hypothetical scale and mix of renewable generation as well as energy storage capacity. Assuming perfect transmission and annual generation equal to annual demand, but no energy storage, we find the most reliable renewable electricity systems are wind-heavy and satisfy countries’ electricity demand in 72–91% of hours (83–94% by adding 12 h of storage). Yet even in systems which meet >90% of demand, hundreds of hours of unmet demand may occur annually. Our analysis helps quantify the power, energy, and utilization rates of additional energy storage, demand management, or curtailment, as well as the benefits of regional aggregation.
Engineering digitizer circuits for chemical and genetic screens in human cells
Authors: Wong Nicole M. , Frias Elizabeth , Sigoillot Frederic D. , Letendre Justin H. , Hild Marc , Wong Wilson W.
Published: October 2021

Cell-based transcriptional reporters are invaluable in high-throughput compound and CRISPR screens for identifying compounds or genes that can impact a pathway of interest. However, many transcriptional reporters have weak activities and transient responses. This can result in overlooking therapeutic targets and compounds that are difficult to detect, necessitating the resource-consuming process of running multiple screens at various timepoints. Here, we present RADAR, a digitizer circuit for amplifying reporter activity and retaining memory of pathway activation. Reporting on the AP-1 pathway, our circuit identifies compounds with known activity against PKC-related pathways and shows an enhanced dynamic range with improved sensitivity compared to a classical reporter in compound screens. In the first genome-wide pooled CRISPR screen for the AP-1 pathway, RADAR identifies canonical genes from the MAPK and PKC pathways, as well as non-canonical regulators. Thus, our scalable system highlights the benefit and versatility of using genetic circuits in large-scale cell-based screening.
Analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling in the activation of neural stem progenitor cells
Authors: Peñailillo Johany , Palacios Miriam , Mounieres Constanza , Muñoz Rosana , Slater Paula G. , De Domenico Elena , Patrushev Ilya , Gilchrist Mike , Larraín Juan
Published: October 2021

Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPCs). Here we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, aiming to identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC-specific ribosome biogenesis factors, and genes involved in stem cell proliferation. Western blot and immunofluorescence analysis showed that mTORC1 is rapidly and transiently activated after SCI, and its pharmacological inhibition impairs spinal cord regeneration and proliferation of NSPC through the downregulation of genes involved in the G1/S transition of cell cycle, with a strong effect on PCNA. We propose that the mTOR signaling pathway is a key player in the activation of NPSCs during the early steps of spinal cord regeneration.
Improving online and offline gain from repetitive practice using anodal tDCS at dorsal premotor cortex
Authors: Kim Taewon , Buchanan John J. , Bernard Jessica A. , Wright David L.
Published: October 2021

Administering anodal transcranial direct current stimulation at the left dorsal premotor cortex (PMd) but not right PMd throughout the repetitive practice of three novel motor sequences resulted in improved offline performance usually only observed after interleaved practice. This gain only emerged following overnight sleep. These data are consistent with the proposed proprietary role of left PMd for motor sequence learning and the more recent claim that PMd is central to sleep-related consolidation of novel skill memory.
Dichotomous metabolic networks govern human ILC2 proliferation and function
Authors: Surace Laura , Doisne Jean-Marc , Croft Carys A. , Thaller Anna , Escoll Pedro , Marie Solenne , Petrosemoli Natalia , Guillemot Vincent , Dardalhon Valerie , Topazio Davide , Cama Antonia , Buchrieser Carmen , Taylor Naomi , Amit Ido , Musumeci Olimpia , Di Santo James P.
Published: October 2021

Group 2 innate lymphoid cells (ILC2s) represent innate homologs of type 2 helper T cells (TH2) that participate in immune defense and tissue homeostasis through production of type 2 cytokines. While T lymphocytes metabolically adapt to microenvironmental changes, knowledge of human ILC2 metabolism is limited, and its key regulators are unknown. Here, we show that circulating ‘naive’ ILC2s have an unexpected metabolic profile with a higher level of oxidative phosphorylation (OXPHOS) than natural killer (NK) cells. Accordingly, ILC2s are severely reduced in individuals with mitochondrial disease (MD) and impaired OXPHOS. Metabolomic and nutrient receptor analysis revealed ILC2 uptake of amino acids to sustain OXPHOS at steady state. Following activation with interleukin-33 (IL-33), ILC2s became highly proliferative, relying on glycolysis and mammalian target of rapamycin (mTOR) to produce IL-13 while continuing to fuel OXPHOS with amino acids to maintain cellular fitness and proliferation. Our results suggest that proliferation and function are metabolically uncoupled in human ILC2s, offering new strategies to target ILC2s in disease settings.
Salivary gland extract from the deer tick, Ixodes scapularis, facilitates neuroinvasion by Powassan virus in BALB/c mice
Authors: Santos Rodrigo I. , Hermance Meghan E. , Reynolds Erin S. , Thangamani Saravanan
Published: October 2021

Powassan virus (POWV) is a neuroinvasive flavivirus transmitted to mammals by the bite of ixodid ticks. In this study, we sought to investigate the impact of tick salivary gland extract (SGE) on POWV neuroinvasion. BALB/c mice were footpad inoculated with either a high dose or a low dose of POWV, with and without Ixodes scapularis salivary gland extract. Brain and spinal cord were extracted daily, and immunohistochemical techniques were used for temporal tracking of POWV antigen. The temporal pattern of POWV staining showed a caudal to rostral spread of POWV in the brains of mice from both high dose infection groups. For the high dose infection groups, the presence of tick SGE did not influence the spread of POWV in the brain. Mice infected with the low dose of virus alone did not present POWV staining in the brain; however, in the presence of SGE, low dose infected mice presented scattered foci of POWV-infected cells throughout the brain. This study shows that tick SGE facilitates POWV neuroinvasion when mice are infected with the lower dose of POWV. We also found two patterns of central nervous system invasion that were directly influenced by the dose of POWV administered.
Effects of interdialytic interval on heart rate variability in chronic hemodialysis patients: a cross-sectional study
Authors: Noppakun Kajohnsak , Putchagarn Phasakorn , Phrommintikul Arintaya , Wongcharoen Wanwarang
Published: October 2021

Previous studies showed that long interdialytic interval of chronic hemodialysis increased risk of sudden cardiac death compared to short interdialytic interval. Diabetes mellitus (DM) and autonomic dysfunction are the strong adverse predictors of survival in ESRD patients. We aimed to compare autonomic function between long and short interdialytic interval of chronic hemodialysis in patients with and without DM. One-hundred sixty-three patients receiving chronic hemodialysis were enrolled. The electrocardiogram recording was performed twice in each patient during 4-h hemodialysis session after long and short interdialytic intervals to assess heart rate variability (HRV). Mean age was 61.4 ± 14.3 years. HRV parameters during hemodialysis did not differ between long and short interdialytic interval in overall population. Nevertheless, in 82 (50.3%) patients, SDNN (47.4 ± 23.8 vs. 43.4 ± 19.5 ms, P = 0.039), ASDNN (24.8 ± 14.3 vs. 22.7 ± 12.3 ms, P = 0.025), LF (8.4 ± 6.8 vs. 7.6 ± 6.6 ms2, P = 0.040) increased after long interdialytic interval. The greater change of SDNN, ASDNN, VLF and LF between long and short interdialytic intervals was noted in DM, compared to non-DM patients. We demonstrated that there was no difference of HRV parameters after short and long interdialytic interval. However, there was greater autonomic alteration observed in DM than non-DM patients between 2 interdialytic intervals.
Optimal time lags from causal prediction model help stratify and forecast nervous system pathology
Authors: Bermperidis Theodoros , Rai Richa , Ryu Jihye , Zanotto Damiano , Agrawal Sunil K. , Lalwani Anil K. , Torres Elizabeth B.
Published: October 2021

Traditional clinical approaches diagnose disorders of the nervous system using standardized observational criteria. Although aiming for homogeneity of symptoms, this method often results in highly heterogeneous disorders. A standing question thus is how to automatically stratify a given random cohort of the population, such that treatment can be better tailored to each cluster’s symptoms, and severity of any given group forecasted to provide neuroprotective therapies. In this work we introduce new methods to automatically stratify a random cohort of the population composed of healthy controls of different ages and patients with different disorders of the nervous systems. Using a simple walking task and measuring micro-fluctuations in their biorhythmic motions, we combine non-linear causal network connectivity analyses in the temporal and frequency domains with stochastic mapping. The methods define a new type of internal motor timings. These are amenable to create personalized clinical interventions tailored to self-emerging clusters signaling fundamentally different types of gait pathologies. We frame our results using the principle of reafference and operationalize them using causal prediction, thus renovating the theory of internal models for the study of neuromotor control.
Enhancement of extreme events through the Allee effect and its mitigation through noise in a three species system
Authors: Sen Deeptajyoti , Sinha Sudeshna
Published: October 2021

We consider the dynamics of a three-species system incorporating the Allee Effect, focussing on its influence on the emergence of extreme events in the system. First we find that under Allee effect the regular periodic dynamics changes to chaotic. Further, we find that the system exhibits unbounded growth in the vegetation population after a critical value of the Allee parameter. The most significant finding is the observation of a critical Allee parameter beyond which the probability of obtaining extreme events becomes non-zero for all three population densities. Though the emergence of extreme events in the predator population is not affected much by the Allee effect, the prey population shows a sharp increase in the probability of obtaining extreme events after a threshold value of the Allee parameter, and the vegetation population also yields extreme events for sufficiently strong Allee effect. Lastly we consider the influence of additive noise on extreme events. First, we find that noise tames the unbounded vegetation growth induced by Allee effect. More interestingly, we demonstrate that stochasticity drastically diminishes the probability of extreme events in all three populations. In fact for sufficiently high noise, we do not observe any more extreme events in the system. This suggests that noise can mitigate extreme events, and has potentially important bearing on the observability of extreme events in naturally occurring systems.
Use of the p-values as a size-dependent function to address practical differences when analyzing large datasets
Authors: Gómez-de-Mariscal Estibaliz , Guerrero Vanesa , Sneider Alexandra , Jayatilaka Hasini , Phillip Jude M. , Wirtz Denis , Muñoz-Barrutia Arrate
Published: October 2021

Biomedical research has come to rely on p-values as a deterministic measure for data-driven decision-making. In the largely extended null hypothesis significance testing for identifying statistically significant differences among groups of observations, a single p-value is computed from sample data. Then, it is routinely compared with a threshold, commonly set to 0.05, to assess the evidence against the hypothesis of having non-significant differences among groups, or the null hypothesis. Because the estimated p-value tends to decrease when the sample size is increased, applying this methodology to datasets with large sample sizes results in the rejection of the null hypothesis, making it not meaningful in this specific situation. We propose a new approach to detect differences based on the dependence of the p-value on the sample size. We introduce new descriptive parameters that overcome the effect of the size in the p-value interpretation in the framework of datasets with large sample sizes, reducing the uncertainty in the decision about the existence of biological differences between the compared experiments. The methodology enables the graphical and quantitative characterization of the differences between the compared experiments guiding the researchers in the decision process. An in-depth study of the methodology is carried out on simulated and experimental data. Code availability at https://github.com/BIIG-UC3M/pMoSS.
Excess soluble alkalis to prepare highly efficient MgO with relative low surface oxygen content applied in DMC synthesis
Authors: Liu Ju , Chen Fei , Yang Wenbing , Guo Jianjun , Xu Guangwen , Jia Fenglei , Shi Lei
Published: October 2021

The activities of various MgO catalysts, which were prepared from different methods such as hydration synthesis, thermal decomposition, combustion, sol–gel and co-precipitation, were conducted in dimethyl carbonate (DMC) synthesis via transesterification of ethylene carbonate with methanol. MgO-P-Na2CO3-3.14 synthesized by the excess Na2CO3 precipitation compared the best catalytic activity and stability, which could be reused for seven times without obvious deactivation. The DMC yield was as high as 69.97% at 68 °C. The transesterification reaction could be separated into two steps, and the samples obtained by NaOH precipitant exhibited better ring-opening capability, while the catalysts acquired by Na2CO3 precipitant displayed superior transesterification ability. The structure-performance relationship was evaluated by multiple characterization methods. The results indicated that the as-synthesized catalyst derived from dried precursors with more crystalline magnesium carbonate was favorable for the promotion of DMC yield, and MgO-P-Na2CO3-3.14 with more Mg-O pairs, which were the active center for the transesterification of 2-hydroxyethyl methyl carbonate (HEMC) intermediate with methanol, resulted in more moderately basic sites left that was in accordance with the DMC yield variation. MgO-P-Na2CO3-3.14 with greater BET surface area and mesopore volume, relative low surface oxygen content and larger moderately basic sites amount compared the excellent activity in DMC synthesis.
Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds
Authors: Sarker Subir
Published: October 2021

Emerging viral pathogens are a significant concern, with potential consequences for human, animal and environmental health. Over the past several decades, many novel viruses have been found in animals, including birds, and often pose a significant threat to vulnerable species. However, despite enormous interest in virus research, little is known about virus communities (viromes) in Australian Neophema birds. Therefore, this study was designed to characterise the viromes of Neophema birds and track the evolutionary relationships of recently emerging psittacine siadenovirus F (PsSiAdV-F) circulating in the critically endangered, orange-bellied parrot (OBP, Neophema chrysogaster), using a viral metagenomic approach. This study identified 16 viruses belonging to the families Adenoviridae, Circoviridae, Endornaviridae, Picobirnaviridae and Picornaviridae. In addition, this study demonstrated a potential evolutionary relationship of a PsSiAdV-F sequenced previously from the critically endangered OBP. Strikingly, five adenoviral contigs identified in this study show the highest identities with human adenovirus 2 and human mastadenovirus C. This highlights an important and unexpected aspects of the avian virome and warrants further studies dedicated to this subject. Finally, the findings of this study emphasise the importance of testing birds used for trade or in experimental settings for potential pathogens to prevent the spread of infections.
Potential and pitfalls of XRF-CS analysis of ion-exchange resins in environmental studies
Authors: Löwemark Ludvig , Liao Alice Chien-Yi , Liou Yu-Hsuan , Godad Shital , Chang Ting-Yi , Kunz Alexander
Published: October 2021

Detecting clandestine, intermittent release of heavy metal pollution into natural and man-made water ways is challenging. Conventional chemical methods are both labor intensive and expensive. A recent approach combining ion-exchange resins with the capabilities of X-ray fluorescence core scanners (XRF-CS) therefore is of great interest. In short, ion-exchange resin is deployed in the water using small sachets, the resin is then collected, dried, filled into sample holders and scanned using XRF-CS. Ion-exchange resins take up heavy metals in proportion to the concentration in the ambient water, with a correlation coefficient (R2) between concentration and XRF-CS counts better than 0.96 for most elements. However, a number of parameters influence the measurements. Different drying methods introduce differences in the XRF counts because of lattice bound water, resin shrinkage, and disaggregation of the resin particles. Furthermore, the newly developed sample carrier, which was constructed using 3D printed polymers, contains trace amounts of elements that may influence the sample measurements through edge effects and secondary fluorescence. In the tested sample carrier materials, substantial levels of Cr, Fe, Co, and Zn were detected, while Ca, Ti, Ni, Cu, Ga showed variable levels. Ba, Tl and Bi show very low levels, and Pb is only of importance in the PLA carrier. It is therefore necessary to streamline the analysis-process to ensure that the variations in sample treatment and drying and filling methods are minimized. It is also recommended that only spectra from the center of the compartments are used for the evaluation to avoid edge effects caused by secondary fluorescence of metals in the compartment walls. Although the technique of using ion-exchange resin sachets and XRF-CS analysis is only semi-quantitative, it is a cost effective and fast way to monitor large areas for environmental pollution, and the new sample carrier greatly contributes to make the process faster and less error prone.
Ultra-low profile solar-cell-integrated antenna with a high form factor
Authors: Ali Ahmed , Wang Heesu , Lee Jaejin , Ahn Yeong Hwan , Park Ikmo
Published: October 2021

This paper presents an ultra-low-profile copper indium gallium selenide (CIGS) based solar cell integrated antenna with a high form factor. A tiny slot was etched from the solar cell to develop an ultra-low-profile solar-cell-integrated antenna. This tiny slot increases the form factor due to the small clearance area from the solar cell. A ground-radiation antenna design method was applied in which lumped elements were employed inside the tiny slot for antenna operation. Another substrate was used under the solar cell for designing the feeding structure with lumped elements connected to the tiny slot using via holes. A prototype was fabricated and measured to verify the operation of a built-in solar-cell antenna and validate the simulated results. The measured results demonstrate that the solar-cell-integrated antenna covers the entire frequency range of the Industrial Scientific Medical band, from 2.4 to 2.5 GHz, with a maximum gain of 2.79 dBi and radiation efficiency higher than 80% within the impedance bandwidth range. Moreover, the proposed design has an ultra-low-profile structure of only 0.0046 λo, where λorepresents the free space wavelength at 2.45 GHz, and a high form factor of 99.1% with no optical blockage. The antenna and solar cell were designed to avoid affecting the performance of each other using the radio-frequency decoupler.
Trends in spectrally resolved outgoing longwave radiation from 10 years of satellite measurements
Authors: Whitburn Simon , Clarisse Lieven , Bouillon Marie , Safieddine Sarah , George Maya , Dewitte Steven , De Longueville Hélène , Coheur Pierre-François , Clerbaux Cathy
Published: October 2021

In recent years, the interest has grown in satellite-derived hyperspectral radiance measurements for assessing the individual impact of climate drivers and their cascade of feedbacks on the outgoing longwave radiation (OLR). In this paper, we use 10 years (2008–2017) of reprocessed radiances from the infrared atmospheric sounding interferometer (IASI) to evaluate the linear trends in clear-sky spectrally resolved OLR (SOLR) in the range [645–2300] cm−1. Spatial inhomogeneities are observed in most of the analyzed spectral regions. These mostly reflected the natural variability of the atmospheric temperature and composition but long-term changes in greenhouse gases concentrations are also highlighted. In particular, the increase of atmospheric CO2 and CH4 led to significant negative trends in the SOLR of −0.05 to −0.3% per year in the spectral region corresponding to the ν2 and the ν3 CO2 and in the ν4 CH4 band. Most of the trends associated with the natural variability of the OLR can be related to the El Niño/Southern Oscillation activity and its teleconnections in the studied period. This is the case for the channels most affected by the temperature variations of the surface and the first layers of the atmosphere but also for the channels corresponding to the ν2 H2O and the ν3 O3 bands.
Using particle swarm optimization to improve visibility-aerosol optical depth retrieval method
Authors: Wu Jian , Zhang Shuang , Yang Qidong , Zhao Deming , Fan Wenxuan , Zhao Jingchuan , Shen Cheng
Published: October 2021

In view of the lack of long-term AOD (Aerosol Optical Depth) data, PSO (Particle Swarm Optimization) algorithm is introduced and joint used with NLSM (the nonlinear least square method) to improve visibility-AOD retrieval method, which is referred to as the PSO-M-Elterman model and significantly increases data available rate by 8% and correlation by about 20% with the true value in the experimental group. The mean absolute error, the proportion of the smaller absolute error and the root mean square error in the PSO-M-Elterman model experimental group are 0.0314 and 91.23%, 0.0509 respectively, which significantly outperforms other groups. The main increase of AOD was found in the eastern region (South China, East China, Central China) and Taklimakan with the trend coefficients of 2.67, 2.46, 2.13, and 1.45 (×10−3 yr−1) in recent 55 years, which may not be interpreted by the influence of relative humidity. Long-term change of AOD in east China is mainly caused by human activity, and the AOD is higher in cities with a larger population and more human activity. The PSO-M-Elterman model can maximize the advantage of visibility sequence length to obtain long-term AOD inversion results.
Hydrolysis of 5-methylfuran-2-yl to 2,5-dioxopentanyl allows for stable bio-orthogonal proximity-induced ligation
Authors: Manicardi Alex , Cadoni Enrico , Madder Annemieke
Published: October 2021

Ligation methodologies featuring bio-orthogonal units and leading to the formation of a stable adduct are the ideal candidates for being applied in a biological context. However, most of the available strategies rely on highly reactive species that require careful handling, or on the activation of pro-reactive functional groups. We here report on a proximity-induced ligation reaction that relies on a stable 2,5-dione, that can be conveniently generated under acidic conditions from a 2,5-dialkylfuran building block, and hydrazine nucleophiles. This bio-orthogonal ligation, which proceeds under physiological conditions, does not require any stimulus or trigger and leads to the formation of a pyridazinium adduct that demonstrates excellent stability under harsh conditions (24 h at 90 °C). The reaction was applied to the formation of PNA-PNA adducts, DNA- and RNA-templated ligations, and for the formation of peptide-peptide adducts in solution. This convenient methodology was further implemented on plastic and glass surfaces to realize self-addressable covalent constructs.
Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea
Authors: Sumi Tomonari , Harada Kouji
Published: October 2021

The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood–Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.
Biomimetic enantioselective synthesis of β,β-difluoro-α-amino acid derivatives
Authors: Peng Qiupeng , Yan Bingjia , Li Fangyi , Lang Ming , Zhang Bei , Guo Donghui , Bierer Donald , Wang Jian
Published: October 2021

Although utilization of fluorine compounds has a long history, synthesis of chiral fluorinated amino acid derivatives with structural diversity and high stereoselectivity is still very appealing and challenging. Here, we report a biomimetic study of enantioselective [1,3]-proton shift ofβ,β-difluoro-α-imine amides catalyzed by chiral quinine derivatives. A wide range of correspondingβ,β-difluoro-α-amino amides were achieved in good yields with high enantioselectivities. The optically pureβ,β-difluoro-α-amino acid derivatives were further obtained, which have high application values in the synthesis of fluoro peptides, fluoro amino alcohols and other valuable fluorine-containing molecules.
Design of solvatomorphic structures based on a polyboronated tetraphenyladamantane molecular tecton
Authors: Drapała Jakub , Marek-Urban Paulina H. , Klimkowski Piotr , Urbanowicz Karolina A. , Gontarczyk Krzysztof , Woźniak Krzysztof , Luliński Sergiusz , Durka Krzysztof
Published: October 2021

A series of solvatomorphic structures of tetrakis(4-dihydroxyborylphenyl)adamantane were investigated.
Eight coordinated mononuclear dysprosium complexes of heptadentate aminophenol ligands: the influence of the phenol substituents and the ancillary donors on the magnetic relaxation
Authors: Fondo Matilde , Corredoira-Vázquez Julio , García-Deibe Ana M. , Sanmartín-Matalobos Jesús , Reta Daniel , Colacio Enrique
Published: October 2021

Distorted square antiprism DyIII SIMs of heptadentate aminophenol ligands decrease their Ueff with the electron-withdrawing ability of the phenol substituents and the increasing electronegativity of auxiliary monodentate donors.
Robust ionic liquid@MOF composite as a versatile superprotonic conductor
Authors: Taksande Kiran , Gkaniatsou Effrosyni , Simonnet-Jégat Corine , Livage Carine , Maurin Guillaume , Steunou Nathalie , Devautour-Vinot Sabine
Published: October 2021

MIL-101(Cr)–SO3H impregnated with EMIMCl ionic liquid is demonstrated as a single protonic superconductor for both low and intermediate temperature applications.
Direct and indirect photodegradation of atrazine and S-metolachlor in agriculturally impacted surface water and associated C and N isotope fractionation
Authors: Drouin Guillaume , Droz Boris , Leresche Frank , Payraudeau Sylvain , Masbou Jérémy , Imfeld Gwenaël
Published: October 2021

Knowledge of direct and indirect photodegradation of pesticides and associated isotope fractionation can help to assess pesticide degradation in surface waters.
Safflower leaf ameliorates cognitive impairment through moderating excessive astrocyte activation in APP/PS1 mice
Authors: Zhang Tiantian , Zhang Shuangxi , Peng Yunhua , Wang Yongyao , Gao Peipei , Hu Yachong , Wang Zhen , Noda Mami , Hiramatsu Midori , Liu Jiankang , Long Jiangang
Published: October 2021

Safflower leaf could protect the cognitive function in APP/PS1 mice possiblely through inhibiting excessive astrocyte activation, which provides a cognitively beneficial food for preventing and alleviating AD-related dementia.
Multifunctional carbon dots with near-infrared absorption and emission for targeted delivery of anticancer drugs, tumor tissue imaging and chemo/photothermal synergistic therapy
Authors: Hu Yuefang , Zhang Liangliang , Chen Shengyu , Hou Li , Zhao Shulin , Huang Yong , Liang Hong
Published: October 2021

A multifunctional nanoprobe for tumor microenvironment- induced cancer imaging and chemo/PTT synergistic targeted therapy was constructed. Tumor microenvironment-specific stimuli responses enable targeted drug accumulation and cancer imaging.
Correction: Enhanced photoluminescence of silicon quantum dots in the presence of both energy transfer enhancement and emission enhancement mechanisms assisted by the double plasmon modes of gold nanorods
Authors: Cao Jiahao , Zhang Hanjie , Pi Xiaodong , Li Dongsheng , Yang Deren
Published: October 2021

Correction for ‘Enhanced photoluminescence of silicon quantum dots in the presence of both energy transfer enhancement and emission enhancement mechanisms assisted by the double plasmon modes of gold nanorods’ by Jiahao Cao et al., Nanoscale Adv., 2021, 3, 4810–4815, DOI: 10.1039/D1NA00287B.
Fe2P encapsulated in carbon nanowalls decorated with well-dispersed Fe3C nanodots for efficient hydrogen evolution and oxygen reduction reactions
Authors: Feng Liangliang , Zhang Xiao , Huang Jianfeng , He Danyang , Li Xiaoyi , Liu Qianqian , Feng Yongqiang , Li Guodong , Xu Guanghui , Cao Liyun
Published: October 2021

A novel “inside-out” gas–solid reaction protocol is reported for the synthesis of an advanced Fe2P@Fe3C/CNT bifunctional electrocatalyst toward the HER and ORR.
Tailoring B-doped silicon nanocrystal surface chemistry via phosphorus pentachloride – mediated surface alkoxylation
Authors: Milliken Sarah , Cui Kai , Klein Brittney A. , Cheong I Teng , Yu Haoyang , Michaelis Vladimir K. , Veinot Jonathan G. C.
Published: October 2021

The reported method provides a straightforward scalable route to preparing solution processable B-doped SiNCs via phosphorus pentachloride-mediated etching induced surface reactivity with alcohols.
Gold-catalyzed oxidative cyclization of amide-alkynes: access to functionalized γ-lactams
Authors: Zheng Yi , Zhang Ting-Ting , Shen Wen-Bo
Published: October 2021

An efficient gold-catalyzed oxidative cyclization of amide-alkynes for the synthesis of functionalized γ-lactams is described.
One-pot synthesis of tetrasubstituted 2-aminofurans via Au(i)-catalyzed cascade reaction of ynamides with propargylic alcohols
Authors: Miyairi Asaki , Oonishi Yoshihiro , Sato Yoshihiro
Published: October 2021

Hydroalkoxylation of ynamide with propargylic alcohol, Saucy–Marbet rearrangement, and cyclization of the resultant 3,4-dienamide sequentially proceeds in a one-pot reaction under highly mild conditions to give fully substituted 2-aminofurans.
Imidazole based dual photo/thermal initiators for highly efficient radical polymerization under air with a metal-free approach
Authors: Ma Qiang , Liu Shaohui , Le Dot Marie , Mokbel Haifaa , Zhang Yijun , Graff Bernadette , Lalevée Jacques
Published: October 2021

A metal-free visible LED photopolymerization process, initiated by imidazole based charge transfer complexes under mild conditions (room temperature, without an inert atmosphere, monomer purification or stabilizer removal), is reported.